src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.analysis.TreeModel;
  30 import jalview.api.AlignExportSettingI;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignViewportI;
  34 import jalview.api.AlignmentViewPanel;
  35 import jalview.api.FeatureSettingsControllerI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenColumns;
  57 import jalview.datamodel.HiddenSequences;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.ext.archaeopteryx.AptxInit;
  64 import jalview.ext.forester.io.SupportedTreeFileFilter;
  65 import jalview.ext.forester.io.TreeParser;
  66 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  67 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  68 import jalview.io.AlignmentProperties;
  69 import jalview.io.AnnotationFile;
  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.jbgui.GAlignFrame;
  88 import jalview.schemes.ColourSchemeI;
  89 import jalview.schemes.ColourSchemes;
  90 import jalview.schemes.ResidueColourScheme;
  91 import jalview.schemes.TCoffeeColourScheme;
  92 import jalview.util.MessageManager;
  93 import jalview.viewmodel.AlignmentViewport;
  94 import jalview.viewmodel.ViewportRanges;
  95 import jalview.ws.DBRefFetcher;
  96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  97 import jalview.ws.jws1.Discoverer;
  98 import jalview.ws.jws2.Jws2Discoverer;
  99 import jalview.ws.jws2.jabaws2.Jws2Instance;
 100 import jalview.ws.seqfetcher.DbSourceProxy;
 101
 102 import java.awt.BorderLayout;
 103 import java.awt.Component;
 104 import java.awt.Dimension;
 105 import java.awt.GridLayout;
 106 import java.awt.Rectangle;
 107 import java.awt.Toolkit;
 108 import java.awt.datatransfer.Clipboard;
 109 import java.awt.datatransfer.DataFlavor;
 110 import java.awt.datatransfer.StringSelection;
 111 import java.awt.datatransfer.Transferable;
 112 import java.awt.dnd.DnDConstants;
 113 import java.awt.dnd.DropTargetDragEvent;
 114 import java.awt.dnd.DropTargetDropEvent;
 115 import java.awt.dnd.DropTargetEvent;
 116 import java.awt.dnd.DropTargetListener;
 117 import java.awt.event.ActionEvent;
 118 import java.awt.event.ActionListener;
 119 import java.awt.event.FocusAdapter;
 120 import java.awt.event.FocusEvent;
 121 import java.awt.event.ItemEvent;
 122 import java.awt.event.ItemListener;
 123 import java.awt.event.KeyAdapter;
 124 import java.awt.event.KeyEvent;
 125 import java.awt.event.MouseEvent;
 126 import java.awt.print.PageFormat;
 127 import java.awt.print.PrinterJob;
 128 import java.beans.PropertyChangeEvent;
 129 import java.io.File;
 130 import java.io.FileWriter;
 131 import java.io.IOException;
 132 import java.io.PrintWriter;
 133 import java.net.URL;
 134 import java.util.ArrayList;
 135 import java.util.Arrays;
 136 import java.util.Deque;
 137 import java.util.Enumeration;
 138 import java.util.Hashtable;
 139 import java.util.List;
 140 import java.util.StringTokenizer;
 141 import java.util.Vector;
 142
 143 import javax.swing.JCheckBoxMenuItem;
 144 import javax.swing.JComboBox;
 145 import javax.swing.JEditorPane;
 146 import javax.swing.JInternalFrame;
 147 import javax.swing.JLabel;
 148 import javax.swing.JLayeredPane;
 149 import javax.swing.JMenu;
 150 import javax.swing.JMenuItem;
 151 import javax.swing.JPanel;
 152 import javax.swing.JScrollPane;
 153 import javax.swing.SwingUtilities;
 154
 155 /**
 156  * DOCUMENT ME!
 157  *
 158  * @author $author$
 159  * @version $Revision$
 160  */
 161 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 162         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 163 {
 164
 165   public static final int DEFAULT_WIDTH = 700;
 166
 167   public static final int DEFAULT_HEIGHT = 500;
 168
 169   /*
 170    * The currently displayed panel (selected tabbed view if more than one)
 171    */
 172   public AlignmentPanel alignPanel;
 173
 174   AlignViewport viewport;
 175
 176   public AlignViewControllerI avc;
 177
 178   List<AlignmentPanel> alignPanels = new ArrayList<>();
 179
 180   /**
 181    * Last format used to load or save alignments in this window
 182    */
 183   FileFormatI currentFileFormat = null;
 184
 185   /**
 186    * Current filename for this alignment
 187    */
 188   String fileName = null;
 189
 190   /**
 191    * Creates a new AlignFrame object with specific width and height.
 192    *
 193    * @param al
 194    * @param width
 195    * @param height
 196    */
 197   public AlignFrame(AlignmentI al, int width, int height)
 198   {
 199     this(al, null, width, height);
 200   }
 201
 202   /**
 203    * Creates a new AlignFrame object with specific width, height and
 204    * sequenceSetId
 205    *
 206    * @param al
 207    * @param width
 208    * @param height
 209    * @param sequenceSetId
 210    */
 211   public AlignFrame(AlignmentI al, int width, int height,
 212           String sequenceSetId)
 213   {
 214     this(al, null, width, height, sequenceSetId);
 215   }
 216
 217   /**
 218    * Creates a new AlignFrame object with specific width, height and
 219    * sequenceSetId
 220    *
 221    * @param al
 222    * @param width
 223    * @param height
 224    * @param sequenceSetId
 225    * @param viewId
 226    */
 227   public AlignFrame(AlignmentI al, int width, int height,
 228           String sequenceSetId, String viewId)
 229   {
 230     this(al, null, width, height, sequenceSetId, viewId);
 231   }
 232
 233   /**
 234    * new alignment window with hidden columns
 235    *
 236    * @param al
 237    *          AlignmentI
 238    * @param hiddenColumns
 239    *          ColumnSelection or null
 240    * @param width
 241    *          Width of alignment frame
 242    * @param height
 243    *          height of frame.
 244    */
 245   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 246           int height)
 247   {
 248     this(al, hiddenColumns, width, height, null);
 249   }
 250
 251   /**
 252    * Create alignment frame for al with hiddenColumns, a specific width and
 253    * height, and specific sequenceId
 254    *
 255    * @param al
 256    * @param hiddenColumns
 257    * @param width
 258    * @param height
 259    * @param sequenceSetId
 260    *          (may be null)
 261    */
 262   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 263           int height, String sequenceSetId)
 264   {
 265     this(al, hiddenColumns, width, height, sequenceSetId, null);
 266   }
 267
 268   /**
 269    * Create alignment frame for al with hiddenColumns, a specific width and
 270    * height, and specific sequenceId
 271    *
 272    * @param al
 273    * @param hiddenColumns
 274    * @param width
 275    * @param height
 276    * @param sequenceSetId
 277    *          (may be null)
 278    * @param viewId
 279    *          (may be null)
 280    */
 281   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 282           int height, String sequenceSetId, String viewId)
 283   {
 284     setSize(width, height);
 285
 286     if (al.getDataset() == null)
 287     {
 288       al.setDataset(null);
 289     }
 290
 291     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 292
 293     alignPanel = new AlignmentPanel(this, viewport);
 294
 295     addAlignmentPanel(alignPanel, true);
 296     init();
 297   }
 298
 299   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 300           HiddenColumns hiddenColumns, int width, int height)
 301   {
 302     setSize(width, height);
 303
 304     if (al.getDataset() == null)
 305     {
 306       al.setDataset(null);
 307     }
 308
 309     viewport = new AlignViewport(al, hiddenColumns);
 310
 311     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 312     {
 313       viewport.hideSequence(hiddenSeqs);
 314     }
 315     alignPanel = new AlignmentPanel(this, viewport);
 316     addAlignmentPanel(alignPanel, true);
 317     init();
 318   }
 319
 320   /**
 321    * Make a new AlignFrame from existing alignmentPanels
 322    *
 323    * @param ap
 324    *          AlignmentPanel
 325    * @param av
 326    *          AlignViewport
 327    */
 328   public AlignFrame(AlignmentPanel ap)
 329   {
 330     viewport = ap.av;
 331     alignPanel = ap;
 332     addAlignmentPanel(ap, false);
 333     init();
 334   }
 335
 336   /**
 337    * initalise the alignframe from the underlying viewport data and the
 338    * configurations
 339    */
 340   void init()
 341   {
 342     if (!Jalview.isHeadlessMode())
 343     {
 344       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 345     }
 346
 347     avc = new jalview.controller.AlignViewController(this, viewport,
 348             alignPanel);
 349     if (viewport.getAlignmentConservationAnnotation() == null)
 350     {
 351       // BLOSUM62Colour.setEnabled(false);
 352       conservationMenuItem.setEnabled(false);
 353       modifyConservation.setEnabled(false);
 354       // PIDColour.setEnabled(false);
 355       // abovePIDThreshold.setEnabled(false);
 356       // modifyPID.setEnabled(false);
 357     }
 358
 359     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 360             "No sort");
 361
 362     if (sortby.equals("Id"))
 363     {
 364       sortIDMenuItem_actionPerformed(null);
 365     }
 366     else if (sortby.equals("Pairwise Identity"))
 367     {
 368       sortPairwiseMenuItem_actionPerformed(null);
 369     }
 370
 371     this.alignPanel.av
 372             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 373
 374     setMenusFromViewport(viewport);
 375     buildSortByAnnotationScoresMenu();
 376     calculateTree.addActionListener(new ActionListener()
 377     {
 378
 379       @Override
 380       public void actionPerformed(ActionEvent e)
 381       {
 382         openTreePcaDialog();
 383       }
 384     });
 385     buildColourMenu();
 386
 387     if (Desktop.desktop != null)
 388     {
 389       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 390       addServiceListeners();
 391       setGUINucleotide();
 392     }
 393
 394     if (viewport.getWrapAlignment())
 395     {
 396       wrapMenuItem_actionPerformed(null);
 397     }
 398
 399     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 400     {
 401       this.overviewMenuItem_actionPerformed(null);
 402     }
 403
 404     addKeyListener();
 405
 406     final List<AlignmentPanel> selviews = new ArrayList<>();
 407     final List<AlignmentPanel> origview = new ArrayList<>();
 408     final String menuLabel = MessageManager
 409             .getString("label.copy_format_from");
 410     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 411             new ViewSetProvider()
 412             {
 413
 414               @Override
 415               public AlignmentPanel[] getAllAlignmentPanels()
 416               {
 417                 origview.clear();
 418                 origview.add(alignPanel);
 419                 // make an array of all alignment panels except for this one
 420                 List<AlignmentPanel> aps = new ArrayList<>(
 421                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 422                 aps.remove(AlignFrame.this.alignPanel);
 423                 return aps.toArray(new AlignmentPanel[aps.size()]);
 424               }
 425             }, selviews, new ItemListener()
 426             {
 427
 428               @Override
 429               public void itemStateChanged(ItemEvent e)
 430               {
 431                 if (origview.size() > 0)
 432                 {
 433                   final AlignmentPanel ap = origview.get(0);
 434
 435                   /*
 436                    * Copy the ViewStyle of the selected panel to 'this one'.
 437                    * Don't change value of 'scaleProteinAsCdna' unless copying
 438                    * from a SplitFrame.
 439                    */
 440                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 441                           .getViewStyle();
 442                   boolean fromSplitFrame = selviews.get(0)
 443                           .getAlignViewport().getCodingComplement() != null;
 444                   if (!fromSplitFrame)
 445                   {
 446                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 447                             .getViewStyle().isScaleProteinAsCdna());
 448                   }
 449                   ap.getAlignViewport().setViewStyle(vs);
 450
 451                   /*
 452                    * Also rescale ViewStyle of SplitFrame complement if there is
 453                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 454                    * the whole ViewStyle (allow cDNA protein to have different
 455                    * fonts)
 456                    */
 457                   AlignViewportI complement = ap.getAlignViewport()
 458                           .getCodingComplement();
 459                   if (complement != null && vs.isScaleProteinAsCdna())
 460                   {
 461                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 462                     ((SplitFrame) af.getSplitViewContainer())
 463                             .adjustLayout();
 464                     af.setMenusForViewport();
 465                   }
 466
 467                   ap.updateLayout();
 468                   ap.setSelected(true);
 469                   ap.alignFrame.setMenusForViewport();
 470
 471                 }
 472               }
 473             });
 474     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 475             .indexOf("devel") > -1
 476             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 477                     .indexOf("test") > -1)
 478     {
 479       formatMenu.add(vsel);
 480     }
 481     addFocusListener(new FocusAdapter()
 482     {
 483       @Override
 484       public void focusGained(FocusEvent e)
 485       {
 486         Jalview.setCurrentAlignFrame(AlignFrame.this);
 487       }
 488     });
 489
 490   }
 491
 492   /**
 493    * Change the filename and format for the alignment, and enable the 'reload'
 494    * button functionality.
 495    *
 496    * @param file
 497    *          valid filename
 498    * @param format
 499    *          format of file
 500    */
 501   public void setFileName(String file, FileFormatI format)
 502   {
 503     fileName = file;
 504     setFileFormat(format);
 505     reload.setEnabled(true);
 506   }
 507
 508   /**
 509    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 510    * events
 511    */
 512   void addKeyListener()
 513   {
 514     addKeyListener(new KeyAdapter()
 515     {
 516       @Override
 517       public void keyPressed(KeyEvent evt)
 518       {
 519         if (viewport.cursorMode
 520                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 521                         && evt.getKeyCode() <= KeyEvent.VK_9)
 522                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 523                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 524                 && Character.isDigit(evt.getKeyChar()))
 525         {
 526           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 527         }
 528
 529         switch (evt.getKeyCode())
 530         {
 531
 532         case 27: // escape key
 533           deselectAllSequenceMenuItem_actionPerformed(null);
 534
 535           break;
 536
 537         case KeyEvent.VK_DOWN:
 538           if (evt.isAltDown() || !viewport.cursorMode)
 539           {
 540             moveSelectedSequences(false);
 541           }
 542           if (viewport.cursorMode)
 543           {
 544             alignPanel.getSeqPanel().moveCursor(0, 1);
 545           }
 546           break;
 547
 548         case KeyEvent.VK_UP:
 549           if (evt.isAltDown() || !viewport.cursorMode)
 550           {
 551             moveSelectedSequences(true);
 552           }
 553           if (viewport.cursorMode)
 554           {
 555             alignPanel.getSeqPanel().moveCursor(0, -1);
 556           }
 557
 558           break;
 559
 560         case KeyEvent.VK_LEFT:
 561           if (evt.isAltDown() || !viewport.cursorMode)
 562           {
 563             slideSequences(false,
 564                     alignPanel.getSeqPanel().getKeyboardNo1());
 565           }
 566           else
 567           {
 568             alignPanel.getSeqPanel().moveCursor(-1, 0);
 569           }
 570
 571           break;
 572
 573         case KeyEvent.VK_RIGHT:
 574           if (evt.isAltDown() || !viewport.cursorMode)
 575           {
 576             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 577           }
 578           else
 579           {
 580             alignPanel.getSeqPanel().moveCursor(1, 0);
 581           }
 582           break;
 583
 584         case KeyEvent.VK_SPACE:
 585           if (viewport.cursorMode)
 586           {
 587             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 588                     || evt.isShiftDown() || evt.isAltDown());
 589           }
 590           break;
 591
 592         // case KeyEvent.VK_A:
 593         // if (viewport.cursorMode)
 594         // {
 595         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 596         // //System.out.println("A");
 597         // }
 598         // break;
 599         /*
 600          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 601          * System.out.println("closing bracket"); } break;
 602          */
 603         case KeyEvent.VK_DELETE:
 604         case KeyEvent.VK_BACK_SPACE:
 605           if (!viewport.cursorMode)
 606           {
 607             cut_actionPerformed(null);
 608           }
 609           else
 610           {
 611             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 612                     || evt.isShiftDown() || evt.isAltDown());
 613           }
 614
 615           break;
 616
 617         case KeyEvent.VK_S:
 618           if (viewport.cursorMode)
 619           {
 620             alignPanel.getSeqPanel().setCursorRow();
 621           }
 622           break;
 623         case KeyEvent.VK_C:
 624           if (viewport.cursorMode && !evt.isControlDown())
 625           {
 626             alignPanel.getSeqPanel().setCursorColumn();
 627           }
 628           break;
 629         case KeyEvent.VK_P:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().setCursorPosition();
 633           }
 634           break;
 635
 636         case KeyEvent.VK_ENTER:
 637         case KeyEvent.VK_COMMA:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setCursorRowAndColumn();
 641           }
 642           break;
 643
 644         case KeyEvent.VK_Q:
 645           if (viewport.cursorMode)
 646           {
 647             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 648           }
 649           break;
 650         case KeyEvent.VK_M:
 651           if (viewport.cursorMode)
 652           {
 653             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 654           }
 655           break;
 656
 657         case KeyEvent.VK_F2:
 658           viewport.cursorMode = !viewport.cursorMode;
 659           statusBar.setText(MessageManager
 660                   .formatMessage("label.keyboard_editing_mode", new String[]
 661                   { (viewport.cursorMode ? "on" : "off") }));
 662           if (viewport.cursorMode)
 663           {
 664             ViewportRanges ranges = viewport.getRanges();
 665             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 666                     .getStartRes();
 667             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 668                     .getStartSeq();
 669           }
 670           alignPanel.getSeqPanel().seqCanvas.repaint();
 671           break;
 672
 673         case KeyEvent.VK_F1:
 674           try
 675           {
 676             Help.showHelpWindow();
 677           } catch (Exception ex)
 678           {
 679             ex.printStackTrace();
 680           }
 681           break;
 682         case KeyEvent.VK_H:
 683         {
 684           boolean toggleSeqs = !evt.isControlDown();
 685           boolean toggleCols = !evt.isShiftDown();
 686           toggleHiddenRegions(toggleSeqs, toggleCols);
 687           break;
 688         }
 689         case KeyEvent.VK_B:
 690         {
 691           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 692           boolean modifyExisting = true; // always modify, don't clear
 693                                          // evt.isShiftDown();
 694           boolean invertHighlighted = evt.isAltDown();
 695           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 696                   toggleSel);
 697           break;
 698         }
 699         case KeyEvent.VK_PAGE_UP:
 700           viewport.getRanges().pageUp();
 701           break;
 702         case KeyEvent.VK_PAGE_DOWN:
 703           viewport.getRanges().pageDown();
 704           break;
 705         }
 706       }
 707
 708       @Override
 709       public void keyReleased(KeyEvent evt)
 710       {
 711         switch (evt.getKeyCode())
 712         {
 713         case KeyEvent.VK_LEFT:
 714           if (evt.isAltDown() || !viewport.cursorMode)
 715           {
 716             viewport.firePropertyChange("alignment", null,
 717                     viewport.getAlignment().getSequences());
 718           }
 719           break;
 720
 721         case KeyEvent.VK_RIGHT:
 722           if (evt.isAltDown() || !viewport.cursorMode)
 723           {
 724             viewport.firePropertyChange("alignment", null,
 725                     viewport.getAlignment().getSequences());
 726           }
 727           break;
 728         }
 729       }
 730     });
 731   }
 732
 733   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 734   {
 735     ap.alignFrame = this;
 736     avc = new jalview.controller.AlignViewController(this, viewport,
 737             alignPanel);
 738
 739     alignPanels.add(ap);
 740
 741     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 742
 743     int aSize = alignPanels.size();
 744
 745     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 746
 747     if (aSize == 1 && ap.av.viewName == null)
 748     {
 749       this.getContentPane().add(ap, BorderLayout.CENTER);
 750     }
 751     else
 752     {
 753       if (aSize == 2)
 754       {
 755         setInitialTabVisible();
 756       }
 757
 758       expandViews.setEnabled(true);
 759       gatherViews.setEnabled(true);
 760       tabbedPane.addTab(ap.av.viewName, ap);
 761
 762       ap.setVisible(false);
 763     }
 764
 765     if (newPanel)
 766     {
 767       if (ap.av.isPadGaps())
 768       {
 769         ap.av.getAlignment().padGaps();
 770       }
 771       ap.av.updateConservation(ap);
 772       ap.av.updateConsensus(ap);
 773       ap.av.updateStrucConsensus(ap);
 774     }
 775   }
 776
 777   public void setInitialTabVisible()
 778   {
 779     expandViews.setEnabled(true);
 780     gatherViews.setEnabled(true);
 781     tabbedPane.setVisible(true);
 782     AlignmentPanel first = alignPanels.get(0);
 783     tabbedPane.addTab(first.av.viewName, first);
 784     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 785   }
 786
 787   public AlignViewport getViewport()
 788   {
 789     return viewport;
 790   }
 791
 792   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 793   private void addServiceListeners()
 794   {
 795     final java.beans.PropertyChangeListener thisListener;
 796     Desktop.instance.addJalviewPropertyChangeListener("services",
 797             thisListener = new java.beans.PropertyChangeListener()
 798             {
 799               @Override
 800               public void propertyChange(PropertyChangeEvent evt)
 801               {
 802                 // // System.out.println("Discoverer property change.");
 803                 // if (evt.getPropertyName().equals("services"))
 804                 {
 805                   SwingUtilities.invokeLater(new Runnable()
 806                   {
 807
 808                     @Override
 809                     public void run()
 810                     {
 811                       System.err.println(
 812                               "Rebuild WS Menu for service change");
 813                       BuildWebServiceMenu();
 814                     }
 815
 816                   });
 817                 }
 818               }
 819             });
 820     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 821     {
 822       @Override
 823       public void internalFrameClosed(
 824               javax.swing.event.InternalFrameEvent evt)
 825       {
 826         // System.out.println("deregistering discoverer listener");
 827         Desktop.instance.removeJalviewPropertyChangeListener("services",
 828                 thisListener);
 829         closeMenuItem_actionPerformed(true);
 830       };
 831     });
 832     // Finally, build the menu once to get current service state
 833     new Thread(new Runnable()
 834     {
 835       @Override
 836       public void run()
 837       {
 838         BuildWebServiceMenu();
 839       }
 840     }).start();
 841   }
 842
 843   /**
 844    * Configure menu items that vary according to whether the alignment is
 845    * nucleotide or protein
 846    */
 847   public void setGUINucleotide()
 848   {
 849     AlignmentI al = getViewport().getAlignment();
 850     boolean nucleotide = al.isNucleotide();
 851
 852     showTranslation.setVisible(nucleotide);
 853     showReverse.setVisible(nucleotide);
 854     showReverseComplement.setVisible(nucleotide);
 855     conservationMenuItem.setEnabled(!nucleotide);
 856     modifyConservation
 857             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 858     showGroupConservation.setEnabled(!nucleotide);
 859
 860     showComplementMenuItem
 861             .setText(nucleotide ? MessageManager.getString("label.protein")
 862                     : MessageManager.getString("label.nucleotide"));
 863   }
 864
 865   /**
 866    * set up menus for the current viewport. This may be called after any
 867    * operation that affects the data in the current view (selection changed,
 868    * etc) to update the menus to reflect the new state.
