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.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  64 import jalview.io.AlignmentProperties;
  65 import jalview.io.AnnotationFile;
  66 import jalview.io.BioJsHTMLOutput;
  67 import jalview.io.DataSourceType;
  68 import jalview.io.FileFormat;
  69 import jalview.io.FileFormatI;
  70 import jalview.io.FileFormats;
  71 import jalview.io.FileLoader;
  72 import jalview.io.FormatAdapter;
  73 import jalview.io.HtmlSvgOutput;
  74 import jalview.io.IdentifyFile;
  75 import jalview.io.JPredFile;
  76 import jalview.io.JalviewFileChooser;
  77 import jalview.io.JalviewFileView;
  78 import jalview.io.JnetAnnotationMaker;
  79 import jalview.io.NewickFile;
  80 import jalview.io.TCoffeeScoreFile;
  81 import jalview.jbgui.GAlignFrame;
  82 import jalview.schemes.ColourSchemeI;
  83 import jalview.schemes.ColourSchemes;
  84 import jalview.schemes.ResidueColourScheme;
  85 import jalview.schemes.ResidueProperties;
  86 import jalview.schemes.TCoffeeColourScheme;
  87 import jalview.util.MessageManager;
  88 import jalview.viewmodel.AlignmentViewport;
  89 import jalview.ws.DBRefFetcher;
  90 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  91 import jalview.ws.jws1.Discoverer;
  92 import jalview.ws.jws2.Jws2Discoverer;
  93 import jalview.ws.jws2.jabaws2.Jws2Instance;
  94 import jalview.ws.seqfetcher.DbSourceProxy;
  95
  96 import java.awt.BorderLayout;
  97 import java.awt.Component;
  98 import java.awt.Rectangle;
  99 import java.awt.Toolkit;
 100 import java.awt.datatransfer.Clipboard;
 101 import java.awt.datatransfer.DataFlavor;
 102 import java.awt.datatransfer.StringSelection;
 103 import java.awt.datatransfer.Transferable;
 104 import java.awt.dnd.DnDConstants;
 105 import java.awt.dnd.DropTargetDragEvent;
 106 import java.awt.dnd.DropTargetDropEvent;
 107 import java.awt.dnd.DropTargetEvent;
 108 import java.awt.dnd.DropTargetListener;
 109 import java.awt.event.ActionEvent;
 110 import java.awt.event.ActionListener;
 111 import java.awt.event.FocusAdapter;
 112 import java.awt.event.FocusEvent;
 113 import java.awt.event.ItemEvent;
 114 import java.awt.event.ItemListener;
 115 import java.awt.event.KeyAdapter;
 116 import java.awt.event.KeyEvent;
 117 import java.awt.event.MouseEvent;
 118 import java.awt.print.PageFormat;
 119 import java.awt.print.PrinterJob;
 120 import java.beans.PropertyChangeEvent;
 121 import java.io.File;
 122 import java.io.FileWriter;
 123 import java.io.PrintWriter;
 124 import java.net.URL;
 125 import java.util.ArrayList;
 126 import java.util.Arrays;
 127 import java.util.Deque;
 128 import java.util.Enumeration;
 129 import java.util.Hashtable;
 130 import java.util.List;
 131 import java.util.Vector;
 132
 133 import javax.swing.JCheckBoxMenuItem;
 134 import javax.swing.JEditorPane;
 135 import javax.swing.JInternalFrame;
 136 import javax.swing.JLayeredPane;
 137 import javax.swing.JMenu;
 138 import javax.swing.JMenuItem;
 139 import javax.swing.JScrollPane;
 140 import javax.swing.SwingUtilities;
 141
 142 /**
 143  * DOCUMENT ME!
 144  *
 145  * @author $author$
 146  * @version $Revision$
 147  */
 148 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 149         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 150 {
 151
 152   public static final int DEFAULT_WIDTH = 700;
 153
 154   public static final int DEFAULT_HEIGHT = 500;
 155
 156   /*
 157    * The currently displayed panel (selected tabbed view if more than one)
 158    */
 159   public AlignmentPanel alignPanel;
 160
 161   AlignViewport viewport;
 162
 163   public AlignViewControllerI avc;
 164
 165   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 166
 167   /**
 168    * Last format used to load or save alignments in this window
 169    */
 170   FileFormatI currentFileFormat = null;
 171
 172   /**
 173    * Current filename for this alignment
 174    */
 175   String fileName = null;
 176
 177   /**
 178    * Creates a new AlignFrame object with specific width and height.
 179    *
 180    * @param al
 181    * @param width
 182    * @param height
 183    */
 184   public AlignFrame(AlignmentI al, int width, int height)
 185   {
 186     this(al, null, width, height);
 187   }
 188
 189   /**
 190    * Creates a new AlignFrame object with specific width, height and
 191    * sequenceSetId
 192    *
 193    * @param al
 194    * @param width
 195    * @param height
 196    * @param sequenceSetId
 197    */
 198   public AlignFrame(AlignmentI al, int width, int height,
 199           String sequenceSetId)
 200   {
 201     this(al, null, width, height, sequenceSetId);
 202   }
 203
 204   /**
 205    * Creates a new AlignFrame object with specific width, height and
 206    * sequenceSetId
 207    *
 208    * @param al
 209    * @param width
 210    * @param height
 211    * @param sequenceSetId
 212    * @param viewId
 213    */
 214   public AlignFrame(AlignmentI al, int width, int height,
 215           String sequenceSetId, String viewId)
 216   {
 217     this(al, null, width, height, sequenceSetId, viewId);
 218   }
 219
 220   /**
 221    * new alignment window with hidden columns
 222    *
 223    * @param al
 224    *          AlignmentI
 225    * @param hiddenColumns
 226    *          ColumnSelection or null
 227    * @param width
 228    *          Width of alignment frame
 229    * @param height
 230    *          height of frame.
 231    */
 232   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 233           int width, int height)
 234   {
 235     this(al, hiddenColumns, width, height, null);
 236   }
 237
 238   /**
 239    * Create alignment frame for al with hiddenColumns, a specific width and
 240    * height, and specific sequenceId
 241    *
 242    * @param al
 243    * @param hiddenColumns
 244    * @param width
 245    * @param height
 246    * @param sequenceSetId
 247    *          (may be null)
 248    */
 249   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 250           int width, int height, String sequenceSetId)
 251   {
 252     this(al, hiddenColumns, width, height, sequenceSetId, null);
 253   }
 254
 255   /**
 256    * Create alignment frame for al with hiddenColumns, a specific width and
 257    * height, and specific sequenceId
 258    *
 259    * @param al
 260    * @param hiddenColumns
 261    * @param width
 262    * @param height
 263    * @param sequenceSetId
 264    *          (may be null)
 265    * @param viewId
 266    *          (may be null)
 267    */
 268   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 269           int width, int height, String sequenceSetId, String viewId)
 270   {
 271     setSize(width, height);
 272
 273     if (al.getDataset() == null)
 274     {
 275       al.setDataset(null);
 276     }
 277
 278     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 279
 280     alignPanel = new AlignmentPanel(this, viewport);
 281
 282     addAlignmentPanel(alignPanel, true);
 283     init();
 284   }
 285
 286   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 287           ColumnSelection hiddenColumns, int width, int height)
 288   {
 289     setSize(width, height);
 290
 291     if (al.getDataset() == null)
 292     {
 293       al.setDataset(null);
 294     }
 295
 296     viewport = new AlignViewport(al, hiddenColumns);
 297
 298     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 299     {
 300       viewport.hideSequence(hiddenSeqs);
 301     }
 302     alignPanel = new AlignmentPanel(this, viewport);
 303     addAlignmentPanel(alignPanel, true);
 304     init();
 305   }
 306
 307   /**
 308    * Make a new AlignFrame from existing alignmentPanels
 309    *
 310    * @param ap
 311    *          AlignmentPanel
 312    * @param av
 313    *          AlignViewport
 314    */
 315   public AlignFrame(AlignmentPanel ap)
 316   {
 317     viewport = ap.av;
 318     alignPanel = ap;
 319     addAlignmentPanel(ap, false);
 320     init();
 321   }
 322
 323   /**
 324    * initalise the alignframe from the underlying viewport data and the
 325    * configurations
 326    */
 327   void init()
 328   {
 329     if (!Jalview.isHeadlessMode())
 330     {
 331       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 332     }
 333
 334     avc = new jalview.controller.AlignViewController(this, viewport,
 335             alignPanel);
 336     if (viewport.getAlignmentConservationAnnotation() == null)
 337     {
 338       // BLOSUM62Colour.setEnabled(false);
 339       conservationMenuItem.setEnabled(false);
 340       modifyConservation.setEnabled(false);
 341       // PIDColour.setEnabled(false);
 342       // abovePIDThreshold.setEnabled(false);
 343       // modifyPID.setEnabled(false);
 344     }
 345
 346     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 347             "No sort");
 348
 349     if (sortby.equals("Id"))
 350     {
 351       sortIDMenuItem_actionPerformed(null);
 352     }
 353     else if (sortby.equals("Pairwise Identity"))
 354     {
 355       sortPairwiseMenuItem_actionPerformed(null);
 356     }
 357
 358     this.alignPanel.av
 359             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 360
 361     setMenusFromViewport(viewport);
 362     buildSortByAnnotationScoresMenu();
 363     buildTreeMenu();
 364     buildColourMenu();
 365
 366     if (Desktop.desktop != null)
 367     {
 368       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 369       addServiceListeners();
 370       setGUINucleotide();
 371     }
 372
 373     if (viewport.getWrapAlignment())
 374     {
 375       wrapMenuItem_actionPerformed(null);
 376     }
 377
 378     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 379     {
 380       this.overviewMenuItem_actionPerformed(null);
 381     }
 382
 383     addKeyListener();
 384
 385     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 386     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 387     final String menuLabel = MessageManager
 388             .getString("label.copy_format_from");
 389     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 390             new ViewSetProvider()
 391             {
 392
 393               @Override
 394               public AlignmentPanel[] getAllAlignmentPanels()
 395               {
 396                 origview.clear();
 397                 origview.add(alignPanel);
 398                 // make an array of all alignment panels except for this one
 399                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 400                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 401                 aps.remove(AlignFrame.this.alignPanel);
 402                 return aps.toArray(new AlignmentPanel[aps.size()]);
 403               }
 404             }, selviews, new ItemListener()
 405             {
 406
 407               @Override
 408               public void itemStateChanged(ItemEvent e)
 409               {
 410                 if (origview.size() > 0)
 411                 {
 412                   final AlignmentPanel ap = origview.get(0);
 413
 414                   /*
 415                    * Copy the ViewStyle of the selected panel to 'this one'.
 416                    * Don't change value of 'scaleProteinAsCdna' unless copying
 417                    * from a SplitFrame.
 418                    */
 419                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 420                           .getViewStyle();
 421                   boolean fromSplitFrame = selviews.get(0)
 422                           .getAlignViewport().getCodingComplement() != null;
 423                   if (!fromSplitFrame)
 424                   {
 425                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 426                             .getViewStyle().isScaleProteinAsCdna());
 427                   }
 428                   ap.getAlignViewport().setViewStyle(vs);
 429
 430                   /*
 431                    * Also rescale ViewStyle of SplitFrame complement if there is
 432                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 433                    * the whole ViewStyle (allow cDNA protein to have different
 434                    * fonts)
 435                    */
 436                   AlignViewportI complement = ap.getAlignViewport()
 437                           .getCodingComplement();
 438                   if (complement != null && vs.isScaleProteinAsCdna())
 439                   {
 440                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 441                     ((SplitFrame) af.getSplitViewContainer())
 442                             .adjustLayout();
 443                     af.setMenusForViewport();
 444                   }
 445
 446                   ap.updateLayout();
 447                   ap.setSelected(true);
 448                   ap.alignFrame.setMenusForViewport();
 449
 450                 }
 451               }
 452             });
 453     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 454             .indexOf("devel") > -1
 455             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 456                     .indexOf("test") > -1)
 457     {
 458       formatMenu.add(vsel);
 459     }
 460     addFocusListener(new FocusAdapter()
 461     {
 462       @Override
 463       public void focusGained(FocusEvent e)
 464       {
 465         Jalview.setCurrentAlignFrame(AlignFrame.this);
 466       }
 467     });
 468
 469   }
 470
 471   /**
 472    * Change the filename and format for the alignment, and enable the 'reload'
 473    * button functionality.
 474    *
 475    * @param file
 476    *          valid filename
 477    * @param format
 478    *          format of file
 479    */
 480   public void setFileName(String file, FileFormatI format)
 481   {
 482     fileName = file;
 483     setFileFormat(format);
 484     reload.setEnabled(true);
 485   }
 486
 487   /**
 488    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 489    * events
 490    */
 491   void addKeyListener()
 492   {
 493     addKeyListener(new KeyAdapter()
 494     {
 495       @Override
 496       public void keyPressed(KeyEvent evt)
 497       {
 498         if (viewport.cursorMode
 499                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 500                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 501                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 502                 && Character.isDigit(evt.getKeyChar()))
 503         {
 504           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 505         }
 506
 507         switch (evt.getKeyCode())
 508         {
 509
 510         case 27: // escape key
 511           deselectAllSequenceMenuItem_actionPerformed(null);
 512
 513           break;
 514
 515         case KeyEvent.VK_DOWN:
 516           if (evt.isAltDown() || !viewport.cursorMode)
 517           {
 518             moveSelectedSequences(false);
 519           }
 520           if (viewport.cursorMode)
 521           {
 522             alignPanel.getSeqPanel().moveCursor(0, 1);
 523           }
 524           break;
 525
 526         case KeyEvent.VK_UP:
 527           if (evt.isAltDown() || !viewport.cursorMode)
 528           {
 529             moveSelectedSequences(true);
 530           }
 531           if (viewport.cursorMode)
 532           {
 533             alignPanel.getSeqPanel().moveCursor(0, -1);
 534           }
 535
 536           break;
 537
 538         case KeyEvent.VK_LEFT:
 539           if (evt.isAltDown() || !viewport.cursorMode)
 540           {
 541             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 542           }
 543           else
 544           {
 545             alignPanel.getSeqPanel().moveCursor(-1, 0);
 546           }
 547
 548           break;
 549
 550         case KeyEvent.VK_RIGHT:
 551           if (evt.isAltDown() || !viewport.cursorMode)
 552           {
 553             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 554           }
 555           else
 556           {
 557             alignPanel.getSeqPanel().moveCursor(1, 0);
 558           }
 559           break;
 560
 561         case KeyEvent.VK_SPACE:
 562           if (viewport.cursorMode)
 563           {
 564             alignPanel.getSeqPanel().insertGapAtCursor(
 565                     evt.isControlDown() || evt.isShiftDown()
 566                             || evt.isAltDown());
 567           }
 568           break;
 569
 570         // case KeyEvent.VK_A:
 571         // if (viewport.cursorMode)
 572         // {
 573         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 574         // //System.out.println("A");
 575         // }
 576         // break;
 577         /*
 578          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 579          * System.out.println("closing bracket"); } break;
 580          */
 581         case KeyEvent.VK_DELETE:
 582         case KeyEvent.VK_BACK_SPACE:
 583           if (!viewport.cursorMode)
 584           {
 585             cut_actionPerformed(null);
 586           }
 587           else
 588           {
 589             alignPanel.getSeqPanel().deleteGapAtCursor(
 590                     evt.isControlDown() || evt.isShiftDown()
 591                             || evt.isAltDown());
 592           }
 593
 594           break;
 595
 596         case KeyEvent.VK_S:
 597           if (viewport.cursorMode)
 598           {
 599             alignPanel.getSeqPanel().setCursorRow();
 600           }
 601           break;
 602         case KeyEvent.VK_C:
 603           if (viewport.cursorMode && !evt.isControlDown())
 604           {
 605             alignPanel.getSeqPanel().setCursorColumn();
 606           }
 607           break;
 608         case KeyEvent.VK_P:
 609           if (viewport.cursorMode)
 610           {
 611             alignPanel.getSeqPanel().setCursorPosition();
 612           }
 613           break;
 614
 615         case KeyEvent.VK_ENTER:
 616         case KeyEvent.VK_COMMA:
 617           if (viewport.cursorMode)
 618           {
 619             alignPanel.getSeqPanel().setCursorRowAndColumn();
 620           }
 621           break;
 622
 623         case KeyEvent.VK_Q:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 627           }
 628           break;
 629         case KeyEvent.VK_M:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 633           }
 634           break;
 635
 636         case KeyEvent.VK_F2:
 637           viewport.cursorMode = !viewport.cursorMode;
 638           statusBar.setText(MessageManager.formatMessage(
 639                   "label.keyboard_editing_mode",
 640                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 641           if (viewport.cursorMode)
 642           {
 643             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 644             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 645           }
 646           alignPanel.getSeqPanel().seqCanvas.repaint();
 647           break;
 648
 649         case KeyEvent.VK_F1:
 650           try
 651           {
 652             Help.showHelpWindow();
 653           } catch (Exception ex)
 654           {
 655             ex.printStackTrace();
 656           }
 657           break;
 658         case KeyEvent.VK_H:
 659         {
 660           boolean toggleSeqs = !evt.isControlDown();
 661           boolean toggleCols = !evt.isShiftDown();
 662           toggleHiddenRegions(toggleSeqs, toggleCols);
 663           break;
 664         }
 665         case KeyEvent.VK_B:
 666         {
 667           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 668           boolean modifyExisting = true; // always modify, don't clear
 669                                          // evt.isShiftDown();
 670           boolean invertHighlighted = evt.isAltDown();
 671           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 672                   toggleSel);
 673           break;
 674         }
 675         case KeyEvent.VK_PAGE_UP:
 676           if (viewport.getWrapAlignment())
 677           {
 678             alignPanel.scrollUp(true);
 679           }
 680           else
 681           {
 682             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 683                     - viewport.endSeq + viewport.startSeq);
 684           }
 685           break;
 686         case KeyEvent.VK_PAGE_DOWN:
 687           if (viewport.getWrapAlignment())
 688           {
 689             alignPanel.scrollUp(false);
 690           }
 691           else
 692           {
 693             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 694                     + viewport.endSeq - viewport.startSeq);
 695           }
 696           break;
 697         }
 698       }
 699
 700       @Override
 701       public void keyReleased(KeyEvent evt)
 702       {
 703         switch (evt.getKeyCode())
 704         {
 705         case KeyEvent.VK_LEFT:
 706           if (evt.isAltDown() || !viewport.cursorMode)
 707           {
 708             viewport.firePropertyChange("alignment", null, viewport
 709                     .getAlignment().getSequences());
 710           }
 711           break;
 712
 713         case KeyEvent.VK_RIGHT:
 714           if (evt.isAltDown() || !viewport.cursorMode)
 715           {
 716             viewport.firePropertyChange("alignment", null, viewport
 717                     .getAlignment().getSequences());
 718           }
 719           break;
 720         }
 721       }
 722     });
 723   }
 724
 725   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 726   {
 727     ap.alignFrame = this;
 728     avc = new jalview.controller.AlignViewController(this, viewport,
 729             alignPanel);
 730
 731     alignPanels.add(ap);
 732
 733     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 734
 735     int aSize = alignPanels.size();
 736
 737     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 738
 739     if (aSize == 1 && ap.av.viewName == null)
 740     {
 741       this.getContentPane().add(ap, BorderLayout.CENTER);
 742     }
 743     else
 744     {
 745       if (aSize == 2)
 746       {
 747         setInitialTabVisible();
 748       }
 749
 750       expandViews.setEnabled(true);
 751       gatherViews.setEnabled(true);
 752       tabbedPane.addTab(ap.av.viewName, ap);
 753
 754       ap.setVisible(false);
 755     }
 756
 757     if (newPanel)
 758     {
 759       if (ap.av.isPadGaps())
 760       {
 761         ap.av.getAlignment().padGaps();
 762       }
 763       ap.av.updateConservation(ap);
 764       ap.av.updateConsensus(ap);
 765       ap.av.updateStrucConsensus(ap);
 766     }
 767   }
 768
 769   public void setInitialTabVisible()
 770   {
 771     expandViews.setEnabled(true);
 772     gatherViews.setEnabled(true);
 773     tabbedPane.setVisible(true);
 774     AlignmentPanel first = alignPanels.get(0);
 775     tabbedPane.addTab(first.av.viewName, first);
 776     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 777   }
 778
 779   public AlignViewport getViewport()
 780   {
 781     return viewport;
 782   }
 783
 784   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 785   private void addServiceListeners()
 786   {
 787     final java.beans.PropertyChangeListener thisListener;
 788     Desktop.instance.addJalviewPropertyChangeListener("services",
 789             thisListener = new java.beans.PropertyChangeListener()
 790             {
 791               @Override
 792               public void propertyChange(PropertyChangeEvent evt)
 793               {
 794                 // // System.out.println("Discoverer property change.");
 795                 // if (evt.getPropertyName().equals("services"))
 796                 {
 797                   SwingUtilities.invokeLater(new Runnable()
 798                   {
 799
 800                     @Override
 801                     public void run()
 802                     {
 803                       System.err
 804                               .println("Rebuild WS Menu for service change");
 805                       BuildWebServiceMenu();
 806                     }
 807
 808                   });
 809                 }
 810               }
 811             });
 812     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 813     {
 814       @Override
 815       public void internalFrameClosed(
 816               javax.swing.event.InternalFrameEvent evt)
 817       {
 818         // System.out.println("deregistering discoverer listener");
 819         Desktop.instance.removeJalviewPropertyChangeListener("services",
 820                 thisListener);
 821         closeMenuItem_actionPerformed(true);
 822       };
 823     });
 824     // Finally, build the menu once to get current service state
 825     new Thread(new Runnable()
 826     {
 827       @Override
 828       public void run()
 829       {
 830         BuildWebServiceMenu();
 831       }
 832     }).start();
 833   }
 834
 835   /**
 836    * Configure menu items that vary according to whether the alignment is
 837    * nucleotide or protein
 838    */
 839   public void setGUINucleotide()
 840   {
 841     AlignmentI al = getViewport().getAlignment();
 842     boolean nucleotide = al.isNucleotide();
 843
 844     showTranslation.setVisible(nucleotide);
 845     showReverse.setVisible(nucleotide);
 846     showReverseComplement.setVisible(nucleotide);
 847     conservationMenuItem.setEnabled(!nucleotide);
 848     modifyConservation.setEnabled(!nucleotide
 849             && conservationMenuItem.isSelected());
 850     showGroupConservation.setEnabled(!nucleotide);
 851
 852     showComplementMenuItem.setText(nucleotide ? MessageManager
 853             .getString("label.protein") : MessageManager
 854             .getString("label.nucleotide"));
 855   }
 856
 857   /**
 858    * set up menus for the current viewport. This may be called after any
 859    * operation that affects the data in the current view (selection changed,
 860    * etc) to update the menus to reflect the new state.
