src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.FeatureSettingsModelI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.ScoreModelI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.DBRefSource;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.FileLoader;
  69 import jalview.io.FormatAdapter;
  70 import jalview.io.HtmlSvgOutput;
  71 import jalview.io.IdentifyFile;
  72 import jalview.io.JalviewFileChooser;
  73 import jalview.io.JalviewFileView;
  74 import jalview.io.JnetAnnotationMaker;
  75 import jalview.io.NewickFile;
  76 import jalview.io.TCoffeeScoreFile;
  77 import jalview.io.gff.SequenceOntologyI;
  78 import jalview.jbgui.GAlignFrame;
  79 import jalview.schemes.Blosum62ColourScheme;
  80 import jalview.schemes.BuriedColourScheme;
  81 import jalview.schemes.ClustalxColourScheme;
  82 import jalview.schemes.ColourSchemeI;
  83 import jalview.schemes.ColourSchemeProperty;
  84 import jalview.schemes.HelixColourScheme;
  85 import jalview.schemes.HydrophobicColourScheme;
  86 import jalview.schemes.NucleotideColourScheme;
  87 import jalview.schemes.PIDColourScheme;
  88 import jalview.schemes.PurinePyrimidineColourScheme;
  89 import jalview.schemes.RNAHelicesColourChooser;
  90 import jalview.schemes.ResidueProperties;
  91 import jalview.schemes.StrandColourScheme;
  92 import jalview.schemes.TCoffeeColourScheme;
  93 import jalview.schemes.TaylorColourScheme;
  94 import jalview.schemes.TurnColourScheme;
  95 import jalview.schemes.UserColourScheme;
  96 import jalview.schemes.ZappoColourScheme;
  97 import jalview.structure.StructureSelectionManager;
  98 import jalview.util.MessageManager;
  99 import jalview.viewmodel.AlignmentViewport;
 100 import jalview.ws.DBRefFetcher;
 101 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 102 import jalview.ws.SequenceFetcher;
 103 import jalview.ws.jws1.Discoverer;
 104 import jalview.ws.jws2.Jws2Discoverer;
 105 import jalview.ws.jws2.jabaws2.Jws2Instance;
 106 import jalview.ws.seqfetcher.DbSourceProxy;
 107
 108 import java.awt.BorderLayout;
 109 import java.awt.Component;
 110 import java.awt.Rectangle;
 111 import java.awt.Toolkit;
 112 import java.awt.datatransfer.Clipboard;
 113 import java.awt.datatransfer.DataFlavor;
 114 import java.awt.datatransfer.StringSelection;
 115 import java.awt.datatransfer.Transferable;
 116 import java.awt.dnd.DropTargetDragEvent;
 117 import java.awt.dnd.DropTargetDropEvent;
 118 import java.awt.dnd.DropTargetEvent;
 119 import java.awt.dnd.DropTargetListener;
 120 import java.awt.event.ActionEvent;
 121 import java.awt.event.ActionListener;
 122 import java.awt.event.FocusAdapter;
 123 import java.awt.event.FocusEvent;
 124 import java.awt.event.ItemEvent;
 125 import java.awt.event.ItemListener;
 126 import java.awt.event.KeyAdapter;
 127 import java.awt.event.KeyEvent;
 128 import java.awt.event.MouseAdapter;
 129 import java.awt.event.MouseEvent;
 130 import java.awt.print.PageFormat;
 131 import java.awt.print.PrinterJob;
 132 import java.beans.PropertyChangeEvent;
 133 import java.io.File;
 134 import java.net.URL;
 135 import java.util.ArrayList;
 136 import java.util.Arrays;
 137 import java.util.Deque;
 138 import java.util.Enumeration;
 139 import java.util.Hashtable;
 140 import java.util.List;
 141 import java.util.Vector;
 142
 143 import javax.swing.JCheckBoxMenuItem;
 144 import javax.swing.JEditorPane;
 145 import javax.swing.JInternalFrame;
 146 import javax.swing.JLayeredPane;
 147 import javax.swing.JMenu;
 148 import javax.swing.JMenuItem;
 149 import javax.swing.JOptionPane;
 150 import javax.swing.JRadioButtonMenuItem;
 151 import javax.swing.JScrollPane;
 152 import javax.swing.SwingUtilities;
 153
 154 /**
 155  * DOCUMENT ME!
 156  *
 157  * @author $author$
 158  * @version $Revision$
 159  */
 160 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 161         IProgressIndicator, AlignViewControllerGuiI
 162 {
 163
 164   public static final int DEFAULT_WIDTH = 700;
 165
 166   public static final int DEFAULT_HEIGHT = 500;
 167
 168   /*
 169    * The currently displayed panel (selected tabbed view if more than one)
 170    */
 171   public AlignmentPanel alignPanel;
 172
 173   AlignViewport viewport;
 174
 175   public AlignViewControllerI avc;
 176
 177   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 178
 179   /**
 180    * Last format used to load or save alignments in this window
 181    */
 182   String currentFileFormat = null;
 183
 184   /**
 185    * Current filename for this alignment
 186    */
 187   String fileName = null;
 188
 189   /**
 190    * Creates a new AlignFrame object with specific width and height.
 191    *
 192    * @param al
 193    * @param width
 194    * @param height
 195    */
 196   public AlignFrame(AlignmentI al, int width, int height)
 197   {
 198     this(al, null, width, height);
 199   }
 200
 201   /**
 202    * Creates a new AlignFrame object with specific width, height and
 203    * sequenceSetId
 204    *
 205    * @param al
 206    * @param width
 207    * @param height
 208    * @param sequenceSetId
 209    */
 210   public AlignFrame(AlignmentI al, int width, int height,
 211           String sequenceSetId)
 212   {
 213     this(al, null, width, height, sequenceSetId);
 214   }
 215
 216   /**
 217    * Creates a new AlignFrame object with specific width, height and
 218    * sequenceSetId
 219    *
 220    * @param al
 221    * @param width
 222    * @param height
 223    * @param sequenceSetId
 224    * @param viewId
 225    */
 226   public AlignFrame(AlignmentI al, int width, int height,
 227           String sequenceSetId, String viewId)
 228   {
 229     this(al, null, width, height, sequenceSetId, viewId);
 230   }
 231
 232   /**
 233    * new alignment window with hidden columns
 234    *
 235    * @param al
 236    *          AlignmentI
 237    * @param hiddenColumns
 238    *          ColumnSelection or null
 239    * @param width
 240    *          Width of alignment frame
 241    * @param height
 242    *          height of frame.
 243    */
 244   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 245           int width, int height)
 246   {
 247     this(al, hiddenColumns, width, height, null);
 248   }
 249
 250   /**
 251    * Create alignment frame for al with hiddenColumns, a specific width and
 252    * height, and specific sequenceId
 253    *
 254    * @param al
 255    * @param hiddenColumns
 256    * @param width
 257    * @param height
 258    * @param sequenceSetId
 259    *          (may be null)
 260    */
 261   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 262           int width, int height, String sequenceSetId)
 263   {
 264     this(al, hiddenColumns, width, height, sequenceSetId, null);
 265   }
 266
 267   /**
 268    * Create alignment frame for al with hiddenColumns, a specific width and
 269    * height, and specific sequenceId
 270    *
 271    * @param al
 272    * @param hiddenColumns
 273    * @param width
 274    * @param height
 275    * @param sequenceSetId
 276    *          (may be null)
 277    * @param viewId
 278    *          (may be null)
 279    */
 280   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 281           int width, int height, String sequenceSetId, String viewId)
 282   {
 283     setSize(width, height);
 284
 285     if (al.getDataset() == null)
 286     {
 287       al.setDataset(null);
 288     }
 289
 290     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 291
 292     alignPanel = new AlignmentPanel(this, viewport);
 293
 294     addAlignmentPanel(alignPanel, true);
 295     init();
 296   }
 297
 298   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 299           ColumnSelection hiddenColumns, int width, int height)
 300   {
 301     setSize(width, height);
 302
 303     if (al.getDataset() == null)
 304     {
 305       al.setDataset(null);
 306     }
 307
 308     viewport = new AlignViewport(al, hiddenColumns);
 309
 310     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 311     {
 312       viewport.hideSequence(hiddenSeqs);
 313     }
 314     alignPanel = new AlignmentPanel(this, viewport);
 315     addAlignmentPanel(alignPanel, true);
 316     init();
 317   }
 318
 319   /**
 320    * Make a new AlignFrame from existing alignmentPanels
 321    *
 322    * @param ap
 323    *          AlignmentPanel
 324    * @param av
 325    *          AlignViewport
 326    */
 327   public AlignFrame(AlignmentPanel ap)
 328   {
 329     viewport = ap.av;
 330     alignPanel = ap;
 331     addAlignmentPanel(ap, false);
 332     init();
 333   }
 334
 335   /**
 336    * initalise the alignframe from the underlying viewport data and the
 337    * configurations
 338    */
 339   void init()
 340   {
 341     if (!Jalview.isHeadlessMode())
 342     {
 343       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 344     }
 345
 346     avc = new jalview.controller.AlignViewController(this, viewport,
 347             alignPanel);
 348     if (viewport.getAlignmentConservationAnnotation() == null)
 349     {
 350       BLOSUM62Colour.setEnabled(false);
 351       conservationMenuItem.setEnabled(false);
 352       modifyConservation.setEnabled(false);
 353       // PIDColour.setEnabled(false);
 354       // abovePIDThreshold.setEnabled(false);
 355       // modifyPID.setEnabled(false);
 356     }
 357
 358     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 359             "No sort");
 360
 361     if (sortby.equals("Id"))
 362     {
 363       sortIDMenuItem_actionPerformed(null);
 364     }
 365     else if (sortby.equals("Pairwise Identity"))
 366     {
 367       sortPairwiseMenuItem_actionPerformed(null);
 368     }
 369
 370     if (Desktop.desktop != null)
 371     {
 372       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 373       addServiceListeners();
 374       setGUINucleotide(viewport.getAlignment().isNucleotide());
 375     }
 376
 377     this.alignPanel.av
 378             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 379
 380     setMenusFromViewport(viewport);
 381     buildSortByAnnotationScoresMenu();
 382     buildTreeMenu();
 383
 384     if (viewport.getWrapAlignment())
 385     {
 386       wrapMenuItem_actionPerformed(null);
 387     }
 388
 389     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 390     {
 391       this.overviewMenuItem_actionPerformed(null);
 392     }
 393
 394     addKeyListener();
 395
 396     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 397     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 398     final String menuLabel = MessageManager
 399             .getString("label.copy_format_from");
 400     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 401             new ViewSetProvider()
 402             {
 403
 404               @Override
 405               public AlignmentPanel[] getAllAlignmentPanels()
 406               {
 407                 origview.clear();
 408                 origview.add(alignPanel);
 409                 // make an array of all alignment panels except for this one
 410                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 411                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 412                 aps.remove(AlignFrame.this.alignPanel);
 413                 return aps.toArray(new AlignmentPanel[aps.size()]);
 414               }
 415             }, selviews, new ItemListener()
 416             {
 417
 418               @Override
 419               public void itemStateChanged(ItemEvent e)
 420               {
 421                 if (origview.size() > 0)
 422                 {
 423                   final AlignmentPanel ap = origview.get(0);
 424
 425                   /*
 426                    * Copy the ViewStyle of the selected panel to 'this one'.
 427                    * Don't change value of 'scaleProteinAsCdna' unless copying
 428                    * from a SplitFrame.
 429                    */
 430                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 431                           .getViewStyle();
 432                   boolean fromSplitFrame = selviews.get(0)
 433                           .getAlignViewport().getCodingComplement() != null;
 434                   if (!fromSplitFrame)
 435                   {
 436                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 437                             .getViewStyle().isScaleProteinAsCdna());
 438                   }
 439                   ap.getAlignViewport().setViewStyle(vs);
 440
 441                   /*
 442                    * Also rescale ViewStyle of SplitFrame complement if there is
 443                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 444                    * the whole ViewStyle (allow cDNA protein to have different
 445                    * fonts)
 446                    */
 447                   AlignViewportI complement = ap.getAlignViewport()
 448                           .getCodingComplement();
 449                   if (complement != null && vs.isScaleProteinAsCdna())
 450                   {
 451                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 452                     ((SplitFrame) af.getSplitViewContainer())
 453                             .adjustLayout();
 454                     af.setMenusForViewport();
 455                   }
 456
 457                   ap.updateLayout();
 458                   ap.setSelected(true);
 459                   ap.alignFrame.setMenusForViewport();
 460
 461                 }
 462               }
 463             });
 464     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 465             .indexOf("devel") > -1
 466             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 467                     .indexOf("test") > -1)
 468     {
 469       formatMenu.add(vsel);
 470     }
 471     addFocusListener(new FocusAdapter()
 472     {
 473       @Override
 474       public void focusGained(FocusEvent e)
 475       {
 476         Desktop.setCurrentAlignFrame(AlignFrame.this);
 477       }
 478     });
 479
 480   }
 481
 482   /**
 483    * Change the filename and format for the alignment, and enable the 'reload'
 484    * button functionality.
 485    *
 486    * @param file
 487    *          valid filename
 488    * @param format
 489    *          format of file
 490    */
 491   public void setFileName(String file, String format)
 492   {
 493     fileName = file;
 494     setFileFormat(format);
 495     reload.setEnabled(true);
 496   }
 497
 498   /**
 499    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 500    * events
 501    */
 502   void addKeyListener()
 503   {
 504     addKeyListener(new KeyAdapter()
 505     {
 506       @Override
 507       public void keyPressed(KeyEvent evt)
 508       {
 509         if (viewport.cursorMode
 510                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 511                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 512                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 513                 && Character.isDigit(evt.getKeyChar()))
 514         {
 515           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 516         }
 517
 518         switch (evt.getKeyCode())
 519         {
 520
 521         case 27: // escape key
 522           deselectAllSequenceMenuItem_actionPerformed(null);
 523
 524           break;
 525
 526         case KeyEvent.VK_DOWN:
 527           if (evt.isAltDown() || !viewport.cursorMode)
 528           {
 529             moveSelectedSequences(false);
 530           }
 531           if (viewport.cursorMode)
 532           {
 533             alignPanel.getSeqPanel().moveCursor(0, 1);
 534           }
 535           break;
 536
 537         case KeyEvent.VK_UP:
 538           if (evt.isAltDown() || !viewport.cursorMode)
 539           {
 540             moveSelectedSequences(true);
 541           }
 542           if (viewport.cursorMode)
 543           {
 544             alignPanel.getSeqPanel().moveCursor(0, -1);
 545           }
 546
 547           break;
 548
 549         case KeyEvent.VK_LEFT:
 550           if (evt.isAltDown() || !viewport.cursorMode)
 551           {
 552             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 553           }
 554           else
 555           {
 556             alignPanel.getSeqPanel().moveCursor(-1, 0);
 557           }
 558
 559           break;
 560
 561         case KeyEvent.VK_RIGHT:
 562           if (evt.isAltDown() || !viewport.cursorMode)
 563           {
 564             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 565           }
 566           else
 567           {
 568             alignPanel.getSeqPanel().moveCursor(1, 0);
 569           }
 570           break;
 571
 572         case KeyEvent.VK_SPACE:
 573           if (viewport.cursorMode)
 574           {
 575             alignPanel.getSeqPanel().insertGapAtCursor(
 576                     evt.isControlDown() || evt.isShiftDown()
 577                             || evt.isAltDown());
 578           }
 579           break;
 580
 581         // case KeyEvent.VK_A:
 582         // if (viewport.cursorMode)
 583         // {
 584         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 585         // //System.out.println("A");
 586         // }
 587         // break;
 588         /*
 589          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 590          * System.out.println("closing bracket"); } break;
 591          */
 592         case KeyEvent.VK_DELETE:
 593         case KeyEvent.VK_BACK_SPACE:
 594           if (!viewport.cursorMode)
 595           {
 596             cut_actionPerformed(null);
 597           }
 598           else
 599           {
 600             alignPanel.getSeqPanel().deleteGapAtCursor(
 601                     evt.isControlDown() || evt.isShiftDown()
 602                             || evt.isAltDown());
 603           }
 604
 605           break;
 606
 607         case KeyEvent.VK_S:
 608           if (viewport.cursorMode)
 609           {
 610             alignPanel.getSeqPanel().setCursorRow();
 611           }
 612           break;
 613         case KeyEvent.VK_C:
 614           if (viewport.cursorMode && !evt.isControlDown())
 615           {
 616             alignPanel.getSeqPanel().setCursorColumn();
 617           }
 618           break;
 619         case KeyEvent.VK_P:
 620           if (viewport.cursorMode)
 621           {
 622             alignPanel.getSeqPanel().setCursorPosition();
 623           }
 624           break;
 625
 626         case KeyEvent.VK_ENTER:
 627         case KeyEvent.VK_COMMA:
 628           if (viewport.cursorMode)
 629           {
 630             alignPanel.getSeqPanel().setCursorRowAndColumn();
 631           }
 632           break;
 633
 634         case KeyEvent.VK_Q:
 635           if (viewport.cursorMode)
 636           {
 637             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 638           }
 639           break;
 640         case KeyEvent.VK_M:
 641           if (viewport.cursorMode)
 642           {
 643             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 644           }
 645           break;
 646
 647         case KeyEvent.VK_F2:
 648           viewport.cursorMode = !viewport.cursorMode;
 649           statusBar.setText(MessageManager.formatMessage(
 650                   "label.keyboard_editing_mode",
 651                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 652           if (viewport.cursorMode)
 653           {
 654             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 655             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 656           }
 657           alignPanel.getSeqPanel().seqCanvas.repaint();
 658           break;
 659
 660         case KeyEvent.VK_F1:
 661           try
 662           {
 663             Help.showHelpWindow();
 664           } catch (Exception ex)
 665           {
 666             ex.printStackTrace();
 667           }
 668           break;
 669         case KeyEvent.VK_H:
 670         {
 671           boolean toggleSeqs = !evt.isControlDown();
 672           boolean toggleCols = !evt.isShiftDown();
 673           toggleHiddenRegions(toggleSeqs, toggleCols);
 674           break;
 675         }
 676         case KeyEvent.VK_PAGE_UP:
 677           if (viewport.getWrapAlignment())
 678           {
 679             alignPanel.scrollUp(true);
 680           }
 681           else
 682           {
 683             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 684                     - viewport.endSeq + viewport.startSeq);
 685           }
 686           break;
 687         case KeyEvent.VK_PAGE_DOWN:
 688           if (viewport.getWrapAlignment())
 689           {
 690             alignPanel.scrollUp(false);
 691           }
 692           else
 693           {
 694             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 695                     + viewport.endSeq - viewport.startSeq);
 696           }
 697           break;
 698         }
 699       }
 700
 701       @Override
 702       public void keyReleased(KeyEvent evt)
 703       {
 704         switch (evt.getKeyCode())
 705         {
 706         case KeyEvent.VK_LEFT:
 707           if (evt.isAltDown() || !viewport.cursorMode)
 708           {
 709             viewport.firePropertyChange("alignment", null, viewport
 710                     .getAlignment().getSequences());
 711           }
 712           break;
 713
 714         case KeyEvent.VK_RIGHT:
 715           if (evt.isAltDown() || !viewport.cursorMode)
 716           {
 717             viewport.firePropertyChange("alignment", null, viewport
 718                     .getAlignment().getSequences());
 719           }
 720           break;
 721         }
 722       }
 723     });
 724   }
 725
 726   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 727   {
 728     ap.alignFrame = this;
 729     avc = new jalview.controller.AlignViewController(this, viewport,
 730             alignPanel);
 731
 732     alignPanels.add(ap);
 733
 734     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 735
 736     int aSize = alignPanels.size();
 737
 738     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 739
 740     if (aSize == 1 && ap.av.viewName == null)
 741     {
 742       this.getContentPane().add(ap, BorderLayout.CENTER);
 743     }
 744     else
 745     {
 746       if (aSize == 2)
 747       {
 748         setInitialTabVisible();
 749       }
 750
 751       expandViews.setEnabled(true);
 752       gatherViews.setEnabled(true);
 753       tabbedPane.addTab(ap.av.viewName, ap);
 754
 755       ap.setVisible(false);
 756     }
 757
 758     if (newPanel)
 759     {
 760       if (ap.av.isPadGaps())
 761       {
 762         ap.av.getAlignment().padGaps();
 763       }
 764       ap.av.updateConservation(ap);
 765       ap.av.updateConsensus(ap);
 766       ap.av.updateStrucConsensus(ap);
 767     }
 768   }
 769
 770   public void setInitialTabVisible()
 771   {
 772     expandViews.setEnabled(true);
 773     gatherViews.setEnabled(true);
 774     tabbedPane.setVisible(true);
 775     AlignmentPanel first = alignPanels.get(0);
 776     tabbedPane.addTab(first.av.viewName, first);
 777     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 778   }
 779
 780   public AlignViewport getViewport()
 781   {
 782     return viewport;
 783   }
 784
 785   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 786   private void addServiceListeners()
 787   {
 788     final java.beans.PropertyChangeListener thisListener;
 789     Desktop.instance.addJalviewPropertyChangeListener("services",
 790             thisListener = new java.beans.PropertyChangeListener()
 791             {
 792               @Override
 793               public void propertyChange(PropertyChangeEvent evt)
 794               {
 795                 // // System.out.println("Discoverer property change.");
 796                 // if (evt.getPropertyName().equals("services"))
 797                 {
 798                   SwingUtilities.invokeLater(new Runnable()
 799                   {
 800
 801                     @Override
 802                     public void run()
 803                     {
 804                       System.err
 805                               .println("Rebuild WS Menu for service change");
 806                       BuildWebServiceMenu();
 807                     }
 808
 809                   });
 810                 }
 811               }
 812             });
 813     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 814     {
 815       @Override
 816       public void internalFrameClosed(
 817               javax.swing.event.InternalFrameEvent evt)
 818       {
 819         // System.out.println("deregistering discoverer listener");
 820         Desktop.instance.removeJalviewPropertyChangeListener("services",
 821                 thisListener);
 822         closeMenuItem_actionPerformed(true);
 823       };
 824     });
 825     // Finally, build the menu once to get current service state
 826     new Thread(new Runnable()
 827     {
 828       @Override
 829       public void run()
 830       {
 831         BuildWebServiceMenu();
 832       }
 833     }).start();
 834   }
 835
 836   /**
 837    * Configure menu items that vary according to whether the alignment is
 838    * nucleotide or protein
 839    *
 840    * @param nucleotide
 841    */
 842   public void setGUINucleotide(boolean nucleotide)
 843   {
 844     showTranslation.setVisible(nucleotide);
 845     showReverse.setVisible(nucleotide);
 846     showReverseComplement.setVisible(nucleotide);
 847     conservationMenuItem.setEnabled(!nucleotide);
 848     modifyConservation.setEnabled(!nucleotide);
 849     showGroupConservation.setEnabled(!nucleotide);
 850     rnahelicesColour.setEnabled(nucleotide);
 851     purinePyrimidineColour.setEnabled(nucleotide);
 852     showComplementMenuItem.setText(MessageManager
 853             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 854     setColourSelected(jalview.bin.Cache.getDefault(
 855             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 856                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 857   }
 858
 859   /**
 860    * set up menus for the current viewport. This may be called after any
 861    * operation that affects the data in the current view (selection changed,
 862    * etc) to update the menus to reflect the new state.