 869    */
 870   @Override
 871   public void setMenusForViewport()
 872   {
 873     setMenusFromViewport(viewport);
 874   }
 875
 876   /**
 877    * Need to call this method when tabs are selected for multiple views, or when
 878    * loading from Jalview2XML.java
 879    *
 880    * @param av
 881    *          AlignViewport
 882    */
 883   void setMenusFromViewport(AlignViewport av)
 884   {
 885     padGapsMenuitem.setSelected(av.isPadGaps());
 886     colourTextMenuItem.setSelected(av.isShowColourText());
 887     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 888     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 889     conservationMenuItem.setSelected(av.getConservationSelected());
 890     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 891     seqLimits.setSelected(av.getShowJVSuffix());
 892     idRightAlign.setSelected(av.isRightAlignIds());
 893     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 894     renderGapsMenuItem.setSelected(av.isRenderGaps());
 895     wrapMenuItem.setSelected(av.getWrapAlignment());
 896     scaleAbove.setVisible(av.getWrapAlignment());
 897     scaleLeft.setVisible(av.getWrapAlignment());
 898     scaleRight.setVisible(av.getWrapAlignment());
 899     annotationPanelMenuItem.setState(av.isShowAnnotation());
 900     /*
 901      * Show/hide annotations only enabled if annotation panel is shown
 902      */
 903     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 904     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 905     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 906     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 907     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 908     viewTextMenuItem.setSelected(av.getShowText());
 909     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 910     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 911     showGroupConservation.setSelected(av.isShowGroupConservation());
 912     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 913     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 914     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 915
 916     ColourMenuHelper.setColourSelected(colourMenu,
 917             av.getGlobalColourScheme());
 918
 919     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 920     hiddenMarkers.setState(av.getShowHiddenMarkers());
 921     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 922     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 923     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 924     autoCalculate.setSelected(av.autoCalculateConsensus);
 925     sortByTree.setSelected(av.sortByTree);
 926     listenToViewSelections.setSelected(av.followSelection);
 927
 928     showProducts.setEnabled(canShowProducts());
 929     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 930
 931     updateEditMenuBar();
 932   }
 933
 934   /**
 935    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 936    *
 937    * @param b
 938    */
 939   public void setGroovyEnabled(boolean b)
 940   {
 941     runGroovy.setEnabled(b);
 942   }
 943
 944   private IProgressIndicator progressBar;
 945
 946   /*
 947    * (non-Javadoc)
 948    *
 949    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 950    */
 951   @Override
 952   public void setProgressBar(String message, long id)
 953   {
 954     progressBar.setProgressBar(message, id);
 955   }
 956
 957   @Override
 958   public void registerHandler(final long id,
 959           final IProgressIndicatorHandler handler)
 960   {
 961     progressBar.registerHandler(id, handler);
 962   }
 963
 964   /**
 965    *
 966    * @return true if any progress bars are still active
 967    */
 968   @Override
 969   public boolean operationInProgress()
 970   {
 971     return progressBar.operationInProgress();
 972   }
 973
 974   @Override
 975   public void setStatus(String text)
 976   {
 977     statusBar.setText(text);
 978   }
 979
 980   /*
 981    * Added so Castor Mapping file can obtain Jalview Version
 982    */
 983   public String getVersion()
 984   {
 985     return jalview.bin.Cache.getProperty("VERSION");
 986   }
 987
 988   public FeatureRenderer getFeatureRenderer()
 989   {
 990     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 991   }
 992
 993   @Override
 994   public void fetchSequence_actionPerformed(ActionEvent e)
 995   {
 996     new jalview.gui.SequenceFetcher(this);
 997   }
 998
 999   @Override
1000   public void addFromFile_actionPerformed(ActionEvent e)
1001   {
1002     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1003   }
1004
1005   @Override
1006   public void reload_actionPerformed(ActionEvent e)
1007   {
1008     if (fileName != null)
1009     {
1010       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1011       // originating file's format
1012       // TODO: work out how to recover feature settings for correct view(s) when
1013       // file is reloaded.
1014       if (FileFormat.Jalview.equals(currentFileFormat))
1015       {
1016         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1017         for (int i = 0; i < frames.length; i++)
1018         {
1019           if (frames[i] instanceof AlignFrame && frames[i] != this
1020                   && ((AlignFrame) frames[i]).fileName != null
1021                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1022           {
1023             try
1024             {
1025               frames[i].setSelected(true);
1026               Desktop.instance.closeAssociatedWindows();
1027             } catch (java.beans.PropertyVetoException ex)
1028             {
1029             }
1030           }
1031
1032         }
1033         Desktop.instance.closeAssociatedWindows();
1034
1035         FileLoader loader = new FileLoader();
1036         DataSourceType protocol = fileName.startsWith("http:")
1037                 ? DataSourceType.URL
1038                 : DataSourceType.FILE;
1039         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1040       }
1041       else
1042       {
1043         Rectangle bounds = this.getBounds();
1044
1045         FileLoader loader = new FileLoader();
1046         DataSourceType protocol = fileName.startsWith("http:")
1047                 ? DataSourceType.URL
1048                 : DataSourceType.FILE;
1049         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1050                 protocol, currentFileFormat);
1051
1052         newframe.setBounds(bounds);
1053         if (featureSettings != null && featureSettings.isShowing())
1054         {
1055           final Rectangle fspos = featureSettings.frame.getBounds();
1056           // TODO: need a 'show feature settings' function that takes bounds -
1057           // need to refactor Desktop.addFrame
1058           newframe.featureSettings_actionPerformed(null);
1059           final FeatureSettings nfs = newframe.featureSettings;
1060           SwingUtilities.invokeLater(new Runnable()
1061           {
1062             @Override
1063             public void run()
1064             {
1065               nfs.frame.setBounds(fspos);
1066             }
1067           });
1068           this.featureSettings.close();
1069           this.featureSettings = null;
1070         }
1071         this.closeMenuItem_actionPerformed(true);
1072       }
1073     }
1074   }
1075
1076   @Override
1077   public void addFromText_actionPerformed(ActionEvent e)
1078   {
1079     Desktop.instance
1080             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1081   }
1082
1083   @Override
1084   public void addFromURL_actionPerformed(ActionEvent e)
1085   {
1086     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1087   }
1088
1089   @Override
1090   public void save_actionPerformed(ActionEvent e)
1091   {
1092     if (fileName == null || (currentFileFormat == null)
1093             || fileName.startsWith("http"))
1094     {
1095       saveAs_actionPerformed(null);
1096     }
1097     else
1098     {
1099       saveAlignment(fileName, currentFileFormat);
1100     }
1101   }
1102
1103   /**
1104    * DOCUMENT ME!
1105    *
1106    * @param e
1107    *          DOCUMENT ME!
1108    */
1109   @Override
1110   public void saveAs_actionPerformed(ActionEvent e)
1111   {
1112     String format = currentFileFormat == null ? null
1113             : currentFileFormat.getName();
1114     JalviewFileChooser chooser = JalviewFileChooser
1115             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1116
1117     chooser.setFileView(new JalviewFileView());
1118     chooser.setDialogTitle(
1119             MessageManager.getString("label.save_alignment_to_file"));
1120     chooser.setToolTipText(MessageManager.getString("action.save"));
1121
1122     int value = chooser.showSaveDialog(this);
1123
1124     if (value == JalviewFileChooser.APPROVE_OPTION)
1125     {
1126       currentFileFormat = chooser.getSelectedFormat();
1127       while (currentFileFormat == null)
1128       {
1129         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1130                 MessageManager.getString(
1131                         "label.select_file_format_before_saving"),
1132                 MessageManager.getString("label.file_format_not_specified"),
1133                 JvOptionPane.WARNING_MESSAGE);
1134         currentFileFormat = chooser.getSelectedFormat();
1135         value = chooser.showSaveDialog(this);
1136         if (value != JalviewFileChooser.APPROVE_OPTION)
1137         {
1138           return;
1139         }
1140       }
1141
1142       fileName = chooser.getSelectedFile().getPath();
1143
1144       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1145
1146       Cache.setProperty("LAST_DIRECTORY", fileName);
1147       saveAlignment(fileName, currentFileFormat);
1148     }
1149   }
1150
1151   public boolean saveAlignment(String file, FileFormatI format)
1152   {
1153     boolean success = true;
1154
1155     if (FileFormat.Jalview.equals(format))
1156     {
1157       String shortName = title;
1158
1159       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1160       {
1161         shortName = shortName.substring(
1162                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1163       }
1164
1165       success = new Jalview2XML().saveAlignment(this, file, 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         try
1198         {
1199           PrintWriter out = new PrintWriter(new FileWriter(file));
1200
1201           out.print(output);
1202           out.close();
1203           this.setTitle(file);
1204           statusBar.setText(MessageManager.formatMessage(
1205                   "label.successfully_saved_to_file_in_format", new Object[]
1206                   { fileName, format.getName() }));
1207         } catch (Exception ex)
1208         {
1209           success = false;
1210           ex.printStackTrace();
1211         }
1212       }
1213     }
1214
1215     if (!success)
1216     {
1217       JvOptionPane.showInternalMessageDialog(this, MessageManager
1218               .formatMessage("label.couldnt_save_file", new Object[]
1219               { fileName }),
1220               MessageManager.getString("label.error_saving_file"),
1221               JvOptionPane.WARNING_MESSAGE);
1222     }
1223
1224     return success;
1225   }
1226
1227   private void warningMessage(String warning, String title)
1228   {
1229     if (new jalview.util.Platform().isHeadless())
1230     {
1231       System.err.println("Warning: " + title + "\nWarning: " + warning);
1232
1233     }
1234     else
1235     {
1236       JvOptionPane.showInternalMessageDialog(this, warning, title,
1237               JvOptionPane.WARNING_MESSAGE);
1238     }
1239     return;
1240   }
1241
1242   /**
1243    * DOCUMENT ME!
1244    *
1245    * @param e
1246    *          DOCUMENT ME!
1247    */
1248   @Override
1249   protected void outputText_actionPerformed(ActionEvent e)
1250   {
1251     FileFormatI fileFormat = FileFormats.getInstance()
1252             .forName(e.getActionCommand());
1253     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1254             viewport, null);
1255     if (exportData.getSettings().isCancelled())
1256     {
1257       return;
1258     }
1259     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1260     cap.setForInput(null);
1261     try
1262     {
1263       FileFormatI format = fileFormat;
1264       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1265               .formatSequences(format, exportData.getAlignment(),
1266                       exportData.getOmitHidden(),
1267                       exportData.getStartEndPostions(),
1268                       viewport.getAlignment().getHiddenColumns()));
1269       Desktop.addInternalFrame(cap, MessageManager
1270               .formatMessage("label.alignment_output_command", new Object[]
1271               { e.getActionCommand() }), 600, 500);
1272     } catch (OutOfMemoryError oom)
1273     {
1274       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1275               oom);
1276       cap.dispose();
1277     }
1278
1279   }
1280
1281   public static AlignmentExportData getAlignmentForExport(
1282           FileFormatI format, AlignViewportI viewport,
1283           AlignExportSettingI exportSettings)
1284   {
1285     AlignmentI alignmentToExport = null;
1286     AlignExportSettingI settings = exportSettings;
1287     String[] omitHidden = null;
1288
1289     HiddenSequences hiddenSeqs = viewport.getAlignment()
1290             .getHiddenSequences();
1291
1292     alignmentToExport = viewport.getAlignment();
1293
1294     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1295     if (settings == null)
1296     {
1297       settings = new AlignExportSettings(hasHiddenSeqs,
1298               viewport.hasHiddenColumns(), format);
1299     }
1300     // settings.isExportAnnotations();
1301
1302     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1303     {
1304       omitHidden = viewport.getViewAsString(false,
1305               settings.isExportHiddenSequences());
1306     }
1307
1308     int[] alignmentStartEnd = new int[2];
1309     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1310     {
1311       alignmentToExport = hiddenSeqs.getFullAlignment();
1312     }
1313     else
1314     {
1315       alignmentToExport = viewport.getAlignment();
1316     }
1317     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1318             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1319     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1320             omitHidden, alignmentStartEnd, settings);
1321     return ed;
1322   }
1323
1324   /**
1325    * DOCUMENT ME!
1326    *
1327    * @param e
1328    *          DOCUMENT ME!
1329    */
1330   @Override
1331   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1332   {
1333     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1334     htmlSVG.exportHTML(null);
1335   }
1336
1337   @Override
1338   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1339   {
1340     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1341     bjs.exportHTML(null);
1342   }
1343
1344   public void createImageMap(File file, String image)
1345   {
1346     alignPanel.makePNGImageMap(file, image);
1347   }
1348
1349   /**
1350    * DOCUMENT ME!
1351    *
1352    * @param e
1353    *          DOCUMENT ME!
1354    */
1355   @Override
1356   public void createPNG(File f)
1357   {
1358     alignPanel.makePNG(f);
1359   }
1360
1361   /**
1362    * DOCUMENT ME!
1363    *
1364    * @param e
1365    *          DOCUMENT ME!
1366    */
1367   @Override
1368   public void createEPS(File f)
1369   {
1370     alignPanel.makeEPS(f);
1371   }
1372
1373   @Override
1374   public void createSVG(File f)
1375   {
1376     alignPanel.makeSVG(f);
1377   }
1378
1379   @Override
1380   public void pageSetup_actionPerformed(ActionEvent e)
1381   {
1382     PrinterJob printJob = PrinterJob.getPrinterJob();
1383     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1384   }
1385
1386   /**
1387    * DOCUMENT ME!
1388    *
1389    * @param e
1390    *          DOCUMENT ME!