 861    */
 862   @Override
 863   public void setMenusForViewport()
 864   {
 865     setMenusFromViewport(viewport);
 866   }
 867
 868   /**
 869    * Need to call this method when tabs are selected for multiple views, or when
 870    * loading from Jalview2XML.java
 871    *
 872    * @param av
 873    *          AlignViewport
 874    */
 875   void setMenusFromViewport(AlignViewport av)
 876   {
 877     padGapsMenuitem.setSelected(av.isPadGaps());
 878     colourTextMenuItem.setSelected(av.isShowColourText());
 879     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 880     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 881     conservationMenuItem.setSelected(av.getConservationSelected());
 882     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 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     ColourMenuHelper.setColourSelected(colourMenu,
 909             av.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
 920     showProducts.setEnabled(canShowProducts());
 921     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 922
 923     updateEditMenuBar();
 924   }
 925
 926   /**
 927    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 928    *
 929    * @param b
 930    */
 931   public void setGroovyEnabled(boolean b)
 932   {
 933     runGroovy.setEnabled(b);
 934   }
 935
 936   private IProgressIndicator progressBar;
 937
 938   /*
 939    * (non-Javadoc)
 940    *
 941    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 942    */
 943   @Override
 944   public void setProgressBar(String message, long id)
 945   {
 946     progressBar.setProgressBar(message, id);
 947   }
 948
 949   @Override
 950   public void registerHandler(final long id,
 951           final IProgressIndicatorHandler handler)
 952   {
 953     progressBar.registerHandler(id, handler);
 954   }
 955
 956   /**
 957    *
 958    * @return true if any progress bars are still active
 959    */
 960   @Override
 961   public boolean operationInProgress()
 962   {
 963     return progressBar.operationInProgress();
 964   }
 965
 966   @Override
 967   public void setStatus(String text)
 968   {
 969     statusBar.setText(text);
 970   }
 971
 972   /*
 973    * Added so Castor Mapping file can obtain Jalview Version
 974    */
 975   public String getVersion()
 976   {
 977     return jalview.bin.Cache.getProperty("VERSION");
 978   }
 979
 980   public FeatureRenderer getFeatureRenderer()
 981   {
 982     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 983   }
 984
 985   @Override
 986   public void fetchSequence_actionPerformed(ActionEvent e)
 987   {
 988     new jalview.gui.SequenceFetcher(this);
 989   }
 990
 991   @Override
 992   public void addFromFile_actionPerformed(ActionEvent e)
 993   {
 994     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 995   }
 996
 997   @Override
 998   public void reload_actionPerformed(ActionEvent e)
 999   {
1000     if (fileName != null)
1001     {
1002       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003       // originating file's format
1004       // TODO: work out how to recover feature settings for correct view(s) when
1005       // file is reloaded.
1006       if (FileFormat.Jalview.equals(currentFileFormat))
1007       {
1008         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009         for (int i = 0; i < frames.length; i++)
1010         {
1011           if (frames[i] instanceof AlignFrame && frames[i] != this
1012                   && ((AlignFrame) frames[i]).fileName != null
1013                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1014           {
1015             try
1016             {
1017               frames[i].setSelected(true);
1018               Desktop.instance.closeAssociatedWindows();
1019             } catch (java.beans.PropertyVetoException ex)
1020             {
1021             }
1022           }
1023
1024         }
1025         Desktop.instance.closeAssociatedWindows();
1026
1027         FileLoader loader = new FileLoader();
1028         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1029                 : DataSourceType.FILE;
1030         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1031       }
1032       else
1033       {
1034         Rectangle bounds = this.getBounds();
1035
1036         FileLoader loader = new FileLoader();
1037         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1038                 : DataSourceType.FILE;
1039         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1040                 protocol, currentFileFormat);
1041
1042         newframe.setBounds(bounds);
1043         if (featureSettings != null && featureSettings.isShowing())
1044         {
1045           final Rectangle fspos = featureSettings.frame.getBounds();
1046           // TODO: need a 'show feature settings' function that takes bounds -
1047           // need to refactor Desktop.addFrame
1048           newframe.featureSettings_actionPerformed(null);
1049           final FeatureSettings nfs = newframe.featureSettings;
1050           SwingUtilities.invokeLater(new Runnable()
1051           {
1052             @Override
1053             public void run()
1054             {
1055               nfs.frame.setBounds(fspos);
1056             }
1057           });
1058           this.featureSettings.close();
1059           this.featureSettings = null;
1060         }
1061         this.closeMenuItem_actionPerformed(true);
1062       }
1063     }
1064   }
1065
1066   @Override
1067   public void addFromText_actionPerformed(ActionEvent e)
1068   {
1069     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1070             .getAlignPanel());
1071   }
1072
1073   @Override
1074   public void addFromURL_actionPerformed(ActionEvent e)
1075   {
1076     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1077   }
1078
1079   @Override
1080   public void save_actionPerformed(ActionEvent e)
1081   {
1082     if (fileName == null || (currentFileFormat == null)
1083             || fileName.startsWith("http"))
1084     {
1085       saveAs_actionPerformed(null);
1086     }
1087     else
1088     {
1089       saveAlignment(fileName, currentFileFormat);
1090     }
1091   }
1092
1093   /**
1094    * DOCUMENT ME!
1095    *
1096    * @param e
1097    *          DOCUMENT ME!
1098    */
1099   @Override
1100   public void saveAs_actionPerformed(ActionEvent e)
1101   {
1102     String format = currentFileFormat == null ? null : currentFileFormat
1103             .getName();
1104     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1105             Cache.getProperty("LAST_DIRECTORY"), format);
1106
1107     chooser.setFileView(new JalviewFileView());
1108     chooser.setDialogTitle(MessageManager
1109             .getString("label.save_alignment_to_file"));
1110     chooser.setToolTipText(MessageManager.getString("action.save"));
1111
1112     int value = chooser.showSaveDialog(this);
1113
1114     if (value == JalviewFileChooser.APPROVE_OPTION)
1115     {
1116       currentFileFormat = chooser.getSelectedFormat();
1117       while (currentFileFormat == null)
1118       {
1119         JvOptionPane
1120                 .showInternalMessageDialog(
1121                         Desktop.desktop,
1122                         MessageManager
1123                                 .getString("label.select_file_format_before_saving"),
1124                         MessageManager
1125                                 .getString("label.file_format_not_specified"),
1126                         JvOptionPane.WARNING_MESSAGE);
1127         currentFileFormat = chooser.getSelectedFormat();
1128         value = chooser.showSaveDialog(this);
1129         if (value != JalviewFileChooser.APPROVE_OPTION)
1130         {
1131           return;
1132         }
1133       }
1134
1135       fileName = chooser.getSelectedFile().getPath();
1136
1137       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1138
1139       Cache.setProperty("LAST_DIRECTORY", fileName);
1140       saveAlignment(fileName, currentFileFormat);
1141     }
1142   }
1143
1144   public boolean saveAlignment(String file, FileFormatI format)
1145   {
1146     boolean success = true;
1147
1148     if (FileFormat.Jalview.equals(format))
1149     {
1150       String shortName = title;
1151
1152       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1153       {
1154         shortName = shortName.substring(shortName
1155                 .lastIndexOf(java.io.File.separatorChar) + 1);
1156       }
1157
1158       success = new Jalview2XML().saveAlignment(this, file, shortName);
1159
1160       statusBar.setText(MessageManager.formatMessage(
1161               "label.successfully_saved_to_file_in_format", new Object[] {
1162                   fileName, format }));
1163
1164     }
1165     else
1166     {
1167       AlignmentExportData exportData = getAlignmentForExport(format,
1168               viewport, null);
1169       if (exportData.getSettings().isCancelled())
1170       {
1171         return false;
1172       }
1173       FormatAdapter f = new FormatAdapter(alignPanel,
1174               exportData.getSettings());
1175       String output = f.formatSequences(
1176               format,
1177               exportData.getAlignment(), // class cast exceptions will
1178               // occur in the distant future
1179               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180               f.getCacheSuffixDefault(format),
1181               viewport.getColumnSelection());
1182
1183       if (output == null)
1184       {
1185         success = false;
1186       }
1187       else
1188       {
1189         try
1190         {
1191           PrintWriter out = new PrintWriter(new FileWriter(file));
1192
1193           out.print(output);
1194           out.close();
1195           this.setTitle(file);
1196           statusBar.setText(MessageManager.formatMessage(
1197                   "label.successfully_saved_to_file_in_format",
1198                   new Object[] { fileName, format.getName() }));
1199         } catch (Exception ex)
1200         {
1201           success = false;
1202           ex.printStackTrace();
1203         }
1204       }
1205     }
1206
1207     if (!success)
1208     {
1209       JvOptionPane.showInternalMessageDialog(this, MessageManager
1210               .formatMessage("label.couldnt_save_file",
1211                       new Object[] { fileName }), MessageManager
1212               .getString("label.error_saving_file"),
1213               JvOptionPane.WARNING_MESSAGE);
1214     }
1215
1216     return success;
1217   }
1218
1219   private void warningMessage(String warning, String title)
1220   {
1221     if (new jalview.util.Platform().isHeadless())
1222     {
1223       System.err.println("Warning: " + title + "\nWarning: " + warning);
1224
1225     }
1226     else
1227     {
1228       JvOptionPane.showInternalMessageDialog(this, warning, title,
1229               JvOptionPane.WARNING_MESSAGE);
1230     }
1231     return;
1232   }
1233
1234   /**
1235    * DOCUMENT ME!
1236    *
1237    * @param e
1238    *          DOCUMENT ME!
1239    */
1240   @Override
1241   protected void outputText_actionPerformed(ActionEvent e)
1242   {
1243     FileFormatI fileFormat = FileFormats.getInstance().forName(
1244             e.getActionCommand());
1245     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1246             viewport, null);
1247     if (exportData.getSettings().isCancelled())
1248     {
1249       return;
1250     }
1251     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252     cap.setForInput(null);
1253     try
1254     {
1255       FileFormatI format = fileFormat;
1256       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1257               .formatSequences(format,
1258                       exportData.getAlignment(),
1259                       exportData.getOmitHidden(),
1260                       exportData.getStartEndPostions(),
1261                       viewport.getColumnSelection()));
1262       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1263               "label.alignment_output_command",
1264               new Object[] { e.getActionCommand() }), 600, 500);
1265     } catch (OutOfMemoryError oom)
1266     {
1267       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1268       cap.dispose();
1269     }
1270
1271   }
1272
1273   public static AlignmentExportData getAlignmentForExport(
1274           FileFormatI format, AlignViewportI viewport,
1275           AlignExportSettingI exportSettings)
1276   {
1277     AlignmentI alignmentToExport = null;
1278     AlignExportSettingI settings = exportSettings;
1279     String[] omitHidden = null;
1280
1281     HiddenSequences hiddenSeqs = viewport.getAlignment()
1282             .getHiddenSequences();
1283
1284     alignmentToExport = viewport.getAlignment();
1285
1286     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1287     if (settings == null)
1288     {
1289       settings = new AlignExportSettings(hasHiddenSeqs,
1290               viewport.hasHiddenColumns(), format);
1291     }
1292     // settings.isExportAnnotations();
1293
1294     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1295     {
1296       omitHidden = viewport.getViewAsString(false,
1297               settings.isExportHiddenSequences());
1298     }
1299
1300     int[] alignmentStartEnd = new int[2];
1301     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1302     {
1303       alignmentToExport = hiddenSeqs.getFullAlignment();
1304     }
1305     else
1306     {
1307       alignmentToExport = viewport.getAlignment();
1308     }
1309     alignmentStartEnd = alignmentToExport
1310             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1311                     .getHiddenColumns());
1312     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1313             omitHidden, alignmentStartEnd, settings);
1314     return ed;
1315   }
1316
1317   /**
1318    * DOCUMENT ME!
1319    *
1320    * @param e
1321    *          DOCUMENT ME!
1322    */
1323   @Override
1324   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1325   {
1326     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1327     htmlSVG.exportHTML(null);
1328   }
1329
1330   @Override
1331   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1332   {
1333     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1334     bjs.exportHTML(null);
1335   }
1336
1337   public void createImageMap(File file, String image)
1338   {
1339     alignPanel.makePNGImageMap(file, image);
1340   }
1341
1342   /**
1343    * DOCUMENT ME!
1344    *
1345    * @param e
1346    *          DOCUMENT ME!
1347    */
1348   @Override
1349   public void createPNG(File f)
1350   {
1351     alignPanel.makePNG(f);
1352   }
1353
1354   /**
1355    * DOCUMENT ME!
1356    *
1357    * @param e
1358    *          DOCUMENT ME!
1359    */
1360   @Override
1361   public void createEPS(File f)
1362   {
1363     alignPanel.makeEPS(f);
1364   }
1365
1366   @Override
1367   public void createSVG(File f)
1368   {
1369     alignPanel.makeSVG(f);
1370   }
1371
1372   @Override
1373   public void pageSetup_actionPerformed(ActionEvent e)
1374   {
1375     PrinterJob printJob = PrinterJob.getPrinterJob();
1376     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1377   }
1378
1379   /**
1380    * DOCUMENT ME!
1381    *
1382    * @param e
1383    *          DOCUMENT ME!
1384    */
1385   @Override
1386   public void printMenuItem_actionPerformed(ActionEvent e)
1387   {
1388     // Putting in a thread avoids Swing painting problems
1389     PrintThread thread = new PrintThread(alignPanel);
1390     thread.start();
1391   }
1392
1393   @Override
1394   public void exportFeatures_actionPerformed(ActionEvent e)
1395   {
1396     new AnnotationExporter().exportFeatures(alignPanel);
1397   }
1398
1399   @Override
1400   public void exportAnnotations_actionPerformed(ActionEvent e)
1401   {
1402     new AnnotationExporter().exportAnnotations(alignPanel);
1403   }
1404
1405   @Override
1406   public void associatedData_actionPerformed(ActionEvent e)
1407   {
1408     // Pick the tree file
1409     JalviewFileChooser chooser = new JalviewFileChooser(
1410             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1411     chooser.setFileView(new JalviewFileView());
1412     chooser.setDialogTitle(MessageManager
1413             .getString("label.load_jalview_annotations"));
1414     chooser.setToolTipText(MessageManager
1415             .getString("label.load_jalview_annotations"));
1416
1417     int value = chooser.showOpenDialog(null);
1418
1419     if (value == JalviewFileChooser.APPROVE_OPTION)
1420     {
1421       String choice = chooser.getSelectedFile().getPath();
1422       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1423       loadJalviewDataFile(choice, null, null, null);
1424     }
1425
1426   }
1427
1428   /**
1429    * Close the current view or all views in the alignment frame. If the frame
1430    * only contains one view then the alignment will be removed from memory.
1431    *
1432    * @param closeAllTabs
1433    */
1434   @Override
1435   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1436   {
1437     if (alignPanels != null && alignPanels.size() < 2)
1438     {
1439       closeAllTabs = true;
1440     }
1441
1442     try
1443     {
1444       if (alignPanels != null)
1445       {
1446         if (closeAllTabs)
1447         {
1448           if (this.isClosed())
1449           {
1450             // really close all the windows - otherwise wait till
1451             // setClosed(true) is called
1452             for (int i = 0; i < alignPanels.size(); i++)
1453             {
1454               AlignmentPanel ap = alignPanels.get(i);
1455               ap.closePanel();
1456             }
1457           }
1458         }
1459         else
1460         {
1461           closeView(alignPanel);
1462         }
1463       }
1464
1465       if (closeAllTabs)
1466       {
1467         /*
1468          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1469          * be called recursively, with the frame now in 'closed' state
1470          */
1471         this.setClosed(true);
1472       }
1473     } catch (Exception ex)
1474     {
1475       ex.printStackTrace();
1476     }
1477   }
1478
1479   /**
1480    * Close the specified panel and close up tabs appropriately.