 863    */
 864   @Override
 865   public void setMenusForViewport()
 866   {
 867     setMenusFromViewport(viewport);
 868   }
 869
 870   /**
 871    * Need to call this method when tabs are selected for multiple views, or when
 872    * loading from Jalview2XML.java
 873    *
 874    * @param av
 875    *          AlignViewport
 876    */
 877   void setMenusFromViewport(AlignViewport av)
 878   {
 879     padGapsMenuitem.setSelected(av.isPadGaps());
 880     colourTextMenuItem.setSelected(av.isShowColourText());
 881     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 882     conservationMenuItem.setSelected(av.getConservationSelected());
 883     seqLimits.setSelected(av.getShowJVSuffix());
 884     idRightAlign.setSelected(av.isRightAlignIds());
 885     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 886     renderGapsMenuItem.setSelected(av.isRenderGaps());
 887     wrapMenuItem.setSelected(av.getWrapAlignment());
 888     scaleAbove.setVisible(av.getWrapAlignment());
 889     scaleLeft.setVisible(av.getWrapAlignment());
 890     scaleRight.setVisible(av.getWrapAlignment());
 891     annotationPanelMenuItem.setState(av.isShowAnnotation());
 892     /*
 893      * Show/hide annotations only enabled if annotation panel is shown
 894      */
 895     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 898     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 900     viewTextMenuItem.setSelected(av.getShowText());
 901     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 902     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 903     showGroupConservation.setSelected(av.isShowGroupConservation());
 904     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 905     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 906     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 907
 908     setColourSelected(ColourSchemeProperty.getColourName(av
 909             .getGlobalColourScheme()));
 910
 911     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 912     hiddenMarkers.setState(av.getShowHiddenMarkers());
 913     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 914     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 915     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 916     autoCalculate.setSelected(av.autoCalculateConsensus);
 917     sortByTree.setSelected(av.sortByTree);
 918     listenToViewSelections.setSelected(av.followSelection);
 919     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 920     rnahelicesColour
 921             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 922
 923     showProducts.setEnabled(canShowProducts());
 924     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 925
 926     updateEditMenuBar();
 927   }
 928
 929   /**
 930    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 931    *
 932    * @param b
 933    */
 934   public void setGroovyEnabled(boolean b)
 935   {
 936     runGroovy.setEnabled(b);
 937   }
 938
 939   private IProgressIndicator progressBar;
 940
 941   /*
 942    * (non-Javadoc)
 943    *
 944    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 945    */
 946   @Override
 947   public void setProgressBar(String message, long id)
 948   {
 949     progressBar.setProgressBar(message, id);
 950   }
 951
 952   @Override
 953   public void registerHandler(final long id,
 954           final IProgressIndicatorHandler handler)
 955   {
 956     progressBar.registerHandler(id, handler);
 957   }
 958
 959   /**
 960    *
 961    * @return true if any progress bars are still active
 962    */
 963   @Override
 964   public boolean operationInProgress()
 965   {
 966     return progressBar.operationInProgress();
 967   }
 968
 969   @Override
 970   public void setStatus(String text)
 971   {
 972     statusBar.setText(text);
 973   }
 974
 975   /*
 976    * Added so Castor Mapping file can obtain Jalview Version
 977    */
 978   public String getVersion()
 979   {
 980     return jalview.bin.Cache.getProperty("VERSION");
 981   }
 982
 983   public FeatureRenderer getFeatureRenderer()
 984   {
 985     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 986   }
 987
 988   @Override
 989   public void fetchSequence_actionPerformed(ActionEvent e)
 990   {
 991     new jalview.gui.SequenceFetcher(this);
 992   }
 993
 994   @Override
 995   public void addFromFile_actionPerformed(ActionEvent e)
 996   {
 997     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 998   }
 999
1000   @Override
1001   public void reload_actionPerformed(ActionEvent e)
1002   {
1003     if (fileName != null)
1004     {
1005       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1006       // originating file's format
1007       // TODO: work out how to recover feature settings for correct view(s) when
1008       // file is reloaded.
1009       if (currentFileFormat.equals("Jalview"))
1010       {
1011         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1012         for (int i = 0; i < frames.length; i++)
1013         {
1014           if (frames[i] instanceof AlignFrame && frames[i] != this
1015                   && ((AlignFrame) frames[i]).fileName != null
1016                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1017           {
1018             try
1019             {
1020               frames[i].setSelected(true);
1021               Desktop.instance.closeAssociatedWindows();
1022             } catch (java.beans.PropertyVetoException ex)
1023             {
1024             }
1025           }
1026
1027         }
1028         Desktop.instance.closeAssociatedWindows();
1029
1030         FileLoader loader = new FileLoader();
1031         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1032         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1033       }
1034       else
1035       {
1036         Rectangle bounds = this.getBounds();
1037
1038         FileLoader loader = new FileLoader();
1039         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1040         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1041                 protocol, currentFileFormat);
1042
1043         newframe.setBounds(bounds);
1044         if (featureSettings != null && featureSettings.isShowing())
1045         {
1046           final Rectangle fspos = featureSettings.frame.getBounds();
1047           // TODO: need a 'show feature settings' function that takes bounds -
1048           // need to refactor Desktop.addFrame
1049           newframe.featureSettings_actionPerformed(null);
1050           final FeatureSettings nfs = newframe.featureSettings;
1051           SwingUtilities.invokeLater(new Runnable()
1052           {
1053             @Override
1054             public void run()
1055             {
1056               nfs.frame.setBounds(fspos);
1057             }
1058           });
1059           this.featureSettings.close();
1060           this.featureSettings = null;
1061         }
1062         this.closeMenuItem_actionPerformed(true);
1063       }
1064     }
1065   }
1066
1067   @Override
1068   public void addFromText_actionPerformed(ActionEvent e)
1069   {
1070     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1071             .getAlignPanel());
1072   }
1073
1074   @Override
1075   public void addFromURL_actionPerformed(ActionEvent e)
1076   {
1077     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1078   }
1079
1080   @Override
1081   public void save_actionPerformed(ActionEvent e)
1082   {
1083     if (fileName == null
1084             || (currentFileFormat == null || !jalview.io.FormatAdapter
1085                     .isValidIOFormat(currentFileFormat, true))
1086             || fileName.startsWith("http"))
1087     {
1088       saveAs_actionPerformed(null);
1089     }
1090     else
1091     {
1092       saveAlignment(fileName, currentFileFormat);
1093     }
1094   }
1095
1096   /**
1097    * DOCUMENT ME!
1098    *
1099    * @param e
1100    *          DOCUMENT ME!
1101    */
1102   @Override
1103   public void saveAs_actionPerformed(ActionEvent e)
1104   {
1105     JalviewFileChooser chooser = new JalviewFileChooser(
1106             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1107             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1108             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1109             currentFileFormat, false);
1110
1111     chooser.setFileView(new JalviewFileView());
1112     chooser.setDialogTitle(MessageManager
1113             .getString("label.save_alignment_to_file"));
1114     chooser.setToolTipText(MessageManager.getString("action.save"));
1115
1116     int value = chooser.showSaveDialog(this);
1117
1118     if (value == JalviewFileChooser.APPROVE_OPTION)
1119     {
1120       currentFileFormat = chooser.getSelectedFormat();
1121       while (currentFileFormat == null)
1122       {
1123         JOptionPane
1124                 .showInternalMessageDialog(
1125                         Desktop.desktop,
1126                         MessageManager
1127                                 .getString("label.select_file_format_before_saving"),
1128                         MessageManager
1129                                 .getString("label.file_format_not_specified"),
1130                         JOptionPane.WARNING_MESSAGE);
1131         currentFileFormat = chooser.getSelectedFormat();
1132         value = chooser.showSaveDialog(this);
1133         if (value != JalviewFileChooser.APPROVE_OPTION)
1134         {
1135           return;
1136         }
1137       }
1138
1139       fileName = chooser.getSelectedFile().getPath();
1140
1141       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1142               currentFileFormat);
1143
1144       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1145       if (currentFileFormat.indexOf(" ") > -1)
1146       {
1147         currentFileFormat = currentFileFormat.substring(0,
1148                 currentFileFormat.indexOf(" "));
1149       }
1150       saveAlignment(fileName, currentFileFormat);
1151     }
1152   }
1153
1154   public boolean saveAlignment(String file, String format)
1155   {
1156     boolean success = true;
1157
1158     if (format.equalsIgnoreCase("Jalview"))
1159     {
1160       String shortName = title;
1161
1162       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1163       {
1164         shortName = shortName.substring(shortName
1165                 .lastIndexOf(java.io.File.separatorChar) + 1);
1166       }
1167
1168       success = new Jalview2XML().saveAlignment(this, file, shortName);
1169
1170       statusBar.setText(MessageManager.formatMessage(
1171               "label.successfully_saved_to_file_in_format", new Object[] {
1172                   fileName, format }));
1173
1174     }
1175     else
1176     {
1177       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1178       {
1179         warningMessage("Cannot save file " + fileName + " using format "
1180                 + format, "Alignment output format not supported");
1181         if (!Jalview.isHeadlessMode())
1182         {
1183           saveAs_actionPerformed(null);
1184         }
1185         return false;
1186       }
1187
1188       AlignmentExportData exportData = getAlignmentForExport(format,
1189               viewport, null);
1190       if (exportData.getSettings().isCancelled())
1191       {
1192         return false;
1193       }
1194       FormatAdapter f = new FormatAdapter(alignPanel,
1195               exportData.getSettings());
1196       String output = f.formatSequences(
1197               format,
1198               exportData.getAlignment(), // class cast exceptions will
1199               // occur in the distant future
1200               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1201               f.getCacheSuffixDefault(format),
1202               viewport.getColumnSelection());
1203
1204       if (output == null)
1205       {
1206         success = false;
1207       }
1208       else
1209       {
1210         try
1211         {
1212           java.io.PrintWriter out = new java.io.PrintWriter(
1213                   new java.io.FileWriter(file));
1214
1215           out.print(output);
1216           out.close();
1217           this.setTitle(file);
1218           statusBar.setText(MessageManager.formatMessage(
1219                   "label.successfully_saved_to_file_in_format",
1220                   new Object[] { fileName, format }));
1221         } catch (Exception ex)
1222         {
1223           success = false;
1224           ex.printStackTrace();
1225         }
1226       }
1227     }
1228
1229     if (!success)
1230     {
1231       JOptionPane.showInternalMessageDialog(this, MessageManager
1232               .formatMessage("label.couldnt_save_file",
1233                       new Object[] { fileName }), MessageManager
1234               .getString("label.error_saving_file"),
1235               JOptionPane.WARNING_MESSAGE);
1236     }
1237
1238     return success;
1239   }
1240
1241   private void warningMessage(String warning, String title)
1242   {
1243     if (new jalview.util.Platform().isHeadless())
1244     {
1245       System.err.println("Warning: " + title + "\nWarning: " + warning);
1246
1247     }
1248     else
1249     {
1250       JOptionPane.showInternalMessageDialog(this, warning, title,
1251               JOptionPane.WARNING_MESSAGE);
1252     }
1253     return;
1254   }
1255
1256   /**
1257    * DOCUMENT ME!
1258    *
1259    * @param e
1260    *          DOCUMENT ME!
1261    */
1262   @Override
1263   protected void outputText_actionPerformed(ActionEvent e)
1264   {
1265
1266     AlignmentExportData exportData = getAlignmentForExport(
1267             e.getActionCommand(), viewport, null);
1268     if (exportData.getSettings().isCancelled())
1269     {
1270       return;
1271     }
1272     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1273     cap.setForInput(null);
1274     try
1275     {
1276       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1277               .formatSequences(e.getActionCommand(),
1278                       exportData.getAlignment(),
1279                       exportData.getOmitHidden(),
1280                       exportData.getStartEndPostions(),
1281                       viewport.getColumnSelection()));
1282       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1283               "label.alignment_output_command",
1284               new Object[] { e.getActionCommand() }), 600, 500);
1285     } catch (OutOfMemoryError oom)
1286     {
1287       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1288       cap.dispose();
1289     }
1290
1291   }
1292
1293   public static AlignmentExportData getAlignmentForExport(
1294           String exportFormat, AlignViewportI viewport,
1295           AlignExportSettingI exportSettings)
1296   {
1297     AlignmentI alignmentToExport = null;
1298     AlignExportSettingI settings = exportSettings;
1299     String[] omitHidden = null;
1300
1301     HiddenSequences hiddenSeqs = viewport.getAlignment()
1302             .getHiddenSequences();
1303
1304     alignmentToExport = viewport.getAlignment();
1305
1306     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1307     if (settings == null)
1308     {
1309       settings = new AlignExportSettings(hasHiddenSeqs,
1310               viewport.hasHiddenColumns(), exportFormat);
1311     }
1312     // settings.isExportAnnotations();
1313
1314     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1315     {
1316       omitHidden = viewport.getViewAsString(false);
1317     }
1318
1319     int[] alignmentStartEnd = new int[2];
1320     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1321     {
1322       alignmentToExport = hiddenSeqs.getFullAlignment();
1323     }
1324     else
1325     {
1326       alignmentToExport = viewport.getAlignment();
1327       alignmentStartEnd = viewport.getAlignment()
1328               .getVisibleStartAndEndIndex(
1329                       viewport.getColumnSelection().getHiddenColumns());
1330     }
1331     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1332             omitHidden, alignmentStartEnd, settings);
1333     return ed;
1334   }
1335
1336   /**
1337    * DOCUMENT ME!
1338    *
1339    * @param e
1340    *          DOCUMENT ME!
1341    */
1342   @Override
1343   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1344   {
1345     new HtmlSvgOutput(null, alignPanel);
1346   }
1347
1348   @Override
1349   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1350   {
1351     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1352     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1353   }
1354
1355   public void createImageMap(File file, String image)
1356   {
1357     alignPanel.makePNGImageMap(file, image);
1358   }
1359
1360   /**
1361    * DOCUMENT ME!
1362    *
1363    * @param e
1364    *          DOCUMENT ME!
1365    */
1366   @Override
1367   public void createPNG(File f)
1368   {
1369     alignPanel.makePNG(f);
1370   }
1371
1372   /**
1373    * DOCUMENT ME!
1374    *
1375    * @param e
1376    *          DOCUMENT ME!
1377    */
1378   @Override
1379   public void createEPS(File f)
1380   {
1381     alignPanel.makeEPS(f);
1382   }
1383
1384   @Override
1385   public void createSVG(File f)
1386   {
1387     alignPanel.makeSVG(f);
1388   }
1389
1390   @Override
1391   public void pageSetup_actionPerformed(ActionEvent e)
1392   {
1393     PrinterJob printJob = PrinterJob.getPrinterJob();
1394     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1395   }
1396
1397   /**
1398    * DOCUMENT ME!
1399    *
1400    * @param e
1401    *          DOCUMENT ME!
1402    */
1403   @Override
1404   public void printMenuItem_actionPerformed(ActionEvent e)
1405   {
1406     // Putting in a thread avoids Swing painting problems
1407     PrintThread thread = new PrintThread(alignPanel);
1408     thread.start();
1409   }
1410
1411   @Override
1412   public void exportFeatures_actionPerformed(ActionEvent e)
1413   {
1414     new AnnotationExporter().exportFeatures(alignPanel);
1415   }
1416
1417   @Override
1418   public void exportAnnotations_actionPerformed(ActionEvent e)
1419   {
1420     new AnnotationExporter().exportAnnotations(alignPanel);
1421   }
1422
1423   @Override
1424   public void associatedData_actionPerformed(ActionEvent e)
1425   {
1426     // Pick the tree file
1427     JalviewFileChooser chooser = new JalviewFileChooser(
1428             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1429     chooser.setFileView(new JalviewFileView());
1430     chooser.setDialogTitle(MessageManager
1431             .getString("label.load_jalview_annotations"));
1432     chooser.setToolTipText(MessageManager
1433             .getString("label.load_jalview_annotations"));
1434
1435     int value = chooser.showOpenDialog(null);
1436
1437     if (value == JalviewFileChooser.APPROVE_OPTION)
1438     {
1439       String choice = chooser.getSelectedFile().getPath();
1440       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1441       loadJalviewDataFile(choice, null, null, null);
1442     }
1443
1444   }
1445
1446   /**
1447    * Close the current view or all views in the alignment frame. If the frame
1448    * only contains one view then the alignment will be removed from memory.
1449    *
1450    * @param closeAllTabs
1451    */
1452   @Override
1453   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1454   {
1455     if (alignPanels != null && alignPanels.size() < 2)
1456     {
1457       closeAllTabs = true;
1458     }
1459
1460     try
1461     {
1462       if (alignPanels != null)
1463       {
1464         if (closeAllTabs)
1465         {
1466           if (this.isClosed())
1467           {
1468             // really close all the windows - otherwise wait till
1469             // setClosed(true) is called
1470             for (int i = 0; i < alignPanels.size(); i++)
1471             {
1472               AlignmentPanel ap = alignPanels.get(i);
1473               ap.closePanel();
1474             }
1475           }
1476         }
1477         else
1478         {
1479           closeView(alignPanel);
1480         }
1481       }
1482
1483       if (closeAllTabs)
1484       {
1485         /*
1486          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1487          * be called recursively, with the frame now in 'closed' state
1488          */
1489         this.setClosed(true);
1490       }
1491     } catch (Exception ex)
1492     {
1493       ex.printStackTrace();
1494     }
1495   }
1496
1497   /**
1498    * Close the specified panel and close up tabs appropriately.
1499    *
1500    * @param panelToClose
1501    */
1502   public void closeView(AlignmentPanel panelToClose)
1503   {
1504     int index = tabbedPane.getSelectedIndex();
1505     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1506     alignPanels.remove(panelToClose);
1507     panelToClose.closePanel();
1508     panelToClose = null;
1509
1510     tabbedPane.removeTabAt(closedindex);
1511     tabbedPane.validate();
1512
1513     if (index > closedindex || index == tabbedPane.getTabCount())
1514     {
1515       // modify currently selected tab index if necessary.