1391    */
1392   @Override
1393   public void printMenuItem_actionPerformed(ActionEvent e)
1394   {
1395     // Putting in a thread avoids Swing painting problems
1396     PrintThread thread = new PrintThread(alignPanel);
1397     thread.start();
1398   }
1399
1400   @Override
1401   public void exportFeatures_actionPerformed(ActionEvent e)
1402   {
1403     new AnnotationExporter().exportFeatures(alignPanel);
1404   }
1405
1406   @Override
1407   public void exportAnnotations_actionPerformed(ActionEvent e)
1408   {
1409     new AnnotationExporter().exportAnnotations(alignPanel);
1410   }
1411
1412   @Override
1413   public void associatedData_actionPerformed(ActionEvent e)
1414   {
1415     // Pick the tree file
1416     JalviewFileChooser chooser = new JalviewFileChooser(
1417             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1418     chooser.setFileView(new JalviewFileView());
1419     chooser.setDialogTitle(
1420             MessageManager.getString("label.load_jalview_annotations"));
1421     chooser.setToolTipText(
1422             MessageManager.getString("label.load_jalview_annotations"));
1423
1424     int value = chooser.showOpenDialog(null);
1425
1426     if (value == JalviewFileChooser.APPROVE_OPTION)
1427     {
1428       String choice = chooser.getSelectedFile().getPath();
1429       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1430       loadJalviewDataFile(choice, null, null, null);
1431     }
1432
1433   }
1434
1435   /**
1436    * Close the current view or all views in the alignment frame. If the frame
1437    * only contains one view then the alignment will be removed from memory.
1438    *
1439    * @param closeAllTabs
1440    */
1441   @Override
1442   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1443   {
1444     if (alignPanels != null && alignPanels.size() < 2)
1445     {
1446       closeAllTabs = true;
1447     }
1448
1449     try
1450     {
1451       if (alignPanels != null)
1452       {
1453         if (closeAllTabs)
1454         {
1455           if (this.isClosed())
1456           {
1457             // really close all the windows - otherwise wait till
1458             // setClosed(true) is called
1459             for (int i = 0; i < alignPanels.size(); i++)
1460             {
1461               AlignmentPanel ap = alignPanels.get(i);
1462               ap.closePanel();
1463             }
1464           }
1465         }
1466         else
1467         {
1468           closeView(alignPanel);
1469         }
1470       }
1471
1472       if (closeAllTabs)
1473       {
1474         /*
1475          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1476          * be called recursively, with the frame now in 'closed' state
1477          */
1478         this.setClosed(true);
1479       }
1480     } catch (Exception ex)
1481     {
1482       ex.printStackTrace();
1483     }
1484   }
1485
1486   /**
1487    * Close the specified panel and close up tabs appropriately.
1488    *
1489    * @param panelToClose
1490    */
1491   public void closeView(AlignmentPanel panelToClose)
1492   {
1493     int index = tabbedPane.getSelectedIndex();
1494     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1495     alignPanels.remove(panelToClose);
1496     panelToClose.closePanel();
1497     panelToClose = null;
1498
1499     tabbedPane.removeTabAt(closedindex);
1500     tabbedPane.validate();
1501
1502     if (index > closedindex || index == tabbedPane.getTabCount())
1503     {
1504       // modify currently selected tab index if necessary.
1505       index--;
1506     }
1507
1508     this.tabSelectionChanged(index);
1509   }
1510
1511   /**
1512    * DOCUMENT ME!
1513    */
1514   void updateEditMenuBar()
1515   {
1516
1517     if (viewport.getHistoryList().size() > 0)
1518     {
1519       undoMenuItem.setEnabled(true);
1520       CommandI command = viewport.getHistoryList().peek();
1521       undoMenuItem.setText(MessageManager
1522               .formatMessage("label.undo_command", new Object[]
1523               { command.getDescription() }));
1524     }
1525     else
1526     {
1527       undoMenuItem.setEnabled(false);
1528       undoMenuItem.setText(MessageManager.getString("action.undo"));
1529     }
1530
1531     if (viewport.getRedoList().size() > 0)
1532     {
1533       redoMenuItem.setEnabled(true);
1534
1535       CommandI command = viewport.getRedoList().peek();
1536       redoMenuItem.setText(MessageManager
1537               .formatMessage("label.redo_command", new Object[]
1538               { command.getDescription() }));
1539     }
1540     else
1541     {
1542       redoMenuItem.setEnabled(false);
1543       redoMenuItem.setText(MessageManager.getString("action.redo"));
1544     }
1545   }
1546
1547   @Override
1548   public void addHistoryItem(CommandI command)
1549   {
1550     if (command.getSize() > 0)
1551     {
1552       viewport.addToHistoryList(command);
1553       viewport.clearRedoList();
1554       updateEditMenuBar();
1555       viewport.updateHiddenColumns();
1556       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1557       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1558       // viewport.getColumnSelection()
1559       // .getHiddenColumns().size() > 0);
1560     }
1561   }
1562
1563   /**
1564    *
1565    * @return alignment objects for all views
1566    */
1567   AlignmentI[] getViewAlignments()
1568   {
1569     if (alignPanels != null)
1570     {
1571       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1572       int i = 0;
1573       for (AlignmentPanel ap : alignPanels)
1574       {
1575         als[i++] = ap.av.getAlignment();
1576       }
1577       return als;
1578     }
1579     if (viewport != null)
1580     {
1581       return new AlignmentI[] { viewport.getAlignment() };
1582     }
1583     return null;
1584   }
1585
1586   /**
1587    * DOCUMENT ME!
1588    *
1589    * @param e
1590    *          DOCUMENT ME!
1591    */
1592   @Override
1593   protected void undoMenuItem_actionPerformed(ActionEvent e)
1594   {
1595     if (viewport.getHistoryList().isEmpty())
1596     {
1597       return;
1598     }
1599     CommandI command = viewport.getHistoryList().pop();
1600     viewport.addToRedoList(command);
1601     command.undoCommand(getViewAlignments());
1602
1603     AlignmentViewport originalSource = getOriginatingSource(command);
1604     updateEditMenuBar();
1605
1606     if (originalSource != null)
1607     {
1608       if (originalSource != viewport)
1609       {
1610         Cache.log.warn(
1611                 "Implementation worry: mismatch of viewport origin for undo");
1612       }
1613       originalSource.updateHiddenColumns();
1614       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1615       // null
1616       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1617       // viewport.getColumnSelection()
1618       // .getHiddenColumns().size() > 0);
1619       originalSource.firePropertyChange("alignment", null,
1620               originalSource.getAlignment().getSequences());
1621     }
1622   }
1623
1624   /**
1625    * DOCUMENT ME!
1626    *
1627    * @param e
1628    *          DOCUMENT ME!
1629    */
1630   @Override
1631   protected void redoMenuItem_actionPerformed(ActionEvent e)
1632   {
1633     if (viewport.getRedoList().size() < 1)
1634     {
1635       return;
1636     }
1637
1638     CommandI command = viewport.getRedoList().pop();
1639     viewport.addToHistoryList(command);
1640     command.doCommand(getViewAlignments());
1641
1642     AlignmentViewport originalSource = getOriginatingSource(command);
1643     updateEditMenuBar();
1644
1645     if (originalSource != null)
1646     {
1647
1648       if (originalSource != viewport)
1649       {
1650         Cache.log.warn(
1651                 "Implementation worry: mismatch of viewport origin for redo");
1652       }
1653       originalSource.updateHiddenColumns();
1654       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1655       // null
1656       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1657       // viewport.getColumnSelection()
1658       // .getHiddenColumns().size() > 0);
1659       originalSource.firePropertyChange("alignment", null,
1660               originalSource.getAlignment().getSequences());
1661     }
1662   }
1663
1664   AlignmentViewport getOriginatingSource(CommandI command)
1665   {
1666     AlignmentViewport originalSource = null;
1667     // For sequence removal and addition, we need to fire
1668     // the property change event FROM the viewport where the
1669     // original alignment was altered
1670     AlignmentI al = null;
1671     if (command instanceof EditCommand)
1672     {
1673       EditCommand editCommand = (EditCommand) command;
1674       al = editCommand.getAlignment();
1675       List<Component> comps = PaintRefresher.components
1676               .get(viewport.getSequenceSetId());
1677
1678       for (Component comp : comps)
1679       {
1680         if (comp instanceof AlignmentPanel)
1681         {
1682           if (al == ((AlignmentPanel) comp).av.getAlignment())
1683           {
1684             originalSource = ((AlignmentPanel) comp).av;
1685             break;
1686           }
1687         }
1688       }
1689     }
1690
1691     if (originalSource == null)
1692     {
1693       // The original view is closed, we must validate
1694       // the current view against the closed view first
1695       if (al != null)
1696       {
1697         PaintRefresher.validateSequences(al, viewport.getAlignment());
1698       }
1699
1700       originalSource = viewport;
1701     }
1702
1703     return originalSource;
1704   }
1705
1706   /**
1707    * DOCUMENT ME!
1708    *
1709    * @param up
1710    *          DOCUMENT ME!
1711    */
1712   public void moveSelectedSequences(boolean up)
1713   {
1714     SequenceGroup sg = viewport.getSelectionGroup();
1715
1716     if (sg == null)
1717     {
1718       return;
1719     }
1720     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1721             viewport.getHiddenRepSequences(), up);
1722     alignPanel.paintAlignment(true, false);
1723   }
1724
1725   synchronized void slideSequences(boolean right, int size)
1726   {
1727     List<SequenceI> sg = new ArrayList<>();
1728     if (viewport.cursorMode)
1729     {
1730       sg.add(viewport.getAlignment()
1731               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1732     }
1733     else if (viewport.getSelectionGroup() != null
1734             && viewport.getSelectionGroup().getSize() != viewport
1735                     .getAlignment().getHeight())
1736     {
1737       sg = viewport.getSelectionGroup()
1738               .getSequences(viewport.getHiddenRepSequences());
1739     }
1740
1741     if (sg.size() < 1)
1742     {
1743       return;
1744     }
1745
1746     List<SequenceI> invertGroup = new ArrayList<>();
1747
1748     for (SequenceI seq : viewport.getAlignment().getSequences())
1749     {
1750       if (!sg.contains(seq))
1751       {
1752         invertGroup.add(seq);
1753       }
1754     }
1755
1756     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1757
1758     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1759     for (int i = 0; i < invertGroup.size(); i++)
1760     {
1761       seqs2[i] = invertGroup.get(i);
1762     }
1763
1764     SlideSequencesCommand ssc;
1765     if (right)
1766     {
1767       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1768               viewport.getGapCharacter());
1769     }
1770     else
1771     {
1772       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1773               viewport.getGapCharacter());
1774     }
1775
1776     int groupAdjustment = 0;
1777     if (ssc.getGapsInsertedBegin() && right)
1778     {
1779       if (viewport.cursorMode)
1780       {
1781         alignPanel.getSeqPanel().moveCursor(size, 0);
1782       }
1783       else
1784       {
1785         groupAdjustment = size;
1786       }
1787     }
1788     else if (!ssc.getGapsInsertedBegin() && !right)
1789     {
1790       if (viewport.cursorMode)
1791       {
1792         alignPanel.getSeqPanel().moveCursor(-size, 0);
1793       }
1794       else
1795       {
1796         groupAdjustment = -size;
1797       }
1798     }
1799
1800     if (groupAdjustment != 0)
1801     {
1802       viewport.getSelectionGroup().setStartRes(
1803               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1804       viewport.getSelectionGroup().setEndRes(
1805               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1806     }
1807
1808     /*
1809      * just extend the last slide command if compatible; but not if in
1810      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1811      */
1812     boolean appendHistoryItem = false;
1813     Deque<CommandI> historyList = viewport.getHistoryList();
1814     boolean inSplitFrame = getSplitViewContainer() != null;
1815     if (!inSplitFrame && historyList != null && historyList.size() > 0
1816             && historyList.peek() instanceof SlideSequencesCommand)
1817     {
1818       appendHistoryItem = ssc.appendSlideCommand(
1819               (SlideSequencesCommand) historyList.peek());
1820     }
1821
1822     if (!appendHistoryItem)
1823     {
1824       addHistoryItem(ssc);
1825     }
1826
1827     repaint();
1828   }
1829
1830   /**
1831    * DOCUMENT ME!
1832    *
1833    * @param e
1834    *          DOCUMENT ME!
1835    */
1836   @Override
1837   protected void copy_actionPerformed(ActionEvent e)
1838   {
1839     System.gc();
1840     if (viewport.getSelectionGroup() == null)
1841     {
1842       return;
1843     }
1844     // TODO: preserve the ordering of displayed alignment annotation in any
1845     // internal paste (particularly sequence associated annotation)
1846     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1847     String[] omitHidden = null;
1848
1849     if (viewport.hasHiddenColumns())
1850     {
1851       omitHidden = viewport.getViewAsString(true);
1852     }
1853
1854     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1855             seqs, omitHidden, null);
1856
1857     StringSelection ss = new StringSelection(output);
1858
1859     try
1860     {
1861       jalview.gui.Desktop.internalCopy = true;
1862       // Its really worth setting the clipboard contents
1863       // to empty before setting the large StringSelection!!
1864       Toolkit.getDefaultToolkit().getSystemClipboard()
1865               .setContents(new StringSelection(""), null);
1866
1867       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1868               Desktop.instance);
1869     } catch (OutOfMemoryError er)
1870     {
1871       new OOMWarning("copying region", er);
1872       return;
1873     }
1874
1875     ArrayList<int[]> hiddenColumns = null;
1876     if (viewport.hasHiddenColumns())
1877     {
1878       hiddenColumns = new ArrayList<>();
1879       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1880       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1881       ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1882               .getHiddenColumns().getHiddenColumnsCopy();
1883       for (int[] region : hiddenRegions)
1884       {
1885         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1886         {
1887           hiddenColumns
1888                   .add(new int[]
1889                   { region[0] - hiddenOffset, region[1] - hiddenOffset });
1890         }
1891       }
1892     }
1893
1894     Desktop.jalviewClipboard = new Object[] { seqs,
1895         viewport.getAlignment().getDataset(), hiddenColumns };
1896     statusBar.setText(MessageManager.formatMessage(
1897             "label.copied_sequences_to_clipboard", new Object[]
1898             { Integer.valueOf(seqs.length).toString() }));
1899   }
1900
1901   /**
1902    * DOCUMENT ME!
1903    *
1904    * @param e
1905    *          DOCUMENT ME!
1906    */
1907   @Override
1908   protected void pasteNew_actionPerformed(ActionEvent e)
1909   {
1910     paste(true);
1911   }
1912
1913   /**
1914    * DOCUMENT ME!
1915    *
1916    * @param e
1917    *          DOCUMENT ME!
1918    */
1919   @Override
1920   protected void pasteThis_actionPerformed(ActionEvent e)
1921   {
1922     paste(false);
1923   }
1924
1925   /**
1926    * Paste contents of Jalview clipboard
1927    *
1928    * @param newAlignment
1929    *          true to paste to a new alignment, otherwise add to this.
1930    */
1931   void paste(boolean newAlignment)
1932   {
1933     boolean externalPaste = true;
1934     try
1935     {
1936       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1937       Transferable contents = c.getContents(this);
1938
1939       if (contents == null)
1940       {
1941         return;
1942       }
1943
1944       String str;
1945       FileFormatI format;
1946       try
1947       {
1948         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1949         if (str.length() < 1)
1950         {
1951           return;
1952         }
1953
1954         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1955
1956       } catch (OutOfMemoryError er)
1957       {
1958         new OOMWarning("Out of memory pasting sequences!!", er);
1959         return;
1960       }
1961
1962       SequenceI[] sequences;
1963       boolean annotationAdded = false;
1964       AlignmentI alignment = null;
1965
1966       if (Desktop.jalviewClipboard != null)
1967       {
1968         // The clipboard was filled from within Jalview, we must use the
1969         // sequences
1970         // And dataset from the copied alignment
1971         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1972         // be doubly sure that we create *new* sequence objects.
1973         sequences = new SequenceI[newseq.length];
1974         for (int i = 0; i < newseq.length; i++)
1975         {
1976           sequences[i] = new Sequence(newseq[i]);
1977         }
1978         alignment = new Alignment(sequences);
1979         externalPaste = false;
1980       }
1981       else
1982       {
1983         // parse the clipboard as an alignment.
1984         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1985                 format);
1986         sequences = alignment.getSequencesArray();
1987       }
1988
1989       int alwidth = 0;
1990       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1991       int fgroup = -1;
1992
1993       if (newAlignment)
1994       {
1995
1996         if (Desktop.jalviewClipboard != null)
1997         {
1998           // dataset is inherited
1999           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2000         }
2001         else
2002         {
2003           // new dataset is constructed
2004           alignment.setDataset(null);
2005         }
2006         alwidth = alignment.getWidth() + 1;
2007       }
2008       else
2009       {
2010         AlignmentI pastedal = alignment; // preserve pasted alignment object
2011         // Add pasted sequences and dataset into existing alignment.
2012         alignment = viewport.getAlignment();
2013         alwidth = alignment.getWidth() + 1;
2014         // decide if we need to import sequences from an existing dataset
2015         boolean importDs = Desktop.jalviewClipboard != null
2016                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2017         // importDs==true instructs us to copy over new dataset sequences from
2018         // an existing alignment
2019         Vector newDs = (importDs) ? new Vector() : null; // used to create
2020         // minimum dataset set
2021
2022         for (int i = 0; i < sequences.length; i++)
2023         {
2024           if (importDs)
2025           {
2026             newDs.addElement(null);
2027           }
2028           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2029           // paste
2030           if (importDs && ds != null)
2031           {
2032             if (!newDs.contains(ds))
2033             {
2034               newDs.setElementAt(ds, i);
2035               ds = new Sequence(ds);
2036               // update with new dataset sequence
2037               sequences[i].setDatasetSequence(ds);
2038             }
2039             else
2040             {
2041               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2042             }
2043           }
2044           else
2045           {
2046             // copy and derive new dataset sequence
2047             sequences[i] = sequences[i].deriveSequence();
2048             alignment.getDataset()
2049                     .addSequence(sequences[i].getDatasetSequence());
2050             // TODO: avoid creation of duplicate dataset sequences with a
2051             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2052           }
2053           alignment.addSequence(sequences[i]); // merges dataset
2054         }
2055         if (newDs != null)
2056         {
2057           newDs.clear(); // tidy up
2058         }
2059         if (alignment.getAlignmentAnnotation() != null)
2060         {
2061           for (AlignmentAnnotation alan : alignment
2062                   .getAlignmentAnnotation())
2063           {
2064             if (alan.graphGroup > fgroup)
2065             {
2066               fgroup = alan.graphGroup;
2067             }
2068           }
2069         }
2070         if (pastedal.getAlignmentAnnotation() != null)
2071         {
2072           // Add any annotation attached to alignment.
