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.FeatureSettingsI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.ScoreModelI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.HiddenSequences;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  64 import jalview.io.AlignmentProperties;
  65 import jalview.io.AnnotationFile;
  66 import jalview.io.BioJsHTMLOutput;
  67 import jalview.io.FileLoader;
  68 import jalview.io.FormatAdapter;
  69 import jalview.io.HtmlSvgOutput;
  70 import jalview.io.IdentifyFile;
  71 import jalview.io.JalviewFileChooser;
  72 import jalview.io.JalviewFileView;
  73 import jalview.io.JnetAnnotationMaker;
  74 import jalview.io.NewickFile;
  75 import jalview.io.TCoffeeScoreFile;
  76 import jalview.jbgui.GAlignFrame;
  77 import jalview.schemes.Blosum62ColourScheme;
  78 import jalview.schemes.BuriedColourScheme;
  79 import jalview.schemes.ClustalxColourScheme;
  80 import jalview.schemes.ColourSchemeI;
  81 import jalview.schemes.ColourSchemeProperty;
  82 import jalview.schemes.HelixColourScheme;
  83 import jalview.schemes.HydrophobicColourScheme;
  84 import jalview.schemes.NucleotideColourScheme;
  85 import jalview.schemes.PIDColourScheme;
  86 import jalview.schemes.PurinePyrimidineColourScheme;
  87 import jalview.schemes.RNAHelicesColourChooser;
  88 import jalview.schemes.ResidueProperties;
  89 import jalview.schemes.StrandColourScheme;
  90 import jalview.schemes.TCoffeeColourScheme;
  91 import jalview.schemes.TaylorColourScheme;
  92 import jalview.schemes.TurnColourScheme;
  93 import jalview.schemes.UserColourScheme;
  94 import jalview.schemes.ZappoColourScheme;
  95 import jalview.structure.StructureSelectionManager;
  96 import jalview.util.MessageManager;
  97 import jalview.viewmodel.AlignmentViewport;
  98 import jalview.ws.SequenceFetcher;
  99 import jalview.ws.jws1.Discoverer;
 100 import jalview.ws.jws2.Jws2Discoverer;
 101 import jalview.ws.jws2.jabaws2.Jws2Instance;
 102 import jalview.ws.seqfetcher.ASequenceFetcher;
 103 import jalview.ws.seqfetcher.DbSourceProxy;
 104
 105 import java.awt.BorderLayout;
 106 import java.awt.Component;
 107 import java.awt.Rectangle;
 108 import java.awt.Toolkit;
 109 import java.awt.datatransfer.Clipboard;
 110 import java.awt.datatransfer.DataFlavor;
 111 import java.awt.datatransfer.StringSelection;
 112 import java.awt.datatransfer.Transferable;
 113 import java.awt.dnd.DnDConstants;
 114 import java.awt.dnd.DropTargetDragEvent;
 115 import java.awt.dnd.DropTargetDropEvent;
 116 import java.awt.dnd.DropTargetEvent;
 117 import java.awt.dnd.DropTargetListener;
 118 import java.awt.event.ActionEvent;
 119 import java.awt.event.ActionListener;
 120 import java.awt.event.ItemEvent;
 121 import java.awt.event.ItemListener;
 122 import java.awt.event.KeyAdapter;
 123 import java.awt.event.KeyEvent;
 124 import java.awt.event.MouseAdapter;
 125 import java.awt.event.MouseEvent;
 126 import java.awt.print.PageFormat;
 127 import java.awt.print.PrinterJob;
 128 import java.beans.PropertyChangeEvent;
 129 import java.io.File;
 130 import java.net.URL;
 131 import java.util.ArrayList;
 132 import java.util.Arrays;
 133 import java.util.Deque;
 134 import java.util.Enumeration;
 135 import java.util.Hashtable;
 136 import java.util.List;
 137 import java.util.Vector;
 138
 139 import javax.swing.JCheckBoxMenuItem;
 140 import javax.swing.JEditorPane;
 141 import javax.swing.JInternalFrame;
 142 import javax.swing.JLayeredPane;
 143 import javax.swing.JMenu;
 144 import javax.swing.JMenuItem;
 145 import javax.swing.JOptionPane;
 146 import javax.swing.JRadioButtonMenuItem;
 147 import javax.swing.JScrollPane;
 148 import javax.swing.SwingUtilities;
 149
 150 /**
 151  * DOCUMENT ME!