1516       index--;
1517     }
1518
1519     this.tabSelectionChanged(index);
1520   }
1521
1522   /**
1523    * DOCUMENT ME!
1524    */
1525   void updateEditMenuBar()
1526   {
1527
1528     if (viewport.getHistoryList().size() > 0)
1529     {
1530       undoMenuItem.setEnabled(true);
1531       CommandI command = viewport.getHistoryList().peek();
1532       undoMenuItem.setText(MessageManager.formatMessage(
1533               "label.undo_command",
1534               new Object[] { command.getDescription() }));
1535     }
1536     else
1537     {
1538       undoMenuItem.setEnabled(false);
1539       undoMenuItem.setText(MessageManager.getString("action.undo"));
1540     }
1541
1542     if (viewport.getRedoList().size() > 0)
1543     {
1544       redoMenuItem.setEnabled(true);
1545
1546       CommandI command = viewport.getRedoList().peek();
1547       redoMenuItem.setText(MessageManager.formatMessage(
1548               "label.redo_command",
1549               new Object[] { command.getDescription() }));
1550     }
1551     else
1552     {
1553       redoMenuItem.setEnabled(false);
1554       redoMenuItem.setText(MessageManager.getString("action.redo"));
1555     }
1556   }
1557
1558   @Override
1559   public void addHistoryItem(CommandI command)
1560   {
1561     if (command.getSize() > 0)
1562     {
1563       viewport.addToHistoryList(command);
1564       viewport.clearRedoList();
1565       updateEditMenuBar();
1566       viewport.updateHiddenColumns();
1567       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1568       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1569       // viewport.getColumnSelection()
1570       // .getHiddenColumns().size() > 0);
1571     }
1572   }
1573
1574   /**
1575    *
1576    * @return alignment objects for all views
1577    */
1578   AlignmentI[] getViewAlignments()
1579   {
1580     if (alignPanels != null)
1581     {
1582       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1583       int i = 0;
1584       for (AlignmentPanel ap : alignPanels)
1585       {
1586         als[i++] = ap.av.getAlignment();
1587       }
1588       return als;
1589     }
1590     if (viewport != null)
1591     {
1592       return new AlignmentI[] { viewport.getAlignment() };
1593     }
1594     return null;
1595   }
1596
1597   /**
1598    * DOCUMENT ME!
1599    *
1600    * @param e
1601    *          DOCUMENT ME!
1602    */
1603   @Override
1604   protected void undoMenuItem_actionPerformed(ActionEvent e)
1605   {
1606     if (viewport.getHistoryList().isEmpty())
1607     {
1608       return;
1609     }
1610     CommandI command = viewport.getHistoryList().pop();
1611     viewport.addToRedoList(command);
1612     command.undoCommand(getViewAlignments());
1613
1614     AlignmentViewport originalSource = getOriginatingSource(command);
1615     updateEditMenuBar();
1616
1617     if (originalSource != null)
1618     {
1619       if (originalSource != viewport)
1620       {
1621         Cache.log
1622                 .warn("Implementation worry: mismatch of viewport origin for undo");
1623       }
1624       originalSource.updateHiddenColumns();
1625       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1626       // null
1627       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1628       // viewport.getColumnSelection()
1629       // .getHiddenColumns().size() > 0);
1630       originalSource.firePropertyChange("alignment", null, originalSource
1631               .getAlignment().getSequences());
1632     }
1633   }
1634
1635   /**
1636    * DOCUMENT ME!
1637    *
1638    * @param e
1639    *          DOCUMENT ME!
1640    */
1641   @Override
1642   protected void redoMenuItem_actionPerformed(ActionEvent e)
1643   {
1644     if (viewport.getRedoList().size() < 1)
1645     {
1646       return;
1647     }
1648
1649     CommandI command = viewport.getRedoList().pop();
1650     viewport.addToHistoryList(command);
1651     command.doCommand(getViewAlignments());
1652
1653     AlignmentViewport originalSource = getOriginatingSource(command);
1654     updateEditMenuBar();
1655
1656     if (originalSource != null)
1657     {
1658
1659       if (originalSource != viewport)
1660       {
1661         Cache.log
1662                 .warn("Implementation worry: mismatch of viewport origin for redo");
1663       }
1664       originalSource.updateHiddenColumns();
1665       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1666       // null
1667       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1668       // viewport.getColumnSelection()
1669       // .getHiddenColumns().size() > 0);
1670       originalSource.firePropertyChange("alignment", null, originalSource
1671               .getAlignment().getSequences());
1672     }
1673   }
1674
1675   AlignmentViewport getOriginatingSource(CommandI command)
1676   {
1677     AlignmentViewport originalSource = null;
1678     // For sequence removal and addition, we need to fire
1679     // the property change event FROM the viewport where the
1680     // original alignment was altered
1681     AlignmentI al = null;
1682     if (command instanceof EditCommand)
1683     {
1684       EditCommand editCommand = (EditCommand) command;
1685       al = editCommand.getAlignment();
1686       List<Component> comps = PaintRefresher.components.get(viewport
1687               .getSequenceSetId());
1688
1689       for (Component comp : comps)
1690       {
1691         if (comp instanceof AlignmentPanel)
1692         {
1693           if (al == ((AlignmentPanel) comp).av.getAlignment())
1694           {
1695             originalSource = ((AlignmentPanel) comp).av;
1696             break;
1697           }
1698         }
1699       }
1700     }
1701
1702     if (originalSource == null)
1703     {
1704       // The original view is closed, we must validate
1705       // the current view against the closed view first
1706       if (al != null)
1707       {
1708         PaintRefresher.validateSequences(al, viewport.getAlignment());
1709       }
1710
1711       originalSource = viewport;
1712     }
1713
1714     return originalSource;
1715   }
1716
1717   /**
1718    * DOCUMENT ME!
1719    *
1720    * @param up
1721    *          DOCUMENT ME!
1722    */
1723   public void moveSelectedSequences(boolean up)
1724   {
1725     SequenceGroup sg = viewport.getSelectionGroup();
1726
1727     if (sg == null)
1728     {
1729       return;
1730     }
1731     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1732             viewport.getHiddenRepSequences(), up);
1733     alignPanel.paintAlignment(true);
1734   }
1735
1736   synchronized void slideSequences(boolean right, int size)
1737   {
1738     List<SequenceI> sg = new ArrayList<SequenceI>();
1739     if (viewport.cursorMode)
1740     {
1741       sg.add(viewport.getAlignment().getSequenceAt(
1742               alignPanel.getSeqPanel().seqCanvas.cursorY));
1743     }
1744     else if (viewport.getSelectionGroup() != null
1745             && viewport.getSelectionGroup().getSize() != viewport
1746                     .getAlignment().getHeight())
1747     {
1748       sg = viewport.getSelectionGroup().getSequences(
1749               viewport.getHiddenRepSequences());
1750     }
1751
1752     if (sg.size() < 1)
1753     {
1754       return;
1755     }
1756
1757     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1758
1759     for (SequenceI seq : viewport.getAlignment().getSequences())
1760     {
1761       if (!sg.contains(seq))
1762       {
1763         invertGroup.add(seq);
1764       }
1765     }
1766
1767     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1768
1769     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1770     for (int i = 0; i < invertGroup.size(); i++)
1771     {
1772       seqs2[i] = invertGroup.get(i);
1773     }
1774
1775     SlideSequencesCommand ssc;
1776     if (right)
1777     {
1778       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1779               size, viewport.getGapCharacter());
1780     }
1781     else
1782     {
1783       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1784               size, viewport.getGapCharacter());
1785     }
1786
1787     int groupAdjustment = 0;
1788     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     else if (!ssc.getGapsInsertedBegin() && !right)
1800     {
1801       if (viewport.cursorMode)
1802       {
1803         alignPanel.getSeqPanel().moveCursor(-size, 0);
1804       }
1805       else
1806       {
1807         groupAdjustment = -size;
1808       }
1809     }
1810
1811     if (groupAdjustment != 0)
1812     {
1813       viewport.getSelectionGroup().setStartRes(
1814               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1815       viewport.getSelectionGroup().setEndRes(
1816               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1817     }
1818
1819     /*
1820      * just extend the last slide command if compatible; but not if in
1821      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1822      */
1823     boolean appendHistoryItem = false;
1824     Deque<CommandI> historyList = viewport.getHistoryList();
1825     boolean inSplitFrame = getSplitViewContainer() != null;
1826     if (!inSplitFrame && historyList != null && historyList.size() > 0
1827             && historyList.peek() instanceof SlideSequencesCommand)
1828     {
1829       appendHistoryItem = ssc
1830               .appendSlideCommand((SlideSequencesCommand) historyList
1831                       .peek());
1832     }
1833
1834     if (!appendHistoryItem)
1835     {
1836       addHistoryItem(ssc);
1837     }
1838
1839     repaint();
1840   }
1841
1842   /**
1843    * DOCUMENT ME!
1844    *
1845    * @param e
1846    *          DOCUMENT ME!
1847    */
1848   @Override
1849   protected void copy_actionPerformed(ActionEvent e)
1850   {
1851     System.gc();
1852     if (viewport.getSelectionGroup() == null)
1853     {
1854       return;
1855     }
1856     // TODO: preserve the ordering of displayed alignment annotation in any
1857     // internal paste (particularly sequence associated annotation)
1858     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1859     String[] omitHidden = null;
1860
1861     if (viewport.hasHiddenColumns())
1862     {
1863       omitHidden = viewport.getViewAsString(true);
1864     }
1865
1866     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1867             omitHidden, null);
1868
1869     StringSelection ss = new StringSelection(output);
1870
1871     try
1872     {
1873       jalview.gui.Desktop.internalCopy = true;
1874       // Its really worth setting the clipboard contents
1875       // to empty before setting the large StringSelection!!
1876       Toolkit.getDefaultToolkit().getSystemClipboard()
1877               .setContents(new StringSelection(""), null);
1878
1879       Toolkit.getDefaultToolkit().getSystemClipboard()
1880               .setContents(ss, Desktop.instance);
1881     } catch (OutOfMemoryError er)
1882     {
1883       new OOMWarning("copying region", er);
1884       return;
1885     }
1886
1887     ArrayList<int[]> hiddenColumns = null;
1888     if (viewport.hasHiddenColumns())
1889     {
1890       hiddenColumns = new ArrayList<int[]>();
1891       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1892               .getSelectionGroup().getEndRes();
1893       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1894       {
1895         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1896         {
1897           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1898               region[1] - hiddenOffset });
1899         }
1900       }
1901     }
1902
1903     Desktop.jalviewClipboard = new Object[] { seqs,
1904         viewport.getAlignment().getDataset(), hiddenColumns };
1905     statusBar.setText(MessageManager.formatMessage(
1906             "label.copied_sequences_to_clipboard", new Object[] { Integer
1907                     .valueOf(seqs.length).toString() }));
1908   }
1909
1910   /**
1911    * DOCUMENT ME!
1912    *
1913    * @param e
1914    *          DOCUMENT ME!
1915    */
1916   @Override
1917   protected void pasteNew_actionPerformed(ActionEvent e)
1918   {
1919     paste(true);
1920   }
1921
1922   /**
1923    * DOCUMENT ME!
1924    *
1925    * @param e
1926    *          DOCUMENT ME!
1927    */
1928   @Override
1929   protected void pasteThis_actionPerformed(ActionEvent e)
1930   {
1931     paste(false);
1932   }
1933
1934   /**
1935    * Paste contents of Jalview clipboard
1936    *
1937    * @param newAlignment
1938    *          true to paste to a new alignment, otherwise add to this.
1939    */
1940   void paste(boolean newAlignment)
1941   {
1942     boolean externalPaste = true;
1943     try
1944     {
1945       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1946       Transferable contents = c.getContents(this);
1947
1948       if (contents == null)
1949       {
1950         return;
1951       }
1952
1953       String str, format;
1954       try
1955       {
1956         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1957         if (str.length() < 1)
1958         {
1959           return;
1960         }
1961
1962         format = new IdentifyFile().identify(str, "Paste");
1963
1964       } catch (OutOfMemoryError er)
1965       {
1966         new OOMWarning("Out of memory pasting sequences!!", er);
1967         return;
1968       }
1969
1970       SequenceI[] sequences;
1971       boolean annotationAdded = false;
1972       AlignmentI alignment = null;
1973
1974       if (Desktop.jalviewClipboard != null)
1975       {
1976         // The clipboard was filled from within Jalview, we must use the
1977         // sequences
1978         // And dataset from the copied alignment
1979         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1980         // be doubly sure that we create *new* sequence objects.
1981         sequences = new SequenceI[newseq.length];
1982         for (int i = 0; i < newseq.length; i++)
1983         {
1984           sequences[i] = new Sequence(newseq[i]);
1985         }
1986         alignment = new Alignment(sequences);
1987         externalPaste = false;
1988       }
1989       else
1990       {
1991         // parse the clipboard as an alignment.
1992         alignment = new FormatAdapter().readFile(str, "Paste", format);
1993         sequences = alignment.getSequencesArray();
1994       }
1995
1996       int alwidth = 0;
1997       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1998       int fgroup = -1;
1999
2000       if (newAlignment)
2001       {
2002
2003         if (Desktop.jalviewClipboard != null)
2004         {
2005           // dataset is inherited
2006           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2007         }
2008         else
2009         {
2010           // new dataset is constructed
2011           alignment.setDataset(null);
2012         }
2013         alwidth = alignment.getWidth() + 1;
2014       }
2015       else
2016       {
2017         AlignmentI pastedal = alignment; // preserve pasted alignment object
2018         // Add pasted sequences and dataset into existing alignment.
2019         alignment = viewport.getAlignment();
2020         alwidth = alignment.getWidth() + 1;
2021         // decide if we need to import sequences from an existing dataset
2022         boolean importDs = Desktop.jalviewClipboard != null
2023                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2024         // importDs==true instructs us to copy over new dataset sequences from
2025         // an existing alignment
2026         Vector newDs = (importDs) ? new Vector() : null; // used to create
2027         // minimum dataset set
2028
2029         for (int i = 0; i < sequences.length; i++)
2030         {
2031           if (importDs)
2032           {
2033             newDs.addElement(null);
2034           }
2035           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2036           // paste
2037           if (importDs && ds != null)
2038           {
2039             if (!newDs.contains(ds))
2040             {
2041               newDs.setElementAt(ds, i);
2042               ds = new Sequence(ds);
2043               // update with new dataset sequence
2044               sequences[i].setDatasetSequence(ds);
2045             }
2046             else
2047             {
2048               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2049             }
2050           }
2051           else
2052           {
2053             // copy and derive new dataset sequence
2054             sequences[i] = sequences[i].deriveSequence();
2055             alignment.getDataset().addSequence(
2056                     sequences[i].getDatasetSequence());
2057             // TODO: avoid creation of duplicate dataset sequences with a
2058             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2059           }
2060           alignment.addSequence(sequences[i]); // merges dataset
2061         }
2062         if (newDs != null)
2063         {
2064           newDs.clear(); // tidy up
2065         }
2066         if (alignment.getAlignmentAnnotation() != null)
2067         {
2068           for (AlignmentAnnotation alan : alignment
2069                   .getAlignmentAnnotation())
2070           {
2071             if (alan.graphGroup > fgroup)
2072             {
2073               fgroup = alan.graphGroup;
2074             }
2075           }
2076         }
2077         if (pastedal.getAlignmentAnnotation() != null)
2078         {
2079           // Add any annotation attached to alignment.
2080           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2081           for (int i = 0; i < alann.length; i++)
2082           {
2083             annotationAdded = true;
2084             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2085             {
2086               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2087               if (newann.graphGroup > -1)
2088               {
2089                 if (newGraphGroups.size() <= newann.graphGroup
2090                         || newGraphGroups.get(newann.graphGroup) == null)
2091                 {
2092                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2093                   {
2094                     newGraphGroups.add(q, null);
2095                   }
2096                   newGraphGroups.set(newann.graphGroup, new Integer(
2097                           ++fgroup));
2098                 }
2099                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2100                         .intValue();
2101               }
2102
2103               newann.padAnnotation(alwidth);
2104               alignment.addAnnotation(newann);
2105             }
2106           }
2107         }
2108       }
2109       if (!newAlignment)
2110       {
2111         // /////
2112         // ADD HISTORY ITEM
2113         //
2114         addHistoryItem(new EditCommand(
2115                 MessageManager.getString("label.add_sequences"),
2116                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2117       }
2118       // Add any annotations attached to sequences
2119       for (int i = 0; i < sequences.length; i++)
2120       {
2121         if (sequences[i].getAnnotation() != null)
2122         {
2123           AlignmentAnnotation newann;
2124           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2125           {
2126             annotationAdded = true;
2127             newann = sequences[i].getAnnotation()[a];
2128             newann.adjustForAlignment();
2129             newann.padAnnotation(alwidth);
2130             if (newann.graphGroup > -1)
2131             {
2132               if (newann.graphGroup > -1)
2133               {
2134                 if (newGraphGroups.size() <= newann.graphGroup
2135                         || newGraphGroups.get(newann.graphGroup) == null)
2136                 {
2137                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2138                   {
2139                     newGraphGroups.add(q, null);
2140                   }
2141                   newGraphGroups.set(newann.graphGroup, new Integer(
2142                           ++fgroup));
2143                 }
2144                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2145                         .intValue();
2146               }
2147             }
2148             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2149             // was
2150             // duplicated
2151             // earlier
2152             alignment
2153                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2154           }
2155         }
2156       }
2157       if (!newAlignment)
2158       {
2159
2160         // propagate alignment changed.
2161         viewport.setEndSeq(alignment.getHeight());
2162         if (annotationAdded)
2163         {
2164           // Duplicate sequence annotation in all views.
2165           AlignmentI[] alview = this.getViewAlignments();
2166           for (int i = 0; i < sequences.length; i++)
2167           {
2168             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2169             if (sann == null)
2170             {
2171               continue;
2172             }
2173             for (int avnum = 0; avnum < alview.length; avnum++)
2174             {
2175               if (alview[avnum] != alignment)
2176               {
2177                 // duplicate in a view other than the one with input focus
2178                 int avwidth = alview[avnum].getWidth() + 1;
2179                 // this relies on sann being preserved after we
2180                 // modify the sequence's annotation array for each duplication
2181                 for (int a = 0; a < sann.length; a++)
2182                 {
2183                   AlignmentAnnotation newann = new AlignmentAnnotation(
2184                           sann[a]);
2185                   sequences[i].addAlignmentAnnotation(newann);
2186                   newann.padAnnotation(avwidth);
2187                   alview[avnum].addAnnotation(newann); // annotation was
2188                   // duplicated earlier
2189                   // TODO JAL-1145 graphGroups are not updated for sequence
2190                   // annotation added to several views. This may cause
2191                   // strangeness
2192                   alview[avnum].setAnnotationIndex(newann, a);
2193                 }
2194               }
2195             }
2196           }
2197           buildSortByAnnotationScoresMenu();
2198         }
2199         viewport.firePropertyChange("alignment", null,
2200                 alignment.getSequences());
2201         if (alignPanels != null)
2202         {
2203           for (AlignmentPanel ap : alignPanels)
2204           {
2205             ap.validateAnnotationDimensions(false);
2206           }
2207         }
2208         else
2209         {
2210           alignPanel.validateAnnotationDimensions(false);
2211         }
2212
2213       }
2214       else
2215       {
2216         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2217                 DEFAULT_HEIGHT);
2218         String newtitle = new String("Copied sequences");
2219
2220         if (Desktop.jalviewClipboard != null
2221                 && Desktop.jalviewClipboard[2] != null)
2222         {
2223           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2224           for (int[] region : hc)
2225           {
2226             af.viewport.hideColumns(region[0], region[1]);
2227           }
2228         }
2229
2230         // >>>This is a fix for the moment, until a better solution is
2231         // found!!<<<
2232         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2233                 .transferSettings(
2234                         alignPanel.getSeqPanel().seqCanvas
2235                                 .getFeatureRenderer());
2236
2237         // TODO: maintain provenance of an alignment, rather than just make the
2238         // title a concatenation of operations.