2073           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2074           for (int i = 0; i < alann.length; i++)
2075           {
2076             annotationAdded = true;
2077             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2078             {
2079               AlignmentAnnotation newann = new AlignmentAnnotation(
2080                       alann[i]);
2081               if (newann.graphGroup > -1)
2082               {
2083                 if (newGraphGroups.size() <= newann.graphGroup
2084                         || newGraphGroups.get(newann.graphGroup) == null)
2085                 {
2086                   for (int q = newGraphGroups
2087                           .size(); q <= newann.graphGroup; q++)
2088                   {
2089                     newGraphGroups.add(q, null);
2090                   }
2091                   newGraphGroups.set(newann.graphGroup,
2092                           new Integer(++fgroup));
2093                 }
2094                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2095                         .intValue();
2096               }
2097
2098               newann.padAnnotation(alwidth);
2099               alignment.addAnnotation(newann);
2100             }
2101           }
2102         }
2103       }
2104       if (!newAlignment)
2105       {
2106         // /////
2107         // ADD HISTORY ITEM
2108         //
2109         addHistoryItem(new EditCommand(
2110                 MessageManager.getString("label.add_sequences"),
2111                 Action.PASTE, sequences, 0, alignment.getWidth(),
2112                 alignment));
2113       }
2114       // Add any annotations attached to sequences
2115       for (int i = 0; i < sequences.length; i++)
2116       {
2117         if (sequences[i].getAnnotation() != null)
2118         {
2119           AlignmentAnnotation newann;
2120           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2121           {
2122             annotationAdded = true;
2123             newann = sequences[i].getAnnotation()[a];
2124             newann.adjustForAlignment();
2125             newann.padAnnotation(alwidth);
2126             if (newann.graphGroup > -1)
2127             {
2128               if (newann.graphGroup > -1)
2129               {
2130                 if (newGraphGroups.size() <= newann.graphGroup
2131                         || newGraphGroups.get(newann.graphGroup) == null)
2132                 {
2133                   for (int q = newGraphGroups
2134                           .size(); q <= newann.graphGroup; q++)
2135                   {
2136                     newGraphGroups.add(q, null);
2137                   }
2138                   newGraphGroups.set(newann.graphGroup,
2139                           new Integer(++fgroup));
2140                 }
2141                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2142                         .intValue();
2143               }
2144             }
2145             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2146             // was
2147             // duplicated
2148             // earlier
2149             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2150                     a);
2151           }
2152         }
2153       }
2154       if (!newAlignment)
2155       {
2156
2157         // propagate alignment changed.
2158         viewport.getRanges().setEndSeq(alignment.getHeight());
2159         if (annotationAdded)
2160         {
2161           // Duplicate sequence annotation in all views.
2162           AlignmentI[] alview = this.getViewAlignments();
2163           for (int i = 0; i < sequences.length; i++)
2164           {
2165             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2166             if (sann == null)
2167             {
2168               continue;
2169             }
2170             for (int avnum = 0; avnum < alview.length; avnum++)
2171             {
2172               if (alview[avnum] != alignment)
2173               {
2174                 // duplicate in a view other than the one with input focus
2175                 int avwidth = alview[avnum].getWidth() + 1;
2176                 // this relies on sann being preserved after we
2177                 // modify the sequence's annotation array for each duplication
2178                 for (int a = 0; a < sann.length; a++)
2179                 {
2180                   AlignmentAnnotation newann = new AlignmentAnnotation(
2181                           sann[a]);
2182                   sequences[i].addAlignmentAnnotation(newann);
2183                   newann.padAnnotation(avwidth);
2184                   alview[avnum].addAnnotation(newann); // annotation was
2185                   // duplicated earlier
2186                   // TODO JAL-1145 graphGroups are not updated for sequence
2187                   // annotation added to several views. This may cause
2188                   // strangeness
2189                   alview[avnum].setAnnotationIndex(newann, a);
2190                 }
2191               }
2192             }
2193           }
2194           buildSortByAnnotationScoresMenu();
2195         }
2196         viewport.firePropertyChange("alignment", null,
2197                 alignment.getSequences());
2198         if (alignPanels != null)
2199         {
2200           for (AlignmentPanel ap : alignPanels)
2201           {
2202             ap.validateAnnotationDimensions(false);
2203           }
2204         }
2205         else
2206         {
2207           alignPanel.validateAnnotationDimensions(false);
2208         }
2209
2210       }
2211       else
2212       {
2213         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2214                 DEFAULT_HEIGHT);
2215         String newtitle = new String("Copied sequences");
2216
2217         if (Desktop.jalviewClipboard != null
2218                 && Desktop.jalviewClipboard[2] != null)
2219         {
2220           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2221           for (int[] region : hc)
2222           {
2223             af.viewport.hideColumns(region[0], region[1]);
2224           }
2225         }
2226
2227         // >>>This is a fix for the moment, until a better solution is
2228         // found!!<<<
2229         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2230                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2231                         .getFeatureRenderer());
2232
2233         // TODO: maintain provenance of an alignment, rather than just make the
2234         // title a concatenation of operations.
2235         if (!externalPaste)
2236         {
2237           if (title.startsWith("Copied sequences"))
2238           {
2239             newtitle = title;
2240           }
2241           else
2242           {
2243             newtitle = newtitle.concat("- from " + title);
2244           }
2245         }
2246         else
2247         {
2248           newtitle = new String("Pasted sequences");
2249         }
2250
2251         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2252                 DEFAULT_HEIGHT);
2253
2254       }
2255
2256     } catch (Exception ex)
2257     {
2258       ex.printStackTrace();
2259       System.out.println("Exception whilst pasting: " + ex);
2260       // could be anything being pasted in here
2261     }
2262
2263   }
2264
2265   @Override
2266   protected void expand_newalign(ActionEvent e)
2267   {
2268     try
2269     {
2270       AlignmentI alignment = AlignmentUtils
2271               .expandContext(getViewport().getAlignment(), -1);
2272       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2273               DEFAULT_HEIGHT);
2274       String newtitle = new String("Flanking alignment");
2275
2276       if (Desktop.jalviewClipboard != null
2277               && Desktop.jalviewClipboard[2] != null)
2278       {
2279         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2280         for (int region[] : hc)
2281         {
2282           af.viewport.hideColumns(region[0], region[1]);
2283         }
2284       }
2285
2286       // >>>This is a fix for the moment, until a better solution is
2287       // found!!<<<
2288       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2289               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2290                       .getFeatureRenderer());
2291
2292       // TODO: maintain provenance of an alignment, rather than just make the
2293       // title a concatenation of operations.
2294       {
2295         if (title.startsWith("Copied sequences"))
2296         {
2297           newtitle = title;
2298         }
2299         else
2300         {
2301           newtitle = newtitle.concat("- from " + title);
2302         }
2303       }
2304
2305       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2306
2307     } catch (Exception ex)
2308     {
2309       ex.printStackTrace();
2310       System.out.println("Exception whilst pasting: " + ex);
2311       // could be anything being pasted in here
2312     } catch (OutOfMemoryError oom)
2313     {
2314       new OOMWarning("Viewing flanking region of alignment", oom);
2315     }
2316   }
2317
2318   /**
2319    * DOCUMENT ME!
2320    *
2321    * @param e
2322    *          DOCUMENT ME!
2323    */
2324   @Override
2325   protected void cut_actionPerformed(ActionEvent e)
2326   {
2327     copy_actionPerformed(null);
2328     delete_actionPerformed(null);
2329   }
2330
2331   /**
2332    * DOCUMENT ME!
2333    *
2334    * @param e
2335    *          DOCUMENT ME!
2336    */
2337   @Override
2338   protected void delete_actionPerformed(ActionEvent evt)
2339   {
2340
2341     SequenceGroup sg = viewport.getSelectionGroup();
2342     if (sg == null)
2343     {
2344       return;
2345     }
2346
2347     /*
2348      * If the cut affects all sequences, warn, remove highlighted columns
2349      */
2350     if (sg.getSize() == viewport.getAlignment().getHeight())
2351     {
2352       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2353               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2354       if (isEntireAlignWidth)
2355       {
2356         int confirm = JvOptionPane.showConfirmDialog(this,
2357                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2358                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2359                 JvOptionPane.OK_CANCEL_OPTION);
2360
2361         if (confirm == JvOptionPane.CANCEL_OPTION
2362                 || confirm == JvOptionPane.CLOSED_OPTION)
2363         {
2364           return;
2365         }
2366       }
2367       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2368               sg.getEndRes() + 1);
2369     }
2370     SequenceI[] cut = sg.getSequences()
2371             .toArray(new SequenceI[sg.getSize()]);
2372
2373     addHistoryItem(new EditCommand(
2374             MessageManager.getString("label.cut_sequences"), Action.CUT,
2375             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2376             viewport.getAlignment()));
2377
2378     viewport.setSelectionGroup(null);
2379     viewport.sendSelection();
2380     viewport.getAlignment().deleteGroup(sg);
2381
2382     viewport.firePropertyChange("alignment", null,
2383             viewport.getAlignment().getSequences());
2384     if (viewport.getAlignment().getHeight() < 1)
2385     {
2386       try
2387       {
2388         this.setClosed(true);
2389       } catch (Exception ex)
2390       {
2391       }
2392     }
2393   }
2394
2395   /**
2396    * DOCUMENT ME!
2397    *
2398    * @param e
2399    *          DOCUMENT ME!
2400    */
2401   @Override
2402   protected void deleteGroups_actionPerformed(ActionEvent e)
2403   {
2404     if (avc.deleteGroups())
2405     {
2406       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2407       alignPanel.updateAnnotation();
2408       alignPanel.paintAlignment(true, true);
2409     }
2410   }
2411
2412   /**
2413    * DOCUMENT ME!
2414    *
2415    * @param e
2416    *          DOCUMENT ME!
2417    */
2418   @Override
2419   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2420   {
2421     SequenceGroup sg = new SequenceGroup();
2422
2423     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2424     {
2425       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2426     }
2427
2428     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2429     viewport.setSelectionGroup(sg);
2430     viewport.sendSelection();
2431     // JAL-2034 - should delegate to
2432     // alignPanel to decide if overview needs
2433     // updating.
2434     alignPanel.paintAlignment(false, false);
2435     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2436   }
2437
2438   /**
2439    * DOCUMENT ME!
2440    *
2441    * @param e
2442    *          DOCUMENT ME!
2443    */
2444   @Override
2445   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2446   {
2447     if (viewport.cursorMode)
2448     {
2449       alignPanel.getSeqPanel().keyboardNo1 = null;
2450       alignPanel.getSeqPanel().keyboardNo2 = null;
2451     }
2452     viewport.setSelectionGroup(null);
2453     viewport.getColumnSelection().clear();
2454     viewport.setSelectionGroup(null);
2455     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2456     // JAL-2034 - should delegate to
2457     // alignPanel to decide if overview needs
2458     // updating.
2459     alignPanel.paintAlignment(false, false);
2460     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2461     viewport.sendSelection();
2462   }
2463
2464   /**
2465    * DOCUMENT ME!
2466    *
2467    * @param e
2468    *          DOCUMENT ME!
2469    */
2470   @Override
2471   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2472   {
2473     SequenceGroup sg = viewport.getSelectionGroup();
2474
2475     if (sg == null)
2476     {
2477       selectAllSequenceMenuItem_actionPerformed(null);
2478
2479       return;
2480     }
2481
2482     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2483     {
2484       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2485     }
2486     // JAL-2034 - should delegate to
2487     // alignPanel to decide if overview needs
2488     // updating.
2489
2490     alignPanel.paintAlignment(true, false);
2491     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2492     viewport.sendSelection();
2493   }
2494
2495   @Override
2496   public void invertColSel_actionPerformed(ActionEvent e)
2497   {
2498     viewport.invertColumnSelection();
2499     alignPanel.paintAlignment(true, false);
2500     viewport.sendSelection();
2501   }
2502
2503   /**
2504    * DOCUMENT ME!
2505    *
2506    * @param e
2507    *          DOCUMENT ME!
2508    */
2509   @Override
2510   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2511   {
2512     trimAlignment(true);
2513   }
2514
2515   /**
2516    * DOCUMENT ME!
2517    *
2518    * @param e
2519    *          DOCUMENT ME!
2520    */
2521   @Override
2522   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2523   {
2524     trimAlignment(false);
2525   }
2526
2527   void trimAlignment(boolean trimLeft)
2528   {
2529     ColumnSelection colSel = viewport.getColumnSelection();
2530     int column;
2531
2532     if (!colSel.isEmpty())
2533     {
2534       if (trimLeft)
2535       {
2536         column = colSel.getMin();
2537       }
2538       else
2539       {
2540         column = colSel.getMax();
2541       }
2542
2543       SequenceI[] seqs;
2544       if (viewport.getSelectionGroup() != null)
2545       {
2546         seqs = viewport.getSelectionGroup()
2547                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2548       }
2549       else
2550       {
2551         seqs = viewport.getAlignment().getSequencesArray();
2552       }
2553
2554       TrimRegionCommand trimRegion;
2555       if (trimLeft)
2556       {
2557         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2558                 column, viewport.getAlignment());
2559         viewport.getRanges().setStartRes(0);
2560       }
2561       else
2562       {
2563         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2564                 column, viewport.getAlignment());
2565       }
2566
2567       statusBar.setText(MessageManager
2568               .formatMessage("label.removed_columns", new String[]
2569               { Integer.valueOf(trimRegion.getSize()).toString() }));
2570
2571       addHistoryItem(trimRegion);
2572
2573       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2574       {
2575         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2576                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2577         {
2578           viewport.getAlignment().deleteGroup(sg);
2579         }
2580       }
2581
2582       viewport.firePropertyChange("alignment", null,
2583               viewport.getAlignment().getSequences());
2584     }
2585   }
2586
2587   /**
2588    * DOCUMENT ME!
2589    *
2590    * @param e
2591    *          DOCUMENT ME!
2592    */
2593   @Override
2594   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2595   {
2596     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2597
2598     SequenceI[] seqs;
2599     if (viewport.getSelectionGroup() != null)
2600     {
2601       seqs = viewport.getSelectionGroup()
2602               .getSequencesAsArray(viewport.getHiddenRepSequences());
2603       start = viewport.getSelectionGroup().getStartRes();
2604       end = viewport.getSelectionGroup().getEndRes();
2605     }
2606     else
2607     {
2608       seqs = viewport.getAlignment().getSequencesArray();
2609     }
2610
2611     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2612             "Remove Gapped Columns", seqs, start, end,
2613             viewport.getAlignment());
2614
2615     addHistoryItem(removeGapCols);
2616
2617     statusBar.setText(MessageManager
2618             .formatMessage("label.removed_empty_columns", new Object[]
2619             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2620
2621     // This is to maintain viewport position on first residue
2622     // of first sequence
2623     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2624     ViewportRanges ranges = viewport.getRanges();
2625     int startRes = seq.findPosition(ranges.getStartRes());
2626     // ShiftList shifts;
2627     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2628     // edit.alColumnChanges=shifts.getInverse();
2629     // if (viewport.hasHiddenColumns)
2630     // viewport.getColumnSelection().compensateForEdits(shifts);
2631     ranges.setStartRes(seq.findIndex(startRes) - 1);
2632     viewport.firePropertyChange("alignment", null,
2633             viewport.getAlignment().getSequences());
2634
2635   }
2636
2637   /**
2638    * DOCUMENT ME!
2639    *
2640    * @param e
2641    *          DOCUMENT ME!
2642    */
2643   @Override
2644   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2645   {
2646     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2647
2648     SequenceI[] seqs;
2649     if (viewport.getSelectionGroup() != null)
2650     {
2651       seqs = viewport.getSelectionGroup()
2652               .getSequencesAsArray(viewport.getHiddenRepSequences());
2653       start = viewport.getSelectionGroup().getStartRes();
2654       end = viewport.getSelectionGroup().getEndRes();
2655     }
2656     else
2657     {
2658       seqs = viewport.getAlignment().getSequencesArray();
2659     }
2660
2661     // This is to maintain viewport position on first residue
2662     // of first sequence
2663     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2664     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2665
2666     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2667             viewport.getAlignment()));
2668
2669     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2670
2671     viewport.firePropertyChange("alignment", null,
2672             viewport.getAlignment().getSequences());
2673
2674   }
2675
2676   /**
2677    * DOCUMENT ME!
2678    *
2679    * @param e
2680    *          DOCUMENT ME!
2681    */
2682   @Override
2683   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2684   {
2685     viewport.setPadGaps(padGapsMenuitem.isSelected());
2686     viewport.firePropertyChange("alignment", null,
2687             viewport.getAlignment().getSequences());
2688   }
2689
2690   /**
2691    * DOCUMENT ME!
2692    *
2693    * @param e
2694    *          DOCUMENT ME!
2695    */
2696   @Override
2697   public void findMenuItem_actionPerformed(ActionEvent e)
2698   {
2699     new Finder();
2700   }
2701
2702   /**
2703    * Create a new view of the current alignment.
2704    */
2705   @Override
2706   public void newView_actionPerformed(ActionEvent e)
2707   {
2708     newView(null, true);
2709   }
2710
2711   /**
2712    * Creates and shows a new view of the current alignment.
2713    *
2714    * @param viewTitle
2715    *          title of newly created view; if null, one will be generated
2716    * @param copyAnnotation
2717    *          if true then duplicate all annnotation, groups and settings
2718    * @return new alignment panel, already displayed.
2719    */
2720   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2721   {
2722     /*
2723      * Create a new AlignmentPanel (with its own, new Viewport)
2724      */
2725     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2726     if (!copyAnnotation)
2727     {
2728       /*
2729        * remove all groups and annotation except for the automatic stuff
2730        */
2731       newap.av.getAlignment().deleteAllGroups();
2732       newap.av.getAlignment().deleteAllAnnotations(false);
2733     }
2734
2735     newap.av.setGatherViewsHere(false);
2736
2737     if (viewport.viewName == null)
2738     {
2739       viewport.viewName = MessageManager
2740               .getString("label.view_name_original");
2741     }
2742
2743     /*
2744      * Views share the same edits undo and redo stacks
2745      */
2746     newap.av.setHistoryList(viewport.getHistoryList());
2747     newap.av.setRedoList(viewport.getRedoList());
2748
2749     /*
2750      * 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.viewName = 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.viewName))
2828         {
2829           existingNames.add(ap.av.viewName);
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(), false);
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.paintAlignment(true, true);
3060     viewport.sendSelection();
3061   }
3062
3063   /*
3064    * (non-Javadoc)
3065    *
3066    * @see
3067    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3068    * ActionEvent)
3069    */
3070   @Override
3071   public void showAllhidden_actionPerformed(ActionEvent e)
3072   {
3073     viewport.showAllHiddenColumns();
3074     viewport.showAllHiddenSeqs();
3075     alignPanel.paintAlignment(true, true);
3076     viewport.sendSelection();
3077   }
3078
3079   @Override
3080   public void hideSelColumns_actionPerformed(ActionEvent e)
3081   {
3082     viewport.hideSelectedColumns();
3083     alignPanel.paintAlignment(true, true);
3084     viewport.sendSelection();
3085   }
3086
3087   @Override
3088   public void hiddenMarkers_actionPerformed(ActionEvent e)
3089   {
3090     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3091     repaint();
3092   }
3093
3094   /**
3095    * DOCUMENT ME!