1481    *
1482    * @param panelToClose
1483    */
1484   public void closeView(AlignmentPanel panelToClose)
1485   {
1486     int index = tabbedPane.getSelectedIndex();
1487     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1488     alignPanels.remove(panelToClose);
1489     panelToClose.closePanel();
1490     panelToClose = null;
1491
1492     tabbedPane.removeTabAt(closedindex);
1493     tabbedPane.validate();
1494
1495     if (index > closedindex || index == tabbedPane.getTabCount())
1496     {
1497       // modify currently selected tab index if necessary.
1498       index--;
1499     }
1500
1501     this.tabSelectionChanged(index);
1502   }
1503
1504   /**
1505    * DOCUMENT ME!
1506    */
1507   void updateEditMenuBar()
1508   {
1509
1510     if (viewport.getHistoryList().size() > 0)
1511     {
1512       undoMenuItem.setEnabled(true);
1513       CommandI command = viewport.getHistoryList().peek();
1514       undoMenuItem.setText(MessageManager.formatMessage(
1515               "label.undo_command",
1516               new Object[] { command.getDescription() }));
1517     }
1518     else
1519     {
1520       undoMenuItem.setEnabled(false);
1521       undoMenuItem.setText(MessageManager.getString("action.undo"));
1522     }
1523
1524     if (viewport.getRedoList().size() > 0)
1525     {
1526       redoMenuItem.setEnabled(true);
1527
1528       CommandI command = viewport.getRedoList().peek();
1529       redoMenuItem.setText(MessageManager.formatMessage(
1530               "label.redo_command",
1531               new Object[] { command.getDescription() }));
1532     }
1533     else
1534     {
1535       redoMenuItem.setEnabled(false);
1536       redoMenuItem.setText(MessageManager.getString("action.redo"));
1537     }
1538   }
1539
1540   @Override
1541   public void addHistoryItem(CommandI command)
1542   {
1543     if (command.getSize() > 0)
1544     {
1545       viewport.addToHistoryList(command);
1546       viewport.clearRedoList();
1547       updateEditMenuBar();
1548       viewport.updateHiddenColumns();
1549       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1550       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1551       // viewport.getColumnSelection()
1552       // .getHiddenColumns().size() > 0);
1553     }
1554   }
1555
1556   /**
1557    *
1558    * @return alignment objects for all views
1559    */
1560   AlignmentI[] getViewAlignments()
1561   {
1562     if (alignPanels != null)
1563     {
1564       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1565       int i = 0;
1566       for (AlignmentPanel ap : alignPanels)
1567       {
1568         als[i++] = ap.av.getAlignment();
1569       }
1570       return als;
1571     }
1572     if (viewport != null)
1573     {
1574       return new AlignmentI[] { viewport.getAlignment() };
1575     }
1576     return null;
1577   }
1578
1579   /**
1580    * DOCUMENT ME!
1581    *
1582    * @param e
1583    *          DOCUMENT ME!
1584    */
1585   @Override
1586   protected void undoMenuItem_actionPerformed(ActionEvent e)
1587   {
1588     if (viewport.getHistoryList().isEmpty())
1589     {
1590       return;
1591     }
1592     CommandI command = viewport.getHistoryList().pop();
1593     viewport.addToRedoList(command);
1594     command.undoCommand(getViewAlignments());
1595
1596     AlignmentViewport originalSource = getOriginatingSource(command);
1597     updateEditMenuBar();
1598
1599     if (originalSource != null)
1600     {
1601       if (originalSource != viewport)
1602       {
1603         Cache.log
1604                 .warn("Implementation worry: mismatch of viewport origin for undo");
1605       }
1606       originalSource.updateHiddenColumns();
1607       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1608       // null
1609       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1610       // viewport.getColumnSelection()
1611       // .getHiddenColumns().size() > 0);
1612       originalSource.firePropertyChange("alignment", null, originalSource
1613               .getAlignment().getSequences());
1614     }
1615   }
1616
1617   /**
1618    * DOCUMENT ME!
1619    *
1620    * @param e
1621    *          DOCUMENT ME!
1622    */
1623   @Override
1624   protected void redoMenuItem_actionPerformed(ActionEvent e)
1625   {
1626     if (viewport.getRedoList().size() < 1)
1627     {
1628       return;
1629     }
1630
1631     CommandI command = viewport.getRedoList().pop();
1632     viewport.addToHistoryList(command);
1633     command.doCommand(getViewAlignments());
1634
1635     AlignmentViewport originalSource = getOriginatingSource(command);
1636     updateEditMenuBar();
1637
1638     if (originalSource != null)
1639     {
1640
1641       if (originalSource != viewport)
1642       {
1643         Cache.log
1644                 .warn("Implementation worry: mismatch of viewport origin for redo");
1645       }
1646       originalSource.updateHiddenColumns();
1647       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1648       // null
1649       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1650       // viewport.getColumnSelection()
1651       // .getHiddenColumns().size() > 0);
1652       originalSource.firePropertyChange("alignment", null, originalSource
1653               .getAlignment().getSequences());
1654     }
1655   }
1656
1657   AlignmentViewport getOriginatingSource(CommandI command)
1658   {
1659     AlignmentViewport originalSource = null;
1660     // For sequence removal and addition, we need to fire
1661     // the property change event FROM the viewport where the
1662     // original alignment was altered
1663     AlignmentI al = null;
1664     if (command instanceof EditCommand)
1665     {
1666       EditCommand editCommand = (EditCommand) command;
1667       al = editCommand.getAlignment();
1668       List<Component> comps = PaintRefresher.components.get(viewport
1669               .getSequenceSetId());
1670
1671       for (Component comp : comps)
1672       {
1673         if (comp instanceof AlignmentPanel)
1674         {
1675           if (al == ((AlignmentPanel) comp).av.getAlignment())
1676           {
1677             originalSource = ((AlignmentPanel) comp).av;
1678             break;
1679           }
1680         }
1681       }
1682     }
1683
1684     if (originalSource == null)
1685     {
1686       // The original view is closed, we must validate
1687       // the current view against the closed view first
1688       if (al != null)
1689       {
1690         PaintRefresher.validateSequences(al, viewport.getAlignment());
1691       }
1692
1693       originalSource = viewport;
1694     }
1695
1696     return originalSource;
1697   }
1698
1699   /**
1700    * DOCUMENT ME!
1701    *
1702    * @param up
1703    *          DOCUMENT ME!
1704    */
1705   public void moveSelectedSequences(boolean up)
1706   {
1707     SequenceGroup sg = viewport.getSelectionGroup();
1708
1709     if (sg == null)
1710     {
1711       return;
1712     }
1713     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1714             viewport.getHiddenRepSequences(), up);
1715     alignPanel.paintAlignment(true);
1716   }
1717
1718   synchronized void slideSequences(boolean right, int size)
1719   {
1720     List<SequenceI> sg = new ArrayList<SequenceI>();
1721     if (viewport.cursorMode)
1722     {
1723       sg.add(viewport.getAlignment().getSequenceAt(
1724               alignPanel.getSeqPanel().seqCanvas.cursorY));
1725     }
1726     else if (viewport.getSelectionGroup() != null
1727             && viewport.getSelectionGroup().getSize() != viewport
1728                     .getAlignment().getHeight())
1729     {
1730       sg = viewport.getSelectionGroup().getSequences(
1731               viewport.getHiddenRepSequences());
1732     }
1733
1734     if (sg.size() < 1)
1735     {
1736       return;
1737     }
1738
1739     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1740
1741     for (SequenceI seq : viewport.getAlignment().getSequences())
1742     {
1743       if (!sg.contains(seq))
1744       {
1745         invertGroup.add(seq);
1746       }
1747     }
1748
1749     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1750
1751     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1752     for (int i = 0; i < invertGroup.size(); i++)
1753     {
1754       seqs2[i] = invertGroup.get(i);
1755     }
1756
1757     SlideSequencesCommand ssc;
1758     if (right)
1759     {
1760       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1761               size, viewport.getGapCharacter());
1762     }
1763     else
1764     {
1765       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1766               size, viewport.getGapCharacter());
1767     }
1768
1769     int groupAdjustment = 0;
1770     if (ssc.getGapsInsertedBegin() && right)
1771     {
1772       if (viewport.cursorMode)
1773       {
1774         alignPanel.getSeqPanel().moveCursor(size, 0);
1775       }
1776       else
1777       {
1778         groupAdjustment = size;
1779       }
1780     }
1781     else if (!ssc.getGapsInsertedBegin() && !right)
1782     {
1783       if (viewport.cursorMode)
1784       {
1785         alignPanel.getSeqPanel().moveCursor(-size, 0);
1786       }
1787       else
1788       {
1789         groupAdjustment = -size;
1790       }
1791     }
1792
1793     if (groupAdjustment != 0)
1794     {
1795       viewport.getSelectionGroup().setStartRes(
1796               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1797       viewport.getSelectionGroup().setEndRes(
1798               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1799     }
1800
1801     /*
1802      * just extend the last slide command if compatible; but not if in
1803      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1804      */
1805     boolean appendHistoryItem = false;
1806     Deque<CommandI> historyList = viewport.getHistoryList();
1807     boolean inSplitFrame = getSplitViewContainer() != null;
1808     if (!inSplitFrame && historyList != null && historyList.size() > 0
1809             && historyList.peek() instanceof SlideSequencesCommand)
1810     {
1811       appendHistoryItem = ssc
1812               .appendSlideCommand((SlideSequencesCommand) historyList
1813                       .peek());
1814     }
1815
1816     if (!appendHistoryItem)
1817     {
1818       addHistoryItem(ssc);
1819     }
1820
1821     repaint();
1822   }
1823
1824   /**
1825    * DOCUMENT ME!
1826    *
1827    * @param e
1828    *          DOCUMENT ME!
1829    */
1830   @Override
1831   protected void copy_actionPerformed(ActionEvent e)
1832   {
1833     System.gc();
1834     if (viewport.getSelectionGroup() == null)
1835     {
1836       return;
1837     }
1838     // TODO: preserve the ordering of displayed alignment annotation in any
1839     // internal paste (particularly sequence associated annotation)
1840     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1841     String[] omitHidden = null;
1842
1843     if (viewport.hasHiddenColumns())
1844     {
1845       omitHidden = viewport.getViewAsString(true);
1846     }
1847
1848     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1849             seqs,
1850             omitHidden, null);
1851
1852     StringSelection ss = new StringSelection(output);
1853
1854     try
1855     {
1856       jalview.gui.Desktop.internalCopy = true;
1857       // Its really worth setting the clipboard contents
1858       // to empty before setting the large StringSelection!!
1859       Toolkit.getDefaultToolkit().getSystemClipboard()
1860               .setContents(new StringSelection(""), null);
1861
1862       Toolkit.getDefaultToolkit().getSystemClipboard()
1863               .setContents(ss, Desktop.instance);
1864     } catch (OutOfMemoryError er)
1865     {
1866       new OOMWarning("copying region", er);
1867       return;
1868     }
1869
1870     ArrayList<int[]> hiddenColumns = null;
1871     if (viewport.hasHiddenColumns())
1872     {
1873       hiddenColumns = new ArrayList<int[]>();
1874       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1875               .getSelectionGroup().getEndRes();
1876       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1877       {
1878         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1879         {
1880           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1881               region[1] - hiddenOffset });
1882         }
1883       }
1884     }
1885
1886     Desktop.jalviewClipboard = new Object[] { seqs,
1887         viewport.getAlignment().getDataset(), hiddenColumns };
1888     statusBar.setText(MessageManager.formatMessage(
1889             "label.copied_sequences_to_clipboard", new Object[] { Integer
1890                     .valueOf(seqs.length).toString() }));
1891   }
1892
1893   /**
1894    * DOCUMENT ME!
1895    *
1896    * @param e
1897    *          DOCUMENT ME!
1898    */
1899   @Override
1900   protected void pasteNew_actionPerformed(ActionEvent e)
1901   {
1902     paste(true);
1903   }
1904
1905   /**
1906    * DOCUMENT ME!
1907    *
1908    * @param e
1909    *          DOCUMENT ME!
1910    */
1911   @Override
1912   protected void pasteThis_actionPerformed(ActionEvent e)
1913   {
1914     paste(false);
1915   }
1916
1917   /**
1918    * Paste contents of Jalview clipboard
1919    *
1920    * @param newAlignment
1921    *          true to paste to a new alignment, otherwise add to this.
1922    */
1923   void paste(boolean newAlignment)
1924   {
1925     boolean externalPaste = true;
1926     try
1927     {
1928       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1929       Transferable contents = c.getContents(this);
1930
1931       if (contents == null)
1932       {
1933         return;
1934       }
1935
1936       String str;
1937       FileFormatI format;
1938       try
1939       {
1940         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1941         if (str.length() < 1)
1942         {
1943           return;
1944         }
1945
1946         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1947
1948       } catch (OutOfMemoryError er)
1949       {
1950         new OOMWarning("Out of memory pasting sequences!!", er);
1951         return;
1952       }
1953
1954       SequenceI[] sequences;
1955       boolean annotationAdded = false;
1956       AlignmentI alignment = null;
1957
1958       if (Desktop.jalviewClipboard != null)
1959       {
1960         // The clipboard was filled from within Jalview, we must use the
1961         // sequences
1962         // And dataset from the copied alignment
1963         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1964         // be doubly sure that we create *new* sequence objects.
1965         sequences = new SequenceI[newseq.length];
1966         for (int i = 0; i < newseq.length; i++)
1967         {
1968           sequences[i] = new Sequence(newseq[i]);
1969         }
1970         alignment = new Alignment(sequences);
1971         externalPaste = false;
1972       }
1973       else
1974       {
1975         // parse the clipboard as an alignment.
1976         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1977                 format);
1978         sequences = alignment.getSequencesArray();
1979       }
1980
1981       int alwidth = 0;
1982       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1983       int fgroup = -1;
1984
1985       if (newAlignment)
1986       {
1987
1988         if (Desktop.jalviewClipboard != null)
1989         {
1990           // dataset is inherited
1991           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1992         }
1993         else
1994         {
1995           // new dataset is constructed
1996           alignment.setDataset(null);
1997         }
1998         alwidth = alignment.getWidth() + 1;
1999       }
2000       else
2001       {
2002         AlignmentI pastedal = alignment; // preserve pasted alignment object
2003         // Add pasted sequences and dataset into existing alignment.
2004         alignment = viewport.getAlignment();
2005         alwidth = alignment.getWidth() + 1;
2006         // decide if we need to import sequences from an existing dataset
2007         boolean importDs = Desktop.jalviewClipboard != null
2008                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2009         // importDs==true instructs us to copy over new dataset sequences from
2010         // an existing alignment
2011         Vector newDs = (importDs) ? new Vector() : null; // used to create
2012         // minimum dataset set
2013
2014         for (int i = 0; i < sequences.length; i++)
2015         {
2016           if (importDs)
2017           {
2018             newDs.addElement(null);
2019           }
2020           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2021           // paste
2022           if (importDs && ds != null)
2023           {
2024             if (!newDs.contains(ds))
2025             {
2026               newDs.setElementAt(ds, i);
2027               ds = new Sequence(ds);
2028               // update with new dataset sequence
2029               sequences[i].setDatasetSequence(ds);
2030             }
2031             else
2032             {
2033               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2034             }
2035           }
2036           else
2037           {
2038             // copy and derive new dataset sequence
2039             sequences[i] = sequences[i].deriveSequence();
2040             alignment.getDataset().addSequence(
2041                     sequences[i].getDatasetSequence());
2042             // TODO: avoid creation of duplicate dataset sequences with a
2043             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2044           }
2045           alignment.addSequence(sequences[i]); // merges dataset
2046         }
2047         if (newDs != null)
2048         {
2049           newDs.clear(); // tidy up
2050         }
2051         if (alignment.getAlignmentAnnotation() != null)
2052         {
2053           for (AlignmentAnnotation alan : alignment
2054                   .getAlignmentAnnotation())
2055           {
2056             if (alan.graphGroup > fgroup)
2057             {
2058               fgroup = alan.graphGroup;
2059             }
2060           }
2061         }
2062         if (pastedal.getAlignmentAnnotation() != null)
2063         {
2064           // Add any annotation attached to alignment.
2065           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2066           for (int i = 0; i < alann.length; i++)
2067           {
2068             annotationAdded = true;
2069             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2070             {
2071               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2072               if (newann.graphGroup > -1)
2073               {
2074                 if (newGraphGroups.size() <= newann.graphGroup
2075                         || newGraphGroups.get(newann.graphGroup) == null)
2076                 {
2077                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2078                   {
2079                     newGraphGroups.add(q, null);
2080                   }
2081                   newGraphGroups.set(newann.graphGroup, new Integer(
2082                           ++fgroup));
2083                 }
2084                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2085                         .intValue();
2086               }
2087
2088               newann.padAnnotation(alwidth);
2089               alignment.addAnnotation(newann);
2090             }
2091           }
2092         }
2093       }
2094       if (!newAlignment)
2095       {
2096         // /////
2097         // ADD HISTORY ITEM
2098         //
2099         addHistoryItem(new EditCommand(
2100                 MessageManager.getString("label.add_sequences"),
2101                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2102       }
2103       // Add any annotations attached to sequences
2104       for (int i = 0; i < sequences.length; i++)
2105       {
2106         if (sequences[i].getAnnotation() != null)
2107         {
2108           AlignmentAnnotation newann;
2109           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2110           {
2111             annotationAdded = true;
2112             newann = sequences[i].getAnnotation()[a];
2113             newann.adjustForAlignment();
2114             newann.padAnnotation(alwidth);
2115             if (newann.graphGroup > -1)
2116             {
2117               if (newann.graphGroup > -1)
2118               {
2119                 if (newGraphGroups.size() <= newann.graphGroup
2120                         || newGraphGroups.get(newann.graphGroup) == null)
2121                 {
2122                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2123                   {
2124                     newGraphGroups.add(q, null);
2125                   }
2126                   newGraphGroups.set(newann.graphGroup, new Integer(
2127                           ++fgroup));
2128                 }
2129                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2130                         .intValue();
2131               }
2132             }
2133             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2134             // was
2135             // duplicated
2136             // earlier
2137             alignment
2138                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2139           }
2140         }
2141       }
2142       if (!newAlignment)
2143       {
2144
2145         // propagate alignment changed.
2146         viewport.setEndSeq(alignment.getHeight());
2147         if (annotationAdded)
2148         {
2149           // Duplicate sequence annotation in all views.
2150           AlignmentI[] alview = this.getViewAlignments();
2151           for (int i = 0; i < sequences.length; i++)
2152           {
2153             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2154             if (sann == null)
2155             {
2156               continue;
2157             }
2158             for (int avnum = 0; avnum < alview.length; avnum++)
2159             {
2160               if (alview[avnum] != alignment)
2161               {
2162                 // duplicate in a view other than the one with input focus
2163                 int avwidth = alview[avnum].getWidth() + 1;
2164                 // this relies on sann being preserved after we
2165                 // modify the sequence's annotation array for each duplication
2166                 for (int a = 0; a < sann.length; a++)
2167                 {
2168                   AlignmentAnnotation newann = new AlignmentAnnotation(
2169                           sann[a]);
2170                   sequences[i].addAlignmentAnnotation(newann);
2171                   newann.padAnnotation(avwidth);
2172                   alview[avnum].addAnnotation(newann); // annotation was
2173                   // duplicated earlier
2174                   // TODO JAL-1145 graphGroups are not updated for sequence
2175                   // annotation added to several views. This may cause
2176                   // strangeness
2177                   alview[avnum].setAnnotationIndex(newann, a);
2178                 }
2179               }
2180             }
2181           }
2182           buildSortByAnnotationScoresMenu();
2183         }
2184         viewport.firePropertyChange("alignment", null,
2185                 alignment.getSequences());
2186         if (alignPanels != null)
2187         {
2188           for (AlignmentPanel ap : alignPanels)
2189           {
2190             ap.validateAnnotationDimensions(false);
2191           }
2192         }
2193         else
2194         {
2195           alignPanel.validateAnnotationDimensions(false);
2196         }
2197
2198       }
2199       else
2200       {
2201         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2202                 DEFAULT_HEIGHT);
2203         String newtitle = new String("Copied sequences");
2204
2205         if (Desktop.jalviewClipboard != null
2206                 && Desktop.jalviewClipboard[2] != null)
2207         {
2208           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2209           for (int[] region : hc)
2210           {
2211             af.viewport.hideColumns(region[0], region[1]);
2212           }
2213         }
2214
2215         // >>>This is a fix for the moment, until a better solution is
2216         // found!!<<<
2217         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2218                 .transferSettings(
2219                         alignPanel.getSeqPanel().seqCanvas
2220                                 .getFeatureRenderer());
2221
2222         // TODO: maintain provenance of an alignment, rather than just make the
2223         // title a concatenation of operations.