2239         if (!externalPaste)
2240         {
2241           if (title.startsWith("Copied sequences"))
2242           {
2243             newtitle = title;
2244           }
2245           else
2246           {
2247             newtitle = newtitle.concat("- from " + title);
2248           }
2249         }
2250         else
2251         {
2252           newtitle = new String("Pasted sequences");
2253         }
2254
2255         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2256                 DEFAULT_HEIGHT);
2257
2258       }
2259
2260     } catch (Exception ex)
2261     {
2262       ex.printStackTrace();
2263       System.out.println("Exception whilst pasting: " + ex);
2264       // could be anything being pasted in here
2265     }
2266
2267   }
2268
2269   @Override
2270   protected void expand_newalign(ActionEvent e)
2271   {
2272     try
2273     {
2274       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2275               .getAlignment(), -1);
2276       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2277               DEFAULT_HEIGHT);
2278       String newtitle = new String("Flanking alignment");
2279
2280       if (Desktop.jalviewClipboard != null
2281               && Desktop.jalviewClipboard[2] != null)
2282       {
2283         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2284         for (int region[] : hc)
2285         {
2286           af.viewport.hideColumns(region[0], region[1]);
2287         }
2288       }
2289
2290       // >>>This is a fix for the moment, until a better solution is
2291       // found!!<<<
2292       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2293               .transferSettings(
2294                       alignPanel.getSeqPanel().seqCanvas
2295                               .getFeatureRenderer());
2296
2297       // TODO: maintain provenance of an alignment, rather than just make the
2298       // title a concatenation of operations.
2299       {
2300         if (title.startsWith("Copied sequences"))
2301         {
2302           newtitle = title;
2303         }
2304         else
2305         {
2306           newtitle = newtitle.concat("- from " + title);
2307         }
2308       }
2309
2310       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2311
2312     } catch (Exception ex)
2313     {
2314       ex.printStackTrace();
2315       System.out.println("Exception whilst pasting: " + ex);
2316       // could be anything being pasted in here
2317     } catch (OutOfMemoryError oom)
2318     {
2319       new OOMWarning("Viewing flanking region of alignment", oom);
2320     }
2321   }
2322
2323   /**
2324    * DOCUMENT ME!
2325    *
2326    * @param e
2327    *          DOCUMENT ME!
2328    */
2329   @Override
2330   protected void cut_actionPerformed(ActionEvent e)
2331   {
2332     copy_actionPerformed(null);
2333     delete_actionPerformed(null);
2334   }
2335
2336   /**
2337    * DOCUMENT ME!
2338    *
2339    * @param e
2340    *          DOCUMENT ME!
2341    */
2342   @Override
2343   protected void delete_actionPerformed(ActionEvent evt)
2344   {
2345
2346     SequenceGroup sg = viewport.getSelectionGroup();
2347     if (sg == null)
2348     {
2349       return;
2350     }
2351
2352     /*
2353      * If the cut affects all sequences, warn, remove highlighted columns
2354      */
2355     if (sg.getSize() == viewport.getAlignment().getHeight())
2356     {
2357       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2358               .getAlignment().getWidth()) ? true : false;
2359       if (isEntireAlignWidth)
2360       {
2361         int confirm = JOptionPane.showConfirmDialog(this,
2362                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2363                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2364                 JOptionPane.OK_CANCEL_OPTION);
2365
2366         if (confirm == JOptionPane.CANCEL_OPTION
2367                 || confirm == JOptionPane.CLOSED_OPTION)
2368         {
2369           return;
2370         }
2371       }
2372       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2373               sg.getEndRes() + 1);
2374     }
2375     SequenceI[] cut = sg.getSequences()
2376             .toArray(new SequenceI[sg.getSize()]);
2377
2378     addHistoryItem(new EditCommand(
2379             MessageManager.getString("label.cut_sequences"), Action.CUT,
2380             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2381             viewport.getAlignment()));
2382
2383     viewport.setSelectionGroup(null);
2384     viewport.sendSelection();
2385     viewport.getAlignment().deleteGroup(sg);
2386
2387     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2388             .getSequences());
2389     if (viewport.getAlignment().getHeight() < 1)
2390     {
2391       try
2392       {
2393         this.setClosed(true);
2394       } catch (Exception ex)
2395       {
2396       }
2397     }
2398   }
2399
2400   /**
2401    * DOCUMENT ME!
2402    *
2403    * @param e
2404    *          DOCUMENT ME!
2405    */
2406   @Override
2407   protected void deleteGroups_actionPerformed(ActionEvent e)
2408   {
2409     if (avc.deleteGroups())
2410     {
2411       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2412       alignPanel.updateAnnotation();
2413       alignPanel.paintAlignment(true);
2414     }
2415   }
2416
2417   /**
2418    * DOCUMENT ME!
2419    *
2420    * @param e
2421    *          DOCUMENT ME!
2422    */
2423   @Override
2424   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2425   {
2426     SequenceGroup sg = new SequenceGroup();
2427
2428     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2429     {
2430       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2431     }
2432
2433     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2434     viewport.setSelectionGroup(sg);
2435     viewport.sendSelection();
2436     // JAL-2034 - should delegate to
2437     // alignPanel to decide if overview needs
2438     // updating.
2439     alignPanel.paintAlignment(false);
2440     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2441   }
2442
2443   /**
2444    * DOCUMENT ME!
2445    *
2446    * @param e
2447    *          DOCUMENT ME!
2448    */
2449   @Override
2450   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2451   {
2452     if (viewport.cursorMode)
2453     {
2454       alignPanel.getSeqPanel().keyboardNo1 = null;
2455       alignPanel.getSeqPanel().keyboardNo2 = null;
2456     }
2457     viewport.setSelectionGroup(null);
2458     viewport.getColumnSelection().clear();
2459     viewport.setSelectionGroup(null);
2460     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2461     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2462     // JAL-2034 - should delegate to
2463     // alignPanel to decide if overview needs
2464     // updating.
2465     alignPanel.paintAlignment(false);
2466     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2467     viewport.sendSelection();
2468   }
2469
2470   /**
2471    * DOCUMENT ME!
2472    *
2473    * @param e
2474    *          DOCUMENT ME!
2475    */
2476   @Override
2477   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2478   {
2479     SequenceGroup sg = viewport.getSelectionGroup();
2480
2481     if (sg == null)
2482     {
2483       selectAllSequenceMenuItem_actionPerformed(null);
2484
2485       return;
2486     }
2487
2488     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2489     {
2490       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2491     }
2492     // JAL-2034 - should delegate to
2493     // alignPanel to decide if overview needs
2494     // updating.
2495
2496     alignPanel.paintAlignment(true);
2497     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2498     viewport.sendSelection();
2499   }
2500
2501   @Override
2502   public void invertColSel_actionPerformed(ActionEvent e)
2503   {
2504     viewport.invertColumnSelection();
2505     alignPanel.paintAlignment(true);
2506     viewport.sendSelection();
2507   }
2508
2509   /**
2510    * DOCUMENT ME!
2511    *
2512    * @param e
2513    *          DOCUMENT ME!
2514    */
2515   @Override
2516   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2517   {
2518     trimAlignment(true);
2519   }
2520
2521   /**
2522    * DOCUMENT ME!
2523    *
2524    * @param e
2525    *          DOCUMENT ME!
2526    */
2527   @Override
2528   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2529   {
2530     trimAlignment(false);
2531   }
2532
2533   void trimAlignment(boolean trimLeft)
2534   {
2535     ColumnSelection colSel = viewport.getColumnSelection();
2536     int column;
2537
2538     if (!colSel.isEmpty())
2539     {
2540       if (trimLeft)
2541       {
2542         column = colSel.getMin();
2543       }
2544       else
2545       {
2546         column = colSel.getMax();
2547       }
2548
2549       SequenceI[] seqs;
2550       if (viewport.getSelectionGroup() != null)
2551       {
2552         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2553                 viewport.getHiddenRepSequences());
2554       }
2555       else
2556       {
2557         seqs = viewport.getAlignment().getSequencesArray();
2558       }
2559
2560       TrimRegionCommand trimRegion;
2561       if (trimLeft)
2562       {
2563         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2564                 column, viewport.getAlignment());
2565         viewport.setStartRes(0);
2566       }
2567       else
2568       {
2569         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2570                 column, viewport.getAlignment());
2571       }
2572
2573       statusBar.setText(MessageManager.formatMessage(
2574               "label.removed_columns",
2575               new String[] { Integer.valueOf(trimRegion.getSize())
2576                       .toString() }));
2577
2578       addHistoryItem(trimRegion);
2579
2580       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2581       {
2582         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2583                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2584         {
2585           viewport.getAlignment().deleteGroup(sg);
2586         }
2587       }
2588
2589       viewport.firePropertyChange("alignment", null, viewport
2590               .getAlignment().getSequences());
2591     }
2592   }
2593
2594   /**
2595    * DOCUMENT ME!
2596    *
2597    * @param e
2598    *          DOCUMENT ME!
2599    */
2600   @Override
2601   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2602   {
2603     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2604
2605     SequenceI[] seqs;
2606     if (viewport.getSelectionGroup() != null)
2607     {
2608       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2609               viewport.getHiddenRepSequences());
2610       start = viewport.getSelectionGroup().getStartRes();
2611       end = viewport.getSelectionGroup().getEndRes();
2612     }
2613     else
2614     {
2615       seqs = viewport.getAlignment().getSequencesArray();
2616     }
2617
2618     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2619             "Remove Gapped Columns", seqs, start, end,
2620             viewport.getAlignment());
2621
2622     addHistoryItem(removeGapCols);
2623
2624     statusBar.setText(MessageManager.formatMessage(
2625             "label.removed_empty_columns",
2626             new Object[] { Integer.valueOf(removeGapCols.getSize())
2627                     .toString() }));
2628
2629     // This is to maintain viewport position on first residue
2630     // of first sequence
2631     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2632     int startRes = seq.findPosition(viewport.startRes);
2633     // ShiftList shifts;
2634     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2635     // edit.alColumnChanges=shifts.getInverse();
2636     // if (viewport.hasHiddenColumns)
2637     // viewport.getColumnSelection().compensateForEdits(shifts);
2638     viewport.setStartRes(seq.findIndex(startRes) - 1);
2639     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2640             .getSequences());
2641
2642   }
2643
2644   /**
2645    * DOCUMENT ME!
2646    *
2647    * @param e
2648    *          DOCUMENT ME!
2649    */
2650   @Override
2651   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2652   {
2653     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2654
2655     SequenceI[] seqs;
2656     if (viewport.getSelectionGroup() != null)
2657     {
2658       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2659               viewport.getHiddenRepSequences());
2660       start = viewport.getSelectionGroup().getStartRes();
2661       end = viewport.getSelectionGroup().getEndRes();
2662     }
2663     else
2664     {
2665       seqs = viewport.getAlignment().getSequencesArray();
2666     }
2667
2668     // This is to maintain viewport position on first residue
2669     // of first sequence
2670     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2671     int startRes = seq.findPosition(viewport.startRes);
2672
2673     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2674             viewport.getAlignment()));
2675
2676     viewport.setStartRes(seq.findIndex(startRes) - 1);
2677
2678     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2679             .getSequences());
2680
2681   }
2682
2683   /**
2684    * DOCUMENT ME!
2685    *
2686    * @param e
2687    *          DOCUMENT ME!
2688    */
2689   @Override
2690   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2691   {
2692     viewport.setPadGaps(padGapsMenuitem.isSelected());
2693     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2694             .getSequences());
2695   }
2696
2697   /**
2698    * DOCUMENT ME!
2699    *
2700    * @param e
2701    *          DOCUMENT ME!
2702    */
2703   @Override
2704   public void findMenuItem_actionPerformed(ActionEvent e)
2705   {
2706     new Finder();
2707   }
2708
2709   /**
2710    * Create a new view of the current alignment.
2711    */
2712   @Override
2713   public void newView_actionPerformed(ActionEvent e)
2714   {
2715     newView(null, true);
2716   }
2717
2718   /**
2719    * Creates and shows a new view of the current alignment.
2720    *
2721    * @param viewTitle
2722    *          title of newly created view; if null, one will be generated
2723    * @param copyAnnotation
2724    *          if true then duplicate all annnotation, groups and settings
2725    * @return new alignment panel, already displayed.
2726    */
2727   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2728   {
2729     /*
2730      * Create a new AlignmentPanel (with its own, new Viewport)
2731      */
2732     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2733             true);
2734     if (!copyAnnotation)
2735     {
2736       /*
2737        * remove all groups and annotation except for the automatic stuff
2738        */
2739       newap.av.getAlignment().deleteAllGroups();
2740       newap.av.getAlignment().deleteAllAnnotations(false);
2741     }
2742
2743     newap.av.setGatherViewsHere(false);
2744
2745     if (viewport.viewName == null)
2746     {
2747       viewport.viewName = MessageManager
2748               .getString("label.view_name_original");
2749     }
2750
2751     /*
2752      * Views share the same edits undo and redo stacks
2753      */
2754     newap.av.setHistoryList(viewport.getHistoryList());
2755     newap.av.setRedoList(viewport.getRedoList());
2756
2757     /*
2758      * Views share the same mappings; need to deregister any new mappings
2759      * created by copyAlignPanel, and register the new reference to the shared
2760      * mappings
2761      */
2762     newap.av.replaceMappings(viewport.getAlignment());
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.get(viewport
2801             .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<String>();
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.instance.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);
2880   }
2881
2882   @Override
2883   public void idRightAlign_actionPerformed(ActionEvent e)
2884   {
2885     viewport.setRightAlignIds(idRightAlign.isSelected());
2886     alignPanel.paintAlignment(true);
2887   }
2888
2889   @Override
2890   public void centreColumnLabels_actionPerformed(ActionEvent e)
2891   {
2892     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2893     alignPanel.paintAlignment(true);
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(
2913               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2914     }
2915   }
2916
2917   /**
2918    * DOCUMENT ME!
2919    *
2920    * @param e
2921    *          DOCUMENT ME!
2922    */
2923   @Override
2924   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2925   {
2926     viewport.setColourText(colourTextMenuItem.isSelected());
2927     alignPanel.paintAlignment(true);
2928   }
2929
2930   /**
2931    * DOCUMENT ME!
2932    *
2933    * @param e
2934    *          DOCUMENT ME!
2935    */
2936   @Override
2937   public void wrapMenuItem_actionPerformed(ActionEvent e)
2938   {
2939     scaleAbove.setVisible(wrapMenuItem.isSelected());
2940     scaleLeft.setVisible(wrapMenuItem.isSelected());
2941     scaleRight.setVisible(wrapMenuItem.isSelected());
2942     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2943     alignPanel.updateLayout();
2944   }
2945
2946   @Override
2947   public void showAllSeqs_actionPerformed(ActionEvent e)
2948   {
2949     viewport.showAllHiddenSeqs();
2950   }
2951
2952   @Override
2953   public void showAllColumns_actionPerformed(ActionEvent e)
2954   {
2955     viewport.showAllHiddenColumns();
2956     repaint();
2957     viewport.sendSelection();
2958   }
2959
2960   @Override
2961   public void hideSelSequences_actionPerformed(ActionEvent e)
2962   {
2963     viewport.hideAllSelectedSeqs();
2964     // alignPanel.paintAlignment(true);
2965   }
2966
2967   /**
2968    * called by key handler and the hide all/show all menu items
2969    *
2970    * @param toggleSeqs
2971    * @param toggleCols
2972    */
2973   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2974   {
2975
2976     boolean hide = false;
2977     SequenceGroup sg = viewport.getSelectionGroup();
2978     if (!toggleSeqs && !toggleCols)
2979     {
2980       // Hide everything by the current selection - this is a hack - we do the
2981       // invert and then hide
2982       // first check that there will be visible columns after the invert.
2983       if ((viewport.getColumnSelection() != null
2984               && viewport.getColumnSelection().getSelected() != null && viewport
2985               .getColumnSelection().getSelected().size() > 0)
2986               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2987                       .getEndRes()))
2988       {
2989         // now invert the sequence set, if required - empty selection implies
2990         // that no hiding is required.
2991         if (sg != null)
2992         {
2993           invertSequenceMenuItem_actionPerformed(null);
2994           sg = viewport.getSelectionGroup();
2995           toggleSeqs = true;
2996
2997         }
2998         viewport.expandColSelection(sg, true);
2999         // finally invert the column selection and get the new sequence
3000         // selection.
3001         invertColSel_actionPerformed(null);
3002         toggleCols = true;
3003       }
3004     }
3005
3006     if (toggleSeqs)
3007     {
3008       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3009       {
3010         hideSelSequences_actionPerformed(null);
3011         hide = true;
3012       }
3013       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3014               .size() > 0))
3015       {
3016         showAllSeqs_actionPerformed(null);
3017       }
3018     }
3019
3020     if (toggleCols)
3021     {
3022       if (viewport.getColumnSelection().getSelected().size() > 0)
3023       {
3024         hideSelColumns_actionPerformed(null);
3025         if (!toggleSeqs)
3026         {
3027           viewport.setSelectionGroup(sg);
3028         }
3029       }
3030       else if (!hide)
3031       {
3032         showAllColumns_actionPerformed(null);
3033       }
3034     }
3035   }
3036
3037   /*
3038    * (non-Javadoc)
3039    *
3040    * @see
3041    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3042    * event.ActionEvent)
3043    */
3044   @Override
3045   public void hideAllButSelection_actionPerformed(ActionEvent e)
3046   {
3047     toggleHiddenRegions(false, false);
3048     viewport.sendSelection();
3049   }
3050
3051   /*
3052    * (non-Javadoc)
3053    *
3054    * @see
3055    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3056    * .ActionEvent)
3057    */
3058   @Override
3059   public void hideAllSelection_actionPerformed(ActionEvent e)
3060   {
3061     SequenceGroup sg = viewport.getSelectionGroup();
3062     viewport.expandColSelection(sg, false);
3063     viewport.hideAllSelectedSeqs();
3064     viewport.hideSelectedColumns();
3065     alignPanel.paintAlignment(true);
3066     viewport.sendSelection();
3067   }
3068
3069   /*
3070    * (non-Javadoc)
3071    *
3072    * @see
3073    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3074    * ActionEvent)
3075    */
3076   @Override
3077   public void showAllhidden_actionPerformed(ActionEvent e)
3078   {
3079     viewport.showAllHiddenColumns();
3080     viewport.showAllHiddenSeqs();
3081     alignPanel.paintAlignment(true);
3082     viewport.sendSelection();
3083   }
3084
3085   @Override
3086   public void hideSelColumns_actionPerformed(ActionEvent e)
3087   {
3088     viewport.hideSelectedColumns();
3089     alignPanel.paintAlignment(true);
3090     viewport.sendSelection();
3091   }
3092
3093   @Override
3094   public void hiddenMarkers_actionPerformed(ActionEvent e)
3095   {
3096     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3097     repaint();
3098   }
3099
3100   /**
3101    * DOCUMENT ME!
3102    *
3103    * @param e
3104    *          DOCUMENT ME!
3105    */
3106   @Override
3107   protected void scaleAbove_actionPerformed(ActionEvent e)
3108   {
3109     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3110     alignPanel.paintAlignment(true);
3111   }
3112
3113   /**
3114    * DOCUMENT ME!
3115    *
3116    * @param e
3117    *          DOCUMENT ME!
3118    */
3119   @Override
3120   protected void scaleLeft_actionPerformed(ActionEvent e)
3121   {
3122     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3123     alignPanel.paintAlignment(true);
3124   }
3125
3126   /**
3127    * DOCUMENT ME!
3128    *
3129    * @param e
3130    *          DOCUMENT ME!
3131    */
3132   @Override
3133   protected void scaleRight_actionPerformed(ActionEvent e)
3134   {
3135     viewport.setScaleRightWrapped(scaleRight.isSelected());
3136     alignPanel.paintAlignment(true);
3137   }
3138
3139   /**
3140    * DOCUMENT ME!
3141    *
3142    * @param e
3143    *          DOCUMENT ME!
3144    */
3145   @Override
3146   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3147   {
3148     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3149     alignPanel.paintAlignment(true);
3150   }
3151
3152   /**
3153    * DOCUMENT ME!
3154    *
3155    * @param e
3156    *          DOCUMENT ME!
3157    */
3158   @Override
3159   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3160   {
3161     viewport.setShowText(viewTextMenuItem.isSelected());
3162     alignPanel.paintAlignment(true);
3163   }
3164
3165   /**
3166    * DOCUMENT ME!
3167    *
3168    * @param e
3169    *          DOCUMENT ME!
3170    */
3171   @Override
3172   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3173   {
3174     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3175     alignPanel.paintAlignment(true);
3176   }
3177
3178   public FeatureSettings featureSettings;
3179
3180   @Override
3181   public FeatureSettingsControllerI getFeatureSettingsUI()
3182   {
3183     return featureSettings;
3184   }
3185
3186   @Override
3187   public void featureSettings_actionPerformed(ActionEvent e)
3188   {
3189     if (featureSettings != null)
3190     {
3191       featureSettings.close();
3192       featureSettings = null;
3193     }
3194     if (!showSeqFeatures.isSelected())
3195     {
3196       // make sure features are actually displayed
3197       showSeqFeatures.setSelected(true);
3198       showSeqFeatures_actionPerformed(null);
3199     }
3200     featureSettings = new FeatureSettings(this);
3201   }
3202
3203   /**
3204    * Set or clear 'Show Sequence Features'
3205    *
3206    * @param evt
3207    *          DOCUMENT ME!