3096    *
3097    * @param e
3098    *          DOCUMENT ME!
3099    */
3100   @Override
3101   protected void scaleAbove_actionPerformed(ActionEvent e)
3102   {
3103     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3104     // TODO: do we actually need to update overview for scale above change ?
3105     alignPanel.paintAlignment(true, false);
3106   }
3107
3108   /**
3109    * DOCUMENT ME!
3110    *
3111    * @param e
3112    *          DOCUMENT ME!
3113    */
3114   @Override
3115   protected void scaleLeft_actionPerformed(ActionEvent e)
3116   {
3117     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3118     alignPanel.paintAlignment(true, false);
3119   }
3120
3121   /**
3122    * DOCUMENT ME!
3123    *
3124    * @param e
3125    *          DOCUMENT ME!
3126    */
3127   @Override
3128   protected void scaleRight_actionPerformed(ActionEvent e)
3129   {
3130     viewport.setScaleRightWrapped(scaleRight.isSelected());
3131     alignPanel.paintAlignment(true, false);
3132   }
3133
3134   /**
3135    * DOCUMENT ME!
3136    *
3137    * @param e
3138    *          DOCUMENT ME!
3139    */
3140   @Override
3141   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3142   {
3143     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3144     alignPanel.paintAlignment(false, false);
3145   }
3146
3147   /**
3148    * DOCUMENT ME!
3149    *
3150    * @param e
3151    *          DOCUMENT ME!
3152    */
3153   @Override
3154   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3155   {
3156     viewport.setShowText(viewTextMenuItem.isSelected());
3157     alignPanel.paintAlignment(false, false);
3158   }
3159
3160   /**
3161    * DOCUMENT ME!
3162    *
3163    * @param e
3164    *          DOCUMENT ME!
3165    */
3166   @Override
3167   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3168   {
3169     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3170     alignPanel.paintAlignment(false, false);
3171   }
3172
3173   public FeatureSettings featureSettings;
3174
3175   @Override
3176   public FeatureSettingsControllerI getFeatureSettingsUI()
3177   {
3178     return featureSettings;
3179   }
3180
3181   @Override
3182   public void featureSettings_actionPerformed(ActionEvent e)
3183   {
3184     if (featureSettings != null)
3185     {
3186       featureSettings.close();
3187       featureSettings = null;
3188     }
3189     if (!showSeqFeatures.isSelected())
3190     {
3191       // make sure features are actually displayed
3192       showSeqFeatures.setSelected(true);
3193       showSeqFeatures_actionPerformed(null);
3194     }
3195     featureSettings = new FeatureSettings(this);
3196   }
3197
3198   /**
3199    * Set or clear 'Show Sequence Features'
3200    *
3201    * @param evt
3202    *          DOCUMENT ME!
3203    */
3204   @Override
3205   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3206   {
3207     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3208     alignPanel.paintAlignment(true, true);
3209   }
3210
3211   /**
3212    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3213    * the annotations panel as a whole.
3214    *
3215    * The options to show/hide all annotations should be enabled when the panel
3216    * is shown, and disabled when the panel is hidden.
3217    *
3218    * @param e
3219    */
3220   @Override
3221   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3222   {
3223     final boolean setVisible = annotationPanelMenuItem.isSelected();
3224     viewport.setShowAnnotation(setVisible);
3225     this.showAllSeqAnnotations.setEnabled(setVisible);
3226     this.hideAllSeqAnnotations.setEnabled(setVisible);
3227     this.showAllAlAnnotations.setEnabled(setVisible);
3228     this.hideAllAlAnnotations.setEnabled(setVisible);
3229     alignPanel.updateLayout();
3230   }
3231
3232   @Override
3233   public void alignmentProperties()
3234   {
3235     JEditorPane editPane = new JEditorPane("text/html", "");
3236     editPane.setEditable(false);
3237     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3238             .formatAsHtml();
3239     editPane.setText(
3240             MessageManager.formatMessage("label.html_content", new Object[]
3241             { contents.toString() }));
3242     JInternalFrame frame = new JInternalFrame();
3243     frame.getContentPane().add(new JScrollPane(editPane));
3244
3245     Desktop.addInternalFrame(frame, MessageManager
3246             .formatMessage("label.alignment_properties", new Object[]
3247             { getTitle() }), 500, 400);
3248   }
3249
3250   /**
3251    * DOCUMENT ME!
3252    *
3253    * @param e
3254    *          DOCUMENT ME!
3255    */
3256   @Override
3257   public void overviewMenuItem_actionPerformed(ActionEvent e)
3258   {
3259     if (alignPanel.overviewPanel != null)
3260     {
3261       return;
3262     }
3263
3264     JInternalFrame frame = new JInternalFrame();
3265     final OverviewPanel overview = new OverviewPanel(alignPanel);
3266     frame.setContentPane(overview);
3267     Desktop.addInternalFrame(frame, MessageManager
3268             .formatMessage("label.overview_params", new Object[]
3269             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3270             true, true);
3271     frame.pack();
3272     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3273     frame.addInternalFrameListener(
3274             new javax.swing.event.InternalFrameAdapter()
3275             {
3276               @Override
3277               public void internalFrameClosed(
3278                       javax.swing.event.InternalFrameEvent evt)
3279               {
3280                 overview.dispose();
3281                 alignPanel.setOverviewPanel(null);
3282               };
3283             });
3284
3285     alignPanel.setOverviewPanel(overview);
3286   }
3287
3288   @Override
3289   public void textColour_actionPerformed()
3290   {
3291     new TextColourChooser().chooseColour(alignPanel, null);
3292   }
3293
3294   /*
3295    * public void covariationColour_actionPerformed() {
3296    * changeColour(new
3297    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3298    * ()[0])); }
3299    */
3300   @Override
3301   public void annotationColour_actionPerformed()
3302   {
3303     new AnnotationColourChooser(viewport, alignPanel);
3304   }
3305
3306   @Override
3307   public void annotationColumn_actionPerformed(ActionEvent e)
3308   {
3309     new AnnotationColumnChooser(viewport, alignPanel);
3310   }
3311
3312   /**
3313    * Action on the user checking or unchecking the option to apply the selected
3314    * colour scheme to all groups. If unchecked, groups may have their own
3315    * independent colour schemes.
3316    *
3317    * @param selected
3318    */
3319   @Override
3320   public void applyToAllGroups_actionPerformed(boolean selected)
3321   {
3322     viewport.setColourAppliesToAllGroups(selected);
3323   }
3324
3325   /**
3326    * Action on user selecting a colour from the colour menu
3327    *
3328    * @param name
3329    *          the name (not the menu item label!) of the colour scheme
3330    */
3331   @Override
3332   public void changeColour_actionPerformed(String name)
3333   {
3334     /*
3335      * 'User Defined' opens a panel to configure or load a
3336      * user-defined colour scheme
3337      */
3338     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3339     {
3340       new UserDefinedColours(alignPanel);
3341       return;
3342     }
3343
3344     /*
3345      * otherwise set the chosen colour scheme (or null for 'None')
3346      */
3347     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3348             viewport.getAlignment(), viewport.getHiddenRepSequences());
3349     changeColour(cs);
3350   }
3351
3352   /**
3353    * Actions on setting or changing the alignment colour scheme
3354    *
3355    * @param cs
3356    */
3357   @Override
3358   public void changeColour(ColourSchemeI cs)
3359   {
3360     // TODO: pull up to controller method
3361     ColourMenuHelper.setColourSelected(colourMenu, cs);
3362
3363     viewport.setGlobalColourScheme(cs);
3364
3365     alignPanel.paintAlignment(true, true);
3366   }
3367
3368   /**
3369    * Show the PID threshold slider panel
3370    */
3371   @Override
3372   protected void modifyPID_actionPerformed()
3373   {
3374     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3375             alignPanel.getViewName());
3376     SliderPanel.showPIDSlider();
3377   }
3378
3379   /**
3380    * Show the Conservation slider panel
3381    */
3382   @Override
3383   protected void modifyConservation_actionPerformed()
3384   {
3385     SliderPanel.setConservationSlider(alignPanel,
3386             viewport.getResidueShading(), alignPanel.getViewName());
3387     SliderPanel.showConservationSlider();
3388   }
3389
3390   /**
3391    * Action on selecting or deselecting (Colour) By Conservation
3392    */
3393   @Override
3394   public void conservationMenuItem_actionPerformed(boolean selected)
3395   {
3396     modifyConservation.setEnabled(selected);
3397     viewport.setConservationSelected(selected);
3398     viewport.getResidueShading().setConservationApplied(selected);
3399
3400     changeColour(viewport.getGlobalColourScheme());
3401     if (selected)
3402     {
3403       modifyConservation_actionPerformed();
3404     }
3405     else
3406     {
3407       SliderPanel.hideConservationSlider();
3408     }
3409   }
3410
3411   /**
3412    * Action on selecting or deselecting (Colour) Above PID Threshold
3413    */
3414   @Override
3415   public void abovePIDThreshold_actionPerformed(boolean selected)
3416   {
3417     modifyPID.setEnabled(selected);
3418     viewport.setAbovePIDThreshold(selected);
3419     if (!selected)
3420     {
3421       viewport.getResidueShading().setThreshold(0,
3422               viewport.isIgnoreGapsConsensus());
3423     }
3424
3425     changeColour(viewport.getGlobalColourScheme());
3426     if (selected)
3427     {
3428       modifyPID_actionPerformed();
3429     }
3430     else
3431     {
3432       SliderPanel.hidePIDSlider();
3433     }
3434   }
3435
3436   /**
3437    * DOCUMENT ME!
3438    *
3439    * @param e
3440    *          DOCUMENT ME!
3441    */
3442   @Override
3443   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3444   {
3445     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3446     AlignmentSorter.sortByPID(viewport.getAlignment(),
3447             viewport.getAlignment().getSequenceAt(0));
3448     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3449             viewport.getAlignment()));
3450     alignPanel.paintAlignment(true, false);
3451   }
3452
3453   /**
3454    * DOCUMENT ME!
3455    *
3456    * @param e
3457    *          DOCUMENT ME!
3458    */
3459   @Override
3460   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3461   {
3462     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3463     AlignmentSorter.sortByID(viewport.getAlignment());
3464     addHistoryItem(
3465             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3466     alignPanel.paintAlignment(true, false);
3467   }
3468
3469   /**
3470    * DOCUMENT ME!
3471    *
3472    * @param e
3473    *          DOCUMENT ME!
3474    */
3475   @Override
3476   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3477   {
3478     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3479     AlignmentSorter.sortByLength(viewport.getAlignment());
3480     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3481             viewport.getAlignment()));
3482     alignPanel.paintAlignment(true, false);
3483   }
3484
3485   /**
3486    * DOCUMENT ME!
3487    *
3488    * @param e
3489    *          DOCUMENT ME!
3490    */
3491   @Override
3492   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3493   {
3494     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3495     AlignmentSorter.sortByGroup(viewport.getAlignment());
3496     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3497             viewport.getAlignment()));
3498
3499     alignPanel.paintAlignment(true, false);
3500   }
3501
3502   /**
3503    * DOCUMENT ME!
3504    *
3505    * @param e
3506    *          DOCUMENT ME!
3507    */
3508   @Override
3509   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3510   {
3511     new RedundancyPanel(alignPanel, this);
3512   }
3513
3514   /**
3515    * DOCUMENT ME!
3516    *
3517    * @param e
3518    *          DOCUMENT ME!
3519    */
3520   @Override
3521   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3522   {
3523     if ((viewport.getSelectionGroup() == null)
3524             || (viewport.getSelectionGroup().getSize() < 2))
3525     {
3526       JvOptionPane.showInternalMessageDialog(this,
3527               MessageManager.getString(
3528                       "label.you_must_select_least_two_sequences"),
3529               MessageManager.getString("label.invalid_selection"),
3530               JvOptionPane.WARNING_MESSAGE);
3531     }
3532     else
3533     {
3534       JInternalFrame frame = new JInternalFrame();
3535       frame.setContentPane(new PairwiseAlignPanel(viewport));
3536       Desktop.addInternalFrame(frame,
3537               MessageManager.getString("action.pairwise_alignment"), 600,
3538               500);
3539     }
3540   }
3541
3542   @Override
3543   public void autoCalculate_actionPerformed(ActionEvent e)
3544   {
3545     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3546     if (viewport.autoCalculateConsensus)
3547     {
3548       viewport.firePropertyChange("alignment", null,
3549               viewport.getAlignment().getSequences());
3550     }
3551   }
3552
3553   @Override
3554   public void sortByTreeOption_actionPerformed(ActionEvent e)
3555   {
3556     viewport.sortByTree = sortByTree.isSelected();
3557   }
3558
3559   @Override
3560   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3561   {
3562     viewport.followSelection = listenToViewSelections.isSelected();
3563   }
3564
3565   /**
3566    * Constructs a tree panel and adds it to the desktop
3567    *
3568    * @param params
3569    * @param treeAlgo
3570    *
3571    * @param tree
3572    *
3573    *
3574    */
3575   void newTreePanel(TreeModel tree, String treeAlgo,
3576           String substitutionMatrix)
3577   {
3578     String frameTitle = "";
3579     TreePanel tp;
3580
3581     boolean onSelection = false;
3582     if (viewport.getSelectionGroup() != null
3583             && viewport.getSelectionGroup().getSize() > 0)
3584     {
3585       SequenceGroup sg = viewport.getSelectionGroup();
3586
3587       /* Decide if the selection is a column region */
3588       for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
3589       {
3590         if (_s.getLength() < sg.getEndRes())
3591         {
3592           JvOptionPane.showMessageDialog(Desktop.desktop,
3593                   MessageManager.getString(
3594                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3595                   MessageManager.getString(
3596                           "label.sequences_selection_not_aligned"),
3597                   JvOptionPane.WARNING_MESSAGE);
3598
3599           return;
3600         }
3601       }
3602       onSelection = true;
3603     }
3604     else
3605     {
3606       if (viewport.getAlignment().getHeight() < 2)
3607       {
3608         return;
3609       }
3610     }
3611
3612     tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
3613     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3614
3615     frameTitle += " from ";
3616
3617     if (viewport.viewName != null)
3618     {
3619       frameTitle += viewport.viewName + " of ";
3620     }
3621
3622     frameTitle += this.title;
3623
3624     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3625   }
3626
3627   /**
3628    * DOCUMENT ME!
3629    *
3630    * @param title
3631    *          DOCUMENT ME!
3632    * @param order
3633    *          DOCUMENT ME!
3634    */
3635   public void addSortByOrderMenuItem(String title,
3636           final AlignmentOrder order)
3637   {
3638     final JMenuItem item = new JMenuItem(MessageManager
3639             .formatMessage("action.by_title_param", new Object[]
3640             { title }));
3641     sort.add(item);
3642     item.addActionListener(new java.awt.event.ActionListener()
3643     {
3644       @Override
3645       public void actionPerformed(ActionEvent e)
3646       {
3647         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3648
3649         // TODO: JBPNote - have to map order entries to curent SequenceI
3650         // pointers
3651         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3652
3653         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3654                 viewport.getAlignment()));
3655
3656         alignPanel.paintAlignment(true, false);
3657       }
3658     });
3659   }
3660
3661   /**
3662    * Add a new sort by annotation score menu item
3663    *
3664    * @param sort
3665    *          the menu to add the option to
3666    * @param scoreLabel
3667    *          the label used to retrieve scores for each sequence on the
3668    *          alignment
3669    */
3670   public void addSortByAnnotScoreMenuItem(JMenu sort,
3671           final String scoreLabel)
3672   {
3673     final JMenuItem item = new JMenuItem(scoreLabel);
3674     sort.add(item);
3675     item.addActionListener(new java.awt.event.ActionListener()
3676     {
3677       @Override
3678       public void actionPerformed(ActionEvent e)
3679       {
3680         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3681         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3682                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3683         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3684                 viewport.getAlignment()));
3685         alignPanel.paintAlignment(true, false);
3686       }
3687     });
3688   }
3689
3690   /**
3691    * last hash for alignment's annotation array - used to minimise cost of
3692    * rebuild.
3693    */
3694   protected int _annotationScoreVectorHash;
3695
3696   /**
3697    * search the alignment and rebuild the sort by annotation score submenu the
3698    * last alignment annotation vector hash is stored to minimize cost of
3699    * rebuilding in subsequence calls.
3700    *
3701    */
3702   @Override
3703   public void buildSortByAnnotationScoresMenu()
3704   {
3705     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3706     {
3707       return;
3708     }
3709
3710     if (viewport.getAlignment().getAlignmentAnnotation()
3711             .hashCode() != _annotationScoreVectorHash)
3712     {
3713       sortByAnnotScore.removeAll();
3714       // almost certainly a quicker way to do this - but we keep it simple
3715       Hashtable scoreSorts = new Hashtable();
3716       AlignmentAnnotation aann[];
3717       for (SequenceI sqa : viewport.getAlignment().getSequences())
3718       {
3719         aann = sqa.getAnnotation();
3720         for (int i = 0; aann != null && i < aann.length; i++)
3721         {
3722           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3723           {
3724             scoreSorts.put(aann[i].label, aann[i].label);
3725           }
3726         }
3727       }
3728       Enumeration labels = scoreSorts.keys();
3729       while (labels.hasMoreElements())
3730       {
3731         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3732                 (String) labels.nextElement());
3733       }
3734       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3735       scoreSorts.clear();
3736
3737       _annotationScoreVectorHash = viewport.getAlignment()
3738               .getAlignmentAnnotation().hashCode();
3739     }
3740   }
3741
3742   /**
3743    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3744    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3745    * call. Listeners are added to remove the menu item when the treePanel is
3746    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3747    * modified.