2224         if (!externalPaste)
2225         {
2226           if (title.startsWith("Copied sequences"))
2227           {
2228             newtitle = title;
2229           }
2230           else
2231           {
2232             newtitle = newtitle.concat("- from " + title);
2233           }
2234         }
2235         else
2236         {
2237           newtitle = new String("Pasted sequences");
2238         }
2239
2240         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2241                 DEFAULT_HEIGHT);
2242
2243       }
2244
2245     } catch (Exception ex)
2246     {
2247       ex.printStackTrace();
2248       System.out.println("Exception whilst pasting: " + ex);
2249       // could be anything being pasted in here
2250     }
2251
2252   }
2253
2254   @Override
2255   protected void expand_newalign(ActionEvent e)
2256   {
2257     try
2258     {
2259       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2260               .getAlignment(), -1);
2261       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2262               DEFAULT_HEIGHT);
2263       String newtitle = new String("Flanking alignment");
2264
2265       if (Desktop.jalviewClipboard != null
2266               && Desktop.jalviewClipboard[2] != null)
2267       {
2268         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2269         for (int region[] : hc)
2270         {
2271           af.viewport.hideColumns(region[0], region[1]);
2272         }
2273       }
2274
2275       // >>>This is a fix for the moment, until a better solution is
2276       // found!!<<<
2277       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2278               .transferSettings(
2279                       alignPanel.getSeqPanel().seqCanvas
2280                               .getFeatureRenderer());
2281
2282       // TODO: maintain provenance of an alignment, rather than just make the
2283       // title a concatenation of operations.
2284       {
2285         if (title.startsWith("Copied sequences"))
2286         {
2287           newtitle = title;
2288         }
2289         else
2290         {
2291           newtitle = newtitle.concat("- from " + title);
2292         }
2293       }
2294
2295       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2296
2297     } catch (Exception ex)
2298     {
2299       ex.printStackTrace();
2300       System.out.println("Exception whilst pasting: " + ex);
2301       // could be anything being pasted in here
2302     } catch (OutOfMemoryError oom)
2303     {
2304       new OOMWarning("Viewing flanking region of alignment", oom);
2305     }
2306   }
2307
2308   /**
2309    * DOCUMENT ME!
2310    *
2311    * @param e
2312    *          DOCUMENT ME!
2313    */
2314   @Override
2315   protected void cut_actionPerformed(ActionEvent e)
2316   {
2317     copy_actionPerformed(null);
2318     delete_actionPerformed(null);
2319   }
2320
2321   /**
2322    * DOCUMENT ME!
2323    *
2324    * @param e
2325    *          DOCUMENT ME!
2326    */
2327   @Override
2328   protected void delete_actionPerformed(ActionEvent evt)
2329   {
2330
2331     SequenceGroup sg = viewport.getSelectionGroup();
2332     if (sg == null)
2333     {
2334       return;
2335     }
2336
2337     /*
2338      * If the cut affects all sequences, warn, remove highlighted columns
2339      */
2340     if (sg.getSize() == viewport.getAlignment().getHeight())
2341     {
2342       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2343               .getAlignment().getWidth()) ? true : false;
2344       if (isEntireAlignWidth)
2345       {
2346         int confirm = JvOptionPane.showConfirmDialog(this,
2347                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2348                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2349                 JvOptionPane.OK_CANCEL_OPTION);
2350
2351         if (confirm == JvOptionPane.CANCEL_OPTION
2352                 || confirm == JvOptionPane.CLOSED_OPTION)
2353         {
2354           return;
2355         }
2356       }
2357       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2358               sg.getEndRes() + 1);
2359     }
2360     SequenceI[] cut = sg.getSequences()
2361             .toArray(new SequenceI[sg.getSize()]);
2362
2363     addHistoryItem(new EditCommand(
2364             MessageManager.getString("label.cut_sequences"), Action.CUT,
2365             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2366             viewport.getAlignment()));
2367
2368     viewport.setSelectionGroup(null);
2369     viewport.sendSelection();
2370     viewport.getAlignment().deleteGroup(sg);
2371
2372     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2373             .getSequences());
2374     if (viewport.getAlignment().getHeight() < 1)
2375     {
2376       try
2377       {
2378         this.setClosed(true);
2379       } catch (Exception ex)
2380       {
2381       }
2382     }
2383   }
2384
2385   /**
2386    * DOCUMENT ME!
2387    *
2388    * @param e
2389    *          DOCUMENT ME!
2390    */
2391   @Override
2392   protected void deleteGroups_actionPerformed(ActionEvent e)
2393   {
2394     if (avc.deleteGroups())
2395     {
2396       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2397       alignPanel.updateAnnotation();
2398       alignPanel.paintAlignment(true);
2399     }
2400   }
2401
2402   /**
2403    * DOCUMENT ME!
2404    *
2405    * @param e
2406    *          DOCUMENT ME!
2407    */
2408   @Override
2409   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2410   {
2411     SequenceGroup sg = new SequenceGroup();
2412
2413     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2414     {
2415       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2416     }
2417
2418     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2419     viewport.setSelectionGroup(sg);
2420     viewport.sendSelection();
2421     // JAL-2034 - should delegate to
2422     // alignPanel to decide if overview needs
2423     // updating.
2424     alignPanel.paintAlignment(false);
2425     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2426   }
2427
2428   /**
2429    * DOCUMENT ME!
2430    *
2431    * @param e
2432    *          DOCUMENT ME!
2433    */
2434   @Override
2435   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2436   {
2437     if (viewport.cursorMode)
2438     {
2439       alignPanel.getSeqPanel().keyboardNo1 = null;
2440       alignPanel.getSeqPanel().keyboardNo2 = null;
2441     }
2442     viewport.setSelectionGroup(null);
2443     viewport.getColumnSelection().clear();
2444     viewport.setSelectionGroup(null);
2445     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2446     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2447     // JAL-2034 - should delegate to
2448     // alignPanel to decide if overview needs
2449     // updating.
2450     alignPanel.paintAlignment(false);
2451     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2452     viewport.sendSelection();
2453   }
2454
2455   /**
2456    * DOCUMENT ME!
2457    *
2458    * @param e
2459    *          DOCUMENT ME!
2460    */
2461   @Override
2462   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2463   {
2464     SequenceGroup sg = viewport.getSelectionGroup();
2465
2466     if (sg == null)
2467     {
2468       selectAllSequenceMenuItem_actionPerformed(null);
2469
2470       return;
2471     }
2472
2473     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2474     {
2475       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2476     }
2477     // JAL-2034 - should delegate to
2478     // alignPanel to decide if overview needs
2479     // updating.
2480
2481     alignPanel.paintAlignment(true);
2482     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2483     viewport.sendSelection();
2484   }
2485
2486   @Override
2487   public void invertColSel_actionPerformed(ActionEvent e)
2488   {
2489     viewport.invertColumnSelection();
2490     alignPanel.paintAlignment(true);
2491     viewport.sendSelection();
2492   }
2493
2494   /**
2495    * DOCUMENT ME!
2496    *
2497    * @param e
2498    *          DOCUMENT ME!
2499    */
2500   @Override
2501   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2502   {
2503     trimAlignment(true);
2504   }
2505
2506   /**
2507    * DOCUMENT ME!
2508    *
2509    * @param e
2510    *          DOCUMENT ME!
2511    */
2512   @Override
2513   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2514   {
2515     trimAlignment(false);
2516   }
2517
2518   void trimAlignment(boolean trimLeft)
2519   {
2520     ColumnSelection colSel = viewport.getColumnSelection();
2521     int column;
2522
2523     if (!colSel.isEmpty())
2524     {
2525       if (trimLeft)
2526       {
2527         column = colSel.getMin();
2528       }
2529       else
2530       {
2531         column = colSel.getMax();
2532       }
2533
2534       SequenceI[] seqs;
2535       if (viewport.getSelectionGroup() != null)
2536       {
2537         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2538                 viewport.getHiddenRepSequences());
2539       }
2540       else
2541       {
2542         seqs = viewport.getAlignment().getSequencesArray();
2543       }
2544
2545       TrimRegionCommand trimRegion;
2546       if (trimLeft)
2547       {
2548         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2549                 column, viewport.getAlignment());
2550         viewport.setStartRes(0);
2551       }
2552       else
2553       {
2554         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2555                 column, viewport.getAlignment());
2556       }
2557
2558       statusBar.setText(MessageManager.formatMessage(
2559               "label.removed_columns",
2560               new String[] { Integer.valueOf(trimRegion.getSize())
2561                       .toString() }));
2562
2563       addHistoryItem(trimRegion);
2564
2565       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2566       {
2567         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2568                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2569         {
2570           viewport.getAlignment().deleteGroup(sg);
2571         }
2572       }
2573
2574       viewport.firePropertyChange("alignment", null, viewport
2575               .getAlignment().getSequences());
2576     }
2577   }
2578
2579   /**
2580    * DOCUMENT ME!
2581    *
2582    * @param e
2583    *          DOCUMENT ME!
2584    */
2585   @Override
2586   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2587   {
2588     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2589
2590     SequenceI[] seqs;
2591     if (viewport.getSelectionGroup() != null)
2592     {
2593       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2594               viewport.getHiddenRepSequences());
2595       start = viewport.getSelectionGroup().getStartRes();
2596       end = viewport.getSelectionGroup().getEndRes();
2597     }
2598     else
2599     {
2600       seqs = viewport.getAlignment().getSequencesArray();
2601     }
2602
2603     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2604             "Remove Gapped Columns", seqs, start, end,
2605             viewport.getAlignment());
2606
2607     addHistoryItem(removeGapCols);
2608
2609     statusBar.setText(MessageManager.formatMessage(
2610             "label.removed_empty_columns",
2611             new Object[] { Integer.valueOf(removeGapCols.getSize())
2612                     .toString() }));
2613
2614     // This is to maintain viewport position on first residue
2615     // of first sequence
2616     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2617     int startRes = seq.findPosition(viewport.startRes);
2618     // ShiftList shifts;
2619     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2620     // edit.alColumnChanges=shifts.getInverse();
2621     // if (viewport.hasHiddenColumns)
2622     // viewport.getColumnSelection().compensateForEdits(shifts);
2623     viewport.setStartRes(seq.findIndex(startRes) - 1);
2624     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2625             .getSequences());
2626
2627   }
2628
2629   /**
2630    * DOCUMENT ME!
2631    *
2632    * @param e
2633    *          DOCUMENT ME!
2634    */
2635   @Override
2636   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2637   {
2638     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2639
2640     SequenceI[] seqs;
2641     if (viewport.getSelectionGroup() != null)
2642     {
2643       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2644               viewport.getHiddenRepSequences());
2645       start = viewport.getSelectionGroup().getStartRes();
2646       end = viewport.getSelectionGroup().getEndRes();
2647     }
2648     else
2649     {
2650       seqs = viewport.getAlignment().getSequencesArray();
2651     }
2652
2653     // This is to maintain viewport position on first residue
2654     // of first sequence
2655     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2656     int startRes = seq.findPosition(viewport.startRes);
2657
2658     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2659             viewport.getAlignment()));
2660
2661     viewport.setStartRes(seq.findIndex(startRes) - 1);
2662
2663     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2664             .getSequences());
2665
2666   }
2667
2668   /**
2669    * DOCUMENT ME!
2670    *
2671    * @param e
2672    *          DOCUMENT ME!
2673    */
2674   @Override
2675   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2676   {
2677     viewport.setPadGaps(padGapsMenuitem.isSelected());
2678     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2679             .getSequences());
2680   }
2681
2682   /**
2683    * DOCUMENT ME!
2684    *
2685    * @param e
2686    *          DOCUMENT ME!
2687    */
2688   @Override
2689   public void findMenuItem_actionPerformed(ActionEvent e)
2690   {
2691     new Finder();
2692   }
2693
2694   /**
2695    * Create a new view of the current alignment.
2696    */
2697   @Override
2698   public void newView_actionPerformed(ActionEvent e)
2699   {
2700     newView(null, true);
2701   }
2702
2703   /**
2704    * Creates and shows a new view of the current alignment.
2705    *
2706    * @param viewTitle
2707    *          title of newly created view; if null, one will be generated
2708    * @param copyAnnotation
2709    *          if true then duplicate all annnotation, groups and settings
2710    * @return new alignment panel, already displayed.
2711    */
2712   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2713   {
2714     /*
2715      * Create a new AlignmentPanel (with its own, new Viewport)
2716      */
2717     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2718             true);
2719     if (!copyAnnotation)
2720     {
2721       /*
2722        * remove all groups and annotation except for the automatic stuff
2723        */
2724       newap.av.getAlignment().deleteAllGroups();
2725       newap.av.getAlignment().deleteAllAnnotations(false);
2726     }
2727
2728     newap.av.setGatherViewsHere(false);
2729
2730     if (viewport.viewName == null)
2731     {
2732       viewport.viewName = MessageManager
2733               .getString("label.view_name_original");
2734     }
2735
2736     /*
2737      * Views share the same edits undo and redo stacks
2738      */
2739     newap.av.setHistoryList(viewport.getHistoryList());
2740     newap.av.setRedoList(viewport.getRedoList());
2741
2742     /*
2743      * Views share the same mappings; need to deregister any new mappings
2744      * created by copyAlignPanel, and register the new reference to the shared
2745      * mappings
2746      */
2747     newap.av.replaceMappings(viewport.getAlignment());
2748
2749     newap.av.viewName = getNewViewName(viewTitle);
2750
2751     addAlignmentPanel(newap, true);
2752     newap.alignmentChanged();
2753
2754     if (alignPanels.size() == 2)
2755     {
2756       viewport.setGatherViewsHere(true);
2757     }
2758     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2759     return newap;
2760   }
2761
2762   /**
2763    * Make a new name for the view, ensuring it is unique within the current
2764    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2765    * these now use viewId. Unique view names are still desirable for usability.)
2766    *
2767    * @param viewTitle
2768    * @return
2769    */
2770   protected String getNewViewName(String viewTitle)
2771   {
2772     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2773     boolean addFirstIndex = false;
2774     if (viewTitle == null || viewTitle.trim().length() == 0)
2775     {
2776       viewTitle = MessageManager.getString("action.view");
2777       addFirstIndex = true;
2778     }
2779     else
2780     {
2781       index = 1;// we count from 1 if given a specific name
2782     }
2783     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2784
2785     List<Component> comps = PaintRefresher.components.get(viewport
2786             .getSequenceSetId());
2787
2788     List<String> existingNames = getExistingViewNames(comps);
2789
2790     while (existingNames.contains(newViewName))
2791     {
2792       newViewName = viewTitle + " " + (++index);
2793     }
2794     return newViewName;
2795   }
2796
2797   /**
2798    * Returns a list of distinct view names found in the given list of
2799    * components. View names are held on the viewport of an AlignmentPanel.
2800    *
2801    * @param comps
2802    * @return
2803    */
2804   protected List<String> getExistingViewNames(List<Component> comps)
2805   {
2806     List<String> existingNames = new ArrayList<String>();
2807     for (Component comp : comps)
2808     {
2809       if (comp instanceof AlignmentPanel)
2810       {
2811         AlignmentPanel ap = (AlignmentPanel) comp;
2812         if (!existingNames.contains(ap.av.viewName))
2813         {
2814           existingNames.add(ap.av.viewName);
2815         }
2816       }
2817     }
2818     return existingNames;
2819   }
2820
2821   /**
2822    * Explode tabbed views into separate windows.
2823    */
2824   @Override
2825   public void expandViews_actionPerformed(ActionEvent e)
2826   {
2827     Desktop.explodeViews(this);
2828   }
2829
2830   /**
2831    * Gather views in separate windows back into a tabbed presentation.
2832    */
2833   @Override
2834   public void gatherViews_actionPerformed(ActionEvent e)
2835   {
2836     Desktop.instance.gatherViews(this);
2837   }
2838
2839   /**
2840    * DOCUMENT ME!
2841    *
2842    * @param e
2843    *          DOCUMENT ME!
2844    */
2845   @Override
2846   public void font_actionPerformed(ActionEvent e)
2847   {
2848     new FontChooser(alignPanel);
2849   }
2850
2851   /**
2852    * DOCUMENT ME!
2853    *
2854    * @param e
2855    *          DOCUMENT ME!
2856    */
2857   @Override
2858   protected void seqLimit_actionPerformed(ActionEvent e)
2859   {
2860     viewport.setShowJVSuffix(seqLimits.isSelected());
2861
2862     alignPanel.getIdPanel().getIdCanvas()
2863             .setPreferredSize(alignPanel.calculateIdWidth());
2864     alignPanel.paintAlignment(true);
2865   }
2866
2867   @Override
2868   public void idRightAlign_actionPerformed(ActionEvent e)
2869   {
2870     viewport.setRightAlignIds(idRightAlign.isSelected());
2871     alignPanel.paintAlignment(true);
2872   }
2873
2874   @Override
2875   public void centreColumnLabels_actionPerformed(ActionEvent e)
2876   {
2877     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2878     alignPanel.paintAlignment(true);
2879   }
2880
2881   /*
2882    * (non-Javadoc)
2883    *
2884    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2885    */
2886   @Override
2887   protected void followHighlight_actionPerformed()
2888   {
2889     /*
2890      * Set the 'follow' flag on the Viewport (and scroll to position if now
2891      * true).
2892      */
2893     final boolean state = this.followHighlightMenuItem.getState();
2894     viewport.setFollowHighlight(state);
2895     if (state)
2896     {
2897       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2898     }
2899   }
2900
2901   /**
2902    * DOCUMENT ME!
2903    *
2904    * @param e
2905    *          DOCUMENT ME!
2906    */
2907   @Override
2908   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2909   {
2910     viewport.setColourText(colourTextMenuItem.isSelected());
2911     alignPanel.paintAlignment(true);
2912   }
2913
2914   /**
2915    * DOCUMENT ME!
2916    *
2917    * @param e
2918    *          DOCUMENT ME!