 152  *
 153  * @author $author$
 154  * @version $Revision$
 155  */
 156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 157         IProgressIndicator, AlignViewControllerGuiI
 158 {
 159
 160   public static final int DEFAULT_WIDTH = 700;
 161
 162   public static final int DEFAULT_HEIGHT = 500;
 163
 164   /*
 165    * The currently displayed panel (selected tabbed view if more than one)
 166    */
 167   public AlignmentPanel alignPanel;
 168
 169   AlignViewport viewport;
 170
 171   public AlignViewControllerI avc;
 172
 173   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 174
 175   /**
 176    * Last format used to load or save alignments in this window
 177    */
 178   String currentFileFormat = null;
 179
 180   /**
 181    * Current filename for this alignment
 182    */
 183   String fileName = null;
 184
 185   /**
 186    * Creates a new AlignFrame object with specific width and height.
 187    *
 188    * @param al
 189    * @param width
 190    * @param height
 191    */
 192   public AlignFrame(AlignmentI al, int width, int height)
 193   {
 194     this(al, null, width, height);
 195   }
 196
 197   /**
 198    * Creates a new AlignFrame object with specific width, height and
 199    * sequenceSetId
 200    *
 201    * @param al
 202    * @param width
 203    * @param height
 204    * @param sequenceSetId
 205    */
 206   public AlignFrame(AlignmentI al, int width, int height,
 207           String sequenceSetId)
 208   {
 209     this(al, null, width, height, sequenceSetId);
 210   }
 211
 212   /**
 213    * Creates a new AlignFrame object with specific width, height and
 214    * sequenceSetId
 215    *
 216    * @param al
 217    * @param width
 218    * @param height
 219    * @param sequenceSetId
 220    * @param viewId
 221    */
 222   public AlignFrame(AlignmentI al, int width, int height,
 223           String sequenceSetId, String viewId)
 224   {
 225     this(al, null, width, height, sequenceSetId, viewId);
 226   }
 227
 228   /**
 229    * new alignment window with hidden columns
 230    *
 231    * @param al
 232    *          AlignmentI
 233    * @param hiddenColumns
 234    *          ColumnSelection or null
 235    * @param width
 236    *          Width of alignment frame
 237    * @param height
 238    *          height of frame.
 239    */
 240   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 241           int width, int height)
 242   {
 243     this(al, hiddenColumns, width, height, null);
 244   }
 245
 246   /**
 247    * Create alignment frame for al with hiddenColumns, a specific width and
 248    * height, and specific sequenceId
 249    *
 250    * @param al
 251    * @param hiddenColumns
 252    * @param width
 253    * @param height
 254    * @param sequenceSetId
 255    *          (may be null)
 256    */
 257   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 258           int width, int height, String sequenceSetId)
 259   {
 260     this(al, hiddenColumns, width, height, sequenceSetId, null);
 261   }
 262
 263   /**
 264    * Create alignment frame for al with hiddenColumns, a specific width and
 265    * height, and specific sequenceId
 266    *
 267    * @param al
 268    * @param hiddenColumns
 269    * @param width
 270    * @param height
 271    * @param sequenceSetId
 272    *          (may be null)
 273    * @param viewId
 274    *          (may be null)
 275    */
 276   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 277           int width, int height, String sequenceSetId, String viewId)
 278   {
 279     setSize(width, height);
 280
 281     if (al.getDataset() == null)
 282     {
 283       al.setDataset(null);
 284     }
 285
 286     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 287
 288     alignPanel = new AlignmentPanel(this, viewport);
 289
 290     addAlignmentPanel(alignPanel, true);
 291     init();
 292   }
 293
 294   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 295           ColumnSelection hiddenColumns, int width, int height)
 296   {
 297     setSize(width, height);
 298
 299     if (al.getDataset() == null)
 300     {
 301       al.setDataset(null);
 302     }
 303
 304     viewport = new AlignViewport(al, hiddenColumns);
 305
 306     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 307     {
 308       viewport.hideSequence(hiddenSeqs);
 309     }
 310     alignPanel = new AlignmentPanel(this, viewport);
 311     addAlignmentPanel(alignPanel, true);
 312     init();
 313   }
 314
 315   /**
 316    * Make a new AlignFrame from existing alignmentPanels
 317    *
 318    * @param ap
 319    *          AlignmentPanel
 320    * @param av
 321    *          AlignViewport
 322    */
 323   public AlignFrame(AlignmentPanel ap)
 324   {
 325     viewport = ap.av;
 326     alignPanel = ap;
 327     addAlignmentPanel(ap, false);
 328     init();
 329   }
 330
 331   /**
 332    * initalise the alignframe from the underlying viewport data and the
 333    * configurations
 334    */
 335   void init()
 336   {
 337     if (!Jalview.isHeadlessMode())
 338     {
 339       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 340     }