3208    */
3209   @Override
3210   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3211   {
3212     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3213     alignPanel.paintAlignment(true);
3214     if (alignPanel.getOverviewPanel() != null)
3215     {
3216       alignPanel.getOverviewPanel().updateOverviewImage();
3217     }
3218   }
3219
3220   /**
3221    * Set or clear 'Show Sequence Features'
3222    *
3223    * @param evt
3224    *          DOCUMENT ME!
3225    */
3226   @Override
3227   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3228   {
3229     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3230             .isSelected());
3231     if (viewport.isShowSequenceFeaturesHeight())
3232     {
3233       // ensure we're actually displaying features
3234       viewport.setShowSequenceFeatures(true);
3235       showSeqFeatures.setSelected(true);
3236     }
3237     alignPanel.paintAlignment(true);
3238     if (alignPanel.getOverviewPanel() != null)
3239     {
3240       alignPanel.getOverviewPanel().updateOverviewImage();
3241     }
3242   }
3243
3244   /**
3245    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3246    * the annotations panel as a whole.
3247    *
3248    * The options to show/hide all annotations should be enabled when the panel
3249    * is shown, and disabled when the panel is hidden.
3250    *
3251    * @param e
3252    */
3253   @Override
3254   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3255   {
3256     final boolean setVisible = annotationPanelMenuItem.isSelected();
3257     viewport.setShowAnnotation(setVisible);
3258     this.showAllSeqAnnotations.setEnabled(setVisible);
3259     this.hideAllSeqAnnotations.setEnabled(setVisible);
3260     this.showAllAlAnnotations.setEnabled(setVisible);
3261     this.hideAllAlAnnotations.setEnabled(setVisible);
3262     alignPanel.updateLayout();
3263   }
3264
3265   @Override
3266   public void alignmentProperties()
3267   {
3268     JEditorPane editPane = new JEditorPane("text/html", "");
3269     editPane.setEditable(false);
3270     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3271             .formatAsHtml();
3272     editPane.setText(MessageManager.formatMessage("label.html_content",
3273             new Object[] { contents.toString() }));
3274     JInternalFrame frame = new JInternalFrame();
3275     frame.getContentPane().add(new JScrollPane(editPane));
3276
3277     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3278             "label.alignment_properties", new Object[] { getTitle() }),
3279             500, 400);
3280   }
3281
3282   /**
3283    * DOCUMENT ME!
3284    *
3285    * @param e
3286    *          DOCUMENT ME!
3287    */
3288   @Override
3289   public void overviewMenuItem_actionPerformed(ActionEvent e)
3290   {
3291     if (alignPanel.overviewPanel != null)
3292     {
3293       return;
3294     }
3295
3296     JInternalFrame frame = new JInternalFrame();
3297     OverviewPanel overview = new OverviewPanel(alignPanel);
3298     frame.setContentPane(overview);
3299     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3300             "label.overview_params", new Object[] { this.getTitle() }),
3301             frame.getWidth(), frame.getHeight());
3302     frame.pack();
3303     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3304     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3305     {
3306       @Override
3307       public void internalFrameClosed(
3308               javax.swing.event.InternalFrameEvent evt)
3309       {
3310         alignPanel.setOverviewPanel(null);
3311       };
3312     });
3313
3314     alignPanel.setOverviewPanel(overview);
3315   }
3316
3317   @Override
3318   public void textColour_actionPerformed(ActionEvent e)
3319   {
3320     new TextColourChooser().chooseColour(alignPanel, null);
3321   }
3322
3323   /**
3324    * DOCUMENT ME!
3325    *
3326    * @param e
3327    *          DOCUMENT ME!
3328    */
3329   @Override
3330   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3331   {
3332     changeColour(null);
3333   }
3334
3335   /**
3336    * DOCUMENT ME!
3337    *
3338    * @param e
3339    *          DOCUMENT ME!
3340    */
3341   @Override
3342   public void clustalColour_actionPerformed(ActionEvent e)
3343   {
3344     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3345             viewport.getHiddenRepSequences()));
3346   }
3347
3348   /**
3349    * DOCUMENT ME!
3350    *
3351    * @param e
3352    *          DOCUMENT ME!
3353    */
3354   @Override
3355   public void zappoColour_actionPerformed(ActionEvent e)
3356   {
3357     changeColour(new ZappoColourScheme());
3358   }
3359
3360   /**
3361    * DOCUMENT ME!
3362    *
3363    * @param e
3364    *          DOCUMENT ME!
3365    */
3366   @Override
3367   public void taylorColour_actionPerformed(ActionEvent e)
3368   {
3369     changeColour(new TaylorColourScheme());
3370   }
3371
3372   /**
3373    * DOCUMENT ME!
3374    *
3375    * @param e
3376    *          DOCUMENT ME!
3377    */
3378   @Override
3379   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3380   {
3381     changeColour(new HydrophobicColourScheme());
3382   }
3383
3384   /**
3385    * DOCUMENT ME!
3386    *
3387    * @param e
3388    *          DOCUMENT ME!
3389    */
3390   @Override
3391   public void helixColour_actionPerformed(ActionEvent e)
3392   {
3393     changeColour(new HelixColourScheme());
3394   }
3395
3396   /**
3397    * DOCUMENT ME!
3398    *
3399    * @param e
3400    *          DOCUMENT ME!
3401    */
3402   @Override
3403   public void strandColour_actionPerformed(ActionEvent e)
3404   {
3405     changeColour(new StrandColourScheme());
3406   }
3407
3408   /**
3409    * DOCUMENT ME!
3410    *
3411    * @param e
3412    *          DOCUMENT ME!
3413    */
3414   @Override
3415   public void turnColour_actionPerformed(ActionEvent e)
3416   {
3417     changeColour(new TurnColourScheme());
3418   }
3419
3420   /**
3421    * DOCUMENT ME!
3422    *
3423    * @param e
3424    *          DOCUMENT ME!
3425    */
3426   @Override
3427   public void buriedColour_actionPerformed(ActionEvent e)
3428   {
3429     changeColour(new BuriedColourScheme());
3430   }
3431
3432   /**
3433    * DOCUMENT ME!
3434    *
3435    * @param e
3436    *          DOCUMENT ME!
3437    */
3438   @Override
3439   public void nucleotideColour_actionPerformed(ActionEvent e)
3440   {
3441     changeColour(new NucleotideColourScheme());
3442   }
3443
3444   @Override
3445   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3446   {
3447     changeColour(new PurinePyrimidineColourScheme());
3448   }
3449
3450   /*
3451    * public void covariationColour_actionPerformed(ActionEvent e) {
3452    * changeColour(new
3453    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3454    * ()[0])); }
3455    */
3456   @Override
3457   public void annotationColour_actionPerformed(ActionEvent e)
3458   {
3459     new AnnotationColourChooser(viewport, alignPanel);
3460   }
3461
3462   @Override
3463   public void annotationColumn_actionPerformed(ActionEvent e)
3464   {
3465     new AnnotationColumnChooser(viewport, alignPanel);
3466   }
3467
3468   @Override
3469   public void rnahelicesColour_actionPerformed(ActionEvent e)
3470   {
3471     new RNAHelicesColourChooser(viewport, alignPanel);
3472   }
3473
3474   /**
3475    * DOCUMENT ME!
3476    *
3477    * @param e
3478    *          DOCUMENT ME!
3479    */
3480   @Override
3481   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3482   {
3483     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3484   }
3485
3486   /**
3487    * DOCUMENT ME!
3488    *
3489    * @param cs
3490    *          DOCUMENT ME!
3491    */
3492   @Override
3493   public void changeColour(ColourSchemeI cs)
3494   {
3495     // TODO: pull up to controller method
3496
3497     if (cs != null)
3498     {
3499       // Make sure viewport is up to date w.r.t. any sliders
3500       if (viewport.getAbovePIDThreshold())
3501       {
3502         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3503                 "Background");
3504         viewport.setThreshold(threshold);
3505       }
3506
3507       if (viewport.getConservationSelected())
3508       {
3509         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3510                 cs, "Background"));
3511       }
3512       if (cs instanceof TCoffeeColourScheme)
3513       {
3514         tcoffeeColour.setEnabled(true);
3515         tcoffeeColour.setSelected(true);
3516       }
3517     }
3518
3519     viewport.setGlobalColourScheme(cs);
3520
3521     alignPanel.paintAlignment(true);
3522   }
3523
3524   /**
3525    * DOCUMENT ME!
3526    *
3527    * @param e
3528    *          DOCUMENT ME!
3529    */
3530   @Override
3531   protected void modifyPID_actionPerformed(ActionEvent e)
3532   {
3533     if (viewport.getAbovePIDThreshold()
3534             && viewport.getGlobalColourScheme() != null)
3535     {
3536       SliderPanel.setPIDSliderSource(alignPanel,
3537               viewport.getGlobalColourScheme(), "Background");
3538       SliderPanel.showPIDSlider();
3539     }
3540   }
3541
3542   /**
3543    * DOCUMENT ME!
3544    *
3545    * @param e
3546    *          DOCUMENT ME!
3547    */
3548   @Override
3549   protected void modifyConservation_actionPerformed(ActionEvent e)
3550   {
3551     if (viewport.getConservationSelected()
3552             && viewport.getGlobalColourScheme() != null)
3553     {
3554       SliderPanel.setConservationSlider(alignPanel,
3555               viewport.getGlobalColourScheme(), "Background");
3556       SliderPanel.showConservationSlider();
3557     }
3558   }
3559
3560   /**
3561    * DOCUMENT ME!
3562    *
3563    * @param e
3564    *          DOCUMENT ME!
3565    */
3566   @Override
3567   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3568   {
3569     viewport.setConservationSelected(conservationMenuItem.isSelected());
3570
3571     viewport.setAbovePIDThreshold(false);
3572     abovePIDThreshold.setSelected(false);
3573
3574     changeColour(viewport.getGlobalColourScheme());
3575
3576     modifyConservation_actionPerformed(null);
3577   }
3578
3579   /**
3580    * DOCUMENT ME!
3581    *
3582    * @param e
3583    *          DOCUMENT ME!
3584    */
3585   @Override
3586   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3587   {
3588     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3589
3590     conservationMenuItem.setSelected(false);
3591     viewport.setConservationSelected(false);
3592
3593     changeColour(viewport.getGlobalColourScheme());
3594
3595     modifyPID_actionPerformed(null);
3596   }
3597
3598   /**
3599    * DOCUMENT ME!
3600    *
3601    * @param e
3602    *          DOCUMENT ME!
3603    */
3604   @Override
3605   public void userDefinedColour_actionPerformed(ActionEvent e)
3606   {
3607     if (e.getActionCommand().equals(
3608             MessageManager.getString("action.user_defined")))
3609     {
3610       new UserDefinedColours(alignPanel, null);
3611     }
3612     else
3613     {
3614       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3615               .getUserColourSchemes().get(e.getActionCommand());
3616
3617       changeColour(udc);
3618     }
3619   }
3620
3621   public void updateUserColourMenu()
3622   {
3623
3624     Component[] menuItems = colourMenu.getMenuComponents();
3625     int iSize = menuItems.length;
3626     for (int i = 0; i < iSize; i++)
3627     {
3628       if (menuItems[i].getName() != null
3629               && menuItems[i].getName().equals("USER_DEFINED"))
3630       {
3631         colourMenu.remove(menuItems[i]);
3632         iSize--;
3633       }
3634     }
3635     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3636     {
3637       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3638               .getUserColourSchemes().keys();
3639
3640       while (userColours.hasMoreElements())
3641       {
3642         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3643                 userColours.nextElement().toString());
3644         radioItem.setName("USER_DEFINED");
3645         radioItem.addMouseListener(new MouseAdapter()
3646         {
3647           @Override
3648           public void mousePressed(MouseEvent evt)
3649           {
3650             if (evt.isPopupTrigger())
3651             {
3652               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3653
3654               int option = JOptionPane.showInternalConfirmDialog(
3655                       jalview.gui.Desktop.desktop,
3656                       MessageManager
3657                               .getString("label.remove_from_default_list"),
3658                       MessageManager
3659                               .getString("label.remove_user_defined_colour"),
3660                       JOptionPane.YES_NO_OPTION);
3661               if (option == JOptionPane.YES_OPTION)
3662               {
3663                 jalview.gui.UserDefinedColours
3664                         .removeColourFromDefaults(radioItem.getText());
3665                 colourMenu.remove(radioItem);
3666               }
3667               else
3668               {
3669                 radioItem.addActionListener(new ActionListener()
3670                 {
3671                   @Override
3672                   public void actionPerformed(ActionEvent evt)
3673                   {
3674                     userDefinedColour_actionPerformed(evt);
3675                   }
3676                 });
3677               }
3678             }
3679           }
3680         });
3681         radioItem.addActionListener(new ActionListener()
3682         {
3683           @Override
3684           public void actionPerformed(ActionEvent evt)
3685           {
3686             userDefinedColour_actionPerformed(evt);
3687           }
3688         });
3689
3690         colourMenu.insert(radioItem, 15);
3691         colours.add(radioItem);
3692       }
3693     }
3694   }
3695
3696   /**
3697    * DOCUMENT ME!
3698    *
3699    * @param e
3700    *          DOCUMENT ME!
3701    */
3702   @Override
3703   public void PIDColour_actionPerformed(ActionEvent e)
3704   {
3705     changeColour(new PIDColourScheme());
3706   }
3707
3708   /**
3709    * DOCUMENT ME!
3710    *
3711    * @param e
3712    *          DOCUMENT ME!
3713    */
3714   @Override
3715   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3716   {
3717     changeColour(new Blosum62ColourScheme());
3718   }
3719
3720   /**
3721    * DOCUMENT ME!
3722    *
3723    * @param e
3724    *          DOCUMENT ME!
3725    */
3726   @Override
3727   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3728   {
3729     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3730     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3731             .getAlignment().getSequenceAt(0), null);
3732     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3733             viewport.getAlignment()));
3734     alignPanel.paintAlignment(true);
3735   }
3736
3737   /**
3738    * DOCUMENT ME!
3739    *
3740    * @param e
3741    *          DOCUMENT ME!
3742    */
3743   @Override
3744   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3745   {
3746     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3747     AlignmentSorter.sortByID(viewport.getAlignment());
3748     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3749             viewport.getAlignment()));
3750     alignPanel.paintAlignment(true);
3751   }
3752
3753   /**
3754    * DOCUMENT ME!
3755    *
3756    * @param e
3757    *          DOCUMENT ME!
3758    */
3759   @Override
3760   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3761   {
3762     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3763     AlignmentSorter.sortByLength(viewport.getAlignment());
3764     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3765             viewport.getAlignment()));
3766     alignPanel.paintAlignment(true);
3767   }
3768
3769   /**
3770    * DOCUMENT ME!
3771    *
3772    * @param e
3773    *          DOCUMENT ME!
3774    */
3775   @Override
3776   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3777   {
3778     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3779     AlignmentSorter.sortByGroup(viewport.getAlignment());
3780     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3781             viewport.getAlignment()));
3782
3783     alignPanel.paintAlignment(true);
3784   }
3785
3786   /**
3787    * DOCUMENT ME!
3788    *
3789    * @param e
3790    *          DOCUMENT ME!
3791    */
3792   @Override
3793   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3794   {
3795     new RedundancyPanel(alignPanel, this);
3796   }
3797
3798   /**
3799    * DOCUMENT ME!
3800    *
3801    * @param e
3802    *          DOCUMENT ME!
3803    */
3804   @Override
3805   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3806   {
3807     if ((viewport.getSelectionGroup() == null)
3808             || (viewport.getSelectionGroup().getSize() < 2))
3809     {
3810       JOptionPane.showInternalMessageDialog(this, MessageManager
3811               .getString("label.you_must_select_least_two_sequences"),
3812               MessageManager.getString("label.invalid_selection"),
3813               JOptionPane.WARNING_MESSAGE);
3814     }
3815     else
3816     {
3817       JInternalFrame frame = new JInternalFrame();
3818       frame.setContentPane(new PairwiseAlignPanel(viewport));
3819       Desktop.addInternalFrame(frame,
3820               MessageManager.getString("action.pairwise_alignment"), 600,
3821               500);
3822     }
3823   }
3824
3825   /**
3826    * DOCUMENT ME!
3827    *
3828    * @param e
3829    *          DOCUMENT ME!
3830    */
3831   @Override
3832   public void PCAMenuItem_actionPerformed(ActionEvent e)
3833   {
3834     if (((viewport.getSelectionGroup() != null)
3835             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3836             .getSelectionGroup().getSize() > 0))
3837             || (viewport.getAlignment().getHeight() < 4))
3838     {
3839       JOptionPane
3840               .showInternalMessageDialog(
3841                       this,
3842                       MessageManager
3843                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3844                       MessageManager
3845                               .getString("label.sequence_selection_insufficient"),
3846                       JOptionPane.WARNING_MESSAGE);
3847
3848       return;
3849     }
3850
3851     new PCAPanel(alignPanel);
3852   }
3853
3854   @Override
3855   public void autoCalculate_actionPerformed(ActionEvent e)
3856   {
3857     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3858     if (viewport.autoCalculateConsensus)
3859     {
3860       viewport.firePropertyChange("alignment", null, viewport
3861               .getAlignment().getSequences());
3862     }
3863   }
3864
3865   @Override
3866   public void sortByTreeOption_actionPerformed(ActionEvent e)
3867   {
3868     viewport.sortByTree = sortByTree.isSelected();
3869   }
3870
3871   @Override
3872   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3873   {
3874     viewport.followSelection = listenToViewSelections.isSelected();
3875   }
3876
3877   /**
3878    * DOCUMENT ME!
3879    *
3880    * @param e
3881    *          DOCUMENT ME!
3882    */
3883   @Override
3884   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3885   {
3886     newTreePanel("AV", "PID", "Average distance tree using PID");
3887   }
3888
3889   /**
3890    * DOCUMENT ME!
3891    *
3892    * @param e
3893    *          DOCUMENT ME!
3894    */
3895   @Override
3896   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3897   {
3898     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3899   }
3900
3901   /**
3902    * DOCUMENT ME!
3903    *
3904    * @param e
3905    *          DOCUMENT ME!
3906    */
3907   @Override
3908   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3909   {
3910     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3911   }
3912
3913   /**
3914    * DOCUMENT ME!
3915    *
3916    * @param e
3917    *          DOCUMENT ME!
3918    */
3919   @Override
3920   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3921   {
3922     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3923   }
3924
3925   /**
3926    * DOCUMENT ME!
3927    *
3928    * @param type
3929    *          DOCUMENT ME!
3930    * @param pwType
3931    *          DOCUMENT ME!
3932    * @param title
3933    *          DOCUMENT ME!
3934    */
3935   void newTreePanel(String type, String pwType, String title)
3936   {
3937     TreePanel tp;
3938
3939     if (viewport.getSelectionGroup() != null
3940             && viewport.getSelectionGroup().getSize() > 0)
3941     {
3942       if (viewport.getSelectionGroup().getSize() < 3)
3943       {
3944         JOptionPane
3945                 .showMessageDialog(
3946                         Desktop.desktop,
3947                         MessageManager
3948                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3949                         MessageManager
3950                                 .getString("label.not_enough_sequences"),
3951                         JOptionPane.WARNING_MESSAGE);
3952         return;
3953       }
3954
3955       SequenceGroup sg = viewport.getSelectionGroup();
3956
3957       /* Decide if the selection is a column region */
3958       for (SequenceI _s : sg.getSequences())
3959       {
3960         if (_s.getLength() < sg.getEndRes())
3961         {
3962           JOptionPane
3963                   .showMessageDialog(
3964                           Desktop.desktop,
3965                           MessageManager
3966                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3967                           MessageManager
3968                                   .getString("label.sequences_selection_not_aligned"),
3969                           JOptionPane.WARNING_MESSAGE);
3970
3971           return;
3972         }
3973       }
3974
3975       title = title + " on region";
3976       tp = new TreePanel(alignPanel, type, pwType);
3977     }
3978     else
3979     {
3980       // are the visible sequences aligned?