2919    */
2920   @Override
2921   public void wrapMenuItem_actionPerformed(ActionEvent e)
2922   {
2923     scaleAbove.setVisible(wrapMenuItem.isSelected());
2924     scaleLeft.setVisible(wrapMenuItem.isSelected());
2925     scaleRight.setVisible(wrapMenuItem.isSelected());
2926     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2927     alignPanel.updateLayout();
2928   }
2929
2930   @Override
2931   public void showAllSeqs_actionPerformed(ActionEvent e)
2932   {
2933     viewport.showAllHiddenSeqs();
2934   }
2935
2936   @Override
2937   public void showAllColumns_actionPerformed(ActionEvent e)
2938   {
2939     viewport.showAllHiddenColumns();
2940     repaint();
2941     viewport.sendSelection();
2942   }
2943
2944   @Override
2945   public void hideSelSequences_actionPerformed(ActionEvent e)
2946   {
2947     viewport.hideAllSelectedSeqs();
2948     // alignPanel.paintAlignment(true);
2949   }
2950
2951   /**
2952    * called by key handler and the hide all/show all menu items
2953    *
2954    * @param toggleSeqs
2955    * @param toggleCols
2956    */
2957   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2958   {
2959
2960     boolean hide = false;
2961     SequenceGroup sg = viewport.getSelectionGroup();
2962     if (!toggleSeqs && !toggleCols)
2963     {
2964       // Hide everything by the current selection - this is a hack - we do the
2965       // invert and then hide
2966       // first check that there will be visible columns after the invert.
2967       if (viewport.hasSelectedColumns()
2968               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2969                       .getEndRes()))
2970       {
2971         // now invert the sequence set, if required - empty selection implies
2972         // that no hiding is required.
2973         if (sg != null)
2974         {
2975           invertSequenceMenuItem_actionPerformed(null);
2976           sg = viewport.getSelectionGroup();
2977           toggleSeqs = true;
2978
2979         }
2980         viewport.expandColSelection(sg, true);
2981         // finally invert the column selection and get the new sequence
2982         // selection.
2983         invertColSel_actionPerformed(null);
2984         toggleCols = true;
2985       }
2986     }
2987
2988     if (toggleSeqs)
2989     {
2990       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2991       {
2992         hideSelSequences_actionPerformed(null);
2993         hide = true;
2994       }
2995       else if (!(toggleCols && viewport.hasSelectedColumns()))
2996       {
2997         showAllSeqs_actionPerformed(null);
2998       }
2999     }
3000
3001     if (toggleCols)
3002     {
3003       if (viewport.hasSelectedColumns())
3004       {
3005         hideSelColumns_actionPerformed(null);
3006         if (!toggleSeqs)
3007         {
3008           viewport.setSelectionGroup(sg);
3009         }
3010       }
3011       else if (!hide)
3012       {
3013         showAllColumns_actionPerformed(null);
3014       }
3015     }
3016   }
3017
3018   /*
3019    * (non-Javadoc)
3020    *
3021    * @see
3022    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3023    * event.ActionEvent)
3024    */
3025   @Override
3026   public void hideAllButSelection_actionPerformed(ActionEvent e)
3027   {
3028     toggleHiddenRegions(false, false);
3029     viewport.sendSelection();
3030   }
3031
3032   /*
3033    * (non-Javadoc)
3034    *
3035    * @see
3036    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3037    * .ActionEvent)
3038    */
3039   @Override
3040   public void hideAllSelection_actionPerformed(ActionEvent e)
3041   {
3042     SequenceGroup sg = viewport.getSelectionGroup();
3043     viewport.expandColSelection(sg, false);
3044     viewport.hideAllSelectedSeqs();
3045     viewport.hideSelectedColumns();
3046     alignPanel.paintAlignment(true);
3047     viewport.sendSelection();
3048   }
3049
3050   /*
3051    * (non-Javadoc)
3052    *
3053    * @see
3054    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3055    * ActionEvent)
3056    */
3057   @Override
3058   public void showAllhidden_actionPerformed(ActionEvent e)
3059   {
3060     viewport.showAllHiddenColumns();
3061     viewport.showAllHiddenSeqs();
3062     alignPanel.paintAlignment(true);
3063     viewport.sendSelection();
3064   }
3065
3066   @Override
3067   public void hideSelColumns_actionPerformed(ActionEvent e)
3068   {
3069     viewport.hideSelectedColumns();
3070     alignPanel.paintAlignment(true);
3071     viewport.sendSelection();
3072   }
3073
3074   @Override
3075   public void hiddenMarkers_actionPerformed(ActionEvent e)
3076   {
3077     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3078     repaint();
3079   }
3080
3081   /**
3082    * DOCUMENT ME!
3083    *
3084    * @param e
3085    *          DOCUMENT ME!
3086    */
3087   @Override
3088   protected void scaleAbove_actionPerformed(ActionEvent e)
3089   {
3090     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3091     alignPanel.paintAlignment(true);
3092   }
3093
3094   /**
3095    * DOCUMENT ME!
3096    *
3097    * @param e
3098    *          DOCUMENT ME!
3099    */
3100   @Override
3101   protected void scaleLeft_actionPerformed(ActionEvent e)
3102   {
3103     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3104     alignPanel.paintAlignment(true);
3105   }
3106
3107   /**
3108    * DOCUMENT ME!
3109    *
3110    * @param e
3111    *          DOCUMENT ME!
3112    */
3113   @Override
3114   protected void scaleRight_actionPerformed(ActionEvent e)
3115   {
3116     viewport.setScaleRightWrapped(scaleRight.isSelected());
3117     alignPanel.paintAlignment(true);
3118   }
3119
3120   /**
3121    * DOCUMENT ME!
3122    *
3123    * @param e
3124    *          DOCUMENT ME!
3125    */
3126   @Override
3127   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3128   {
3129     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3130     alignPanel.paintAlignment(true);
3131   }
3132
3133   /**
3134    * DOCUMENT ME!
3135    *
3136    * @param e
3137    *          DOCUMENT ME!
3138    */
3139   @Override
3140   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3141   {
3142     viewport.setShowText(viewTextMenuItem.isSelected());
3143     alignPanel.paintAlignment(true);
3144   }
3145
3146   /**
3147    * DOCUMENT ME!
3148    *
3149    * @param e
3150    *          DOCUMENT ME!
3151    */
3152   @Override
3153   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3154   {
3155     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3156     alignPanel.paintAlignment(true);
3157   }
3158
3159   public FeatureSettings featureSettings;
3160
3161   @Override
3162   public FeatureSettingsControllerI getFeatureSettingsUI()
3163   {
3164     return featureSettings;
3165   }
3166
3167   @Override
3168   public void featureSettings_actionPerformed(ActionEvent e)
3169   {
3170     if (featureSettings != null)
3171     {
3172       featureSettings.close();
3173       featureSettings = null;
3174     }
3175     if (!showSeqFeatures.isSelected())
3176     {
3177       // make sure features are actually displayed
3178       showSeqFeatures.setSelected(true);
3179       showSeqFeatures_actionPerformed(null);
3180     }
3181     featureSettings = new FeatureSettings(this);
3182   }
3183
3184   /**
3185    * Set or clear 'Show Sequence Features'
3186    *
3187    * @param evt
3188    *          DOCUMENT ME!
3189    */
3190   @Override
3191   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3192   {
3193     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3194     alignPanel.paintAlignment(true);
3195     if (alignPanel.getOverviewPanel() != null)
3196     {
3197       alignPanel.getOverviewPanel().updateOverviewImage();
3198     }
3199   }
3200
3201   /**
3202    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3203    * the annotations panel as a whole.
3204    *
3205    * The options to show/hide all annotations should be enabled when the panel
3206    * is shown, and disabled when the panel is hidden.
3207    *
3208    * @param e
3209    */
3210   @Override
3211   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3212   {
3213     final boolean setVisible = annotationPanelMenuItem.isSelected();
3214     viewport.setShowAnnotation(setVisible);
3215     this.showAllSeqAnnotations.setEnabled(setVisible);
3216     this.hideAllSeqAnnotations.setEnabled(setVisible);
3217     this.showAllAlAnnotations.setEnabled(setVisible);
3218     this.hideAllAlAnnotations.setEnabled(setVisible);
3219     alignPanel.updateLayout();
3220   }
3221
3222   @Override
3223   public void alignmentProperties()
3224   {
3225     JEditorPane editPane = new JEditorPane("text/html", "");
3226     editPane.setEditable(false);
3227     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3228             .formatAsHtml();
3229     editPane.setText(MessageManager.formatMessage("label.html_content",
3230             new Object[] { contents.toString() }));
3231     JInternalFrame frame = new JInternalFrame();
3232     frame.getContentPane().add(new JScrollPane(editPane));
3233
3234     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3235             "label.alignment_properties", new Object[] { getTitle() }),
3236             500, 400);
3237   }
3238
3239   /**
3240    * DOCUMENT ME!
3241    *
3242    * @param e
3243    *          DOCUMENT ME!
3244    */
3245   @Override
3246   public void overviewMenuItem_actionPerformed(ActionEvent e)
3247   {
3248     if (alignPanel.overviewPanel != null)
3249     {
3250       return;
3251     }
3252
3253     JInternalFrame frame = new JInternalFrame();
3254     OverviewPanel overview = new OverviewPanel(alignPanel);
3255     frame.setContentPane(overview);
3256     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3257             "label.overview_params", new Object[] { this.getTitle() }),
3258             frame.getWidth(), frame.getHeight());
3259     frame.pack();
3260     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3261     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3262     {
3263       @Override
3264       public void internalFrameClosed(
3265               javax.swing.event.InternalFrameEvent evt)
3266       {
3267         alignPanel.setOverviewPanel(null);
3268       };
3269     });
3270
3271     alignPanel.setOverviewPanel(overview);
3272   }
3273
3274   @Override
3275   public void textColour_actionPerformed()
3276   {
3277     new TextColourChooser().chooseColour(alignPanel, null);
3278   }
3279
3280   /*
3281    * public void covariationColour_actionPerformed() {
3282    * changeColour(new
3283    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3284    * ()[0])); }
3285    */
3286   @Override
3287   public void annotationColour_actionPerformed()
3288   {
3289     new AnnotationColourChooser(viewport, alignPanel);
3290   }
3291
3292   @Override
3293   public void annotationColumn_actionPerformed(ActionEvent e)
3294   {
3295     new AnnotationColumnChooser(viewport, alignPanel);
3296   }
3297
3298   /**
3299    * Action on the user checking or unchecking the option to apply the selected
3300    * colour scheme to all groups. If unchecked, groups may have their own
3301    * independent colour schemes.
3302    *
3303    */
3304   @Override
3305   protected void applyToAllGroups_actionPerformed()
3306   {
3307     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3308   }
3309
3310   /**
3311    * Action on user selecting a colour from the colour menu
3312    *
3313    * @param name
3314    *          the name (not the menu item label!) of the colour scheme
3315    */
3316   @Override
3317   public void changeColour_actionPerformed(String name)
3318   {
3319     /*
3320      * 'User Defined' opens a panel to configure or load a
3321      * user-defined colour scheme
3322      */
3323     if (ResidueColourScheme.USER_DEFINED.equals(name))
3324     {
3325       new UserDefinedColours(alignPanel, null);
3326       return;
3327     }
3328
3329     /*
3330      * otherwise set the chosen colour scheme (or null for 'None')
3331      */
3332     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3333             viewport.getAlignment(), viewport.getHiddenRepSequences());
3334     changeColour(cs);
3335   }
3336
3337   /**
3338    * Actions on setting or changing the alignment colour scheme
3339    *
3340    * @param cs
3341    */
3342   @Override
3343   public void changeColour(ColourSchemeI cs)
3344   {
3345     // TODO: pull up to controller method
3346     if (cs != null)
3347     {
3348       ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3349       // Make sure viewport is up to date w.r.t. any sliders
3350       // ? not needed as handled by SliderPanel.valueChanged?
3351 //       if (viewport.getAbovePIDThreshold())
3352 //       {
3353       // int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3354 //       "Background");
3355        //todo is threshold held in viewport style or in colour scheme?
3356 //       viewport.setThreshold(threshold);
3357       // }
3358       //
3359       // if (viewport.getConservationSelected())
3360       // {
3361       // cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3362       // cs, "Background"));
3363       // }
3364     }
3365
3366     viewport.setGlobalColourScheme(cs);
3367     if (viewport.getConservationSelected())
3368     {
3369       int conservationInc = SliderPanel.getConservationValue();
3370       viewport.getViewportColourScheme()
3371               .setConservationInc(conservationInc);
3372     }
3373
3374     alignPanel.paintAlignment(true);
3375   }
3376
3377   /**
3378    * DOCUMENT ME!
3379    *
3380    * @param e
3381    *          DOCUMENT ME!
3382    */
3383   @Override
3384   protected void modifyPID_actionPerformed()
3385   {
3386     if (viewport.getAbovePIDThreshold())
3387     {
3388       SliderPanel.setPIDSliderSource(alignPanel,
3389               viewport.getViewportColourScheme(), "Background");
3390       SliderPanel.showPIDSlider();
3391     }
3392   }
3393
3394   /**
3395    * DOCUMENT ME!
3396    *
3397    * @param e
3398    *          DOCUMENT ME!
3399    */
3400   @Override
3401   protected void modifyConservation_actionPerformed()
3402   {
3403     if (viewport.getConservationSelected()
3404             && viewport.getGlobalColourScheme() != null)
3405     {
3406       SliderPanel.setConservationSlider(alignPanel,
3407               viewport.getViewportColourScheme(), "Background");
3408       SliderPanel.showConservationSlider();
3409     }
3410   }
3411
3412   /**
3413    * Action on selecting or deselecting (Colour) By Conservation
3414    */
3415   @Override
3416   protected void conservationMenuItem_actionPerformed()
3417   {
3418     boolean selected = conservationMenuItem.isSelected();
3419     modifyConservation.setEnabled(selected);
3420     viewport.setConservationSelected(selected);
3421
3422     changeColour(viewport.getGlobalColourScheme());
3423     if (selected)
3424     {
3425       modifyConservation_actionPerformed();
3426     }
3427     else
3428     {
3429       SliderPanel.hideConservationSlider();
3430     }
3431   }
3432
3433   /**
3434    * Action on selecting or deselecting (Colour) Above PID Threshold
3435    */
3436   @Override
3437   public void abovePIDThreshold_actionPerformed()
3438   {
3439     boolean selected = abovePIDThreshold.isSelected();
3440     modifyPID.setEnabled(selected);
3441     viewport.setAbovePIDThreshold(selected);
3442
3443     changeColour(viewport.getGlobalColourScheme());
3444     if (selected)
3445     {
3446       modifyPID_actionPerformed();
3447     }
3448     else
3449     {
3450       SliderPanel.hidePIDSlider();
3451     }
3452   }
3453
3454   /**
3455    * DOCUMENT ME!
3456    *
3457    * @param e
3458    *          DOCUMENT ME!
3459    */
3460   @Override
3461   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3462   {
3463     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3464     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3465             .getAlignment().getSequenceAt(0), null);
3466     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3467             viewport.getAlignment()));
3468     alignPanel.paintAlignment(true);
3469   }
3470
3471   /**
3472    * DOCUMENT ME!
3473    *
3474    * @param e
3475    *          DOCUMENT ME!
3476    */
3477   @Override
3478   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3479   {
3480     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3481     AlignmentSorter.sortByID(viewport.getAlignment());
3482     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3483             viewport.getAlignment()));
3484     alignPanel.paintAlignment(true);
3485   }
3486
3487   /**
3488    * DOCUMENT ME!
3489    *
3490    * @param e
3491    *          DOCUMENT ME!
3492    */
3493   @Override
3494   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3495   {
3496     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3497     AlignmentSorter.sortByLength(viewport.getAlignment());
3498     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3499             viewport.getAlignment()));
3500     alignPanel.paintAlignment(true);
3501   }
3502
3503   /**
3504    * DOCUMENT ME!
3505    *
3506    * @param e
3507    *          DOCUMENT ME!
3508    */
3509   @Override
3510   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3511   {
3512     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3513     AlignmentSorter.sortByGroup(viewport.getAlignment());
3514     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3515             viewport.getAlignment()));
3516
3517     alignPanel.paintAlignment(true);
3518   }
3519
3520   /**
3521    * DOCUMENT ME!
3522    *
3523    * @param e
3524    *          DOCUMENT ME!
3525    */
3526   @Override
3527   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3528   {
3529     new RedundancyPanel(alignPanel, this);
3530   }
3531
3532   /**
3533    * DOCUMENT ME!
3534    *
3535    * @param e
3536    *          DOCUMENT ME!
3537    */
3538   @Override
3539   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3540   {
3541     if ((viewport.getSelectionGroup() == null)
3542             || (viewport.getSelectionGroup().getSize() < 2))
3543     {
3544       JvOptionPane.showInternalMessageDialog(this, MessageManager
3545               .getString("label.you_must_select_least_two_sequences"),
3546               MessageManager.getString("label.invalid_selection"),
3547               JvOptionPane.WARNING_MESSAGE);
3548     }
3549     else
3550     {
3551       JInternalFrame frame = new JInternalFrame();
3552       frame.setContentPane(new PairwiseAlignPanel(viewport));
3553       Desktop.addInternalFrame(frame,
3554               MessageManager.getString("action.pairwise_alignment"), 600,
3555               500);
3556     }
3557   }
3558
3559   /**
3560    * DOCUMENT ME!
3561    *
3562    * @param e
3563    *          DOCUMENT ME!
3564    */
3565   @Override
3566   public void PCAMenuItem_actionPerformed(ActionEvent e)
3567   {
3568     if (((viewport.getSelectionGroup() != null)
3569             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3570             .getSelectionGroup().getSize() > 0))
3571             || (viewport.getAlignment().getHeight() < 4))
3572     {
3573       JvOptionPane
3574               .showInternalMessageDialog(
3575                       this,
3576                       MessageManager
3577                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3578                       MessageManager
3579                               .getString("label.sequence_selection_insufficient"),
3580                       JvOptionPane.WARNING_MESSAGE);
3581
3582       return;
3583     }
3584
3585     new PCAPanel(alignPanel);
3586   }
3587
3588   @Override
3589   public void autoCalculate_actionPerformed(ActionEvent e)
3590   {
3591     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3592     if (viewport.autoCalculateConsensus)
3593     {
3594       viewport.firePropertyChange("alignment", null, viewport
3595               .getAlignment().getSequences());
3596     }
3597   }
3598
3599   @Override
3600   public void sortByTreeOption_actionPerformed(ActionEvent e)
3601   {
3602     viewport.sortByTree = sortByTree.isSelected();
3603   }
3604
3605   @Override
3606   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3607   {
3608     viewport.followSelection = listenToViewSelections.isSelected();
3609   }
3610
3611   /**
3612    * DOCUMENT ME!
3613    *
3614    * @param e
3615    *          DOCUMENT ME!
3616    */
3617   @Override
3618   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3619   {
3620     newTreePanel("AV", "PID", "Average distance tree using PID");
3621   }
3622
3623   /**
3624    * DOCUMENT ME!
3625    *
3626    * @param e
3627    *          DOCUMENT ME!
3628    */
3629   @Override
3630   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3631   {
3632     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3633   }
3634
3635   /**
3636    * DOCUMENT ME!
3637    *
3638    * @param e
3639    *          DOCUMENT ME!
3640    */
3641   @Override
3642   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3643   {
3644     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3645   }
3646
3647   /**
3648    * DOCUMENT ME!
3649    *
3650    * @param e
3651    *          DOCUMENT ME!
3652    */
3653   @Override
3654   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3655   {
3656     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3657   }
3658
3659   /**
3660    * DOCUMENT ME!
3661    *
3662    * @param type
3663    *          DOCUMENT ME!
3664    * @param pwType
3665    *          DOCUMENT ME!
3666    * @param title
3667    *          DOCUMENT ME!