 341
 342     avc = new jalview.controller.AlignViewController(this, viewport,
 343             alignPanel);
 344     if (viewport.getAlignmentConservationAnnotation() == null)
 345     {
 346       BLOSUM62Colour.setEnabled(false);
 347       conservationMenuItem.setEnabled(false);
 348       modifyConservation.setEnabled(false);
 349       // PIDColour.setEnabled(false);
 350       // abovePIDThreshold.setEnabled(false);
 351       // modifyPID.setEnabled(false);
 352     }
 353
 354     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 355             "No sort");
 356
 357     if (sortby.equals("Id"))
 358     {
 359       sortIDMenuItem_actionPerformed(null);
 360     }
 361     else if (sortby.equals("Pairwise Identity"))
 362     {
 363       sortPairwiseMenuItem_actionPerformed(null);
 364     }
 365
 366     if (Desktop.desktop != null)
 367     {
 368       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 369       addServiceListeners();
 370       setGUINucleotide(viewport.getAlignment().isNucleotide());
 371     }
 372
 373     this.alignPanel.av
 374             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 375
 376     setMenusFromViewport(viewport);
 377     buildSortByAnnotationScoresMenu();
 378     buildTreeMenu();
 379
 380     if (viewport.getWrapAlignment())
 381     {
 382       wrapMenuItem_actionPerformed(null);
 383     }
 384
 385     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 386     {
 387       this.overviewMenuItem_actionPerformed(null);
 388     }
 389
 390     addKeyListener();
 391
 392     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 393     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 394     final String menuLabel = MessageManager
 395             .getString("label.copy_format_from");
 396     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 397             new ViewSetProvider()
 398             {
 399
 400               @Override
 401               public AlignmentPanel[] getAllAlignmentPanels()
 402               {
 403                 origview.clear();
 404                 origview.add(alignPanel);
 405                 // make an array of all alignment panels except for this one
 406                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 407                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 408                 aps.remove(AlignFrame.this.alignPanel);
 409                 return aps.toArray(new AlignmentPanel[aps.size()]);
 410               }
 411             }, selviews, new ItemListener()
 412             {
 413
 414               @Override
 415               public void itemStateChanged(ItemEvent e)
 416               {
 417                 if (origview.size() > 0)
 418                 {
 419                   final AlignmentPanel ap = origview.get(0);
 420
 421                   /*
 422                    * Copy the ViewStyle of the selected panel to 'this one'.
 423                    * Don't change value of 'scaleProteinAsCdna' unless copying
 424                    * from a SplitFrame.
 425                    */
 426                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 427                           .getViewStyle();
 428                   boolean fromSplitFrame = selviews.get(0)
 429                           .getAlignViewport().getCodingComplement() != null;
 430                   if (!fromSplitFrame)
 431                   {
 432                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 433                             .getViewStyle().isScaleProteinAsCdna());
 434                   }
 435                   ap.getAlignViewport().setViewStyle(vs);
 436
 437                   /*
 438                    * Also rescale ViewStyle of SplitFrame complement if there is
 439                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 440                    * the whole ViewStyle (allow cDNA protein to have different
 441                    * fonts)
 442                    */
 443                   AlignViewportI complement = ap.getAlignViewport()
 444                           .getCodingComplement();
 445                   if (complement != null && vs.isScaleProteinAsCdna())
 446                   {
 447                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 448                     ((SplitFrame) af.getSplitViewContainer())
 449                             .adjustLayout();
 450                     af.setMenusForViewport();
 451                   }
 452
 453                   ap.updateLayout();
 454                   ap.setSelected(true);
 455                   ap.alignFrame.setMenusForViewport();
 456
 457                 }
 458               }
 459             });
 460     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 461             .indexOf("devel") > -1
 462             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 463                     .indexOf("test") > -1)
 464     {
 465       formatMenu.add(vsel);
 466     }
 467
 468   }
 469
 470   /**
 471    * Change the filename and format for the alignment, and enable the 'reload'
 472    * button functionality.