3748    */
3749   @Override
3750   public void buildTreeSortMenu()
3751   {
3752     sortByTreeMenu.removeAll();
3753
3754     List<Component> comps = PaintRefresher.components
3755             .get(viewport.getSequenceSetId());
3756     List<TreePanel> treePanels = new ArrayList<>();
3757     for (Component comp : comps)
3758     {
3759       if (comp instanceof TreePanel)
3760       {
3761         treePanels.add((TreePanel) comp);
3762       }
3763     }
3764
3765     if (treePanels.size() < 1)
3766     {
3767       sortByTreeMenu.setVisible(false);
3768       return;
3769     }
3770
3771     sortByTreeMenu.setVisible(true);
3772
3773     for (final TreePanel tp : treePanels)
3774     {
3775       final JMenuItem item = new JMenuItem(tp.getTitle());
3776       item.addActionListener(new java.awt.event.ActionListener()
3777       {
3778         @Override
3779         public void actionPerformed(ActionEvent e)
3780         {
3781           // adapt to Aptx
3782           tp.sortByTree_actionPerformed();
3783           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3784
3785         }
3786       });
3787
3788       sortByTreeMenu.add(item);
3789     }
3790   }
3791
3792   public boolean sortBy(AlignmentOrder alorder, String undoname)
3793   {
3794     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3795     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3796     if (undoname != null)
3797     {
3798       addHistoryItem(new OrderCommand(undoname, oldOrder,
3799               viewport.getAlignment()));
3800     }
3801     alignPanel.paintAlignment(true, false);
3802     return true;
3803   }
3804
3805   /**
3806    * Work out whether the whole set of sequences or just the selected set will
3807    * be submitted for multiple alignment.
3808    *
3809    */
3810   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3811   {
3812     // Now, check we have enough sequences
3813     AlignmentView msa = null;
3814
3815     if ((viewport.getSelectionGroup() != null)
3816             && (viewport.getSelectionGroup().getSize() > 1))
3817     {
3818       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3819       // some common interface!
3820       /*
3821        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3822        * SequenceI[sz = seqs.getSize(false)];
3823        *
3824        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3825        * seqs.getSequenceAt(i); }
3826        */
3827       msa = viewport.getAlignmentView(true);
3828     }
3829     else if (viewport.getSelectionGroup() != null
3830             && viewport.getSelectionGroup().getSize() == 1)
3831     {
3832       int option = JvOptionPane.showConfirmDialog(this,
3833               MessageManager.getString("warn.oneseq_msainput_selection"),
3834               MessageManager.getString("label.invalid_selection"),
3835               JvOptionPane.OK_CANCEL_OPTION);
3836       if (option == JvOptionPane.OK_OPTION)
3837       {
3838         msa = viewport.getAlignmentView(false);
3839       }
3840     }
3841     else
3842     {
3843       msa = viewport.getAlignmentView(false);
3844     }
3845     return msa;
3846   }
3847
3848   /**
3849    * Decides what is submitted to a secondary structure prediction service: the
3850    * first sequence in the alignment, or in the current selection, or, if the
3851    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3852    * region or the whole alignment. (where the first sequence in the set is the
3853    * one that the prediction will be for).
3854    */
3855   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3856   {
3857     AlignmentView seqs = null;
3858
3859     if ((viewport.getSelectionGroup() != null)
3860             && (viewport.getSelectionGroup().getSize() > 0))
3861     {
3862       seqs = viewport.getAlignmentView(true);
3863     }
3864     else
3865     {
3866       seqs = viewport.getAlignmentView(false);
3867     }
3868     // limit sequences - JBPNote in future - could spawn multiple prediction
3869     // jobs
3870     // TODO: viewport.getAlignment().isAligned is a global state - the local
3871     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3872     if (!viewport.getAlignment().isAligned(false))
3873     {
3874       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3875       // TODO: if seqs.getSequences().length>1 then should really have warned
3876       // user!
3877
3878     }
3879     return seqs;
3880   }
3881
3882   /**
3883    * DOCUMENT ME!
3884    *
3885    * @param e
3886    *          DOCUMENT ME!
3887    */
3888   @Override
3889   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3890   {
3891     chooseTreeFile();
3892   }
3893
3894   @Override
3895   protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
3896   {
3897     chooseTreeUrl();
3898   }
3899
3900   @Override
3901   protected void loadTreeDbItem_actionPerformed(ActionEvent e)
3902   {
3903     chooseTreeDb();
3904   }
3905
3906   public void chooseTreeFile()
3907   {
3908     // Pick the tree file
3909     JalviewFileChooser chooser = new JalviewFileChooser(
3910             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3911     chooser.setFileView(new JalviewFileView());
3912     chooser.setDialogTitle(
3913             MessageManager.getString("label.select_tree_file")); // modify
3914     chooser.setToolTipText(
3915             MessageManager.getString("label.load_tree_for_sequence_set"));
3916     for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter
3917             .values())
3918     {
3919       chooser.setFileFilter(treeFormat.getTreeFilter());
3920     }
3921
3922     int value = chooser.showOpenDialog(null);
3923
3924     if (value == JalviewFileChooser.APPROVE_OPTION)
3925     {
3926       String filePath = chooser.getSelectedFile().getPath();
3927       Cache.setProperty("LAST_DIRECTORY", filePath);
3928
3929       TreeParser treeParser = new TreeParser(filePath);
3930       treeParser.loadTree(viewport);
3931
3932     }
3933   }
3934
3935   /**
3936    * Break up and move to TreeParser?
3937    */
3938   public void chooseTreeUrl()
3939   {
3940
3941
3942     JLabel label = new JLabel(
3943             MessageManager.getString("label.tree_url_example"));
3944     // add "example" button
3945     final JComboBox<String> history = new JComboBox<>();
3946
3947     JPanel panel = new JPanel(new GridLayout(2, 1));
3948     panel.add(label);
3949     panel.add(history);
3950     history.setPreferredSize(new Dimension(400, 20));
3951     history.setEditable(true);
3952     history.addItem("http://www.");
3953
3954     String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
3955
3956     StringTokenizer st;
3957
3958     if (historyItems != null)
3959       {
3960       st = new StringTokenizer(historyItems, "\t");
3961
3962       while (st.hasMoreTokens())
3963       {
3964         history.addItem(st.nextToken());
3965       }
3966       }
3967
3968     int reply = JvOptionPane.showInternalConfirmDialog(this, panel,
3969             MessageManager.getString("label.load_tree_url"),
3970             JvOptionPane.OK_CANCEL_OPTION);
3971
3972     if (reply == JvOptionPane.OK_OPTION)
3973     {
3974
3975       String urlString = history.getSelectedItem().toString();
3976       URL treeUrl;
3977
3978       try
3979       {
3980         FileFormatI format = null;
3981
3982         format = new IdentifyFile().identify(urlString, DataSourceType.URL);
3983         // add actual use for the format identification (jalview .jar files)
3984         treeUrl = new URL(urlString);
3985         AptxInit.createInstanceFromUrl(treeUrl, viewport);
3986
3987       } catch (IOException | RuntimeException e)
3988       {
3989         JvOptionPane.showMessageDialog(this, MessageManager.formatMessage(
3990                 "exception.failed_to_read_data_from_source", new String[]
3991                 { urlString }),
3992                 MessageManager.getString("label.url_not_found"),
3993                 JvOptionPane.ERROR_MESSAGE);
3994         e.printStackTrace();
3995       }
3996     }
3997     else
3998     {
3999
4000     }
4001   }
4002
4003   public void chooseTreeDb()
4004   {
4005
4006
4007   }
4008
4009   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4010   {
4011     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4012   }
4013
4014   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4015           int h, int x, int y)
4016   {
4017     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4018   }
4019
4020   /**
4021    * Add a treeviewer for the tree extracted from a Newick file object to the
4022    * current alignment view
4023    *
4024    * @param nf
4025    *          the tree
4026    * @param title
4027    *          tree viewer title
4028    * @param input
4029    *          Associated alignment input data (or null)
4030    * @param w
4031    *          width
4032    * @param h
4033    *          height
4034    * @param x
4035    *          position
4036    * @param y
4037    *          position
4038    * @return TreePanel handle
4039    */
4040   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4041           AlignmentView input, int w, int h, int x, int y)
4042   {
4043     TreePanel tp = null;
4044
4045     try
4046     {
4047       nf.parse();
4048
4049       if (nf.getTree() != null)
4050       {
4051         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4052
4053         tp.setSize(w, h);
4054
4055         if (x > 0 && y > 0)
4056         {
4057           tp.setLocation(x, y);
4058         }
4059
4060         Desktop.addInternalFrame(tp, treeTitle, w, h);
4061       }
4062     } catch (Exception ex)
4063     {
4064       ex.printStackTrace();
4065     }
4066
4067     return tp;
4068   }
4069
4070   private boolean buildingMenu = false;
4071
4072   /**
4073    * Generates menu items and listener event actions for web service clients
4074    *
4075    */
4076   public void BuildWebServiceMenu()
4077   {
4078     while (buildingMenu)
4079     {
4080       try
4081       {
4082         System.err.println("Waiting for building menu to finish.");
4083         Thread.sleep(10);
4084       } catch (Exception e)
4085       {
4086       }
4087     }
4088     final AlignFrame me = this;
4089     buildingMenu = true;
4090     new Thread(new Runnable()
4091     {
4092       @Override
4093       public void run()
4094       {
4095         final List<JMenuItem> legacyItems = new ArrayList<>();
4096         try
4097         {
4098           // System.err.println("Building ws menu again "
4099           // + Thread.currentThread());
4100           // TODO: add support for context dependent disabling of services based
4101           // on
4102           // alignment and current selection
4103           // TODO: add additional serviceHandle parameter to specify abstract
4104           // handler
4105           // class independently of AbstractName
4106           // TODO: add in rediscovery GUI function to restart discoverer
4107           // TODO: group services by location as well as function and/or
4108           // introduce
4109           // object broker mechanism.
4110           final Vector<JMenu> wsmenu = new Vector<>();
4111           final IProgressIndicator af = me;
4112
4113           /*
4114            * do not i18n these strings - they are hard-coded in class
4115            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4116            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4117            */
4118           final JMenu msawsmenu = new JMenu("Alignment");
4119           final JMenu secstrmenu = new JMenu(
4120                   "Secondary Structure Prediction");
4121           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4122           final JMenu analymenu = new JMenu("Analysis");
4123           final JMenu dismenu = new JMenu("Protein Disorder");
4124           final JMenu phylogenmenu = new JMenu("Phylogenetic inference");
4125
4126           // JAL-940 - only show secondary structure prediction services from
4127           // the legacy server
4128           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4129               // &&
4130           Discoverer.services != null && (Discoverer.services.size() > 0))
4131           {
4132             // TODO: refactor to allow list of AbstractName/Handler bindings to
4133             // be
4134             // stored or retrieved from elsewhere
4135             // No MSAWS used any more:
4136             // Vector msaws = null; // (Vector)
4137             // Discoverer.services.get("MsaWS");
4138             Vector secstrpr = (Vector) Discoverer.services
4139                     .get("SecStrPred");
4140             if (secstrpr != null)
4141             {
4142               // Add any secondary structure prediction services
4143               for (int i = 0, j = secstrpr.size(); i < j; i++)
4144               {
4145                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4146                         .get(i);
4147                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4148                         .getServiceClient(sh);
4149                 int p = secstrmenu.getItemCount();
4150                 impl.attachWSMenuEntry(secstrmenu, me);
4151                 int q = secstrmenu.getItemCount();
4152                 for (int litm = p; litm < q; litm++)
4153                 {
4154                   legacyItems.add(secstrmenu.getItem(litm));
4155                 }
4156               }
4157             }
4158           }
4159
4160           // Add all submenus in the order they should appear on the web
4161           // services menu
4162           wsmenu.add(msawsmenu);
4163           wsmenu.add(secstrmenu);
4164           wsmenu.add(dismenu);
4165           wsmenu.add(analymenu);
4166           wsmenu.add(phylogenmenu);
4167           // No search services yet
4168           // wsmenu.add(seqsrchmenu);
4169
4170           javax.swing.SwingUtilities.invokeLater(new Runnable()
4171           {
4172             @Override
4173             public void run()
4174             {
4175               try
4176               {
4177                 webService.removeAll();
4178                 // first, add discovered services onto the webservices menu
4179                 if (wsmenu.size() > 0)
4180                 {
4181                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4182                   {
4183                     webService.add(wsmenu.get(i));
4184                   }
4185                 }
4186                 else
4187                 {
4188                   webService.add(me.webServiceNoServices);
4189                 }
4190                 // TODO: move into separate menu builder class.
4191                 boolean new_sspred = false;
4192                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4193                 {
4194                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4195                   if (jws2servs != null)
4196                   {
4197                     if (jws2servs.hasServices())
4198                     {
4199                       jws2servs.attachWSMenuEntry(webService, me);
4200                       for (Jws2Instance sv : jws2servs.getServices())
4201                       {
4202                         if (sv.description.toLowerCase().contains("jpred"))
4203                         {
4204                           for (JMenuItem jmi : legacyItems)
4205                           {
4206                             jmi.setVisible(false);
4207                           }
4208                         }
4209                       }
4210
4211                     }
4212                     if (jws2servs.isRunning())
4213                     {
4214                       JMenuItem tm = new JMenuItem(
4215                               "Still discovering JABA Services");
4216                       tm.setEnabled(false);
4217                       webService.add(tm);
4218                     }
4219                   }
4220                 }
4221                 build_urlServiceMenu(me.webService);
4222                 build_fetchdbmenu(webService);
4223                 for (JMenu item : wsmenu)
4224                 {
4225                   if (item.getItemCount() == 0)
4226                   {
4227                     item.setEnabled(false);
4228                   }
4229                   else
4230                   {
4231                     item.setEnabled(true);
4232                   }
4233                 }
4234               } catch (Exception e)
4235               {
4236                 Cache.log.debug(
4237                         "Exception during web service menu building process.",
4238                         e);
4239               }
4240             }
4241           });
4242         } catch (Exception e)
4243         {
4244         }
4245         buildingMenu = false;
4246       }
4247     }, "BuildWebServiceThread").start();
4248
4249   }
4250
4251   /**
4252    * construct any groupURL type service menu entries.
4253    *
4254    * @param webService
4255    */
4256   private void build_urlServiceMenu(JMenu webService)
4257   {
4258     // TODO: remove this code when 2.7 is released
4259     // DEBUG - alignmentView
4260     /*
4261      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4262      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4263      *
4264      * @Override public void actionPerformed(ActionEvent e) {
4265      * jalview.datamodel.AlignmentView
4266      * .testSelectionViews(af.viewport.getAlignment(),
4267      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4268      *
4269      * }); webService.add(testAlView);
4270      */
4271     // TODO: refactor to RestClient discoverer and merge menu entries for
4272     // rest-style services with other types of analysis/calculation service
4273     // SHmmr test client - still being implemented.
4274     // DEBUG - alignmentView
4275
4276     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4277             .getRestClients())
4278     {
4279       client.attachWSMenuEntry(
4280               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4281               this);
4282     }
4283   }
4284
4285   /**
4286    * Searches the alignment sequences for xRefs and builds the Show
4287    * Cross-References menu (formerly called Show Products), with database
4288    * sources for which cross-references are found (protein sources for a
4289    * nucleotide alignment and vice versa)
4290    *
4291    * @return true if Show Cross-references menu should be enabled
4292    */
4293   public boolean canShowProducts()
4294   {
4295     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4296     AlignmentI dataset = viewport.getAlignment().getDataset();
4297
4298     showProducts.removeAll();
4299     final boolean dna = viewport.getAlignment().isNucleotide();
4300
4301     if (seqs == null || seqs.length == 0)
4302     {
4303       // nothing to see here.
4304       return false;
4305     }
4306
4307     boolean showp = false;
4308     try
4309     {
4310       List<String> ptypes = new CrossRef(seqs, dataset)
4311               .findXrefSourcesForSequences(dna);
4312
4313       for (final String source : ptypes)
4314       {
4315         showp = true;
4316         final AlignFrame af = this;
4317         JMenuItem xtype = new JMenuItem(source);
4318         xtype.addActionListener(new ActionListener()
4319         {
4320           @Override
4321           public void actionPerformed(ActionEvent e)
4322           {
4323             showProductsFor(af.viewport.getSequenceSelection(), dna,
4324                     source);
4325           }
4326         });
4327         showProducts.add(xtype);
4328       }
4329       showProducts.setVisible(showp);
4330       showProducts.setEnabled(showp);
4331     } catch (Exception e)
4332     {
4333       Cache.log.warn(
4334               "canShowProducts threw an exception - please report to help@jalview.org",
4335               e);
4336       return false;
4337     }
4338     return showp;
4339   }
4340
4341   /**
4342    * Finds and displays cross-references for the selected sequences (protein
4343    * products for nucleotide sequences, dna coding sequences for peptides).
4344    *
4345    * @param sel
4346    *          the sequences to show cross-references for
4347    * @param dna
4348    *          true if from a nucleotide alignment (so showing proteins)
4349    * @param source
4350    *          the database to show cross-references for
4351    */
4352   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4353           final String source)
4354   {
4355     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
4356             "CrossReferencesThread")
4357             .start();
4358   }
4359
4360   /**
4361    * Construct and display a new frame containing the translation of this
4362    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4363    */
4364   @Override
4365   public void showTranslation_actionPerformed(ActionEvent e)
4366   {
4367     AlignmentI al = null;
4368     try
4369     {
4370       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4371
4372       al = dna.translateCdna();
4373     } catch (Exception ex)
4374     {
4375       jalview.bin.Cache.log.error(
4376               "Exception during translation. Please report this !", ex);
4377       final String msg = MessageManager.getString(
4378               "label.error_when_translating_sequences_submit_bug_report");
4379       final String errorTitle = MessageManager
4380               .getString("label.implementation_error")
4381               + MessageManager.getString("label.translation_failed");
4382       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4383               JvOptionPane.ERROR_MESSAGE);
4384       return;
4385     }
4386     if (al == null || al.getHeight() == 0)
4387     {
4388       final String msg = MessageManager.getString(
4389               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4390       final String errorTitle = MessageManager
4391               .getString("label.translation_failed");
4392       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4393               JvOptionPane.WARNING_MESSAGE);
4394     }
4395     else
4396     {
4397       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4398       af.setFileFormat(this.currentFileFormat);
4399       final String newTitle = MessageManager
4400               .formatMessage("label.translation_of_params", new Object[]
4401               { this.getTitle() });
4402       af.setTitle(newTitle);
4403       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4404       {
4405         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4406         viewport.openSplitFrame(af, new Alignment(seqs));
4407       }
4408       else
4409       {
4410         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4411                 DEFAULT_HEIGHT);
4412       }
4413     }
4414   }
4415
4416   /**
4417    * Set the file format
4418    *
4419    * @param format
4420    */
4421   public void setFileFormat(FileFormatI format)
4422   {
4423     this.currentFileFormat = format;
4424   }
4425
4426   /**
4427    * Try to load a features file onto the alignment.
4428    *
4429    * @param file
4430    *          contents or path to retrieve file
4431    * @param sourceType
4432    *          access mode of file (see jalview.io.AlignFile)
4433    * @return true if features file was parsed correctly.