3668    */
3669   void newTreePanel(String type, String pwType, String title)
3670   {
3671     TreePanel tp;
3672
3673     if (viewport.getSelectionGroup() != null
3674             && viewport.getSelectionGroup().getSize() > 0)
3675     {
3676       if (viewport.getSelectionGroup().getSize() < 3)
3677       {
3678         JvOptionPane
3679                 .showMessageDialog(
3680                         Desktop.desktop,
3681                         MessageManager
3682                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3683                         MessageManager
3684                                 .getString("label.not_enough_sequences"),
3685                         JvOptionPane.WARNING_MESSAGE);
3686         return;
3687       }
3688
3689       SequenceGroup sg = viewport.getSelectionGroup();
3690
3691       /* Decide if the selection is a column region */
3692       for (SequenceI _s : sg.getSequences())
3693       {
3694         if (_s.getLength() < sg.getEndRes())
3695         {
3696           JvOptionPane
3697                   .showMessageDialog(
3698                           Desktop.desktop,
3699                           MessageManager
3700                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3701                           MessageManager
3702                                   .getString("label.sequences_selection_not_aligned"),
3703                           JvOptionPane.WARNING_MESSAGE);
3704
3705           return;
3706         }
3707       }
3708
3709       title = title + " on region";
3710       tp = new TreePanel(alignPanel, type, pwType);
3711     }
3712     else
3713     {
3714       // are the visible sequences aligned?
3715       if (!viewport.getAlignment().isAligned(false))
3716       {
3717         JvOptionPane
3718                 .showMessageDialog(
3719                         Desktop.desktop,
3720                         MessageManager
3721                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3722                         MessageManager
3723                                 .getString("label.sequences_not_aligned"),
3724                         JvOptionPane.WARNING_MESSAGE);
3725
3726         return;
3727       }
3728
3729       if (viewport.getAlignment().getHeight() < 2)
3730       {
3731         return;
3732       }
3733
3734       tp = new TreePanel(alignPanel, type, pwType);
3735     }
3736
3737     title += " from ";
3738
3739     if (viewport.viewName != null)
3740     {
3741       title += viewport.viewName + " of ";
3742     }
3743
3744     title += this.title;
3745
3746     Desktop.addInternalFrame(tp, title, 600, 500);
3747   }
3748
3749   /**
3750    * DOCUMENT ME!
3751    *
3752    * @param title
3753    *          DOCUMENT ME!
3754    * @param order
3755    *          DOCUMENT ME!
3756    */
3757   public void addSortByOrderMenuItem(String title,
3758           final AlignmentOrder order)
3759   {
3760     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3761             "action.by_title_param", new Object[] { title }));
3762     sort.add(item);
3763     item.addActionListener(new java.awt.event.ActionListener()
3764     {
3765       @Override
3766       public void actionPerformed(ActionEvent e)
3767       {
3768         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3769
3770         // TODO: JBPNote - have to map order entries to curent SequenceI
3771         // pointers
3772         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3773
3774         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3775                 .getAlignment()));
3776
3777         alignPanel.paintAlignment(true);
3778       }
3779     });
3780   }
3781
3782   /**
3783    * Add a new sort by annotation score menu item
3784    *
3785    * @param sort
3786    *          the menu to add the option to
3787    * @param scoreLabel
3788    *          the label used to retrieve scores for each sequence on the
3789    *          alignment
3790    */
3791   public void addSortByAnnotScoreMenuItem(JMenu sort,
3792           final String scoreLabel)
3793   {
3794     final JMenuItem item = new JMenuItem(scoreLabel);
3795     sort.add(item);
3796     item.addActionListener(new java.awt.event.ActionListener()
3797     {
3798       @Override
3799       public void actionPerformed(ActionEvent e)
3800       {
3801         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3802         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3803                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3804         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3805                 viewport.getAlignment()));
3806         alignPanel.paintAlignment(true);
3807       }
3808     });
3809   }
3810
3811   /**
3812    * last hash for alignment's annotation array - used to minimise cost of
3813    * rebuild.
3814    */
3815   protected int _annotationScoreVectorHash;
3816
3817   /**
3818    * search the alignment and rebuild the sort by annotation score submenu the
3819    * last alignment annotation vector hash is stored to minimize cost of
3820    * rebuilding in subsequence calls.
3821    *
3822    */
3823   @Override
3824   public void buildSortByAnnotationScoresMenu()
3825   {
3826     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3827     {
3828       return;
3829     }
3830
3831     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3832     {
3833       sortByAnnotScore.removeAll();
3834       // almost certainly a quicker way to do this - but we keep it simple
3835       Hashtable scoreSorts = new Hashtable();
3836       AlignmentAnnotation aann[];
3837       for (SequenceI sqa : viewport.getAlignment().getSequences())
3838       {
3839         aann = sqa.getAnnotation();
3840         for (int i = 0; aann != null && i < aann.length; i++)
3841         {
3842           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3843           {
3844             scoreSorts.put(aann[i].label, aann[i].label);
3845           }
3846         }
3847       }
3848       Enumeration labels = scoreSorts.keys();
3849       while (labels.hasMoreElements())
3850       {
3851         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3852                 (String) labels.nextElement());
3853       }
3854       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3855       scoreSorts.clear();
3856
3857       _annotationScoreVectorHash = viewport.getAlignment()
3858               .getAlignmentAnnotation().hashCode();
3859     }
3860   }
3861
3862   /**
3863    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3864    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3865    * call. Listeners are added to remove the menu item when the treePanel is
3866    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3867    * modified.
3868    *
3869    * @param treePanel
3870    *          Displayed tree window.
3871    * @param title
3872    *          SortBy menu item title.
3873    */
3874   @Override
3875   public void buildTreeMenu()
3876   {
3877     calculateTree.removeAll();
3878     // build the calculate menu
3879
3880     for (final String type : new String[] { "NJ", "AV" })
3881     {
3882       String treecalcnm = MessageManager.getString("label.tree_calc_"
3883               + type.toLowerCase());
3884       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3885       {
3886         JMenuItem tm = new JMenuItem();
3887         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3888         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3889                 || sm.isProtein() == !viewport.getAlignment()
3890                         .isNucleotide())
3891         {
3892           String smn = MessageManager.getStringOrReturn(
3893                   "label.score_model_", sm.getName());
3894           final String title = MessageManager.formatMessage(
3895                   "label.treecalc_title", treecalcnm, smn);
3896           tm.setText(title);//
3897           tm.addActionListener(new java.awt.event.ActionListener()
3898           {
3899             @Override
3900             public void actionPerformed(ActionEvent e)
3901             {
3902               newTreePanel(type, pwtype, title);
3903             }
3904           });
3905           calculateTree.add(tm);
3906         }
3907
3908       }
3909     }
3910     sortByTreeMenu.removeAll();
3911
3912     List<Component> comps = PaintRefresher.components.get(viewport
3913             .getSequenceSetId());
3914     List<TreePanel> treePanels = new ArrayList<TreePanel>();
3915     for (Component comp : comps)
3916     {
3917       if (comp instanceof TreePanel)
3918       {
3919         treePanels.add((TreePanel) comp);
3920       }
3921     }
3922
3923     if (treePanels.size() < 1)
3924     {
3925       sortByTreeMenu.setVisible(false);
3926       return;
3927     }
3928
3929     sortByTreeMenu.setVisible(true);
3930
3931     for (final TreePanel tp : treePanels)
3932     {
3933       final JMenuItem item = new JMenuItem(tp.getTitle());
3934       item.addActionListener(new java.awt.event.ActionListener()
3935       {
3936         @Override
3937         public void actionPerformed(ActionEvent e)
3938         {
3939           tp.sortByTree_actionPerformed();
3940           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3941
3942         }
3943       });
3944
3945       sortByTreeMenu.add(item);
3946     }
3947   }
3948
3949   public boolean sortBy(AlignmentOrder alorder, String undoname)
3950   {
3951     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3952     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3953     if (undoname != null)
3954     {
3955       addHistoryItem(new OrderCommand(undoname, oldOrder,
3956               viewport.getAlignment()));
3957     }
3958     alignPanel.paintAlignment(true);
3959     return true;
3960   }
3961
3962   /**
3963    * Work out whether the whole set of sequences or just the selected set will
3964    * be submitted for multiple alignment.
3965    *
3966    */
3967   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3968   {
3969     // Now, check we have enough sequences
3970     AlignmentView msa = null;
3971
3972     if ((viewport.getSelectionGroup() != null)
3973             && (viewport.getSelectionGroup().getSize() > 1))
3974     {
3975       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3976       // some common interface!
3977       /*
3978        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3979        * SequenceI[sz = seqs.getSize(false)];
3980        *
3981        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3982        * seqs.getSequenceAt(i); }
3983        */
3984       msa = viewport.getAlignmentView(true);
3985     }
3986     else if (viewport.getSelectionGroup() != null
3987             && viewport.getSelectionGroup().getSize() == 1)
3988     {
3989       int option = JvOptionPane.showConfirmDialog(this,
3990               MessageManager.getString("warn.oneseq_msainput_selection"),
3991               MessageManager.getString("label.invalid_selection"),
3992               JvOptionPane.OK_CANCEL_OPTION);
3993       if (option == JvOptionPane.OK_OPTION)
3994       {
3995         msa = viewport.getAlignmentView(false);
3996       }
3997     }
3998     else
3999     {
4000       msa = viewport.getAlignmentView(false);
4001     }
4002     return msa;
4003   }
4004
4005   /**
4006    * Decides what is submitted to a secondary structure prediction service: the
4007    * first sequence in the alignment, or in the current selection, or, if the
4008    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4009    * region or the whole alignment. (where the first sequence in the set is the
4010    * one that the prediction will be for).
4011    */
4012   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4013   {
4014     AlignmentView seqs = null;
4015
4016     if ((viewport.getSelectionGroup() != null)
4017             && (viewport.getSelectionGroup().getSize() > 0))
4018     {
4019       seqs = viewport.getAlignmentView(true);
4020     }
4021     else
4022     {
4023       seqs = viewport.getAlignmentView(false);
4024     }
4025     // limit sequences - JBPNote in future - could spawn multiple prediction
4026     // jobs
4027     // TODO: viewport.getAlignment().isAligned is a global state - the local
4028     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4029     if (!viewport.getAlignment().isAligned(false))
4030     {
4031       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4032       // TODO: if seqs.getSequences().length>1 then should really have warned
4033       // user!
4034
4035     }
4036     return seqs;
4037   }
4038
4039   /**
4040    * DOCUMENT ME!
4041    *
4042    * @param e
4043    *          DOCUMENT ME!
4044    */
4045   @Override
4046   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4047   {
4048     // Pick the tree file
4049     JalviewFileChooser chooser = new JalviewFileChooser(
4050             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4051     chooser.setFileView(new JalviewFileView());
4052     chooser.setDialogTitle(MessageManager
4053             .getString("label.select_newick_like_tree_file"));
4054     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4055
4056     int value = chooser.showOpenDialog(null);
4057
4058     if (value == JalviewFileChooser.APPROVE_OPTION)
4059     {
4060       String choice = chooser.getSelectedFile().getPath();
4061       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4062       jalview.io.NewickFile fin = null;
4063       try
4064       {
4065         fin = new NewickFile(choice, DataSourceType.FILE);
4066         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4067       } catch (Exception ex)
4068       {
4069         JvOptionPane
4070                 .showMessageDialog(
4071                         Desktop.desktop,
4072                         ex.getMessage(),
4073                         MessageManager
4074                                 .getString("label.problem_reading_tree_file"),
4075                         JvOptionPane.WARNING_MESSAGE);
4076         ex.printStackTrace();
4077       }
4078       if (fin != null && fin.hasWarningMessage())
4079       {
4080         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4081                 .getWarningMessage(), MessageManager
4082                 .getString("label.possible_problem_with_tree_file"),
4083                 JvOptionPane.WARNING_MESSAGE);
4084       }
4085     }
4086   }
4087
4088   public TreePanel ShowNewickTree(NewickFile nf, String title)
4089   {
4090     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4091   }
4092
4093   public TreePanel ShowNewickTree(NewickFile nf, String title,
4094           AlignmentView input)
4095   {
4096     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4097   }
4098
4099   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4100           int h, int x, int y)
4101   {
4102     return ShowNewickTree(nf, title, null, w, h, x, y);
4103   }
4104
4105   /**
4106    * Add a treeviewer for the tree extracted from a newick file object to the
4107    * current alignment view
4108    *
4109    * @param nf
4110    *          the tree
4111    * @param title
4112    *          tree viewer title
4113    * @param input
4114    *          Associated alignment input data (or null)
4115    * @param w
4116    *          width
4117    * @param h
4118    *          height
4119    * @param x
4120    *          position
4121    * @param y
4122    *          position
4123    * @return TreePanel handle
4124    */
4125   public TreePanel ShowNewickTree(NewickFile nf, String title,
4126           AlignmentView input, int w, int h, int x, int y)
4127   {
4128     TreePanel tp = null;
4129
4130     try
4131     {
4132       nf.parse();
4133
4134       if (nf.getTree() != null)
4135       {
4136         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4137
4138         tp.setSize(w, h);
4139
4140         if (x > 0 && y > 0)
4141         {
4142           tp.setLocation(x, y);
4143         }
4144
4145         Desktop.addInternalFrame(tp, title, w, h);
4146       }
4147     } catch (Exception ex)
4148     {
4149       ex.printStackTrace();
4150     }
4151
4152     return tp;
4153   }
4154
4155   private boolean buildingMenu = false;
4156
4157   /**
4158    * Generates menu items and listener event actions for web service clients
4159    *
4160    */
4161   public void BuildWebServiceMenu()
4162   {
4163     while (buildingMenu)
4164     {
4165       try
4166       {
4167         System.err.println("Waiting for building menu to finish.");
4168         Thread.sleep(10);
4169       } catch (Exception e)
4170       {
4171       }
4172     }
4173     final AlignFrame me = this;
4174     buildingMenu = true;
4175     new Thread(new Runnable()
4176     {
4177       @Override
4178       public void run()
4179       {
4180         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4181         try
4182         {
4183           // System.err.println("Building ws menu again "
4184           // + Thread.currentThread());
4185           // TODO: add support for context dependent disabling of services based
4186           // on
4187           // alignment and current selection
4188           // TODO: add additional serviceHandle parameter to specify abstract
4189           // handler
4190           // class independently of AbstractName
4191           // TODO: add in rediscovery GUI function to restart discoverer
4192           // TODO: group services by location as well as function and/or
4193           // introduce
4194           // object broker mechanism.
4195           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4196           final IProgressIndicator af = me;
4197
4198           /*
4199            * do not i18n these strings - they are hard-coded in class
4200            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4201            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4202            */
4203           final JMenu msawsmenu = new JMenu("Alignment");
4204           final JMenu secstrmenu = new JMenu(
4205                   "Secondary Structure Prediction");
4206           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4207           final JMenu analymenu = new JMenu("Analysis");
4208           final JMenu dismenu = new JMenu("Protein Disorder");
4209           // JAL-940 - only show secondary structure prediction services from
4210           // the legacy server
4211           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4212               // &&
4213           Discoverer.services != null && (Discoverer.services.size() > 0))
4214           {
4215             // TODO: refactor to allow list of AbstractName/Handler bindings to
4216             // be
4217             // stored or retrieved from elsewhere
4218             // No MSAWS used any more:
4219             // Vector msaws = null; // (Vector)
4220             // Discoverer.services.get("MsaWS");
4221             Vector secstrpr = (Vector) Discoverer.services
4222                     .get("SecStrPred");
4223             if (secstrpr != null)
4224             {
4225               // Add any secondary structure prediction services
4226               for (int i = 0, j = secstrpr.size(); i < j; i++)
4227               {
4228                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4229                         .get(i);
4230                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4231                         .getServiceClient(sh);
4232                 int p = secstrmenu.getItemCount();
4233                 impl.attachWSMenuEntry(secstrmenu, me);
4234                 int q = secstrmenu.getItemCount();
4235                 for (int litm = p; litm < q; litm++)
4236                 {
4237                   legacyItems.add(secstrmenu.getItem(litm));
4238                 }
4239               }
4240             }
4241           }
4242
4243           // Add all submenus in the order they should appear on the web
4244           // services menu
4245           wsmenu.add(msawsmenu);
4246           wsmenu.add(secstrmenu);
4247           wsmenu.add(dismenu);
4248           wsmenu.add(analymenu);
4249           // No search services yet
4250           // wsmenu.add(seqsrchmenu);
4251
4252           javax.swing.SwingUtilities.invokeLater(new Runnable()
4253           {
4254             @Override
4255             public void run()
4256             {
4257               try
4258               {
4259                 webService.removeAll();
4260                 // first, add discovered services onto the webservices menu
4261                 if (wsmenu.size() > 0)
4262                 {
4263                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4264                   {
4265                     webService.add(wsmenu.get(i));
4266                   }
4267                 }
4268                 else
4269                 {
4270                   webService.add(me.webServiceNoServices);
4271                 }
4272                 // TODO: move into separate menu builder class.
4273                 boolean new_sspred = false;
4274                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4275                 {
4276                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4277                   if (jws2servs != null)
4278                   {
4279                     if (jws2servs.hasServices())
4280                     {
4281                       jws2servs.attachWSMenuEntry(webService, me);
4282                       for (Jws2Instance sv : jws2servs.getServices())
4283                       {
4284                         if (sv.description.toLowerCase().contains("jpred"))
4285                         {
4286                           for (JMenuItem jmi : legacyItems)
4287                           {
4288                             jmi.setVisible(false);
4289                           }
4290                         }
4291                       }
4292
4293                     }
4294                     if (jws2servs.isRunning())
4295                     {
4296                       JMenuItem tm = new JMenuItem(
4297                               "Still discovering JABA Services");
4298                       tm.setEnabled(false);
4299                       webService.add(tm);
4300                     }
4301                   }
4302                 }
4303                 build_urlServiceMenu(me.webService);
4304                 build_fetchdbmenu(webService);
4305                 for (JMenu item : wsmenu)
4306                 {
4307                   if (item.getItemCount() == 0)
4308                   {
4309                     item.setEnabled(false);
4310                   }
4311                   else
4312                   {
4313                     item.setEnabled(true);
4314                   }
4315                 }
4316               } catch (Exception e)
4317               {
4318                 Cache.log
4319                         .debug("Exception during web service menu building process.",
4320                                 e);
4321               }
4322             }
4323           });
4324         } catch (Exception e)
4325         {
4326         }
4327         buildingMenu = false;
4328       }
4329     }).start();
4330
4331   }
4332
4333   /**
4334    * construct any groupURL type service menu entries.
4335    *
4336    * @param webService
4337    */
4338   private void build_urlServiceMenu(JMenu webService)
4339   {
4340     // TODO: remove this code when 2.7 is released
4341     // DEBUG - alignmentView
4342     /*
4343      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4344      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4345      *
4346      * @Override public void actionPerformed(ActionEvent e) {
4347      * jalview.datamodel.AlignmentView
4348      * .testSelectionViews(af.viewport.getAlignment(),
4349      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4350      *
4351      * }); webService.add(testAlView);
4352      */
4353     // TODO: refactor to RestClient discoverer and merge menu entries for
4354     // rest-style services with other types of analysis/calculation service
4355     // SHmmr test client - still being implemented.