 473    *
 474    * @param file
 475    *          valid filename
 476    * @param format
 477    *          format of file
 478    */
 479   public void setFileName(String file, String format)
 480   {
 481     fileName = file;
 482     setFileFormat(format);
 483     reload.setEnabled(true);
 484   }
 485
 486   /**
 487    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 488    * events
 489    */
 490   void addKeyListener()
 491   {
 492     addKeyListener(new KeyAdapter()
 493     {
 494       @Override
 495       public void keyPressed(KeyEvent evt)
 496       {
 497         if (viewport.cursorMode
 498                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 499                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 500                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 501                 && Character.isDigit(evt.getKeyChar()))
 502         {
 503           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 504         }
 505
 506         switch (evt.getKeyCode())
 507         {
 508
 509         case 27: // escape key
 510           deselectAllSequenceMenuItem_actionPerformed(null);
 511
 512           break;
 513
 514         case KeyEvent.VK_DOWN:
 515           if (evt.isAltDown() || !viewport.cursorMode)
 516           {
 517             moveSelectedSequences(false);
 518           }
 519           if (viewport.cursorMode)
 520           {
 521             alignPanel.getSeqPanel().moveCursor(0, 1);
 522           }
 523           break;
 524
 525         case KeyEvent.VK_UP:
 526           if (evt.isAltDown() || !viewport.cursorMode)
 527           {
 528             moveSelectedSequences(true);
 529           }
 530           if (viewport.cursorMode)
 531           {
 532             alignPanel.getSeqPanel().moveCursor(0, -1);
 533           }
 534
 535           break;
 536
 537         case KeyEvent.VK_LEFT:
 538           if (evt.isAltDown() || !viewport.cursorMode)
 539           {
 540             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 541           }
 542           else
 543           {
 544             alignPanel.getSeqPanel().moveCursor(-1, 0);
 545           }
 546
 547           break;
 548
 549         case KeyEvent.VK_RIGHT:
 550           if (evt.isAltDown() || !viewport.cursorMode)
 551           {
 552             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 553           }
 554           else
 555           {
 556             alignPanel.getSeqPanel().moveCursor(1, 0);
 557           }
 558           break;
 559
 560         case KeyEvent.VK_SPACE:
 561           if (viewport.cursorMode)
 562           {
 563             alignPanel.getSeqPanel().insertGapAtCursor(
 564                     evt.isControlDown() || evt.isShiftDown()
 565                             || evt.isAltDown());
 566           }
 567           break;
 568
 569         // case KeyEvent.VK_A:
 570         // if (viewport.cursorMode)
 571         // {
 572         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 573         // //System.out.println("A");
 574         // }
 575         // break;
 576         /*
 577          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 578          * System.out.println("closing bracket"); } break;
 579          */
 580         case KeyEvent.VK_DELETE:
 581         case KeyEvent.VK_BACK_SPACE:
 582           if (!viewport.cursorMode)
 583           {
 584             cut_actionPerformed(null);
 585           }
 586           else
 587           {
 588             alignPanel.getSeqPanel().deleteGapAtCursor(
 589                     evt.isControlDown() || evt.isShiftDown()
 590                             || evt.isAltDown());
 591           }
 592
 593           break;
 594
 595         case KeyEvent.VK_S:
 596           if (viewport.cursorMode)
 597           {
 598             alignPanel.getSeqPanel().setCursorRow();
 599           }
 600           break;
 601         case KeyEvent.VK_C:
 602           if (viewport.cursorMode && !evt.isControlDown())
 603           {
 604             alignPanel.getSeqPanel().setCursorColumn();
 605           }
 606           break;
 607         case KeyEvent.VK_P:
 608           if (viewport.cursorMode)
 609           {
 610             alignPanel.getSeqPanel().setCursorPosition();
 611           }
 612           break;
 613
 614         case KeyEvent.VK_ENTER:
 615         case KeyEvent.VK_COMMA:
 616           if (viewport.cursorMode)
 617           {
 618             alignPanel.getSeqPanel().setCursorRowAndColumn();
 619           }
 620           break;
 621
 622         case KeyEvent.VK_Q:
 623           if (viewport.cursorMode)
 624           {
 625             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 626           }
 627           break;
 628         case KeyEvent.VK_M:
 629           if (viewport.cursorMode)
 630           {
 631             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 632           }
 633           break;
 634
 635         case KeyEvent.VK_F2:
 636           viewport.cursorMode = !viewport.cursorMode;
 637           statusBar.setText(MessageManager.formatMessage(
 638                   "label.keyboard_editing_mode",
 639                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 640           if (viewport.cursorMode)
 641           {
 642             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 643             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 644           }
 645           alignPanel.getSeqPanel().seqCanvas.repaint();
 646           break;
 647
 648         case KeyEvent.VK_F1:
 649           try
 650           {
 651             Help.showHelpWindow();
 652           } catch (Exception ex)
 653           {
 654             ex.printStackTrace();
 655           }
 656           break;
 657         case KeyEvent.VK_H:
 658         {
 659           boolean toggleSeqs = !evt.isControlDown();
 660           boolean toggleCols = !evt.isShiftDown();
 661           toggleHiddenRegions(toggleSeqs, toggleCols);
 662           break;
 663         }
 664         case KeyEvent.VK_PAGE_UP:
 665           if (viewport.getWrapAlignment())
 666           {
 667             alignPanel.scrollUp(true);
 668           }
 669           else
 670           {
 671             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 672                     - viewport.endSeq + viewport.startSeq);
 673           }
 674           break;
 675         case KeyEvent.VK_PAGE_DOWN:
 676           if (viewport.getWrapAlignment())
 677           {
 678             alignPanel.scrollUp(false);
 679           }
 680           else
 681           {
 682             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 683                     + viewport.endSeq - viewport.startSeq);
 684           }
 685           break;
 686         }
 687       }
 688
 689       @Override
 690       public void keyReleased(KeyEvent evt)
 691       {
 692         switch (evt.getKeyCode())
 693         {
 694         case KeyEvent.VK_LEFT:
 695           if (evt.isAltDown() || !viewport.cursorMode)
 696           {
 697             viewport.firePropertyChange("alignment", null, viewport
 698                     .getAlignment().getSequences());
 699           }
 700           break;
 701
 702         case KeyEvent.VK_RIGHT:
 703           if (evt.isAltDown() || !viewport.cursorMode)
 704           {
 705             viewport.firePropertyChange("alignment", null, viewport
 706                     .getAlignment().getSequences());
 707           }
 708           break;
 709         }
 710       }
 711     });
 712   }
 713
 714   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 715   {
 716     ap.alignFrame = this;
 717     avc = new jalview.controller.AlignViewController(this, viewport,
 718             alignPanel);
 719
 720     alignPanels.add(ap);
 721
 722     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 723
 724     int aSize = alignPanels.size();
 725
 726     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 727
 728     if (aSize == 1 && ap.av.viewName == null)
 729     {
 730       this.getContentPane().add(ap, BorderLayout.CENTER);
 731     }
 732     else
 733     {
 734       if (aSize == 2)
 735       {
 736         setInitialTabVisible();
 737       }
 738
 739       expandViews.setEnabled(true);
 740       gatherViews.setEnabled(true);
 741       tabbedPane.addTab(ap.av.viewName, ap);
 742
 743       ap.setVisible(false);
 744     }
 745
 746     if (newPanel)
 747     {
 748       if (ap.av.isPadGaps())
 749       {
 750         ap.av.getAlignment().padGaps();
 751       }
 752       ap.av.updateConservation(ap);
 753       ap.av.updateConsensus(ap);
 754       ap.av.updateStrucConsensus(ap);
 755     }
 756   }
 757
 758   public void setInitialTabVisible()
 759   {
 760     expandViews.setEnabled(true);
 761     gatherViews.setEnabled(true);
 762     tabbedPane.setVisible(true);
 763     AlignmentPanel first = alignPanels.get(0);
 764     tabbedPane.addTab(first.av.viewName, first);
 765     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 766   }
 767
 768   public AlignViewport getViewport()
 769   {
 770     return viewport;
 771   }
 772
 773   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 774   private void addServiceListeners()
 775   {
 776     final java.beans.PropertyChangeListener thisListener;
 777     Desktop.instance.addJalviewPropertyChangeListener("services",
 778             thisListener = new java.beans.PropertyChangeListener()
 779             {
 780               @Override
 781               public void propertyChange(PropertyChangeEvent evt)
 782               {
 783                 // // System.out.println("Discoverer property change.");
 784                 // if (evt.getPropertyName().equals("services"))
 785                 {
 786                   SwingUtilities.invokeLater(new Runnable()
 787                   {
 788
 789                     @Override
 790                     public void run()
 791                     {