4434    */
4435   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4436   {
4437     return avc.parseFeaturesFile(file, sourceType,
4438             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4439
4440   }
4441
4442   @Override
4443   public void refreshFeatureUI(boolean enableIfNecessary)
4444   {
4445     // note - currently this is only still here rather than in the controller
4446     // because of the featureSettings hard reference that is yet to be
4447     // abstracted
4448     if (enableIfNecessary)
4449     {
4450       viewport.setShowSequenceFeatures(true);
4451       showSeqFeatures.setSelected(true);
4452     }
4453
4454   }
4455
4456   @Override
4457   public void dragEnter(DropTargetDragEvent evt)
4458   {
4459   }
4460
4461   @Override
4462   public void dragExit(DropTargetEvent evt)
4463   {
4464   }
4465
4466   @Override
4467   public void dragOver(DropTargetDragEvent evt)
4468   {
4469   }
4470
4471   @Override
4472   public void dropActionChanged(DropTargetDragEvent evt)
4473   {
4474   }
4475
4476   @Override
4477   public void drop(DropTargetDropEvent evt)
4478   {
4479     // JAL-1552 - acceptDrop required before getTransferable call for
4480     // Java's Transferable for native dnd
4481     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4482     Transferable t = evt.getTransferable();
4483     final AlignFrame thisaf = this;
4484     final List<String> files = new ArrayList<>();
4485     List<DataSourceType> protocols = new ArrayList<>();
4486
4487     try
4488     {
4489       Desktop.transferFromDropTarget(files, protocols, evt, t);
4490     } catch (Exception e)
4491     {
4492       e.printStackTrace();
4493     }
4494     if (files != null)
4495     {
4496       new Thread(new Runnable()
4497       {
4498         @Override
4499         public void run()
4500         {
4501           try
4502           {
4503             // check to see if any of these files have names matching sequences
4504             // in
4505             // the alignment
4506             SequenceIdMatcher idm = new SequenceIdMatcher(
4507                     viewport.getAlignment().getSequencesArray());
4508             /**
4509              * Object[] { String,SequenceI}
4510              */
4511             ArrayList<Object[]> filesmatched = new ArrayList<>();
4512             ArrayList<String> filesnotmatched = new ArrayList<>();
4513             for (int i = 0; i < files.size(); i++)
4514             {
4515               String file = files.get(i).toString();
4516               String pdbfn = "";
4517               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4518               if (protocol == DataSourceType.FILE)
4519               {
4520                 File fl = new File(file);
4521                 pdbfn = fl.getName();
4522               }
4523               else if (protocol == DataSourceType.URL)
4524               {
4525                 URL url = new URL(file);
4526                 pdbfn = url.getFile();
4527               }
4528               if (pdbfn.length() > 0)
4529               {
4530                 // attempt to find a match in the alignment
4531                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4532                 int l = 0, c = pdbfn.indexOf(".");
4533                 while (mtch == null && c != -1)
4534                 {
4535                   do
4536                   {
4537                     l = c;
4538                   } while ((c = pdbfn.indexOf(".", l)) > l);
4539                   if (l > -1)
4540                   {
4541                     pdbfn = pdbfn.substring(0, l);
4542                   }
4543                   mtch = idm.findAllIdMatches(pdbfn);
4544                 }
4545                 if (mtch != null)
4546                 {
4547                   FileFormatI type = null;
4548                   try
4549                   {
4550                     type = new IdentifyFile().identify(file, protocol);
4551                   } catch (Exception ex)
4552                   {
4553                     type = null;
4554                   }
4555                   if (type != null && type.isStructureFile())
4556                   {
4557                     filesmatched.add(new Object[] { file, protocol, mtch });
4558                     continue;
4559                   }
4560                 }
4561                 // File wasn't named like one of the sequences or wasn't a PDB
4562                 // file.
4563                 filesnotmatched.add(file);
4564               }
4565             }
4566             int assocfiles = 0;
4567             if (filesmatched.size() > 0)
4568             {
4569               if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4570                       || JvOptionPane.showConfirmDialog(thisaf,
4571                               MessageManager.formatMessage(
4572                                       "label.automatically_associate_structure_files_with_sequences_same_name",
4573                                       new Object[]
4574                                       { Integer.valueOf(filesmatched.size())
4575                                               .toString() }),
4576                               MessageManager.getString(
4577                                       "label.automatically_associate_structure_files_by_name"),
4578                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4579
4580               {
4581                 for (Object[] fm : filesmatched)
4582                 {
4583                   // try and associate
4584                   // TODO: may want to set a standard ID naming formalism for
4585                   // associating PDB files which have no IDs.
4586                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4587                   {
4588                     PDBEntry pe = new AssociatePdbFileWithSeq()
4589                             .associatePdbWithSeq((String) fm[0],
4590                                     (DataSourceType) fm[1], toassoc, false,
4591                                     Desktop.instance);
4592                     if (pe != null)
4593                     {
4594                       System.err.println("Associated file : "
4595                               + ((String) fm[0]) + " with "
4596                               + toassoc.getDisplayId(true));
4597                       assocfiles++;
4598                     }
4599                   }
4600                   // TODO: do we need to update overview ? only if features are
4601                   // shown I guess
4602                   alignPanel.paintAlignment(true, false);
4603                 }
4604               }
4605             }
4606             if (filesnotmatched.size() > 0)
4607             {
4608               if (assocfiles > 0 && (Cache.getDefault(
4609                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4610                       || JvOptionPane.showConfirmDialog(thisaf,
4611                               "<html>" + MessageManager.formatMessage(
4612                                       "label.ignore_unmatched_dropped_files_info",
4613                                       new Object[]
4614                                       { Integer.valueOf(
4615                                               filesnotmatched.size())
4616                                               .toString() })
4617                                       + "</html>",
4618                               MessageManager.getString(
4619                                       "label.ignore_unmatched_dropped_files"),
4620                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4621               {
4622                 return;
4623               }
4624               for (String fn : filesnotmatched)
4625               {
4626                 loadJalviewDataFile(fn, null, null, null);
4627               }
4628
4629             }
4630           } catch (Exception ex)
4631           {
4632             ex.printStackTrace();
4633           }
4634         }
4635       }, "DropFileThread").start();
4636     }
4637   }
4638
4639   /**
4640    * Attempt to load a "dropped" file or URL string, by testing in turn for
4641    * <ul>
4642    * <li>an Annotation file</li>
4643    * <li>a JNet file</li>
4644    * <li>a features file</li>
4645    * <li>else try to interpret as an alignment file</li>
4646    * </ul>
4647    *
4648    * @param file
4649    *          either a filename or a URL string.
4650    */
4651   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4652           FileFormatI format, SequenceI assocSeq)
4653   {
4654     try
4655     {
4656       if (sourceType == null)
4657       {
4658         sourceType = FormatAdapter.checkProtocol(file);
4659       }
4660       // if the file isn't identified, or not positively identified as some
4661       // other filetype (PFAM is default unidentified alignment file type) then
4662       // try to parse as annotation.
4663       boolean isAnnotation = (format == null
4664               || FileFormat.Pfam.equals(format))
4665                       ? new AnnotationFile().annotateAlignmentView(viewport,
4666                               file, sourceType)
4667                       : false;
4668
4669       if (!isAnnotation)
4670       {
4671         // first see if its a T-COFFEE score file
4672         TCoffeeScoreFile tcf = null;
4673         try
4674         {
4675           tcf = new TCoffeeScoreFile(file, sourceType);
4676           if (tcf.isValid())
4677           {
4678             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4679             {
4680               buildColourMenu();
4681               changeColour(
4682                       new TCoffeeColourScheme(viewport.getAlignment()));
4683               isAnnotation = true;
4684               statusBar.setText(MessageManager.getString(
4685                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4686             }
4687             else
4688             {
4689               // some problem - if no warning its probable that the ID matching
4690               // process didn't work
4691               JvOptionPane.showMessageDialog(Desktop.desktop,
4692                       tcf.getWarningMessage() == null
4693                               ? MessageManager.getString(
4694                                       "label.check_file_matches_sequence_ids_alignment")
4695                               : tcf.getWarningMessage(),
4696                       MessageManager.getString(
4697                               "label.problem_reading_tcoffee_score_file"),
4698                       JvOptionPane.WARNING_MESSAGE);
4699             }
4700           }
4701           else
4702           {
4703             tcf = null;
4704           }
4705         } catch (Exception x)
4706         {
4707           Cache.log.debug(
4708                   "Exception when processing data source as T-COFFEE score file",
4709                   x);
4710           tcf = null;
4711         }
4712         if (tcf == null)
4713         {
4714           // try to see if its a JNet 'concise' style annotation file *before*
4715           // we
4716           // try to parse it as a features file
4717           if (format == null)
4718           {
4719             format = new IdentifyFile().identify(file, sourceType);
4720           }
4721           if (FileFormat.ScoreMatrix == format)
4722           {
4723             ScoreMatrixFile sm = new ScoreMatrixFile(
4724                     new FileParse(file, sourceType));
4725             sm.parse();
4726             // todo: i18n this message
4727             statusBar.setText(MessageManager.formatMessage(
4728                     "label.successfully_loaded_matrix",
4729                     sm.getMatrixName()));
4730           }
4731           else if (FileFormat.Jnet.equals(format))
4732           {
4733             JPredFile predictions = new JPredFile(file, sourceType);
4734             new JnetAnnotationMaker();
4735             JnetAnnotationMaker.add_annotation(predictions,
4736                     viewport.getAlignment(), 0, false);
4737             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4738             viewport.getAlignment().setSeqrep(repseq);
4739             HiddenColumns cs = new HiddenColumns();
4740             cs.hideInsertionsFor(repseq);
4741             viewport.getAlignment().setHiddenColumns(cs);
4742             isAnnotation = true;
4743           }
4744           // else if (IdentifyFile.FeaturesFile.equals(format))
4745           else if (FileFormat.Features.equals(format))
4746           {
4747             if (parseFeaturesFile(file, sourceType))
4748             {
4749               alignPanel.paintAlignment(true, true);
4750             }
4751           }
4752           else
4753           {
4754             new FileLoader().LoadFile(viewport, file, sourceType, format);
4755           }
4756         }
4757       }
4758       if (isAnnotation)
4759       {
4760
4761         alignPanel.adjustAnnotationHeight();
4762         viewport.updateSequenceIdColours();
4763         buildSortByAnnotationScoresMenu();
4764         alignPanel.paintAlignment(true, true);
4765       }
4766     } catch (Exception ex)
4767     {
4768       ex.printStackTrace();
4769     } catch (OutOfMemoryError oom)
4770     {
4771       try
4772       {
4773         System.gc();
4774       } catch (Exception x)
4775       {
4776       }
4777       new OOMWarning(
4778               "loading data "
4779                       + (sourceType != null
4780                               ? (sourceType == DataSourceType.PASTE
4781                                       ? "from clipboard."
4782                                       : "using " + sourceType + " from "
4783                                               + file)
4784                               : ".")
4785                       + (format != null
4786                               ? "(parsing as '" + format + "' file)"
4787                               : ""),
4788               oom, Desktop.desktop);
4789     }
4790   }
4791
4792   /**
4793    * Method invoked by the ChangeListener on the tabbed pane, in other words
4794    * when a different tabbed pane is selected by the user or programmatically.
4795    */
4796   @Override
4797   public void tabSelectionChanged(int index)
4798   {
4799     if (index > -1)
4800     {
4801       alignPanel = alignPanels.get(index);
4802       viewport = alignPanel.av;
4803       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4804       setMenusFromViewport(viewport);
4805     }
4806
4807     /*
4808      * 'focus' any colour slider that is open to the selected viewport
4809      */
4810     if (viewport.getConservationSelected())
4811     {
4812       SliderPanel.setConservationSlider(alignPanel,
4813               viewport.getResidueShading(), alignPanel.getViewName());
4814     }
4815     else
4816     {
4817       SliderPanel.hideConservationSlider();
4818     }
4819     if (viewport.getAbovePIDThreshold())
4820     {
4821       SliderPanel.setPIDSliderSource(alignPanel,
4822               viewport.getResidueShading(), alignPanel.getViewName());
4823     }
4824     else
4825     {
4826       SliderPanel.hidePIDSlider();
4827     }
4828
4829     /*
4830      * If there is a frame linked to this one in a SplitPane, switch it to the
4831      * same view tab index. No infinite recursion of calls should happen, since
4832      * tabSelectionChanged() should not get invoked on setting the selected
4833      * index to an unchanged value. Guard against setting an invalid index
4834      * before the new view peer tab has been created.
4835      */
4836     final AlignViewportI peer = viewport.getCodingComplement();
4837     if (peer != null)
4838     {
4839       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4840               .getAlignPanel().alignFrame;
4841       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4842       {
4843         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4844       }
4845     }
4846   }
4847
4848   /**
4849    * On right mouse click on view tab, prompt for and set new view name.
4850    */
4851   @Override
4852   public void tabbedPane_mousePressed(MouseEvent e)
4853   {
4854     if (e.isPopupTrigger())
4855     {
4856       String msg = MessageManager.getString("label.enter_view_name");
4857       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4858               JvOptionPane.QUESTION_MESSAGE);
4859
4860       if (reply != null)
4861       {
4862         viewport.viewName = reply;
4863         // TODO warn if reply is in getExistingViewNames()?
4864         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4865       }
4866     }
4867   }
4868
4869   public AlignViewport getCurrentView()
4870   {
4871     return viewport;
4872   }
4873
4874   /**
4875    * Open the dialog for regex description parsing.
4876    */
4877   @Override
4878   protected void extractScores_actionPerformed(ActionEvent e)
4879   {
4880     ParseProperties pp = new jalview.analysis.ParseProperties(
4881             viewport.getAlignment());
4882     // TODO: verify regex and introduce GUI dialog for version 2.5
4883     // if (pp.getScoresFromDescription("col", "score column ",
4884     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4885     // true)>0)
4886     if (pp.getScoresFromDescription("description column",
4887             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4888     {
4889       buildSortByAnnotationScoresMenu();
4890     }
4891   }
4892
4893   /*
4894    * (non-Javadoc)
4895    *
4896    * @see
4897    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4898    * )
4899    */
4900   @Override
4901   protected void showDbRefs_actionPerformed(ActionEvent e)
4902   {
4903     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4904   }
4905
4906   /*
4907    * (non-Javadoc)
4908    *
4909    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4910    * ActionEvent)
4911    */
4912   @Override
4913   protected void showNpFeats_actionPerformed(ActionEvent e)
4914   {
4915     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4916   }
4917
4918   /**
4919    * find the viewport amongst the tabs in this alignment frame and close that
4920    * tab
4921    *
4922    * @param av
4923    */
4924   public boolean closeView(AlignViewportI av)
4925   {
4926     if (viewport == av)
4927     {
4928       this.closeMenuItem_actionPerformed(false);
4929       return true;
4930     }
4931     Component[] comp = tabbedPane.getComponents();
4932     for (int i = 0; comp != null && i < comp.length; i++)
4933     {
4934       if (comp[i] instanceof AlignmentPanel)
4935       {
4936         if (((AlignmentPanel) comp[i]).av == av)
4937         {
4938           // close the view.
4939           closeView((AlignmentPanel) comp[i]);
4940           return true;
4941         }
4942       }
4943     }
4944     return false;
4945   }
4946
4947   protected void build_fetchdbmenu(JMenu webService)
4948   {
4949     // Temporary hack - DBRef Fetcher always top level ws entry.
