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