 792                       System.err
 793                               .println("Rebuild WS Menu for service change");
 794                       BuildWebServiceMenu();
 795                     }
 796
 797                   });
 798                 }
 799               }
 800             });
 801     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 802     {
 803       @Override
 804       public void internalFrameClosed(
 805               javax.swing.event.InternalFrameEvent evt)
 806       {
 807         // System.out.println("deregistering discoverer listener");
 808         Desktop.instance.removeJalviewPropertyChangeListener("services",
 809                 thisListener);
 810         closeMenuItem_actionPerformed(true);
 811       };
 812     });
 813     // Finally, build the menu once to get current service state
 814     new Thread(new Runnable()
 815     {
 816       @Override
 817       public void run()
 818       {
 819         BuildWebServiceMenu();
 820       }
 821     }).start();
 822   }
 823
 824   /**
 825    * Configure menu items that vary according to whether the alignment is
 826    * nucleotide or protein
 827    *
 828    * @param nucleotide
 829    */
 830   public void setGUINucleotide(boolean nucleotide)
 831   {
 832     showTranslation.setVisible(nucleotide);
 833     showReverse.setVisible(nucleotide);
 834     showReverseComplement.setVisible(nucleotide);
 835     conservationMenuItem.setEnabled(!nucleotide);
 836     modifyConservation.setEnabled(!nucleotide);
 837     showGroupConservation.setEnabled(!nucleotide);
 838     rnahelicesColour.setEnabled(nucleotide);
 839     purinePyrimidineColour.setEnabled(nucleotide);
 840     showComplementMenuItem.setText(MessageManager
 841             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 842     setColourSelected(jalview.bin.Cache.getDefault(
 843             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 844                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 845   }
 846
 847   /**
 848    * set up menus for the current viewport. This may be called after any
 849    * operation that affects the data in the current view (selection changed,
 850    * etc) to update the menus to reflect the new state.
 851    */
 852   @Override
 853   public void setMenusForViewport()
 854   {
 855     setMenusFromViewport(viewport);
 856   }
 857
 858   /**
 859    * Need to call this method when tabs are selected for multiple views, or when
 860    * loading from Jalview2XML.java
 861    *
 862    * @param av
 863    *          AlignViewport
 864    */
 865   void setMenusFromViewport(AlignViewport av)
 866   {
 867     padGapsMenuitem.setSelected(av.isPadGaps());
 868     colourTextMenuItem.setSelected(av.isShowColourText());
 869     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 870     conservationMenuItem.setSelected(av.getConservationSelected());
 871     seqLimits.setSelected(av.getShowJVSuffix());
 872     idRightAlign.setSelected(av.isRightAlignIds());
 873     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 874     renderGapsMenuItem.setSelected(av.isRenderGaps());
 875     wrapMenuItem.setSelected(av.getWrapAlignment());
 876     scaleAbove.setVisible(av.getWrapAlignment());
 877     scaleLeft.setVisible(av.getWrapAlignment());
 878     scaleRight.setVisible(av.getWrapAlignment());
 879     annotationPanelMenuItem.setState(av.isShowAnnotation());
 880     /*
 881      * Show/hide annotations only enabled if annotation panel is shown
 882      */
 883     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 884     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 885     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 886     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 887     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 888     viewTextMenuItem.setSelected(av.getShowText());
 889     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 890     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 891     showGroupConservation.setSelected(av.isShowGroupConservation());
 892     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 893     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 894     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 895
 896     setColourSelected(ColourSchemeProperty.getColourName(av
 897             .getGlobalColourScheme()));
 898
 899     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 900     hiddenMarkers.setState(av.getShowHiddenMarkers());
 901     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 902     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 903     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 904     autoCalculate.setSelected(av.autoCalculateConsensus);
 905     sortByTree.setSelected(av.sortByTree);
 906     listenToViewSelections.setSelected(av.followSelection);
 907     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 908     rnahelicesColour
 909             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 910