4356     // DEBUG - alignmentView
4357
4358     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4359             .getRestClients())
4360     {
4361       client.attachWSMenuEntry(
4362               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4363               this);
4364     }
4365   }
4366
4367   /**
4368    * Searches the alignment sequences for xRefs and builds the Show
4369    * Cross-References menu (formerly called Show Products), with database
4370    * sources for which cross-references are found (protein sources for a
4371    * nucleotide alignment and vice versa)
4372    *
4373    * @return true if Show Cross-references menu should be enabled
4374    */
4375   public boolean canShowProducts()
4376   {
4377     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4378     AlignmentI dataset = viewport.getAlignment().getDataset();
4379
4380     showProducts.removeAll();
4381     final boolean dna = viewport.getAlignment().isNucleotide();
4382
4383     if (seqs == null || seqs.length == 0)
4384     {
4385       // nothing to see here.
4386       return false;
4387     }
4388
4389     boolean showp = false;
4390     try
4391     {
4392       List<String> ptypes = new CrossRef(seqs, dataset)
4393               .findXrefSourcesForSequences(dna);
4394
4395       for (final String source : ptypes)
4396       {
4397         showp = true;
4398         final AlignFrame af = this;
4399         JMenuItem xtype = new JMenuItem(source);
4400         xtype.addActionListener(new ActionListener()
4401         {
4402           @Override
4403           public void actionPerformed(ActionEvent e)
4404           {
4405             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4406           }
4407         });
4408         showProducts.add(xtype);
4409       }
4410       showProducts.setVisible(showp);
4411       showProducts.setEnabled(showp);
4412     } catch (Exception e)
4413     {
4414       Cache.log
4415               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4416                       e);
4417       return false;
4418     }
4419     return showp;
4420   }
4421
4422   /**
4423    * Finds and displays cross-references for the selected sequences (protein
4424    * products for nucleotide sequences, dna coding sequences for peptides).
4425    *
4426    * @param sel
4427    *          the sequences to show cross-references for
4428    * @param dna
4429    *          true if from a nucleotide alignment (so showing proteins)
4430    * @param source
4431    *          the database to show cross-references for
4432    */
4433   protected void showProductsFor(final SequenceI[] sel,
4434           final boolean _odna, final String source)
4435   {
4436     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4437             .start();
4438   }
4439
4440   /**
4441    * Construct and display a new frame containing the translation of this
4442    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4443    */
4444   @Override
4445   public void showTranslation_actionPerformed(ActionEvent e)
4446   {
4447     AlignmentI al = null;
4448     try
4449     {
4450       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4451
4452       al = dna.translateCdna();
4453     } catch (Exception ex)
4454     {
4455       jalview.bin.Cache.log.error(
4456               "Exception during translation. Please report this !", ex);
4457       final String msg = MessageManager
4458               .getString("label.error_when_translating_sequences_submit_bug_report");
4459       final String errorTitle = MessageManager
4460               .getString("label.implementation_error")
4461               + MessageManager.getString("label.translation_failed");
4462       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4463               JvOptionPane.ERROR_MESSAGE);
4464       return;
4465     }
4466     if (al == null || al.getHeight() == 0)
4467     {
4468       final String msg = MessageManager
4469               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4470       final String errorTitle = MessageManager
4471               .getString("label.translation_failed");
4472       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4473               JvOptionPane.WARNING_MESSAGE);
4474     }
4475     else
4476     {
4477       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4478       af.setFileFormat(this.currentFileFormat);
4479       final String newTitle = MessageManager.formatMessage(
4480               "label.translation_of_params",
4481               new Object[] { this.getTitle() });
4482       af.setTitle(newTitle);
4483       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4484       {
4485         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4486         viewport.openSplitFrame(af, new Alignment(seqs));
4487       }
4488       else
4489       {
4490         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4491                 DEFAULT_HEIGHT);
4492       }
4493     }
4494   }
4495
4496   /**
4497    * Set the file format
4498    *
4499    * @param format
4500    */
4501   public void setFileFormat(FileFormatI format)
4502   {
4503     this.currentFileFormat = format;
4504   }
4505
4506   /**
4507    * Try to load a features file onto the alignment.
4508    *
4509    * @param file
4510    *          contents or path to retrieve file
4511    * @param sourceType
4512    *          access mode of file (see jalview.io.AlignFile)
4513    * @return true if features file was parsed correctly.
4514    */
4515   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4516   {
4517     return avc.parseFeaturesFile(file, sourceType,
4518             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4519
4520   }
4521
4522   @Override
4523   public void refreshFeatureUI(boolean enableIfNecessary)
4524   {
4525     // note - currently this is only still here rather than in the controller
4526     // because of the featureSettings hard reference that is yet to be
4527     // abstracted
4528     if (enableIfNecessary)
4529     {
4530       viewport.setShowSequenceFeatures(true);
4531       showSeqFeatures.setSelected(true);
4532     }
4533
4534   }
4535
4536   @Override
4537   public void dragEnter(DropTargetDragEvent evt)
4538   {
4539   }
4540
4541   @Override
4542   public void dragExit(DropTargetEvent evt)
4543   {
4544   }
4545
4546   @Override
4547   public void dragOver(DropTargetDragEvent evt)
4548   {
4549   }
4550
4551   @Override
4552   public void dropActionChanged(DropTargetDragEvent evt)
4553   {
4554   }
4555
4556   @Override
4557   public void drop(DropTargetDropEvent evt)
4558   {
4559     // JAL-1552 - acceptDrop required before getTransferable call for
4560     // Java's Transferable for native dnd
4561     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4562     Transferable t = evt.getTransferable();
4563     List<String> files = new ArrayList<String>();
4564     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4565
4566     try
4567     {
4568       Desktop.transferFromDropTarget(files, protocols, evt, t);
4569     } catch (Exception e)
4570     {
4571       e.printStackTrace();
4572     }
4573     if (files != null)
4574     {
4575       try
4576       {
4577         // check to see if any of these files have names matching sequences in
4578         // the alignment
4579         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4580                 .getAlignment().getSequencesArray());
4581         /**
4582          * Object[] { String,SequenceI}
4583          */
4584         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4585         ArrayList<String> filesnotmatched = new ArrayList<String>();
4586         for (int i = 0; i < files.size(); i++)
4587         {
4588           String file = files.get(i).toString();
4589           String pdbfn = "";
4590           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4591           if (protocol == DataSourceType.FILE)
4592           {
4593             File fl = new File(file);
4594             pdbfn = fl.getName();
4595           }
4596           else if (protocol == DataSourceType.URL)
4597           {
4598             URL url = new URL(file);
4599             pdbfn = url.getFile();
4600           }
4601           if (pdbfn.length() > 0)
4602           {
4603             // attempt to find a match in the alignment
4604             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4605             int l = 0, c = pdbfn.indexOf(".");
4606             while (mtch == null && c != -1)
4607             {
4608               do
4609               {
4610                 l = c;
4611               } while ((c = pdbfn.indexOf(".", l)) > l);
4612               if (l > -1)
4613               {
4614                 pdbfn = pdbfn.substring(0, l);
4615               }
4616               mtch = idm.findAllIdMatches(pdbfn);
4617             }
4618             if (mtch != null)
4619             {
4620               FileFormatI type = null;
4621               try
4622               {
4623                 type = new IdentifyFile().identify(file, protocol);
4624               } catch (Exception ex)
4625               {
4626                 type = null;
4627               }
4628               if (type != null && type.isStructureFile())
4629               {
4630                 filesmatched.add(new Object[] { file, protocol, mtch });
4631                 continue;
4632               }
4633             }
4634             // File wasn't named like one of the sequences or wasn't a PDB file.
4635             filesnotmatched.add(file);
4636           }
4637         }
4638         int assocfiles = 0;
4639         if (filesmatched.size() > 0)
4640         {
4641           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4642                   || JvOptionPane
4643                           .showConfirmDialog(
4644                                   this,
4645                                   MessageManager
4646                                           .formatMessage(
4647                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4648                                                   new Object[] { Integer
4649                                                           .valueOf(
4650                                                                   filesmatched
4651                                                                           .size())
4652                                                           .toString() }),
4653                                   MessageManager
4654                                           .getString("label.automatically_associate_structure_files_by_name"),
4655                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4656
4657           {
4658             for (Object[] fm : filesmatched)
4659             {
4660               // try and associate
4661               // TODO: may want to set a standard ID naming formalism for
4662               // associating PDB files which have no IDs.
4663               for (SequenceI toassoc : (SequenceI[]) fm[2])
4664               {
4665                 PDBEntry pe = new AssociatePdbFileWithSeq()
4666                         .associatePdbWithSeq((String) fm[0],
4667                                 (DataSourceType) fm[1], toassoc, false,
4668                                 Desktop.instance);
4669                 if (pe != null)
4670                 {
4671                   System.err.println("Associated file : "
4672                           + ((String) fm[0]) + " with "
4673                           + toassoc.getDisplayId(true));
4674                   assocfiles++;
4675                 }
4676               }
4677               alignPanel.paintAlignment(true);
4678             }
4679           }
4680         }
4681         if (filesnotmatched.size() > 0)
4682         {
4683           if (assocfiles > 0
4684                   && (Cache.getDefault(
4685                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4686                           .showConfirmDialog(
4687                                   this,
4688                                   "<html>"
4689                                           + MessageManager
4690                                                   .formatMessage(
4691                                                           "label.ignore_unmatched_dropped_files_info",
4692                                                           new Object[] { Integer
4693                                                                   .valueOf(
4694                                                                           filesnotmatched
4695                                                                                   .size())
4696                                                                   .toString() })
4697                                           + "</html>",
4698                                   MessageManager
4699                                           .getString("label.ignore_unmatched_dropped_files"),
4700                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4701           {
4702             return;
4703           }
4704           for (String fn : filesnotmatched)
4705           {
4706             loadJalviewDataFile(fn, null, null, null);
4707           }
4708
4709         }
4710       } catch (Exception ex)
4711       {
4712         ex.printStackTrace();
4713       }
4714     }
4715   }
4716
4717   /**
4718    * Attempt to load a "dropped" file or URL string: First by testing whether
4719    * it's an Annotation file, then a JNet file, and finally a features file. If
4720    * all are false then the user may have dropped an alignment file onto this
4721    * AlignFrame.
4722    *
4723    * @param file
4724    *          either a filename or a URL string.
4725    */
4726   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4727           FileFormatI format, SequenceI assocSeq)
4728   {
4729     try
4730     {
4731       if (sourceType == null)
4732       {
4733         sourceType = FormatAdapter.checkProtocol(file);
4734       }
4735       // if the file isn't identified, or not positively identified as some
4736       // other filetype (PFAM is default unidentified alignment file type) then
4737       // try to parse as annotation.
4738       boolean isAnnotation = (format == null || FileFormat.Pfam
4739               .equals(format)) ? new AnnotationFile()
4740               .annotateAlignmentView(viewport, file, sourceType) : false;
4741
4742       if (!isAnnotation)
4743       {
4744         // first see if its a T-COFFEE score file
4745         TCoffeeScoreFile tcf = null;
4746         try
4747         {
4748           tcf = new TCoffeeScoreFile(file, sourceType);
4749           if (tcf.isValid())
4750           {
4751             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4752             {
4753               buildColourMenu();
4754               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4755               isAnnotation = true;
4756               statusBar
4757                       .setText(MessageManager
4758                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4759             }
4760             else
4761             {
4762               // some problem - if no warning its probable that the ID matching
4763               // process didn't work
4764               JvOptionPane
4765                       .showMessageDialog(
4766                               Desktop.desktop,
4767                               tcf.getWarningMessage() == null ? MessageManager
4768                                       .getString("label.check_file_matches_sequence_ids_alignment")
4769                                       : tcf.getWarningMessage(),
4770                               MessageManager
4771                                       .getString("label.problem_reading_tcoffee_score_file"),
4772                               JvOptionPane.WARNING_MESSAGE);
4773             }
4774           }
4775           else
4776           {
4777             tcf = null;
4778           }
4779         } catch (Exception x)
4780         {
4781           Cache.log
4782                   .debug("Exception when processing data source as T-COFFEE score file",
4783                           x);
4784           tcf = null;
4785         }
4786         if (tcf == null)
4787         {
4788           // try to see if its a JNet 'concise' style annotation file *before*
4789           // we
4790           // try to parse it as a features file
4791           if (format == null)
4792           {
4793             format = new IdentifyFile().identify(file, sourceType);
4794           }
4795           if (FileFormat.Jnet.equals(format))
4796           {
4797             JPredFile predictions = new JPredFile(
4798                     file, sourceType);
4799             new JnetAnnotationMaker();
4800             JnetAnnotationMaker.add_annotation(predictions,
4801                     viewport.getAlignment(), 0, false);
4802             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4803             viewport.getAlignment().setSeqrep(repseq);
4804             ColumnSelection cs = new ColumnSelection();
4805             cs.hideInsertionsFor(repseq);
4806             viewport.setColumnSelection(cs);
4807             isAnnotation = true;
4808           }
4809           // else if (IdentifyFile.FeaturesFile.equals(format))
4810           else if (FileFormat.Features.equals(format))
4811           {
4812             if (parseFeaturesFile(file, sourceType))
4813             {
4814               alignPanel.paintAlignment(true);
4815             }
4816           }
4817           else
4818           {
4819             new FileLoader().LoadFile(viewport, file, sourceType, format);
4820           }
4821         }
4822       }
4823       if (isAnnotation)
4824       {
4825
4826         alignPanel.adjustAnnotationHeight();
4827         viewport.updateSequenceIdColours();
4828         buildSortByAnnotationScoresMenu();
4829         alignPanel.paintAlignment(true);
4830       }
4831     } catch (Exception ex)
4832     {
4833       ex.printStackTrace();
4834     } catch (OutOfMemoryError oom)
4835     {
4836       try
4837       {
4838         System.gc();
4839       } catch (Exception x)
4840       {
4841       }
4842       new OOMWarning(
4843               "loading data "
4844                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4845                               : "using " + sourceType + " from " + file)
4846                               : ".")
4847                       + (format != null ? "(parsing as '" + format
4848                               + "' file)" : ""), oom, Desktop.desktop);
4849     }
4850   }
4851
4852   /**
4853    * Method invoked by the ChangeListener on the tabbed pane, in other words
4854    * when a different tabbed pane is selected by the user or programmatically.
4855    */
4856   @Override
4857   public void tabSelectionChanged(int index)
4858   {
4859     if (index > -1)
4860     {
4861       alignPanel = alignPanels.get(index);
4862       viewport = alignPanel.av;
4863       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4864       setMenusFromViewport(viewport);
4865     }
4866
4867     /*
4868      * If there is a frame linked to this one in a SplitPane, switch it to the
4869      * same view tab index. No infinite recursion of calls should happen, since
4870      * tabSelectionChanged() should not get invoked on setting the selected
4871      * index to an unchanged value. Guard against setting an invalid index
4872      * before the new view peer tab has been created.
4873      */
4874     final AlignViewportI peer = viewport.getCodingComplement();
4875     if (peer != null)
4876     {
4877       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4878       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4879       {
4880         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4881       }
4882     }
4883   }
4884
4885   /**
4886    * On right mouse click on view tab, prompt for and set new view name.
4887    */
4888   @Override
4889   public void tabbedPane_mousePressed(MouseEvent e)
4890   {
4891     if (e.isPopupTrigger())
4892     {
4893       String msg = MessageManager.getString("label.enter_view_name");
4894       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4895               JvOptionPane.QUESTION_MESSAGE);
4896
4897       if (reply != null)
4898       {
4899         viewport.viewName = reply;
4900         // TODO warn if reply is in getExistingViewNames()?
4901         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4902       }
4903     }
4904   }
4905
4906   public AlignViewport getCurrentView()
4907   {
4908     return viewport;
4909   }
4910
4911   /**
4912    * Open the dialog for regex description parsing.
4913    */
4914   @Override
4915   protected void extractScores_actionPerformed(ActionEvent e)
4916   {
4917     ParseProperties pp = new jalview.analysis.ParseProperties(
4918             viewport.getAlignment());
4919     // TODO: verify regex and introduce GUI dialog for version 2.5
4920     // if (pp.getScoresFromDescription("col", "score column ",
4921     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4922     // true)>0)
4923     if (pp.getScoresFromDescription("description column",
4924             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4925     {
4926       buildSortByAnnotationScoresMenu();
4927     }
4928   }
4929
4930   /*
4931    * (non-Javadoc)
4932    *
4933    * @see
4934    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4935    * )
4936    */
4937   @Override
4938   protected void showDbRefs_actionPerformed(ActionEvent e)
4939   {
4940     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4941   }
4942
4943   /*
4944    * (non-Javadoc)
4945    *
4946    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4947    * ActionEvent)
4948    */
4949   @Override
4950   protected void showNpFeats_actionPerformed(ActionEvent e)
4951   {
4952     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4953   }
4954
4955   /**
4956    * find the viewport amongst the tabs in this alignment frame and close that
4957    * tab
4958    *
4959    * @param av
4960    */
4961   public boolean closeView(AlignViewportI av)
4962   {
4963     if (viewport == av)
4964     {
4965       this.closeMenuItem_actionPerformed(false);
4966       return true;
4967     }
4968     Component[] comp = tabbedPane.getComponents();
4969     for (int i = 0; comp != null && i < comp.length; i++)
4970     {
4971       if (comp[i] instanceof AlignmentPanel)
4972       {
4973         if (((AlignmentPanel) comp[i]).av == av)
4974         {
4975           // close the view.
4976           closeView((AlignmentPanel) comp[i]);
4977           return true;
4978         }
4979       }
4980     }
4981     return false;
4982   }
4983
4984   protected void build_fetchdbmenu(JMenu webService)
4985   {
4986     // Temporary hack - DBRef Fetcher always top level ws entry.