3981       if (!viewport.getAlignment().isAligned(false))
3982       {
3983         JOptionPane
3984                 .showMessageDialog(
3985                         Desktop.desktop,
3986                         MessageManager
3987                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3988                         MessageManager
3989                                 .getString("label.sequences_not_aligned"),
3990                         JOptionPane.WARNING_MESSAGE);
3991
3992         return;
3993       }
3994
3995       if (viewport.getAlignment().getHeight() < 2)
3996       {
3997         return;
3998       }
3999
4000       tp = new TreePanel(alignPanel, type, pwType);
4001     }
4002
4003     title += " from ";
4004
4005     if (viewport.viewName != null)
4006     {
4007       title += viewport.viewName + " of ";
4008     }
4009
4010     title += this.title;
4011
4012     Desktop.addInternalFrame(tp, title, 600, 500);
4013   }
4014
4015   /**
4016    * DOCUMENT ME!
4017    *
4018    * @param title
4019    *          DOCUMENT ME!
4020    * @param order
4021    *          DOCUMENT ME!
4022    */
4023   public void addSortByOrderMenuItem(String title,
4024           final AlignmentOrder order)
4025   {
4026     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4027             "action.by_title_param", new Object[] { title }));
4028     sort.add(item);
4029     item.addActionListener(new java.awt.event.ActionListener()
4030     {
4031       @Override
4032       public void actionPerformed(ActionEvent e)
4033       {
4034         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4035
4036         // TODO: JBPNote - have to map order entries to curent SequenceI
4037         // pointers
4038         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4039
4040         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4041                 .getAlignment()));
4042
4043         alignPanel.paintAlignment(true);
4044       }
4045     });
4046   }
4047
4048   /**
4049    * Add a new sort by annotation score menu item
4050    *
4051    * @param sort
4052    *          the menu to add the option to
4053    * @param scoreLabel
4054    *          the label used to retrieve scores for each sequence on the
4055    *          alignment
4056    */
4057   public void addSortByAnnotScoreMenuItem(JMenu sort,
4058           final String scoreLabel)
4059   {
4060     final JMenuItem item = new JMenuItem(scoreLabel);
4061     sort.add(item);
4062     item.addActionListener(new java.awt.event.ActionListener()
4063     {
4064       @Override
4065       public void actionPerformed(ActionEvent e)
4066       {
4067         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4068         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4069                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4070         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4071                 viewport.getAlignment()));
4072         alignPanel.paintAlignment(true);
4073       }
4074     });
4075   }
4076
4077   /**
4078    * last hash for alignment's annotation array - used to minimise cost of
4079    * rebuild.
4080    */
4081   protected int _annotationScoreVectorHash;
4082
4083   /**
4084    * search the alignment and rebuild the sort by annotation score submenu the
4085    * last alignment annotation vector hash is stored to minimize cost of
4086    * rebuilding in subsequence calls.
4087    *
4088    */
4089   @Override
4090   public void buildSortByAnnotationScoresMenu()
4091   {
4092     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4093     {
4094       return;
4095     }
4096
4097     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4098     {
4099       sortByAnnotScore.removeAll();
4100       // almost certainly a quicker way to do this - but we keep it simple
4101       Hashtable scoreSorts = new Hashtable();
4102       AlignmentAnnotation aann[];
4103       for (SequenceI sqa : viewport.getAlignment().getSequences())
4104       {
4105         aann = sqa.getAnnotation();
4106         for (int i = 0; aann != null && i < aann.length; i++)
4107         {
4108           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4109           {
4110             scoreSorts.put(aann[i].label, aann[i].label);
4111           }
4112         }
4113       }
4114       Enumeration labels = scoreSorts.keys();
4115       while (labels.hasMoreElements())
4116       {
4117         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4118                 (String) labels.nextElement());
4119       }
4120       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4121       scoreSorts.clear();
4122
4123       _annotationScoreVectorHash = viewport.getAlignment()
4124               .getAlignmentAnnotation().hashCode();
4125     }
4126   }
4127
4128   /**
4129    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4130    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4131    * call. Listeners are added to remove the menu item when the treePanel is
4132    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4133    * modified.
4134    *
4135    * @param treePanel
4136    *          Displayed tree window.
4137    * @param title
4138    *          SortBy menu item title.
4139    */
4140   @Override
4141   public void buildTreeMenu()
4142   {
4143     calculateTree.removeAll();
4144     // build the calculate menu
4145
4146     for (final String type : new String[] { "NJ", "AV" })
4147     {
4148       String treecalcnm = MessageManager.getString("label.tree_calc_"
4149               + type.toLowerCase());
4150       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4151       {
4152         JMenuItem tm = new JMenuItem();
4153         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4154         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4155                 || sm.isProtein() == !viewport.getAlignment()
4156                         .isNucleotide())
4157         {
4158           String smn = MessageManager.getStringOrReturn(
4159                   "label.score_model_", sm.getName());
4160           final String title = MessageManager.formatMessage(
4161                   "label.treecalc_title", treecalcnm, smn);
4162           tm.setText(title);//
4163           tm.addActionListener(new java.awt.event.ActionListener()
4164           {
4165             @Override
4166             public void actionPerformed(ActionEvent e)
4167             {
4168               newTreePanel(type, pwtype, title);
4169             }
4170           });
4171           calculateTree.add(tm);
4172         }
4173
4174       }
4175     }
4176     sortByTreeMenu.removeAll();
4177
4178     List<Component> comps = PaintRefresher.components.get(viewport
4179             .getSequenceSetId());
4180     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4181     for (Component comp : comps)
4182     {
4183       if (comp instanceof TreePanel)
4184       {
4185         treePanels.add((TreePanel) comp);
4186       }
4187     }
4188
4189     if (treePanels.size() < 1)
4190     {
4191       sortByTreeMenu.setVisible(false);
4192       return;
4193     }
4194
4195     sortByTreeMenu.setVisible(true);
4196
4197     for (final TreePanel tp : treePanels)
4198     {
4199       final JMenuItem item = new JMenuItem(tp.getTitle());
4200       item.addActionListener(new java.awt.event.ActionListener()
4201       {
4202         @Override
4203         public void actionPerformed(ActionEvent e)
4204         {
4205           tp.sortByTree_actionPerformed();
4206           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4207
4208         }
4209       });
4210
4211       sortByTreeMenu.add(item);
4212     }
4213   }
4214
4215   public boolean sortBy(AlignmentOrder alorder, String undoname)
4216   {
4217     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4218     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4219     if (undoname != null)
4220     {
4221       addHistoryItem(new OrderCommand(undoname, oldOrder,
4222               viewport.getAlignment()));
4223     }
4224     alignPanel.paintAlignment(true);
4225     return true;
4226   }
4227
4228   /**
4229    * Work out whether the whole set of sequences or just the selected set will
4230    * be submitted for multiple alignment.
4231    *
4232    */
4233   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4234   {
4235     // Now, check we have enough sequences
4236     AlignmentView msa = null;
4237
4238     if ((viewport.getSelectionGroup() != null)
4239             && (viewport.getSelectionGroup().getSize() > 1))
4240     {
4241       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4242       // some common interface!
4243       /*
4244        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4245        * SequenceI[sz = seqs.getSize(false)];
4246        *
4247        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4248        * seqs.getSequenceAt(i); }
4249        */
4250       msa = viewport.getAlignmentView(true);
4251     }
4252     else if (viewport.getSelectionGroup() != null
4253             && viewport.getSelectionGroup().getSize() == 1)
4254     {
4255       int option = JOptionPane.showConfirmDialog(this,
4256               MessageManager.getString("warn.oneseq_msainput_selection"),
4257               MessageManager.getString("label.invalid_selection"),
4258               JOptionPane.OK_CANCEL_OPTION);
4259       if (option == JOptionPane.OK_OPTION)
4260       {
4261         msa = viewport.getAlignmentView(false);
4262       }
4263     }
4264     else
4265     {
4266       msa = viewport.getAlignmentView(false);
4267     }
4268     return msa;
4269   }
4270
4271   /**
4272    * Decides what is submitted to a secondary structure prediction service: the
4273    * first sequence in the alignment, or in the current selection, or, if the
4274    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4275    * region or the whole alignment. (where the first sequence in the set is the
4276    * one that the prediction will be for).
4277    */
4278   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4279   {
4280     AlignmentView seqs = null;
4281
4282     if ((viewport.getSelectionGroup() != null)
4283             && (viewport.getSelectionGroup().getSize() > 0))
4284     {
4285       seqs = viewport.getAlignmentView(true);
4286     }
4287     else
4288     {
4289       seqs = viewport.getAlignmentView(false);
4290     }
4291     // limit sequences - JBPNote in future - could spawn multiple prediction
4292     // jobs
4293     // TODO: viewport.getAlignment().isAligned is a global state - the local
4294     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4295     if (!viewport.getAlignment().isAligned(false))
4296     {
4297       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4298       // TODO: if seqs.getSequences().length>1 then should really have warned
4299       // user!
4300
4301     }
4302     return seqs;
4303   }
4304
4305   /**
4306    * DOCUMENT ME!
4307    *
4308    * @param e
4309    *          DOCUMENT ME!
4310    */
4311   @Override
4312   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4313   {
4314     // Pick the tree file
4315     JalviewFileChooser chooser = new JalviewFileChooser(
4316             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4317     chooser.setFileView(new JalviewFileView());
4318     chooser.setDialogTitle(MessageManager
4319             .getString("label.select_newick_like_tree_file"));
4320     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4321
4322     int value = chooser.showOpenDialog(null);
4323
4324     if (value == JalviewFileChooser.APPROVE_OPTION)
4325     {
4326       String choice = chooser.getSelectedFile().getPath();
4327       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4328       jalview.io.NewickFile fin = null;
4329       try
4330       {
4331         fin = new jalview.io.NewickFile(choice, "File");
4332         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4333       } catch (Exception ex)
4334       {
4335         JOptionPane
4336                 .showMessageDialog(
4337                         Desktop.desktop,
4338                         ex.getMessage(),
4339                         MessageManager
4340                                 .getString("label.problem_reading_tree_file"),
4341                         JOptionPane.WARNING_MESSAGE);
4342         ex.printStackTrace();
4343       }
4344       if (fin != null && fin.hasWarningMessage())
4345       {
4346         JOptionPane.showMessageDialog(Desktop.desktop, fin
4347                 .getWarningMessage(), MessageManager
4348                 .getString("label.possible_problem_with_tree_file"),
4349                 JOptionPane.WARNING_MESSAGE);
4350       }
4351     }
4352   }
4353
4354   @Override
4355   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4356   {
4357     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4358   }
4359
4360   public TreePanel ShowNewickTree(NewickFile nf, String title)
4361   {
4362     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4363   }
4364
4365   public TreePanel ShowNewickTree(NewickFile nf, String title,
4366           AlignmentView input)
4367   {
4368     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4369   }
4370
4371   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4372           int h, int x, int y)
4373   {
4374     return ShowNewickTree(nf, title, null, w, h, x, y);
4375   }
4376
4377   /**
4378    * Add a treeviewer for the tree extracted from a newick file object to the
4379    * current alignment view
4380    *
4381    * @param nf
4382    *          the tree
4383    * @param title
4384    *          tree viewer title
4385    * @param input
4386    *          Associated alignment input data (or null)
4387    * @param w
4388    *          width
4389    * @param h
4390    *          height
4391    * @param x
4392    *          position
4393    * @param y
4394    *          position
4395    * @return TreePanel handle
4396    */
4397   public TreePanel ShowNewickTree(NewickFile nf, String title,
4398           AlignmentView input, int w, int h, int x, int y)
4399   {
4400     TreePanel tp = null;
4401
4402     try
4403     {
4404       nf.parse();
4405
4406       if (nf.getTree() != null)
4407       {
4408         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4409
4410         tp.setSize(w, h);
4411
4412         if (x > 0 && y > 0)
4413         {
4414           tp.setLocation(x, y);
4415         }
4416
4417         Desktop.addInternalFrame(tp, title, w, h);
4418       }
4419     } catch (Exception ex)
4420     {
4421       ex.printStackTrace();
4422     }
4423
4424     return tp;
4425   }
4426
4427   private boolean buildingMenu = false;
4428
4429   /**
4430    * Generates menu items and listener event actions for web service clients
4431    *
4432    */
4433   public void BuildWebServiceMenu()
4434   {
4435     while (buildingMenu)
4436     {
4437       try
4438       {
4439         System.err.println("Waiting for building menu to finish.");
4440         Thread.sleep(10);
4441       } catch (Exception e)
4442       {
4443       }
4444     }
4445     final AlignFrame me = this;
4446     buildingMenu = true;
4447     new Thread(new Runnable()
4448     {
4449       @Override
4450       public void run()
4451       {
4452         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4453         try
4454         {
4455           // System.err.println("Building ws menu again "
4456           // + Thread.currentThread());
4457           // TODO: add support for context dependent disabling of services based
4458           // on
4459           // alignment and current selection
4460           // TODO: add additional serviceHandle parameter to specify abstract
4461           // handler
4462           // class independently of AbstractName
4463           // TODO: add in rediscovery GUI function to restart discoverer
4464           // TODO: group services by location as well as function and/or
4465           // introduce
4466           // object broker mechanism.
4467           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4468           final IProgressIndicator af = me;
4469           final JMenu msawsmenu = new JMenu("Alignment");
4470           final JMenu secstrmenu = new JMenu(
4471                   "Secondary Structure Prediction");
4472           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4473           final JMenu analymenu = new JMenu("Analysis");
4474           final JMenu dismenu = new JMenu("Protein Disorder");
4475           // final JMenu msawsmenu = new
4476           // JMenu(MessageManager.getString("label.alignment"));
4477           // final JMenu secstrmenu = new
4478           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4479           // final JMenu seqsrchmenu = new
4480           // JMenu(MessageManager.getString("label.sequence_database_search"));
4481           // final JMenu analymenu = new
4482           // JMenu(MessageManager.getString("label.analysis"));
4483           // final JMenu dismenu = new
4484           // JMenu(MessageManager.getString("label.protein_disorder"));
4485           // JAL-940 - only show secondary structure prediction services from
4486           // the legacy server
4487           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4488               // &&
4489           Discoverer.services != null && (Discoverer.services.size() > 0))
4490           {
4491             // TODO: refactor to allow list of AbstractName/Handler bindings to
4492             // be
4493             // stored or retrieved from elsewhere
4494             // No MSAWS used any more:
4495             // Vector msaws = null; // (Vector)
4496             // Discoverer.services.get("MsaWS");
4497             Vector secstrpr = (Vector) Discoverer.services
4498                     .get("SecStrPred");
4499             if (secstrpr != null)
4500             {
4501               // Add any secondary structure prediction services
4502               for (int i = 0, j = secstrpr.size(); i < j; i++)
4503               {
4504                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4505                         .get(i);
4506                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4507                         .getServiceClient(sh);
4508                 int p = secstrmenu.getItemCount();
4509                 impl.attachWSMenuEntry(secstrmenu, me);
4510                 int q = secstrmenu.getItemCount();
4511                 for (int litm = p; litm < q; litm++)
4512                 {
4513                   legacyItems.add(secstrmenu.getItem(litm));
4514                 }
4515               }
4516             }
4517           }
4518
4519           // Add all submenus in the order they should appear on the web
4520           // services menu
4521           wsmenu.add(msawsmenu);
4522           wsmenu.add(secstrmenu);
4523           wsmenu.add(dismenu);
4524           wsmenu.add(analymenu);
4525           // No search services yet
4526           // wsmenu.add(seqsrchmenu);
4527
4528           javax.swing.SwingUtilities.invokeLater(new Runnable()
4529           {
4530             @Override
4531             public void run()
4532             {
4533               try
4534               {
4535                 webService.removeAll();
4536                 // first, add discovered services onto the webservices menu
4537                 if (wsmenu.size() > 0)
4538                 {
4539                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4540                   {
4541                     webService.add(wsmenu.get(i));
4542                   }
4543                 }
4544                 else
4545                 {
4546                   webService.add(me.webServiceNoServices);
4547                 }
4548                 // TODO: move into separate menu builder class.
4549                 boolean new_sspred = false;
4550                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4551                 {
4552                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4553                   if (jws2servs != null)
4554                   {
4555                     if (jws2servs.hasServices())
4556                     {
4557                       jws2servs.attachWSMenuEntry(webService, me);
4558                       for (Jws2Instance sv : jws2servs.getServices())
4559                       {
4560                         if (sv.description.toLowerCase().contains("jpred"))
4561                         {
4562                           for (JMenuItem jmi : legacyItems)
4563                           {
4564                             jmi.setVisible(false);
4565                           }
4566                         }
4567                       }
4568
4569                     }
4570                     if (jws2servs.isRunning())
4571                     {
4572                       JMenuItem tm = new JMenuItem(
4573                               "Still discovering JABA Services");
4574                       tm.setEnabled(false);
4575                       webService.add(tm);
4576                     }
4577                   }
4578                 }
4579                 build_urlServiceMenu(me.webService);
4580                 build_fetchdbmenu(webService);
4581                 for (JMenu item : wsmenu)
4582                 {
4583                   if (item.getItemCount() == 0)
4584                   {
4585                     item.setEnabled(false);
4586                   }
4587                   else
4588                   {
4589                     item.setEnabled(true);
4590                   }
4591                 }
4592               } catch (Exception e)
4593               {
4594                 Cache.log
4595                         .debug("Exception during web service menu building process.",
4596                                 e);
4597               }
4598             }
4599           });
4600         } catch (Exception e)
4601         {
4602         }
4603         buildingMenu = false;
4604       }
4605     }).start();
4606
4607   }
4608
4609   /**
4610    * construct any groupURL type service menu entries.
4611    *
4612    * @param webService
4613    */
4614   private void build_urlServiceMenu(JMenu webService)
4615   {
4616     // TODO: remove this code when 2.7 is released
4617     // DEBUG - alignmentView
4618     /*
4619      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4620      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4621      *
4622      * @Override public void actionPerformed(ActionEvent e) {
4623      * jalview.datamodel.AlignmentView
4624      * .testSelectionViews(af.viewport.getAlignment(),
4625      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4626      *
4627      * }); webService.add(testAlView);
4628      */
4629     // TODO: refactor to RestClient discoverer and merge menu entries for
4630     // rest-style services with other types of analysis/calculation service
4631     // SHmmr test client - still being implemented.
4632     // DEBUG - alignmentView
4633
4634     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4635             .getRestClients())
4636     {
4637       client.attachWSMenuEntry(
4638               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4639               this);
4640     }
4641   }
4642
4643   /**
4644    * Searches selected sequences for xRef products and builds the Show
4645    * Cross-References menu (formerly called Show Products)
4646    *
4647    * @return true if Show Cross-references menu should be enabled.