4950     // TODO We probably want to store a sequence database checklist in
4951     // preferences and have checkboxes.. rather than individual sources selected
4952     // here
4953     final JMenu rfetch = new JMenu(
4954             MessageManager.getString("action.fetch_db_references"));
4955     rfetch.setToolTipText(MessageManager.getString(
4956             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4957     webService.add(rfetch);
4958
4959     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4960             MessageManager.getString("option.trim_retrieved_seqs"));
4961     trimrs.setToolTipText(
4962             MessageManager.getString("label.trim_retrieved_sequences"));
4963     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4964     trimrs.addActionListener(new ActionListener()
4965     {
4966       @Override
4967       public void actionPerformed(ActionEvent e)
4968       {
4969         trimrs.setSelected(trimrs.isSelected());
4970         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4971                 Boolean.valueOf(trimrs.isSelected()).toString());
4972       };
4973     });
4974     rfetch.add(trimrs);
4975     JMenuItem fetchr = new JMenuItem(
4976             MessageManager.getString("label.standard_databases"));
4977     fetchr.setToolTipText(
4978             MessageManager.getString("label.fetch_embl_uniprot"));
4979     fetchr.addActionListener(new ActionListener()
4980     {
4981
4982       @Override
4983       public void actionPerformed(ActionEvent e)
4984       {
4985         new Thread(new Runnable()
4986         {
4987           @Override
4988           public void run()
4989           {
4990             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4991                     .getAlignment().isNucleotide();
4992             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4993                     alignPanel.av.getSequenceSelection(),
4994                     alignPanel.alignFrame, null,
4995                     alignPanel.alignFrame.featureSettings, isNucleotide);
4996             dbRefFetcher.addListener(new FetchFinishedListenerI()
4997             {
4998               @Override
4999               public void finished()
5000               {
5001                 AlignFrame.this.setMenusForViewport();
5002               }
5003             });
5004             dbRefFetcher.fetchDBRefs(false);
5005           }
5006         }, "BuildFetchDBMenuThread").start();
5007
5008       }
5009
5010     });
5011     rfetch.add(fetchr);
5012     final AlignFrame me = this;
5013     new Thread(new Runnable()
5014     {
5015       @Override
5016       public void run()
5017       {
5018         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5019                 .getSequenceFetcherSingleton(me);
5020         javax.swing.SwingUtilities.invokeLater(new Runnable()
5021         {
5022           @Override
5023           public void run()
5024           {
5025             String[] dbclasses = sf.getOrderedSupportedSources();
5026             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5027             // jalview.util.QuickSort.sort(otherdb, otherdb);
5028             List<DbSourceProxy> otherdb;
5029             JMenu dfetch = new JMenu();
5030             JMenu ifetch = new JMenu();
5031             JMenuItem fetchr = null;
5032             int comp = 0, icomp = 0, mcomp = 15;
5033             String mname = null;
5034             int dbi = 0;
5035             for (String dbclass : dbclasses)
5036             {
5037               otherdb = sf.getSourceProxy(dbclass);
5038               // add a single entry for this class, or submenu allowing 'fetch
5039               // all' or pick one
5040               if (otherdb == null || otherdb.size() < 1)
5041               {
5042                 continue;
5043               }
5044               // List<DbSourceProxy> dbs=otherdb;
5045               // otherdb=new ArrayList<DbSourceProxy>();
5046               // for (DbSourceProxy db:dbs)
5047               // {
5048               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5049               // }
5050               if (mname == null)
5051               {
5052                 mname = "From " + dbclass;
5053               }
5054               if (otherdb.size() == 1)
5055               {
5056                 final DbSourceProxy[] dassource = otherdb
5057                         .toArray(new DbSourceProxy[0]);
5058                 DbSourceProxy src = otherdb.get(0);
5059                 fetchr = new JMenuItem(src.getDbSource());
5060                 fetchr.addActionListener(new ActionListener()
5061                 {
5062
5063                   @Override
5064                   public void actionPerformed(ActionEvent e)
5065                   {
5066                     new Thread(new Runnable()
5067                     {
5068
5069                       @Override
5070                       public void run()
5071                       {
5072                         boolean isNucleotide = alignPanel.alignFrame
5073                                 .getViewport().getAlignment()
5074                                 .isNucleotide();
5075                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5076                                 alignPanel.av.getSequenceSelection(),
5077                                 alignPanel.alignFrame, dassource,
5078                                 alignPanel.alignFrame.featureSettings,
5079                                 isNucleotide);
5080                         dbRefFetcher
5081                                 .addListener(new FetchFinishedListenerI()
5082                                 {
5083                                   @Override
5084                                   public void finished()
5085                                   {
5086                                     AlignFrame.this.setMenusForViewport();
5087                                   }
5088                                 });
5089                         dbRefFetcher.fetchDBRefs(false);
5090                       }
5091                     }).start();
5092                   }
5093
5094                 });
5095                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5096                         MessageManager.formatMessage(
5097                                 "label.fetch_retrieve_from", new Object[]
5098                                 { src.getDbName() })));
5099                 dfetch.add(fetchr);
5100                 comp++;
5101               }
5102               else
5103               {
5104                 final DbSourceProxy[] dassource = otherdb
5105                         .toArray(new DbSourceProxy[0]);
5106                 // fetch all entry
5107                 DbSourceProxy src = otherdb.get(0);
5108                 fetchr = new JMenuItem(MessageManager
5109                         .formatMessage("label.fetch_all_param", new Object[]
5110                         { src.getDbSource() }));
5111                 fetchr.addActionListener(new ActionListener()
5112                 {
5113                   @Override
5114                   public void actionPerformed(ActionEvent e)
5115                   {
5116                     new Thread(new Runnable()
5117                     {
5118
5119                       @Override
5120                       public void run()
5121                       {
5122                         boolean isNucleotide = alignPanel.alignFrame
5123                                 .getViewport().getAlignment()
5124                                 .isNucleotide();
5125                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5126                                 alignPanel.av.getSequenceSelection(),
5127                                 alignPanel.alignFrame, dassource,
5128                                 alignPanel.alignFrame.featureSettings,
5129                                 isNucleotide);
5130                         dbRefFetcher
5131                                 .addListener(new FetchFinishedListenerI()
5132                                 {
5133                                   @Override
5134                                   public void finished()
5135                                   {
5136                                     AlignFrame.this.setMenusForViewport();
5137                                   }
5138                                 });
5139                         dbRefFetcher.fetchDBRefs(false);
5140                       }
5141                     }).start();
5142                   }
5143                 });
5144
5145                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5146                         MessageManager.formatMessage(
5147                                 "label.fetch_retrieve_from_all_sources",
5148                                 new Object[]
5149                                 { Integer.valueOf(otherdb.size())
5150                                         .toString(),
5151                                     src.getDbSource(), src.getDbName() })));
5152                 dfetch.add(fetchr);
5153                 comp++;
5154                 // and then build the rest of the individual menus
5155                 ifetch = new JMenu(MessageManager.formatMessage(
5156                         "label.source_from_db_source", new Object[]
5157                         { src.getDbSource() }));
5158                 icomp = 0;
5159                 String imname = null;
5160                 int i = 0;
5161                 for (DbSourceProxy sproxy : otherdb)
5162                 {
5163                   String dbname = sproxy.getDbName();
5164                   String sname = dbname.length() > 5
5165                           ? dbname.substring(0, 5) + "..."
5166                           : dbname;
5167                   String msname = dbname.length() > 10
5168                           ? dbname.substring(0, 10) + "..."
5169                           : dbname;
5170                   if (imname == null)
5171                   {
5172                     imname = MessageManager
5173                             .formatMessage("label.from_msname", new Object[]
5174                             { sname });
5175                   }
5176                   fetchr = new JMenuItem(msname);
5177                   final DbSourceProxy[] dassrc = { sproxy };
5178                   fetchr.addActionListener(new ActionListener()
5179                   {
5180
5181                     @Override
5182                     public void actionPerformed(ActionEvent e)
5183                     {
5184                       new Thread(new Runnable()
5185                       {
5186
5187                         @Override
5188                         public void run()
5189                         {
5190                           boolean isNucleotide = alignPanel.alignFrame
5191                                   .getViewport().getAlignment()
5192                                   .isNucleotide();
5193                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5194                                   alignPanel.av.getSequenceSelection(),
5195                                   alignPanel.alignFrame, dassrc,
5196                                   alignPanel.alignFrame.featureSettings,
5197                                   isNucleotide);
5198                           dbRefFetcher
5199                                   .addListener(new FetchFinishedListenerI()
5200                                   {
5201                                     @Override
5202                                     public void finished()
5203                                     {
5204                                       AlignFrame.this.setMenusForViewport();
5205                                     }
5206                                   });
5207                           dbRefFetcher.fetchDBRefs(false);
5208                         }
5209                       }).start();
5210                     }
5211
5212                   });
5213                   fetchr.setToolTipText(
5214                           "<html>" + MessageManager.formatMessage(
5215                                   "label.fetch_retrieve_from", new Object[]
5216                                   { dbname }));
5217                   ifetch.add(fetchr);
5218                   ++i;
5219                   if (++icomp >= mcomp || i == (otherdb.size()))
5220                   {
5221                     ifetch.setText(MessageManager.formatMessage(
5222                             "label.source_to_target", imname, sname));
5223                     dfetch.add(ifetch);
5224                     ifetch = new JMenu();
5225                     imname = null;
5226                     icomp = 0;
5227                     comp++;
5228                   }
5229                 }
5230               }
5231               ++dbi;
5232               if (comp >= mcomp || dbi >= (dbclasses.length))
5233               {
5234                 dfetch.setText(MessageManager.formatMessage(
5235                         "label.source_to_target", mname, dbclass));
5236                 rfetch.add(dfetch);
5237                 dfetch = new JMenu();
5238                 mname = null;
5239                 comp = 0;
5240               }
5241             }
5242           }
5243         });
5244       }
5245     }).start();
5246
5247   }
5248
5249   /**
5250    * Left justify the whole alignment.
5251    */
5252   @Override
5253   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5254   {
5255     AlignmentI al = viewport.getAlignment();
5256     al.justify(false);
5257     viewport.firePropertyChange("alignment", null, al);
5258   }
5259
5260   /**
5261    * Right justify the whole alignment.
5262    */
5263   @Override
5264   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5265   {
5266     AlignmentI al = viewport.getAlignment();
5267     al.justify(true);
5268     viewport.firePropertyChange("alignment", null, al);
5269   }
5270
5271   @Override
5272   public void setShowSeqFeatures(boolean b)
5273   {
5274     showSeqFeatures.setSelected(b);
5275     viewport.setShowSequenceFeatures(b);
5276   }
5277
5278   /*
5279    * (non-Javadoc)
5280    *
5281    * @see
5282    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5283    * awt.event.ActionEvent)
5284    */
5285   @Override
5286   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5287   {
5288     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5289     alignPanel.paintAlignment(false, false);
5290   }
5291
5292   /*
5293    * (non-Javadoc)
5294    *
5295    * @see
5296    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5297    * .ActionEvent)
5298    */
5299   @Override
5300   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5301   {
5302     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5303     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5304
5305   }
5306
5307   /*
5308    * (non-Javadoc)
5309    *
5310    * @see
5311    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5312    * .event.ActionEvent)
5313    */
5314   @Override
5315   protected void showGroupConservation_actionPerformed(ActionEvent e)
5316   {
5317     viewport.setShowGroupConservation(showGroupConservation.getState());
5318     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5319   }
5320
5321   /*
5322    * (non-Javadoc)
5323    *
5324    * @see
5325    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5326    * .event.ActionEvent)
5327    */
5328   @Override
5329   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5330   {
5331     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5332     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5333   }
5334
5335   /*
5336    * (non-Javadoc)
5337    *
5338    * @see
5339    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5340    * .event.ActionEvent)
5341    */
5342   @Override
5343   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5344   {
5345     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5346     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5347   }
5348
5349   @Override
5350   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5351   {
5352     showSequenceLogo.setState(true);
5353     viewport.setShowSequenceLogo(true);
5354     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5355     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5356   }
5357
5358   @Override
5359   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5360   {
5361     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5362   }
5363
5364   /*
5365    * (non-Javadoc)
5366    *
5367    * @see
5368    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5369    * .event.ActionEvent)
5370    */
5371   @Override
5372   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5373   {
5374     if (avc.makeGroupsFromSelection())
5375     {
5376       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5377       alignPanel.updateAnnotation();
5378       alignPanel.paintAlignment(true, true);
5379     }
5380   }
5381
5382   public void clearAlignmentSeqRep()
5383   {
5384     // TODO refactor alignmentseqrep to controller
5385     if (viewport.getAlignment().hasSeqrep())
5386     {
5387       viewport.getAlignment().setSeqrep(null);
5388       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5389       alignPanel.updateAnnotation();
5390       alignPanel.paintAlignment(true, true);
5391     }
5392   }
5393
5394   @Override
5395   protected void createGroup_actionPerformed(ActionEvent e)
5396   {
5397     if (avc.createGroup())
5398     {
5399       alignPanel.alignmentChanged();
5400     }
5401   }
5402
5403   @Override
5404   protected void unGroup_actionPerformed(ActionEvent e)
5405   {
5406     if (avc.unGroup())
5407     {
5408       alignPanel.alignmentChanged();
5409     }
5410   }
5411
5412   /**
5413    * make the given alignmentPanel the currently selected tab
5414    *
5415    * @param alignmentPanel
5416    */
5417   public void setDisplayedView(AlignmentPanel alignmentPanel)
5418   {
5419     if (!viewport.getSequenceSetId()
5420             .equals(alignmentPanel.av.getSequenceSetId()))
5421     {
5422       throw new Error(MessageManager.getString(
5423               "error.implementation_error_cannot_show_view_alignment_frame"));
5424     }
5425     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5426             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5427     {
5428       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5429     }
5430   }
5431
5432   /**
5433    * Action on selection of menu options to Show or Hide annotations.
5434    *
5435    * @param visible
5436    * @param forSequences
5437    *          update sequence-related annotations
5438    * @param forAlignment
5439    *          update non-sequence-related annotations
5440    */
5441   @Override
5442   protected void setAnnotationsVisibility(boolean visible,
5443           boolean forSequences, boolean forAlignment)
5444   {
5445     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5446             .getAlignmentAnnotation();
5447     if (anns == null)
5448     {
5449       return;
5450     }
5451     for (AlignmentAnnotation aa : anns)
5452     {
5453       /*
5454        * don't display non-positional annotations on an alignment
5455        */
5456       if (aa.annotations == null)
5457       {
5458         continue;
5459       }
5460       boolean apply = (aa.sequenceRef == null && forAlignment)
5461               || (aa.sequenceRef != null && forSequences);
5462       if (apply)
5463       {
5464         aa.visible = visible;
5465       }
5466     }
5467     alignPanel.validateAnnotationDimensions(true);
5468     alignPanel.alignmentChanged();
5469   }
5470
5471   /**
5472    * Store selected annotation sort order for the view and repaint.
5473    */
5474   @Override
5475   protected void sortAnnotations_actionPerformed()
5476   {
5477     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5478     this.alignPanel.av
5479             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5480     alignPanel.paintAlignment(false, false);
5481   }
5482
5483   /**
5484    *
5485    * @return alignment panels in this alignment frame
5486    */
5487   public List<? extends AlignmentViewPanel> getAlignPanels()
5488   {
5489     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5490   }
5491
5492   /**
5493    * Open a new alignment window, with the cDNA associated with this (protein)
5494    * alignment, aligned as is the protein.
5495    */
5496   protected void viewAsCdna_actionPerformed()
5497   {
5498     // TODO no longer a menu action - refactor as required
5499     final AlignmentI alignment = getViewport().getAlignment();
5500     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5501     if (mappings == null)
5502     {
5503       return;
5504     }
5505     List<SequenceI> cdnaSeqs = new ArrayList<>();
5506     for (SequenceI aaSeq : alignment.getSequences())
5507     {
5508       for (AlignedCodonFrame acf : mappings)
5509       {
5510         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5511         if (dnaSeq != null)
5512         {
5513           /*
5514            * There is a cDNA mapping for this protein sequence - add to new
5515            * alignment. It will share the same dataset sequence as other mapped
5516            * cDNA (no new mappings need to be created).
5517            */
5518           final Sequence newSeq = new Sequence(dnaSeq);
5519           newSeq.setDatasetSequence(dnaSeq);
5520           cdnaSeqs.add(newSeq);
5521         }
5522       }
5523     }
5524     if (cdnaSeqs.size() == 0)
5525     {
5526       // show a warning dialog no mapped cDNA
5527       return;
5528     }
5529     AlignmentI cdna = new Alignment(
5530             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5531     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5532             AlignFrame.DEFAULT_HEIGHT);
5533     cdna.alignAs(alignment);
5534     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5535             + this.title;
5536     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5537             AlignFrame.DEFAULT_HEIGHT);
5538   }
5539
5540   /**
5541    * Set visibility of dna/protein complement view (available when shown in a
5542    * split frame).
5543    *
5544    * @param show
5545    */
5546   @Override
5547   protected void showComplement_actionPerformed(boolean show)
5548   {
5549     SplitContainerI sf = getSplitViewContainer();
5550     if (sf != null)
5551     {
5552       sf.setComplementVisible(this, show);
5553     }
5554   }
5555
5556   /**
5557    * Generate the reverse (optionally complemented) of the selected sequences,
5558    * and add them to the alignment
5559    */
5560   @Override
5561   protected void showReverse_actionPerformed(boolean complement)
5562   {
5563     AlignmentI al = null;
5564     try
5565     {
5566       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5567       al = dna.reverseCdna(complement);
5568       viewport.addAlignment(al, "");
5569       addHistoryItem(new EditCommand(
5570               MessageManager.getString("label.add_sequences"), Action.PASTE,
5571               al.getSequencesArray(), 0, al.getWidth(),
5572               viewport.getAlignment()));
5573     } catch (Exception ex)
5574     {
5575       System.err.println(ex.getMessage());
5576       return;
5577     }
5578   }
5579
5580   /**
5581    * Try to run a script in the Groovy console, having first ensured that this
5582    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5583    * be targeted at this alignment.
5584    */
5585   @Override
5586   protected void runGroovy_actionPerformed()
5587   {
5588     Jalview.setCurrentAlignFrame(this);
5589     groovy.ui.Console console = Desktop.getGroovyConsole();
5590     if (console != null)
5591     {
5592       try
5593       {
5594         console.runScript();
5595       } catch (Exception ex)
5596       {
5597         System.err.println((ex.toString()));
5598         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5599                 MessageManager.getString("label.couldnt_run_groovy_script"),
5600                 MessageManager.getString("label.groovy_support_failed"),
5601                 JvOptionPane.ERROR_MESSAGE);
5602       }
5603     }
5604     else
5605     {
5606       System.err.println("Can't run Groovy script as console not found");
5607     }
5608   }
5609
5610   /**
5611    * Hides columns containing (or not containing) a specified feature, provided
5612    * that would not leave all columns hidden
5613    *
5614    * @param featureType
5615    * @param columnsContaining
5616    * @return
5617    */
5618   public boolean hideFeatureColumns(String featureType,
5619           boolean columnsContaining)
5620   {
5621     boolean notForHiding = avc.markColumnsContainingFeatures(
5622             columnsContaining, false, false, featureType);
5623     if (notForHiding)
5624     {
5625       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5626               false, featureType))
5627       {
5628         getViewport().hideSelectedColumns();
5629         return true;
5630       }
5631     }
5632     return false;
5633   }
5634
5635   @Override
5636   protected void selectHighlightedColumns_actionPerformed(
5637           ActionEvent actionEvent)
5638   {
5639     // include key modifier check in case user selects from menu
5640     avc.markHighlightedColumns(
5641             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5642             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5643                     | ActionEvent.CTRL_MASK)) != 0);
5644   }
5645
5646   /**
5647    * Rebuilds the Colour menu, including any user-defined colours which have
5648    * been loaded either on startup or during the session
5649    */
5650   public void buildColourMenu()
5651   {
5652     colourMenu.removeAll();
5653
5654     colourMenu.add(applyToAllGroups);
5655     colourMenu.add(textColour);
5656     colourMenu.addSeparator();
5657
5658     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5659             false);
5660
5661     colourMenu.addSeparator();
5662     colourMenu.add(conservationMenuItem);
5663     colourMenu.add(modifyConservation);
5664     colourMenu.add(abovePIDThreshold);
5665     colourMenu.add(modifyPID);
5666     colourMenu.add(annotationColour);
5667
5668     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5669     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5670   }
5671
5672   /**
5673    * Open a dialog (if not already open) that allows the user to select and
5674    * calculate PCA or Tree analysis
5675    */
5676   protected void openTreePcaDialog()
5677   {
5678     if (alignPanel.getCalculationDialog() == null)
5679     {
5680       new CalculationChooser(AlignFrame.this);
5681     }
5682   }
5683 }
5684
5685 class PrintThread extends Thread
5686 {
5687   AlignmentPanel ap;
5688
5689   public PrintThread(AlignmentPanel ap)
5690   {
5691     this.ap = ap;
5692   }
5693
5694   static PageFormat pf;
5695
5696   @Override
5697   public void run()
5698   {
5699     PrinterJob printJob = PrinterJob.getPrinterJob();
5700
5701     if (pf != null)
5702     {
5703       printJob.setPrintable(ap, pf);
5704     }
5705     else
5706     {
5707       printJob.setPrintable(ap);
5708     }
5709
5710     if (printJob.printDialog())
5711     {
5712       try
5713       {
5714         printJob.print();
5715       } catch (Exception PrintException)
5716       {
5717         PrintException.printStackTrace();
5718       }
5719     }
5720   }
5721 }