 911     showProducts.setEnabled(canShowProducts());
 912
 913     updateEditMenuBar();
 914   }
 915
 916   private IProgressIndicator progressBar;
 917
 918   /*
 919    * (non-Javadoc)
 920    *
 921    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 922    */
 923   @Override
 924   public void setProgressBar(String message, long id)
 925   {
 926     progressBar.setProgressBar(message, id);
 927   }
 928
 929   @Override
 930   public void registerHandler(final long id,
 931           final IProgressIndicatorHandler handler)
 932   {
 933     progressBar.registerHandler(id, handler);
 934   }
 935
 936   /**
 937    *
 938    * @return true if any progress bars are still active
 939    */
 940   @Override
 941   public boolean operationInProgress()
 942   {
 943     return progressBar.operationInProgress();
 944   }
 945
 946   @Override
 947   public void setStatus(String text)
 948   {
 949     statusBar.setText(text);
 950   }
 951
 952   /*
 953    * Added so Castor Mapping file can obtain Jalview Version
 954    */
 955   public String getVersion()
 956   {
 957     return jalview.bin.Cache.getProperty("VERSION");
 958   }
 959
 960   public FeatureRenderer getFeatureRenderer()
 961   {
 962     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 963   }
 964
 965   @Override
 966   public void fetchSequence_actionPerformed(ActionEvent e)
 967   {
 968     new jalview.gui.SequenceFetcher(this);
 969   }
 970
 971   @Override
 972   public void addFromFile_actionPerformed(ActionEvent e)
 973   {
 974     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 975   }
 976
 977   @Override
 978   public void reload_actionPerformed(ActionEvent e)
 979   {
 980     if (fileName != null)
 981     {
 982       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 983       // originating file's format
 984       // TODO: work out how to recover feature settings for correct view(s) when
 985       // file is reloaded.
 986       if (currentFileFormat.equals("Jalview"))
 987       {
 988         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 989         for (int i = 0; i < frames.length; i++)
 990         {
 991           if (frames[i] instanceof AlignFrame && frames[i] != this
 992                   && ((AlignFrame) frames[i]).fileName != null
 993                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 994           {
 995             try
 996             {
 997               frames[i].setSelected(true);
 998               Desktop.instance.closeAssociatedWindows();
 999             } catch (java.beans.PropertyVetoException ex)
1000             {
1001             }
1002           }
1003
1004         }
1005         Desktop.instance.closeAssociatedWindows();
1006
1007         FileLoader loader = new FileLoader();
1008         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1009         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1010       }
1011       else
1012       {
1013         Rectangle bounds = this.getBounds();
1014
1015         FileLoader loader = new FileLoader();
1016         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1017         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1018                 protocol, currentFileFormat);
1019
1020         newframe.setBounds(bounds);
1021         if (featureSettings != null && featureSettings.isShowing())
1022         {
1023           final Rectangle fspos = featureSettings.frame.getBounds();
1024           // TODO: need a 'show feature settings' function that takes bounds -
1025           // need to refactor Desktop.addFrame
1026           newframe.featureSettings_actionPerformed(null);
1027           final FeatureSettings nfs = newframe.featureSettings;
1028           SwingUtilities.invokeLater(new Runnable()
1029           {
1030             @Override
1031             public void run()
1032             {
1033               nfs.frame.setBounds(fspos);
1034             }
1035           });
1036           this.featureSettings.close();
1037           this.featureSettings = null;
1038         }
1039         this.closeMenuItem_actionPerformed(true);
1040       }
1041     }
1042   }
1043
1044   @Override
1045   public void addFromText_actionPerformed(ActionEvent e)
1046   {
1047     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1048             .getAlignPanel());
1049   }
1050
1051   @Override
1052   public void addFromURL_actionPerformed(ActionEvent e)
1053   {
1054     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1055   }
1056
1057   @Override
1058   public void save_actionPerformed(ActionEvent e)
1059   {
1060     if (fileName == null
1061             || (currentFileFormat == null || !jalview.io.FormatAdapter
1062                     .isValidIOFormat(currentFileFormat, true))
1063             || fileName.startsWith("http"))
1064     {
1065       saveAs_actionPerformed(null);
1066     }
1067     else
1068     {
1069       saveAlignment(fileName, currentFileFormat);
1070     }
1071   }
1072
1073   /**
1074    * DOCUMENT ME!