4648    */
4649   public boolean canShowProducts()
4650   {
4651     SequenceI[] selection = viewport.getSequenceSelection();
4652     AlignmentI dataset = viewport.getAlignment().getDataset();
4653     boolean showp = false;
4654     try
4655     {
4656       showProducts.removeAll();
4657       final boolean dna = viewport.getAlignment().isNucleotide();
4658       String[] ptypes = (selection == null || selection.length == 0) ? null
4659               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4660
4661       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4662       {
4663         showp = true;
4664         final AlignFrame af = this;
4665         final String source = ptypes[t];
4666         JMenuItem xtype = new JMenuItem(ptypes[t]);
4667         xtype.addActionListener(new ActionListener()
4668         {
4669
4670           @Override
4671           public void actionPerformed(ActionEvent e)
4672           {
4673             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4674           }
4675
4676         });
4677         showProducts.add(xtype);
4678       }
4679       showProducts.setVisible(showp);
4680       showProducts.setEnabled(showp);
4681     } catch (Exception e)
4682     {
4683       jalview.bin.Cache.log
4684               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4685                       e);
4686       return false;
4687     }
4688     return showp;
4689   }
4690
4691   protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4692           final String source)
4693   {
4694     Runnable foo = new Runnable()
4695     {
4696
4697       @Override
4698       public void run()
4699       {
4700         final long sttime = System.currentTimeMillis();
4701         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4702                 "status.searching_for_sequences_from",
4703                 new Object[] { source }), sttime);
4704         try
4705         {
4706           AlignmentI alignment = AlignFrame.this.getViewport()
4707                   .getAlignment();
4708           AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4709                   alignment);
4710           if (xrefs != null)
4711           {
4712             /*
4713              * get display scheme (if any) to apply to features
4714              */
4715             FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4716                     .getFeatureColourScheme(source);
4717
4718             AlignmentI al = makeCrossReferencesAlignment(
4719                     alignment.getDataset(), xrefs);
4720
4721             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4722                     DEFAULT_HEIGHT);
4723             if (Cache.getDefault("HIDE_INTRONS", true))
4724             {
4725               newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
4726             }
4727             String newtitle = String.format("%s %s %s",
4728                     MessageManager.getString(dna ? "label.proteins"
4729                             : "label.nucleotides"), MessageManager
4730                             .getString("label.for"), getTitle());
4731             newFrame.setTitle(newtitle);
4732
4733             if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4734             {
4735               /*
4736                * split frame display is turned off in preferences file
4737                */
4738               Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4739                       DEFAULT_HEIGHT);
4740               return; // via finally clause
4741             }
4742
4743             /*
4744              * Make a copy of this alignment (sharing the same dataset
4745              * sequences). If we are DNA, drop introns and update mappings
4746              */
4747             AlignmentI copyAlignment = null;
4748             final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4749                     .getSequenceSelection();
4750             List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4751             boolean copyAlignmentIsAligned = false;
4752             if (dna)
4753             {
4754               copyAlignment = AlignmentUtils.makeCdsAlignment(
4755                       sequenceSelection, cf, alignment);
4756               if (copyAlignment.getHeight() == 0)
4757               {
4758                 System.err.println("Failed to make CDS alignment");
4759               }
4760               al.getCodonFrames().clear();
4761               al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
4762
4763               /*
4764                * pending getting Embl transcripts to 'align',
4765                * we are only doing this for Ensembl
4766                */
4767               // TODO proper criteria for 'can align as cdna'
4768               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4769                       || AlignmentUtils.looksLikeEnsembl(alignment))
4770               {
4771                 copyAlignment.alignAs(alignment);
4772                 copyAlignmentIsAligned = true;
4773               }
4774             }
4775             else
4776             {
4777               copyAlignment = AlignmentUtils.makeCopyAlignment(
4778                       sequenceSelection, xrefs.getSequencesArray());
4779               copyAlignment.getCodonFrames().addAll(cf);
4780             }
4781             copyAlignment.setGapCharacter(AlignFrame.this.viewport
4782                     .getGapCharacter());
4783
4784             StructureSelectionManager ssm = StructureSelectionManager
4785                     .getStructureSelectionManager(Desktop.instance);
4786             ssm.registerMappings(cf);
4787
4788             if (copyAlignment.getHeight() <= 0)
4789             {
4790               System.err.println("No Sequences generated for xRef type "
4791                       + source);
4792               return;
4793             }
4794             /*
4795              * align protein to dna
4796              */
4797             if (dna && copyAlignmentIsAligned)
4798             {
4799               al.alignAs(copyAlignment);
4800             }
4801             else
4802             {
4803               /*
4804                * align cdna to protein - currently only if
4805                * fetching and aligning Ensembl transcripts!
4806                */
4807               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4808               {
4809                 copyAlignment.alignAs(al);
4810               }
4811             }
4812
4813             AlignFrame copyThis = new AlignFrame(copyAlignment,
4814                     AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4815             copyThis.setTitle(AlignFrame.this.getTitle());
4816
4817             boolean showSequenceFeatures = viewport
4818                     .isShowSequenceFeatures();
4819             newFrame.setShowSeqFeatures(showSequenceFeatures);
4820             copyThis.setShowSeqFeatures(showSequenceFeatures);
4821             FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4822                     .getFeatureRenderer();
4823
4824             /*
4825              * copy feature rendering settings to split frame
4826              */
4827             newFrame.alignPanel.getSeqPanel().seqCanvas
4828                     .getFeatureRenderer()
4829                     .transferSettings(myFeatureStyling);
4830             copyThis.alignPanel.getSeqPanel().seqCanvas
4831                     .getFeatureRenderer()
4832                     .transferSettings(myFeatureStyling);
4833
4834             /*
4835              * apply 'database source' feature configuration
4836              * if any was found
4837              */
4838             // TODO is this the feature colouring for the original
4839             // alignment or the fetched xrefs? either could be Ensembl
4840             newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4841             copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4842
4843             SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4844                     dna ? newFrame : copyThis);
4845             newFrame.setVisible(true);
4846             copyThis.setVisible(true);
4847             String linkedTitle = MessageManager
4848                     .getString("label.linked_view_title");
4849             Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4850             sf.adjustDivider();
4851           }
4852         } catch (Exception e)
4853         {
4854           Cache.log.error("Exception when finding crossreferences", e);
4855         } catch (OutOfMemoryError e)
4856         {
4857           new OOMWarning("whilst fetching crossreferences", e);
4858         } catch (Throwable e)
4859         {
4860           Cache.log.error("Error when finding crossreferences", e);
4861         } finally
4862         {
4863           AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4864                   "status.finished_searching_for_sequences_from",
4865                   new Object[] { source }), sttime);
4866         }
4867       }
4868
4869       /**
4870        * Makes an alignment containing the given sequences. If this is of the
4871        * same type as the given dataset (nucleotide/protein), then the new
4872        * alignment shares the same dataset, and its dataset sequences are added
4873        * to it. Otherwise a new dataset sequence is created for the
4874        * cross-references.
4875        *
4876        * @param dataset
4877        * @param seqs
4878        * @return
4879        */
4880       protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4881               AlignmentI seqs)
4882       {
4883         boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4884
4885         SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4886         for (int s = 0; s < sprods.length; s++)
4887         {
4888           sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4889           if (sameType)
4890           {
4891             if (dataset.getSequences() == null
4892                     || !dataset.getSequences().contains(
4893                             sprods[s].getDatasetSequence()))
4894             {
4895               dataset.addSequence(sprods[s].getDatasetSequence());
4896             }
4897           }
4898           sprods[s].updatePDBIds();
4899         }
4900         Alignment al = new Alignment(sprods);
4901         if (sameType)
4902         {
4903           al.setDataset((Alignment) dataset);
4904         }
4905         else
4906         {
4907           al.createDatasetAlignment();
4908         }
4909         return al;
4910       }
4911
4912     };
4913     Thread frunner = new Thread(foo);
4914     frunner.start();
4915   }
4916
4917   /**
4918    * Construct and display a new frame containing the translation of this
4919    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4920    */
4921   @Override
4922   public void showTranslation_actionPerformed(ActionEvent e)
4923   {
4924     AlignmentI al = null;
4925     try
4926     {
4927       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4928
4929       al = dna.translateCdna();
4930     } catch (Exception ex)
4931     {
4932       jalview.bin.Cache.log.error(
4933               "Exception during translation. Please report this !", ex);
4934       final String msg = MessageManager
4935               .getString("label.error_when_translating_sequences_submit_bug_report");
4936       final String errorTitle = MessageManager
4937               .getString("label.implementation_error")
4938               + MessageManager.getString("translation_failed");
4939       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4940               JOptionPane.ERROR_MESSAGE);
4941       return;
4942     }
4943     if (al == null || al.getHeight() == 0)
4944     {
4945       final String msg = MessageManager
4946               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4947       final String errorTitle = MessageManager
4948               .getString("label.translation_failed");
4949       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4950               JOptionPane.WARNING_MESSAGE);
4951     }
4952     else
4953     {
4954       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4955       af.setFileFormat(this.currentFileFormat);
4956       final String newTitle = MessageManager.formatMessage(
4957               "label.translation_of_params",
4958               new Object[] { this.getTitle() });
4959       af.setTitle(newTitle);
4960       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4961       {
4962         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4963         viewport.openSplitFrame(af, new Alignment(seqs));
4964       }
4965       else
4966       {
4967         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4968                 DEFAULT_HEIGHT);
4969       }
4970     }
4971   }
4972
4973   /**
4974    * Set the file format
4975    *
4976    * @param fileFormat
4977    */
4978   public void setFileFormat(String fileFormat)
4979   {
4980     this.currentFileFormat = fileFormat;
4981   }
4982
4983   /**
4984    * Try to load a features file onto the alignment.
4985    *
4986    * @param file
4987    *          contents or path to retrieve file
4988    * @param type
4989    *          access mode of file (see jalview.io.AlignFile)
4990    * @return true if features file was parsed correctly.
4991    */
4992   public boolean parseFeaturesFile(String file, String type)
4993   {
4994     return avc.parseFeaturesFile(file, type,
4995             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4996
4997   }
4998
4999   @Override
5000   public void refreshFeatureUI(boolean enableIfNecessary)
5001   {
5002     // note - currently this is only still here rather than in the controller
5003     // because of the featureSettings hard reference that is yet to be
5004     // abstracted
5005     if (enableIfNecessary)
5006     {
5007       viewport.setShowSequenceFeatures(true);
5008       showSeqFeatures.setSelected(true);
5009     }
5010
5011   }
5012
5013   @Override
5014   public void dragEnter(DropTargetDragEvent evt)
5015   {
5016   }
5017
5018   @Override
5019   public void dragExit(DropTargetEvent evt)
5020   {
5021   }
5022
5023   @Override
5024   public void dragOver(DropTargetDragEvent evt)
5025   {
5026   }
5027
5028   @Override
5029   public void dropActionChanged(DropTargetDragEvent evt)
5030   {
5031   }
5032
5033   @Override
5034   public void drop(DropTargetDropEvent evt)
5035   {
5036     Transferable t = evt.getTransferable();
5037     java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
5038
5039     try
5040     {
5041       Desktop.transferFromDropTarget(files, protocols, evt, t);
5042     } catch (Exception e)
5043     {
5044       e.printStackTrace();
5045     }
5046     if (files != null)
5047     {
5048       try
5049       {
5050         // check to see if any of these files have names matching sequences in
5051         // the alignment
5052         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5053                 .getAlignment().getSequencesArray());
5054         /**
5055          * Object[] { String,SequenceI}
5056          */
5057         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5058         ArrayList<String> filesnotmatched = new ArrayList<String>();
5059         for (int i = 0; i < files.size(); i++)
5060         {
5061           String file = files.get(i).toString();
5062           String pdbfn = "";
5063           String protocol = FormatAdapter.checkProtocol(file);
5064           if (protocol == jalview.io.FormatAdapter.FILE)
5065           {
5066             File fl = new File(file);
5067             pdbfn = fl.getName();
5068           }
5069           else if (protocol == jalview.io.FormatAdapter.URL)
5070           {
5071             URL url = new URL(file);
5072             pdbfn = url.getFile();
5073           }
5074           if (pdbfn.length() > 0)
5075           {
5076             // attempt to find a match in the alignment
5077             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5078             int l = 0, c = pdbfn.indexOf(".");
5079             while (mtch == null && c != -1)
5080             {
5081               do
5082               {
5083                 l = c;
5084               } while ((c = pdbfn.indexOf(".", l)) > l);
5085               if (l > -1)
5086               {
5087                 pdbfn = pdbfn.substring(0, l);
5088               }
5089               mtch = idm.findAllIdMatches(pdbfn);
5090             }
5091             if (mtch != null)
5092             {
5093               String type = null;
5094               try
5095               {
5096                 type = new IdentifyFile().identify(file, protocol);
5097               } catch (Exception ex)
5098               {
5099                 type = null;
5100               }
5101               if (type != null)
5102               {
5103                 if (type.equalsIgnoreCase("PDB"))
5104                 {
5105                   filesmatched.add(new Object[] { file, protocol, mtch });
5106                   continue;
5107                 }
5108               }
5109             }
5110             // File wasn't named like one of the sequences or wasn't a PDB file.
5111             filesnotmatched.add(file);
5112           }
5113         }
5114         int assocfiles = 0;
5115         if (filesmatched.size() > 0)
5116         {
5117           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5118                   || JOptionPane
5119                           .showConfirmDialog(
5120                                   this,
5121                                   MessageManager
5122                                           .formatMessage(
5123                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5124                                                   new Object[] { Integer
5125                                                           .valueOf(
5126                                                                   filesmatched
5127                                                                           .size())
5128                                                           .toString() }),
5129                                   MessageManager
5130                                           .getString("label.automatically_associate_pdb_files_by_name"),
5131                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5132
5133           {
5134             for (Object[] fm : filesmatched)
5135             {
5136               // try and associate
5137               // TODO: may want to set a standard ID naming formalism for
5138               // associating PDB files which have no IDs.
5139               for (SequenceI toassoc : (SequenceI[]) fm[2])
5140               {
5141                 PDBEntry pe = new AssociatePdbFileWithSeq()
5142                         .associatePdbWithSeq((String) fm[0],
5143                                 (String) fm[1], toassoc, false,
5144                                 Desktop.instance);
5145                 if (pe != null)
5146                 {
5147                   System.err.println("Associated file : "
5148                           + ((String) fm[0]) + " with "
5149                           + toassoc.getDisplayId(true));
5150                   assocfiles++;
5151                 }
5152               }
5153               alignPanel.paintAlignment(true);
5154             }
5155           }
5156         }
5157         if (filesnotmatched.size() > 0)
5158         {
5159           if (assocfiles > 0
5160                   && (Cache.getDefault(
5161                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5162                           .showConfirmDialog(
5163                                   this,
5164                                   "<html>"
5165                                           + MessageManager
5166                                                   .formatMessage(
5167                                                           "label.ignore_unmatched_dropped_files_info",
5168                                                           new Object[] { Integer
5169                                                                   .valueOf(
5170                                                                           filesnotmatched
5171                                                                                   .size())
5172                                                                   .toString() })
5173                                           + "</html>",
5174                                   MessageManager
5175                                           .getString("label.ignore_unmatched_dropped_files"),
5176                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5177           {
5178             return;
5179           }
5180           for (String fn : filesnotmatched)
5181           {
5182             loadJalviewDataFile(fn, null, null, null);
5183           }
5184
5185         }
5186       } catch (Exception ex)
5187       {
5188         ex.printStackTrace();
5189       }
5190     }
5191   }
5192
5193   /**
5194    * Attempt to load a "dropped" file or URL string: First by testing whether
5195    * it's an Annotation file, then a JNet file, and finally a features file. If
5196    * all are false then the user may have dropped an alignment file onto this
5197    * AlignFrame.
5198    *
5199    * @param file
5200    *          either a filename or a URL string.
5201    */
5202   public void loadJalviewDataFile(String file, String protocol,
5203           String format, SequenceI assocSeq)
5204   {
5205     try
5206     {
5207       if (protocol == null)
5208       {
5209         protocol = FormatAdapter.checkProtocol(file);
5210       }
5211       // if the file isn't identified, or not positively identified as some
5212       // other filetype (PFAM is default unidentified alignment file type) then
5213       // try to parse as annotation.
5214       boolean isAnnotation = (format == null || format
5215               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5216               .annotateAlignmentView(viewport, file, protocol) : false;
5217
5218       if (!isAnnotation)
5219       {
5220         // first see if its a T-COFFEE score file
5221         TCoffeeScoreFile tcf = null;
5222         try
5223         {
5224           tcf = new TCoffeeScoreFile(file, protocol);
5225           if (tcf.isValid())
5226           {
5227             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5228             {
5229               tcoffeeColour.setEnabled(true);
5230               tcoffeeColour.setSelected(true);
5231               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5232               isAnnotation = true;
5233               statusBar
5234                       .setText(MessageManager
5235                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5236             }
5237             else
5238             {
5239               // some problem - if no warning its probable that the ID matching
5240               // process didn't work
5241               JOptionPane
5242                       .showMessageDialog(
5243                               Desktop.desktop,
5244                               tcf.getWarningMessage() == null ? MessageManager
5245                                       .getString("label.check_file_matches_sequence_ids_alignment")
5246                                       : tcf.getWarningMessage(),
5247                               MessageManager
5248                                       .getString("label.problem_reading_tcoffee_score_file"),
5249                               JOptionPane.WARNING_MESSAGE);
5250             }
5251           }
5252           else
5253           {
5254             tcf = null;
5255           }
5256         } catch (Exception x)
5257         {
5258           Cache.log
5259                   .debug("Exception when processing data source as T-COFFEE score file",
5260                           x);
5261           tcf = null;
5262         }
5263         if (tcf == null)
5264         {
5265           // try to see if its a JNet 'concise' style annotation file *before*
5266           // we
5267           // try to parse it as a features file
5268           if (format == null)
5269           {
5270             format = new IdentifyFile().identify(file, protocol);
5271           }
5272           if (format.equalsIgnoreCase("JnetFile"))
5273           {
5274             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5275                     file, protocol);
5276             new JnetAnnotationMaker();
5277             JnetAnnotationMaker.add_annotation(predictions,
5278                     viewport.getAlignment(), 0, false);
5279             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5280             viewport.getAlignment().setSeqrep(repseq);
5281             ColumnSelection cs = new ColumnSelection();
5282             cs.hideInsertionsFor(repseq);
5283             viewport.setColumnSelection(cs);
5284             isAnnotation = true;
5285           }
5286           else if (IdentifyFile.FeaturesFile.equals(format))
5287           {
5288             if (parseFeaturesFile(file, protocol))
5289             {
5290               alignPanel.paintAlignment(true);
5291             }
5292           }
5293           else
5294           {
5295             new FileLoader().LoadFile(viewport, file, protocol, format);
5296           }
5297         }
5298       }
5299       if (isAnnotation)
5300       {
5301
5302         alignPanel.adjustAnnotationHeight();
5303         viewport.updateSequenceIdColours();
5304         buildSortByAnnotationScoresMenu();
5305         alignPanel.paintAlignment(true);
5306       }
5307     } catch (Exception ex)
5308     {
5309       ex.printStackTrace();
5310     } catch (OutOfMemoryError oom)
5311     {
5312       try
5313       {
5314         System.gc();
5315       } catch (Exception x)
5316       {
5317       }
5318       new OOMWarning(
5319               "loading data "
5320                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5321                               : "using " + protocol + " from " + file)
5322                               : ".")
5323                       + (format != null ? "(parsing as '" + format
5324                               + "' file)" : ""), oom, Desktop.desktop);
5325     }
5326   }
5327
5328   /**
5329    * Method invoked by the ChangeListener on the tabbed pane, in other words
5330    * when a different tabbed pane is selected by the user or programmatically.
5331    */
5332   @Override
5333   public void tabSelectionChanged(int index)
5334   {
5335     if (index > -1)
5336     {
5337       alignPanel = alignPanels.get(index);
5338       viewport = alignPanel.av;
5339       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5340       setMenusFromViewport(viewport);
5341     }
5342
5343     /*
5344      * If there is a frame linked to this one in a SplitPane, switch it to the
5345      * same view tab index. No infinite recursion of calls should happen, since
5346      * tabSelectionChanged() should not get invoked on setting the selected
5347      * index to an unchanged value. Guard against setting an invalid index
5348      * before the new view peer tab has been created.
5349      */
5350     final AlignViewportI peer = viewport.getCodingComplement();
5351     if (peer != null)
5352     {
5353       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5354       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5355       {
5356         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5357       }
5358     }
5359   }
5360
5361   /**
5362    * On right mouse click on view tab, prompt for and set new view name.
5363    */
5364   @Override
5365   public void tabbedPane_mousePressed(MouseEvent e)
5366   {
5367     if (e.isPopupTrigger())
5368     {
5369       String msg = MessageManager.getString("label.enter_view_name");
5370       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5371               JOptionPane.QUESTION_MESSAGE);
5372
5373       if (reply != null)
5374       {
5375         viewport.viewName = reply;
5376         // TODO warn if reply is in getExistingViewNames()?
5377         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5378       }
5379     }
5380   }
5381
5382   public AlignViewport getCurrentView()
5383   {
5384     return viewport;
5385   }
5386
5387   /**
5388    * Open the dialog for regex description parsing.
5389    */
5390   @Override
5391   protected void extractScores_actionPerformed(ActionEvent e)
5392   {
5393     ParseProperties pp = new jalview.analysis.ParseProperties(
5394             viewport.getAlignment());
5395     // TODO: verify regex and introduce GUI dialog for version 2.5
5396     // if (pp.getScoresFromDescription("col", "score column ",
5397     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5398     // true)>0)
5399     if (pp.getScoresFromDescription("description column",
5400             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5401     {
5402       buildSortByAnnotationScoresMenu();
5403     }
5404   }
5405
5406   /*
5407    * (non-Javadoc)
5408    *
5409    * @see
5410    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5411    * )
5412    */
5413   @Override
5414   protected void showDbRefs_actionPerformed(ActionEvent e)
5415   {
5416     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5417   }
5418
5419   /*
5420    * (non-Javadoc)
5421    *
5422    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5423    * ActionEvent)
5424    */
5425   @Override
5426   protected void showNpFeats_actionPerformed(ActionEvent e)
5427   {
5428     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5429   }
5430
5431   /**
5432    * find the viewport amongst the tabs in this alignment frame and close that
5433    * tab
5434    *
5435    * @param av
5436    */
5437   public boolean closeView(AlignViewportI av)
5438   {
5439     if (viewport == av)
5440     {
5441       this.closeMenuItem_actionPerformed(false);
5442       return true;
5443     }
5444     Component[] comp = tabbedPane.getComponents();
5445     for (int i = 0; comp != null && i < comp.length; i++)
5446     {
5447       if (comp[i] instanceof AlignmentPanel)
5448       {
5449         if (((AlignmentPanel) comp[i]).av == av)
5450         {
5451           // close the view.