4987     // TODO We probably want to store a sequence database checklist in
4988     // preferences and have checkboxes.. rather than individual sources selected
4989     // here
4990     final JMenu rfetch = new JMenu(
4991             MessageManager.getString("action.fetch_db_references"));
4992     rfetch.setToolTipText(MessageManager
4993             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4994     webService.add(rfetch);
4995
4996     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4997             MessageManager.getString("option.trim_retrieved_seqs"));
4998     trimrs.setToolTipText(MessageManager
4999             .getString("label.trim_retrieved_sequences"));
5000     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5001     trimrs.addActionListener(new ActionListener()
5002     {
5003       @Override
5004       public void actionPerformed(ActionEvent e)
5005       {
5006         trimrs.setSelected(trimrs.isSelected());
5007         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5008                 Boolean.valueOf(trimrs.isSelected()).toString());
5009       };
5010     });
5011     rfetch.add(trimrs);
5012     JMenuItem fetchr = new JMenuItem(
5013             MessageManager.getString("label.standard_databases"));
5014     fetchr.setToolTipText(MessageManager
5015             .getString("label.fetch_embl_uniprot"));
5016     fetchr.addActionListener(new ActionListener()
5017     {
5018
5019       @Override
5020       public void actionPerformed(ActionEvent e)
5021       {
5022         new Thread(new Runnable()
5023         {
5024           @Override
5025           public void run()
5026           {
5027             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5028                     .getAlignment().isNucleotide();
5029             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5030                     .getSequenceSelection(), alignPanel.alignFrame, null,
5031                     alignPanel.alignFrame.featureSettings, isNucleotide);
5032             dbRefFetcher.addListener(new FetchFinishedListenerI()
5033             {
5034               @Override
5035               public void finished()
5036               {
5037                 AlignFrame.this.setMenusForViewport();
5038               }
5039             });
5040             dbRefFetcher.fetchDBRefs(false);
5041           }
5042         }).start();
5043
5044       }
5045
5046     });
5047     rfetch.add(fetchr);
5048     final AlignFrame me = this;
5049     new Thread(new Runnable()
5050     {
5051       @Override
5052       public void run()
5053       {
5054         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5055                 .getSequenceFetcherSingleton(me);
5056         javax.swing.SwingUtilities.invokeLater(new Runnable()
5057         {
5058           @Override
5059           public void run()
5060           {
5061             String[] dbclasses = sf.getOrderedSupportedSources();
5062             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5063             // jalview.util.QuickSort.sort(otherdb, otherdb);
5064             List<DbSourceProxy> otherdb;
5065             JMenu dfetch = new JMenu();
5066             JMenu ifetch = new JMenu();
5067             JMenuItem fetchr = null;
5068             int comp = 0, icomp = 0, mcomp = 15;
5069             String mname = null;
5070             int dbi = 0;
5071             for (String dbclass : dbclasses)
5072             {
5073               otherdb = sf.getSourceProxy(dbclass);
5074               // add a single entry for this class, or submenu allowing 'fetch
5075               // all' or pick one
5076               if (otherdb == null || otherdb.size() < 1)
5077               {
5078                 continue;
5079               }
5080               // List<DbSourceProxy> dbs=otherdb;
5081               // otherdb=new ArrayList<DbSourceProxy>();
5082               // for (DbSourceProxy db:dbs)
5083               // {
5084               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5085               // }
5086               if (mname == null)
5087               {
5088                 mname = "From " + dbclass;
5089               }
5090               if (otherdb.size() == 1)
5091               {
5092                 final DbSourceProxy[] dassource = otherdb
5093                         .toArray(new DbSourceProxy[0]);
5094                 DbSourceProxy src = otherdb.get(0);
5095                 fetchr = new JMenuItem(src.getDbSource());
5096                 fetchr.addActionListener(new ActionListener()
5097                 {
5098
5099                   @Override
5100                   public void actionPerformed(ActionEvent e)
5101                   {
5102                     new Thread(new Runnable()
5103                     {
5104
5105                       @Override
5106                       public void run()
5107                       {
5108                         boolean isNucleotide = alignPanel.alignFrame
5109                                 .getViewport().getAlignment()
5110                                 .isNucleotide();
5111                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5112                                 alignPanel.av.getSequenceSelection(),
5113                                 alignPanel.alignFrame, dassource,
5114                                 alignPanel.alignFrame.featureSettings,
5115                                 isNucleotide);
5116                         dbRefFetcher
5117                                 .addListener(new FetchFinishedListenerI()
5118                                 {
5119                                   @Override
5120                                   public void finished()
5121                                   {
5122                                     AlignFrame.this.setMenusForViewport();
5123                                   }
5124                                 });
5125                         dbRefFetcher.fetchDBRefs(false);
5126                       }
5127                     }).start();
5128                   }
5129
5130                 });
5131                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5132                         MessageManager.formatMessage(
5133                                 "label.fetch_retrieve_from",
5134                                 new Object[] { src.getDbName() })));
5135                 dfetch.add(fetchr);
5136                 comp++;
5137               }
5138               else
5139               {
5140                 final DbSourceProxy[] dassource = otherdb
5141                         .toArray(new DbSourceProxy[0]);
5142                 // fetch all entry
5143                 DbSourceProxy src = otherdb.get(0);
5144                 fetchr = new JMenuItem(MessageManager.formatMessage(
5145                         "label.fetch_all_param",
5146                         new Object[] { src.getDbSource() }));
5147                 fetchr.addActionListener(new ActionListener()
5148                 {
5149                   @Override
5150                   public void actionPerformed(ActionEvent e)
5151                   {
5152                     new Thread(new Runnable()
5153                     {
5154
5155                       @Override
5156                       public void run()
5157                       {
5158                         boolean isNucleotide = alignPanel.alignFrame
5159                                 .getViewport().getAlignment()
5160                                 .isNucleotide();
5161                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5162                                 alignPanel.av.getSequenceSelection(),
5163                                 alignPanel.alignFrame, dassource,
5164                                 alignPanel.alignFrame.featureSettings,
5165                                 isNucleotide);
5166                         dbRefFetcher
5167                                 .addListener(new FetchFinishedListenerI()
5168                                 {
5169                                   @Override
5170                                   public void finished()
5171                                   {
5172                                     AlignFrame.this.setMenusForViewport();
5173                                   }
5174                                 });
5175                         dbRefFetcher.fetchDBRefs(false);
5176                       }
5177                     }).start();
5178                   }
5179                 });
5180
5181                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5182                         MessageManager.formatMessage(
5183                                 "label.fetch_retrieve_from_all_sources",
5184                                 new Object[] {
5185                                     Integer.valueOf(otherdb.size())
5186                                             .toString(), src.getDbSource(),
5187                                     src.getDbName() })));
5188                 dfetch.add(fetchr);
5189                 comp++;
5190                 // and then build the rest of the individual menus
5191                 ifetch = new JMenu(MessageManager.formatMessage(
5192                         "label.source_from_db_source",
5193                         new Object[] { src.getDbSource() }));
5194                 icomp = 0;
5195                 String imname = null;
5196                 int i = 0;
5197                 for (DbSourceProxy sproxy : otherdb)
5198                 {
5199                   String dbname = sproxy.getDbName();
5200                   String sname = dbname.length() > 5 ? dbname.substring(0,
5201                           5) + "..." : dbname;
5202                   String msname = dbname.length() > 10 ? dbname.substring(
5203                           0, 10) + "..." : dbname;
5204                   if (imname == null)
5205                   {
5206                     imname = MessageManager.formatMessage(
5207                             "label.from_msname", new Object[] { sname });
5208                   }
5209                   fetchr = new JMenuItem(msname);
5210                   final DbSourceProxy[] dassrc = { sproxy };
5211                   fetchr.addActionListener(new ActionListener()
5212                   {
5213
5214                     @Override
5215                     public void actionPerformed(ActionEvent e)
5216                     {
5217                       new Thread(new Runnable()
5218                       {
5219
5220                         @Override
5221                         public void run()
5222                         {
5223                           boolean isNucleotide = alignPanel.alignFrame
5224                                   .getViewport().getAlignment()
5225                                   .isNucleotide();
5226                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5227                                   alignPanel.av.getSequenceSelection(),
5228                                   alignPanel.alignFrame, dassrc,
5229                                   alignPanel.alignFrame.featureSettings,
5230                                   isNucleotide);
5231                           dbRefFetcher
5232                                   .addListener(new FetchFinishedListenerI()
5233                                   {
5234                                     @Override
5235                                     public void finished()
5236                                     {
5237                                       AlignFrame.this.setMenusForViewport();
5238                                     }
5239                                   });
5240                           dbRefFetcher.fetchDBRefs(false);
5241                         }
5242                       }).start();
5243                     }
5244
5245                   });
5246                   fetchr.setToolTipText("<html>"
5247                           + MessageManager.formatMessage(
5248                                   "label.fetch_retrieve_from", new Object[]
5249                                   { dbname }));
5250                   ifetch.add(fetchr);
5251                   ++i;
5252                   if (++icomp >= mcomp || i == (otherdb.size()))
5253                   {
5254                     ifetch.setText(MessageManager.formatMessage(
5255                             "label.source_to_target", imname, sname));
5256                     dfetch.add(ifetch);
5257                     ifetch = new JMenu();
5258                     imname = null;
5259                     icomp = 0;
5260                     comp++;
5261                   }
5262                 }
5263               }
5264               ++dbi;
5265               if (comp >= mcomp || dbi >= (dbclasses.length))
5266               {
5267                 dfetch.setText(MessageManager.formatMessage(
5268                         "label.source_to_target", mname, dbclass));
5269                 rfetch.add(dfetch);
5270                 dfetch = new JMenu();
5271                 mname = null;
5272                 comp = 0;
5273               }
5274             }
5275           }
5276         });
5277       }
5278     }).start();
5279
5280   }
5281
5282   /**
5283    * Left justify the whole alignment.
5284    */
5285   @Override
5286   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5287   {
5288     AlignmentI al = viewport.getAlignment();
5289     al.justify(false);
5290     viewport.firePropertyChange("alignment", null, al);
5291   }
5292
5293   /**
5294    * Right justify the whole alignment.
5295    */
5296   @Override
5297   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5298   {
5299     AlignmentI al = viewport.getAlignment();
5300     al.justify(true);
5301     viewport.firePropertyChange("alignment", null, al);
5302   }
5303
5304   @Override
5305   public void setShowSeqFeatures(boolean b)
5306   {
5307     showSeqFeatures.setSelected(b);
5308     viewport.setShowSequenceFeatures(b);
5309   }
5310
5311   /*
5312    * (non-Javadoc)
5313    *
5314    * @see
5315    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5316    * awt.event.ActionEvent)
5317    */
5318   @Override
5319   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5320   {
5321     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5322     alignPanel.paintAlignment(true);
5323   }
5324
5325   /*
5326    * (non-Javadoc)
5327    *
5328    * @see
5329    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5330    * .ActionEvent)
5331    */
5332   @Override
5333   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5334   {
5335     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5336     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5337
5338   }
5339
5340   /*
5341    * (non-Javadoc)
5342    *
5343    * @see
5344    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5345    * .event.ActionEvent)
5346    */
5347   @Override
5348   protected void showGroupConservation_actionPerformed(ActionEvent e)
5349   {
5350     viewport.setShowGroupConservation(showGroupConservation.getState());
5351     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5352   }
5353
5354   /*
5355    * (non-Javadoc)
5356    *
5357    * @see
5358    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5359    * .event.ActionEvent)
5360    */
5361   @Override
5362   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5363   {
5364     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5365     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5366   }
5367
5368   /*
5369    * (non-Javadoc)
5370    *
5371    * @see
5372    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5373    * .event.ActionEvent)
5374    */
5375   @Override
5376   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5377   {
5378     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5379     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5380   }
5381
5382   @Override
5383   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5384   {
5385     showSequenceLogo.setState(true);
5386     viewport.setShowSequenceLogo(true);
5387     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5388     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5389   }
5390
5391   @Override
5392   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5393   {
5394     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5395   }
5396
5397   /*
5398    * (non-Javadoc)
5399    *
5400    * @see
5401    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5402    * .event.ActionEvent)
5403    */
5404   @Override
5405   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5406   {
5407     if (avc.makeGroupsFromSelection())
5408     {
5409       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5410       alignPanel.updateAnnotation();
5411       alignPanel.paintAlignment(true);
5412     }
5413   }
5414
5415   public void clearAlignmentSeqRep()
5416   {
5417     // TODO refactor alignmentseqrep to controller
5418     if (viewport.getAlignment().hasSeqrep())
5419     {
5420       viewport.getAlignment().setSeqrep(null);
5421       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5422       alignPanel.updateAnnotation();
5423       alignPanel.paintAlignment(true);
5424     }
5425   }
5426
5427   @Override
5428   protected void createGroup_actionPerformed(ActionEvent e)
5429   {
5430     if (avc.createGroup())
5431     {
5432       alignPanel.alignmentChanged();
5433     }
5434   }
5435
5436   @Override
5437   protected void unGroup_actionPerformed(ActionEvent e)
5438   {
5439     if (avc.unGroup())
5440     {
5441       alignPanel.alignmentChanged();
5442     }
5443   }
5444
5445   /**
5446    * make the given alignmentPanel the currently selected tab
5447    *
5448    * @param alignmentPanel
5449    */
5450   public void setDisplayedView(AlignmentPanel alignmentPanel)
5451   {
5452     if (!viewport.getSequenceSetId().equals(
5453             alignmentPanel.av.getSequenceSetId()))
5454     {
5455       throw new Error(
5456               MessageManager
5457                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5458     }
5459     if (tabbedPane != null
5460             && tabbedPane.getTabCount() > 0
5461             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5462                     .getSelectedIndex())
5463     {
5464       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5465     }
5466   }
5467
5468   /**
5469    * Action on selection of menu options to Show or Hide annotations.
5470    *
5471    * @param visible
5472    * @param forSequences
5473    *          update sequence-related annotations
5474    * @param forAlignment
5475    *          update non-sequence-related annotations
5476    */
5477   @Override
5478   protected void setAnnotationsVisibility(boolean visible,
5479           boolean forSequences, boolean forAlignment)
5480   {
5481     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5482             .getAlignmentAnnotation();
5483     if (anns == null)
5484     {
5485       return;
5486     }
5487     for (AlignmentAnnotation aa : anns)
5488     {
5489       /*
5490        * don't display non-positional annotations on an alignment
5491        */
5492       if (aa.annotations == null)
5493       {
5494         continue;
5495       }
5496       boolean apply = (aa.sequenceRef == null && forAlignment)
5497               || (aa.sequenceRef != null && forSequences);
5498       if (apply)
5499       {
5500         aa.visible = visible;
5501       }
5502     }
5503     alignPanel.validateAnnotationDimensions(true);
5504     alignPanel.alignmentChanged();
5505   }
5506
5507   /**
5508    * Store selected annotation sort order for the view and repaint.
5509    */
5510   @Override
5511   protected void sortAnnotations_actionPerformed()
5512   {
5513     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5514     this.alignPanel.av
5515             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5516     alignPanel.paintAlignment(true);
5517   }
5518
5519   /**
5520    *
5521    * @return alignment panels in this alignment frame
5522    */
5523   public List<? extends AlignmentViewPanel> getAlignPanels()
5524   {
5525     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5526   }
5527
5528   /**
5529    * Open a new alignment window, with the cDNA associated with this (protein)
5530    * alignment, aligned as is the protein.
5531    */
5532   protected void viewAsCdna_actionPerformed()
5533   {
5534     // TODO no longer a menu action - refactor as required
5535     final AlignmentI alignment = getViewport().getAlignment();
5536     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5537     if (mappings == null)
5538     {
5539       return;
5540     }
5541     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5542     for (SequenceI aaSeq : alignment.getSequences())
5543     {
5544       for (AlignedCodonFrame acf : mappings)
5545       {
5546         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5547         if (dnaSeq != null)
5548         {
5549           /*
5550            * There is a cDNA mapping for this protein sequence - add to new
5551            * alignment. It will share the same dataset sequence as other mapped
5552            * cDNA (no new mappings need to be created).
5553            */
5554           final Sequence newSeq = new Sequence(dnaSeq);
5555           newSeq.setDatasetSequence(dnaSeq);
5556           cdnaSeqs.add(newSeq);
5557         }
5558       }
5559     }
5560     if (cdnaSeqs.size() == 0)
5561     {
5562       // show a warning dialog no mapped cDNA
5563       return;
5564     }
5565     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5566             .size()]));
5567     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5568             AlignFrame.DEFAULT_HEIGHT);
5569     cdna.alignAs(alignment);
5570     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5571             + this.title;
5572     Desktop.addInternalFrame(alignFrame, newtitle,
5573             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5574   }
5575
5576   /**
5577    * Set visibility of dna/protein complement view (available when shown in a
5578    * split frame).
5579    *
5580    * @param show
5581    */
5582   @Override
5583   protected void showComplement_actionPerformed(boolean show)
5584   {
5585     SplitContainerI sf = getSplitViewContainer();
5586     if (sf != null)
5587     {
5588       sf.setComplementVisible(this, show);
5589     }
5590   }
5591
5592   /**
5593    * Generate the reverse (optionally complemented) of the selected sequences,
5594    * and add them to the alignment
5595    */
5596   @Override
5597   protected void showReverse_actionPerformed(boolean complement)
5598   {
5599     AlignmentI al = null;
5600     try
5601     {
5602       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5603       al = dna.reverseCdna(complement);
5604       viewport.addAlignment(al, "");
5605       addHistoryItem(new EditCommand(
5606               MessageManager.getString("label.add_sequences"),
5607               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5608               viewport.getAlignment()));
5609     } catch (Exception ex)
5610     {
5611       System.err.println(ex.getMessage());
5612       return;
5613     }
5614   }
5615
5616   /**
5617    * Try to run a script in the Groovy console, having first ensured that this
5618    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5619    * be targeted at this alignment.
5620    */
5621   @Override
5622   protected void runGroovy_actionPerformed()
5623   {
5624     Jalview.setCurrentAlignFrame(this);
5625     groovy.ui.Console console = Desktop.getGroovyConsole();
5626     if (console != null)
5627     {
5628       try
5629       {
5630         console.runScript();
5631       } catch (Exception ex)
5632       {
5633         System.err.println((ex.toString()));
5634         JvOptionPane
5635                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5636                         .getString("label.couldnt_run_groovy_script"),
5637                         MessageManager
5638                                 .getString("label.groovy_support_failed"),
5639                         JvOptionPane.ERROR_MESSAGE);
5640       }
5641     }
5642     else
5643     {
5644       System.err.println("Can't run Groovy script as console not found");
5645     }
5646   }
5647
5648   /**
5649    * Hides columns containing (or not containing) a specified feature, provided
5650    * that would not leave all columns hidden
5651    *
5652    * @param featureType
5653    * @param columnsContaining
5654    * @return
5655    */
5656   public boolean hideFeatureColumns(String featureType,
5657           boolean columnsContaining)
5658   {
5659     boolean notForHiding = avc.markColumnsContainingFeatures(
5660             columnsContaining, false, false, featureType);
5661     if (notForHiding)
5662     {
5663       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5664               false, featureType))
5665       {
5666         getViewport().hideSelectedColumns();
5667         return true;
5668       }
5669     }
5670     return false;
5671   }
5672
5673   @Override
5674   protected void selectHighlightedColumns_actionPerformed(
5675           ActionEvent actionEvent)
5676   {
5677     // include key modifier check in case user selects from menu
5678     avc.markHighlightedColumns(
5679             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5680             true,
5681             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5682   }
5683
5684   /**
5685    * Rebuilds the Colour menu, including any user-defined colours which have
5686    * been loaded either on startup or during the session
5687    */
5688   public void buildColourMenu()
5689   {
5690     colourMenu.removeAll();
5691
5692     colourMenu.add(applyToAllGroups);
5693     colourMenu.add(textColour);
5694     colourMenu.addSeparator();
5695
5696     ColourMenuHelper.addMenuItems(colourMenu, this,
5697             viewport.getAlignment(), false);
5698
5699     colourMenu.addSeparator();
5700     colourMenu.add(conservationMenuItem);
5701     colourMenu.add(modifyConservation);
5702     colourMenu.add(abovePIDThreshold);
5703     colourMenu.add(modifyPID);
5704     colourMenu.add(annotationColour);
5705
5706     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5707     String schemeName = colourScheme == null ? null : colourScheme
5708             .getSchemeName();
5709
5710     ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5711   }
5712 }
5713
5714 class PrintThread extends Thread
5715 {
5716   AlignmentPanel ap;
5717
5718   public PrintThread(AlignmentPanel ap)
5719   {
5720     this.ap = ap;
5721   }
5722
5723   static PageFormat pf;
5724
5725   @Override
5726   public void run()
5727   {
5728     PrinterJob printJob = PrinterJob.getPrinterJob();
5729
5730     if (pf != null)
5731     {
5732       printJob.setPrintable(ap, pf);
5733     }
5734     else
5735     {
5736       printJob.setPrintable(ap);
5737     }
5738
5739     if (printJob.printDialog())
5740     {
5741       try
5742       {
5743         printJob.print();
5744       } catch (Exception PrintException)
5745       {
5746         PrintException.printStackTrace();
5747       }
5748     }
5749   }
5750 }