5452           closeView((AlignmentPanel) comp[i]);
5453           return true;
5454         }
5455       }
5456     }
5457     return false;
5458   }
5459
5460   protected void build_fetchdbmenu(JMenu webService)
5461   {
5462     // Temporary hack - DBRef Fetcher always top level ws entry.
5463     // TODO We probably want to store a sequence database checklist in
5464     // preferences and have checkboxes.. rather than individual sources selected
5465     // here
5466     final JMenu rfetch = new JMenu(
5467             MessageManager.getString("action.fetch_db_references"));
5468     rfetch.setToolTipText(MessageManager
5469             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5470     webService.add(rfetch);
5471
5472     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5473             MessageManager.getString("option.trim_retrieved_seqs"));
5474     trimrs.setToolTipText(MessageManager
5475             .getString("label.trim_retrieved_sequences"));
5476     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5477     trimrs.addActionListener(new ActionListener()
5478     {
5479       @Override
5480       public void actionPerformed(ActionEvent e)
5481       {
5482         trimrs.setSelected(trimrs.isSelected());
5483         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5484                 Boolean.valueOf(trimrs.isSelected()).toString());
5485       };
5486     });
5487     rfetch.add(trimrs);
5488     JMenuItem fetchr = new JMenuItem(
5489             MessageManager.getString("label.standard_databases"));
5490     fetchr.setToolTipText(MessageManager
5491             .getString("label.fetch_embl_uniprot"));
5492     fetchr.addActionListener(new ActionListener()
5493     {
5494
5495       @Override
5496       public void actionPerformed(ActionEvent e)
5497       {
5498         new Thread(new Runnable()
5499         {
5500           @Override
5501           public void run()
5502           {
5503             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5504                     .getAlignment().isNucleotide();
5505             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5506                     .getSequenceSelection(), alignPanel.alignFrame, null,
5507                     alignPanel.alignFrame.featureSettings, isNucleotide);
5508             dbRefFetcher.addListener(new FetchFinishedListenerI()
5509             {
5510               @Override
5511               public void finished()
5512               {
5513                 AlignFrame.this.setMenusForViewport();
5514               }
5515             });
5516             dbRefFetcher.fetchDBRefs(false);
5517           }
5518         }).start();
5519
5520       }
5521
5522     });
5523     rfetch.add(fetchr);
5524     final AlignFrame me = this;
5525     new Thread(new Runnable()
5526     {
5527       @Override
5528       public void run()
5529       {
5530         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5531                 .getSequenceFetcherSingleton(me);
5532         javax.swing.SwingUtilities.invokeLater(new Runnable()
5533         {
5534           @Override
5535           public void run()
5536           {
5537             String[] dbclasses = sf.getOrderedSupportedSources();
5538             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5539             // jalview.util.QuickSort.sort(otherdb, otherdb);
5540             List<DbSourceProxy> otherdb;
5541             JMenu dfetch = new JMenu();
5542             JMenu ifetch = new JMenu();
5543             JMenuItem fetchr = null;
5544             int comp = 0, icomp = 0, mcomp = 15;
5545             String mname = null;
5546             int dbi = 0;
5547             for (String dbclass : dbclasses)
5548             {
5549               otherdb = sf.getSourceProxy(dbclass);
5550               // add a single entry for this class, or submenu allowing 'fetch
5551               // all' or pick one
5552               if (otherdb == null || otherdb.size() < 1)
5553               {
5554                 continue;
5555               }
5556               // List<DbSourceProxy> dbs=otherdb;
5557               // otherdb=new ArrayList<DbSourceProxy>();
5558               // for (DbSourceProxy db:dbs)
5559               // {
5560               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5561               // }
5562               if (mname == null)
5563               {
5564                 mname = "From " + dbclass;
5565               }
5566               if (otherdb.size() == 1)
5567               {
5568                 final DbSourceProxy[] dassource = otherdb
5569                         .toArray(new DbSourceProxy[0]);
5570                 DbSourceProxy src = otherdb.get(0);
5571                 fetchr = new JMenuItem(src.getDbSource());
5572                 fetchr.addActionListener(new ActionListener()
5573                 {
5574
5575                   @Override
5576                   public void actionPerformed(ActionEvent e)
5577                   {
5578                     new Thread(new Runnable()
5579                     {
5580
5581                       @Override
5582                       public void run()
5583                       {
5584                         boolean isNucleotide = alignPanel.alignFrame
5585                                 .getViewport().getAlignment()
5586                                 .isNucleotide();
5587                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5588                                 alignPanel.av.getSequenceSelection(),
5589                                 alignPanel.alignFrame, dassource,
5590                                 alignPanel.alignFrame.featureSettings,
5591                                 isNucleotide);
5592                         dbRefFetcher
5593                                 .addListener(new FetchFinishedListenerI()
5594                                 {
5595                                   @Override
5596                                   public void finished()
5597                                   {
5598                                     AlignFrame.this.setMenusForViewport();
5599                                   }
5600                                 });
5601                         dbRefFetcher.fetchDBRefs(false);
5602                       }
5603                     }).start();
5604                   }
5605
5606                 });
5607                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5608                         MessageManager.formatMessage(
5609                                 "label.fetch_retrieve_from",
5610                                 new Object[] { src.getDbName() })));
5611                 dfetch.add(fetchr);
5612                 comp++;
5613               }
5614               else
5615               {
5616                 final DbSourceProxy[] dassource = otherdb
5617                         .toArray(new DbSourceProxy[0]);
5618                 // fetch all entry
5619                 DbSourceProxy src = otherdb.get(0);
5620                 fetchr = new JMenuItem(MessageManager.formatMessage(
5621                         "label.fetch_all_param",
5622                         new Object[] { src.getDbSource() }));
5623                 fetchr.addActionListener(new ActionListener()
5624                 {
5625                   @Override
5626                   public void actionPerformed(ActionEvent e)
5627                   {
5628                     new Thread(new Runnable()
5629                     {
5630
5631                       @Override
5632                       public void run()
5633                       {
5634                         boolean isNucleotide = alignPanel.alignFrame
5635                                 .getViewport().getAlignment()
5636                                 .isNucleotide();
5637                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5638                                 alignPanel.av.getSequenceSelection(),
5639                                 alignPanel.alignFrame, dassource,
5640                                 alignPanel.alignFrame.featureSettings,
5641                                 isNucleotide);
5642                         dbRefFetcher
5643                                 .addListener(new FetchFinishedListenerI()
5644                                 {
5645                                   @Override
5646                                   public void finished()
5647                                   {
5648                                     AlignFrame.this.setMenusForViewport();
5649                                   }
5650                                 });
5651                         dbRefFetcher.fetchDBRefs(false);
5652                       }
5653                     }).start();
5654                   }
5655                 });
5656
5657                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5658                         MessageManager.formatMessage(
5659                                 "label.fetch_retrieve_from_all_sources",
5660                                 new Object[] {
5661                                     Integer.valueOf(otherdb.size())
5662                                             .toString(), src.getDbSource(),
5663                                     src.getDbName() })));
5664                 dfetch.add(fetchr);
5665                 comp++;
5666                 // and then build the rest of the individual menus
5667                 ifetch = new JMenu(MessageManager.formatMessage(
5668                         "label.source_from_db_source",
5669                         new Object[] { src.getDbSource() }));
5670                 icomp = 0;
5671                 String imname = null;
5672                 int i = 0;
5673                 for (DbSourceProxy sproxy : otherdb)
5674                 {
5675                   String dbname = sproxy.getDbName();
5676                   String sname = dbname.length() > 5 ? dbname.substring(0,
5677                           5) + "..." : dbname;
5678                   String msname = dbname.length() > 10 ? dbname.substring(
5679                           0, 10) + "..." : dbname;
5680                   if (imname == null)
5681                   {
5682                     imname = MessageManager.formatMessage(
5683                             "label.from_msname", new Object[] { sname });
5684                   }
5685                   fetchr = new JMenuItem(msname);
5686                   final DbSourceProxy[] dassrc = { sproxy };
5687                   fetchr.addActionListener(new ActionListener()
5688                   {
5689
5690                     @Override
5691                     public void actionPerformed(ActionEvent e)
5692                     {
5693                       new Thread(new Runnable()
5694                       {
5695
5696                         @Override
5697                         public void run()
5698                         {
5699                           boolean isNucleotide = alignPanel.alignFrame
5700                                   .getViewport().getAlignment()
5701                                   .isNucleotide();
5702                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5703                                   alignPanel.av.getSequenceSelection(),
5704                                   alignPanel.alignFrame, dassrc,
5705                                   alignPanel.alignFrame.featureSettings,
5706                                   isNucleotide);
5707                           dbRefFetcher
5708                                   .addListener(new FetchFinishedListenerI()
5709                                   {
5710                                     @Override
5711                                     public void finished()
5712                                     {
5713                                       AlignFrame.this.setMenusForViewport();
5714                                     }
5715                                   });
5716                           dbRefFetcher.fetchDBRefs(false);
5717                         }
5718                       }).start();
5719                     }
5720
5721                   });
5722                   fetchr.setToolTipText("<html>"
5723                           + MessageManager.formatMessage(
5724                                   "label.fetch_retrieve_from", new Object[]
5725                                   { dbname }));
5726                   ifetch.add(fetchr);
5727                   ++i;
5728                   if (++icomp >= mcomp || i == (otherdb.size()))
5729                   {
5730                     ifetch.setText(MessageManager.formatMessage(
5731                             "label.source_to_target", imname, sname));
5732                     dfetch.add(ifetch);
5733                     ifetch = new JMenu();
5734                     imname = null;
5735                     icomp = 0;
5736                     comp++;
5737                   }
5738                 }
5739               }
5740               ++dbi;
5741               if (comp >= mcomp || dbi >= (dbclasses.length))
5742               {
5743                 dfetch.setText(MessageManager.formatMessage(
5744                         "label.source_to_target", mname, dbclass));
5745                 rfetch.add(dfetch);
5746                 dfetch = new JMenu();
5747                 mname = null;
5748                 comp = 0;
5749               }
5750             }
5751           }
5752         });
5753       }
5754     }).start();
5755
5756   }
5757
5758   /**
5759    * Left justify the whole alignment.
5760    */
5761   @Override
5762   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5763   {
5764     AlignmentI al = viewport.getAlignment();
5765     al.justify(false);
5766     viewport.firePropertyChange("alignment", null, al);
5767   }
5768
5769   /**
5770    * Right justify the whole alignment.
5771    */
5772   @Override
5773   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5774   {
5775     AlignmentI al = viewport.getAlignment();
5776     al.justify(true);
5777     viewport.firePropertyChange("alignment", null, al);
5778   }
5779
5780   @Override
5781   public void setShowSeqFeatures(boolean b)
5782   {
5783     showSeqFeatures.setSelected(b);
5784     viewport.setShowSequenceFeatures(b);
5785   }
5786
5787   /*
5788    * (non-Javadoc)
5789    *
5790    * @see
5791    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5792    * awt.event.ActionEvent)
5793    */
5794   @Override
5795   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5796   {
5797     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5798     alignPanel.paintAlignment(true);
5799   }
5800
5801   /*
5802    * (non-Javadoc)
5803    *
5804    * @see
5805    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5806    * .ActionEvent)
5807    */
5808   @Override
5809   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5810   {
5811     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5812     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5813
5814   }
5815
5816   /*
5817    * (non-Javadoc)
5818    *
5819    * @see
5820    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5821    * .event.ActionEvent)
5822    */
5823   @Override
5824   protected void showGroupConservation_actionPerformed(ActionEvent e)
5825   {
5826     viewport.setShowGroupConservation(showGroupConservation.getState());
5827     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5828   }
5829
5830   /*
5831    * (non-Javadoc)
5832    *
5833    * @see
5834    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5835    * .event.ActionEvent)
5836    */
5837   @Override
5838   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5839   {
5840     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5841     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5842   }
5843
5844   /*
5845    * (non-Javadoc)
5846    *
5847    * @see
5848    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5849    * .event.ActionEvent)
5850    */
5851   @Override
5852   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5853   {
5854     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5855     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5856   }
5857
5858   @Override
5859   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5860   {
5861     showSequenceLogo.setState(true);
5862     viewport.setShowSequenceLogo(true);
5863     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5864     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5865   }
5866
5867   @Override
5868   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5869   {
5870     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5871   }
5872
5873   /*
5874    * (non-Javadoc)
5875    *
5876    * @see
5877    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5878    * .event.ActionEvent)
5879    */
5880   @Override
5881   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5882   {
5883     if (avc.makeGroupsFromSelection())
5884     {
5885       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5886       alignPanel.updateAnnotation();
5887       alignPanel.paintAlignment(true);
5888     }
5889   }
5890
5891   public void clearAlignmentSeqRep()
5892   {
5893     // TODO refactor alignmentseqrep to controller
5894     if (viewport.getAlignment().hasSeqrep())
5895     {
5896       viewport.getAlignment().setSeqrep(null);
5897       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5898       alignPanel.updateAnnotation();
5899       alignPanel.paintAlignment(true);
5900     }
5901   }
5902
5903   @Override
5904   protected void createGroup_actionPerformed(ActionEvent e)
5905   {
5906     if (avc.createGroup())
5907     {
5908       alignPanel.alignmentChanged();
5909     }
5910   }
5911
5912   @Override
5913   protected void unGroup_actionPerformed(ActionEvent e)
5914   {
5915     if (avc.unGroup())
5916     {
5917       alignPanel.alignmentChanged();
5918     }
5919   }
5920
5921   /**
5922    * make the given alignmentPanel the currently selected tab
5923    *
5924    * @param alignmentPanel
5925    */
5926   public void setDisplayedView(AlignmentPanel alignmentPanel)
5927   {
5928     if (!viewport.getSequenceSetId().equals(
5929             alignmentPanel.av.getSequenceSetId()))
5930     {
5931       throw new Error(
5932               MessageManager
5933                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5934     }
5935     if (tabbedPane != null
5936             && tabbedPane.getTabCount() > 0
5937             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5938                     .getSelectedIndex())
5939     {
5940       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5941     }
5942   }
5943
5944   /**
5945    * Action on selection of menu options to Show or Hide annotations.
5946    *
5947    * @param visible
5948    * @param forSequences
5949    *          update sequence-related annotations
5950    * @param forAlignment
5951    *          update non-sequence-related annotations
5952    */
5953   @Override
5954   protected void setAnnotationsVisibility(boolean visible,
5955           boolean forSequences, boolean forAlignment)
5956   {
5957     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5958             .getAlignmentAnnotation())
5959     {
5960       /*
5961        * don't display non-positional annotations on an alignment
5962        */
5963       if (aa.annotations == null)
5964       {
5965         continue;
5966       }
5967       boolean apply = (aa.sequenceRef == null && forAlignment)
5968               || (aa.sequenceRef != null && forSequences);
5969       if (apply)
5970       {
5971         aa.visible = visible;
5972       }
5973     }
5974     alignPanel.validateAnnotationDimensions(true);
5975     alignPanel.alignmentChanged();
5976   }
5977
5978   /**
5979    * Store selected annotation sort order for the view and repaint.
5980    */
5981   @Override
5982   protected void sortAnnotations_actionPerformed()
5983   {
5984     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5985     this.alignPanel.av
5986             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5987     alignPanel.paintAlignment(true);
5988   }
5989
5990   /**
5991    *
5992    * @return alignment panels in this alignment frame
5993    */
5994   public List<? extends AlignmentViewPanel> getAlignPanels()
5995   {
5996     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5997   }
5998
5999   /**
6000    * Open a new alignment window, with the cDNA associated with this (protein)
6001    * alignment, aligned as is the protein.
6002    */
6003   protected void viewAsCdna_actionPerformed()
6004   {
6005     // TODO no longer a menu action - refactor as required
6006     final AlignmentI alignment = getViewport().getAlignment();
6007     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6008     if (mappings == null)
6009     {
6010       return;
6011     }
6012     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6013     for (SequenceI aaSeq : alignment.getSequences())
6014     {
6015       for (AlignedCodonFrame acf : mappings)
6016       {
6017         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6018         if (dnaSeq != null)
6019         {
6020           /*
6021            * There is a cDNA mapping for this protein sequence - add to new
6022            * alignment. It will share the same dataset sequence as other mapped
6023            * cDNA (no new mappings need to be created).
6024            */
6025           final Sequence newSeq = new Sequence(dnaSeq);
6026           newSeq.setDatasetSequence(dnaSeq);
6027           cdnaSeqs.add(newSeq);
6028         }
6029       }
6030     }
6031     if (cdnaSeqs.size() == 0)
6032     {
6033       // show a warning dialog no mapped cDNA
6034       return;
6035     }
6036     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6037             .size()]));
6038     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6039             AlignFrame.DEFAULT_HEIGHT);
6040     cdna.alignAs(alignment);
6041     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6042             + this.title;
6043     Desktop.addInternalFrame(alignFrame, newtitle,
6044             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6045   }
6046
6047   /**
6048    * Set visibility of dna/protein complement view (available when shown in a
6049    * split frame).
6050    *
6051    * @param show
6052    */
6053   @Override
6054   protected void showComplement_actionPerformed(boolean show)
6055   {
6056     SplitContainerI sf = getSplitViewContainer();
6057     if (sf != null)
6058     {
6059       sf.setComplementVisible(this, show);
6060     }
6061   }
6062
6063   /**
6064    * Generate the reverse (optionally complemented) of the selected sequences,
6065    * and add them to the alignment
6066    */
6067   @Override
6068   protected void showReverse_actionPerformed(boolean complement)
6069   {
6070     AlignmentI al = null;
6071     try
6072     {
6073       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6074       al = dna.reverseCdna(complement);
6075       viewport.addAlignment(al, "");
6076       addHistoryItem(new EditCommand(
6077               MessageManager.getString("label.add_sequences"),
6078               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
6079               viewport.getAlignment()));
6080     } catch (Exception ex)
6081     {
6082       System.err.println(ex.getMessage());
6083       return;
6084     }
6085   }
6086
6087   /**
6088    * Try to run a script in the Groovy console, having first ensured that this
6089    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
6090    * be targeted at this alignment.
6091    */
6092   @Override
6093   protected void runGroovy_actionPerformed()
6094   {
6095     Desktop.setCurrentAlignFrame(this);
6096     groovy.ui.Console console = Desktop.getGroovyConsole();
6097     if (console != null)
6098     {
6099       try
6100       {
6101         console.runScript();
6102       } catch (Exception ex)
6103       {
6104         System.err.println((ex.toString()));
6105         JOptionPane
6106                 .showInternalMessageDialog(Desktop.desktop, MessageManager
6107                         .getString("label.couldnt_run_groovy_script"),
6108                         MessageManager
6109                                 .getString("label.groovy_support_failed"),
6110                         JOptionPane.ERROR_MESSAGE);
6111       }
6112     }
6113     else
6114     {
6115       System.err.println("Can't run Groovy script as console not found");
6116     }
6117   }
6118
6119   /**
6120    * Hides columns containing (or not containing) a specified feature, provided
6121    * that would not leave all columns hidden
6122    *
6123    * @param featureType
6124    * @param columnsContaining
6125    * @return
6126    */
6127   public boolean hideFeatureColumns(String featureType,
6128           boolean columnsContaining)
6129   {
6130     boolean notForHiding = avc.markColumnsContainingFeatures(
6131             columnsContaining, false, false, featureType);
6132     if (notForHiding)
6133     {
6134       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
6135               false, featureType))
6136       {
6137         getViewport().hideSelectedColumns();
6138         return true;
6139       }
6140     }
6141     return false;
6142   }
6143 }
6144
6145 class PrintThread extends Thread
6146 {
6147   AlignmentPanel ap;
6148
6149   public PrintThread(AlignmentPanel ap)
6150   {
6151     this.ap = ap;
6152   }
6153
6154   static PageFormat pf;
6155
6156   @Override
6157   public void run()
6158   {
6159     PrinterJob printJob = PrinterJob.getPrinterJob();
6160
6161     if (pf != null)
6162     {
6163       printJob.setPrintable(ap, pf);
6164     }
6165     else
6166     {
6167       printJob.setPrintable(ap);
6168     }
6169
6170     if (printJob.printDialog())
6171     {
6172       try
6173       {
6174         printJob.print();
6175       } catch (Exception PrintException)
6176       {
6177         PrintException.printStackTrace();
6178       }
6179     }
6180   }
6181 }