1075    *
1076    * @param e
1077    *          DOCUMENT ME!
1078    */
1079   @Override
1080   public void saveAs_actionPerformed(ActionEvent e)
1081   {
1082     JalviewFileChooser chooser = new JalviewFileChooser(
1083             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1084             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1085             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1086             currentFileFormat, false);
1087
1088     chooser.setFileView(new JalviewFileView());
1089     chooser.setDialogTitle(MessageManager
1090             .getString("label.save_alignment_to_file"));
1091     chooser.setToolTipText(MessageManager.getString("action.save"));
1092
1093     int value = chooser.showSaveDialog(this);
1094
1095     if (value == JalviewFileChooser.APPROVE_OPTION)
1096     {
1097       currentFileFormat = chooser.getSelectedFormat();
1098       while (currentFileFormat == null)
1099       {
1100         JOptionPane
1101                 .showInternalMessageDialog(
1102                         Desktop.desktop,
1103                         MessageManager
1104                                 .getString("label.select_file_format_before_saving"),
1105                         MessageManager
1106                                 .getString("label.file_format_not_specified"),
1107                         JOptionPane.WARNING_MESSAGE);
1108         currentFileFormat = chooser.getSelectedFormat();
1109         value = chooser.showSaveDialog(this);
1110         if (value != JalviewFileChooser.APPROVE_OPTION)
1111         {
1112           return;
1113         }
1114       }
1115
1116       fileName = chooser.getSelectedFile().getPath();
1117
1118       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1119               currentFileFormat);
1120
1121       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1122       if (currentFileFormat.indexOf(" ") > -1)
1123       {
1124         currentFileFormat = currentFileFormat.substring(0,
1125                 currentFileFormat.indexOf(" "));
1126       }
1127       saveAlignment(fileName, currentFileFormat);
1128     }
1129   }
1130
1131   public boolean saveAlignment(String file, String format)
1132   {
1133     boolean success = true;
1134
1135     if (format.equalsIgnoreCase("Jalview"))
1136     {
1137       String shortName = title;
1138
1139       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1140       {
1141         shortName = shortName.substring(shortName
1142                 .lastIndexOf(java.io.File.separatorChar) + 1);
1143       }
1144
1145       success = new Jalview2XML().saveAlignment(this, file, shortName);
1146
1147       statusBar.setText(MessageManager.formatMessage(
1148               "label.successfully_saved_to_file_in_format", new Object[] {
1149                   fileName, format }));
1150
1151     }
1152     else
1153     {
1154       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1155       {
1156         warningMessage("Cannot save file " + fileName + " using format "
1157                 + format, "Alignment output format not supported");
1158         if (!Jalview.isHeadlessMode())
1159         {
1160           saveAs_actionPerformed(null);
1161         }
1162         return false;
1163       }
1164
1165       AlignmentExportData exportData = getAlignmentForExport(format,
1166               viewport, null);
1167       if (exportData.getSettings().isCancelled())
1168       {
1169         return false;
1170       }
1171       FormatAdapter f = new FormatAdapter(alignPanel,
1172               exportData.getSettings());
1173       String output = f.formatSequences(
1174               format,
1175               exportData.getAlignment(), // class cast exceptions will
1176               // occur in the distant future
1177               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1178               f.getCacheSuffixDefault(format),
1179               viewport.getColumnSelection());
1180
1181       if (output == null)
1182       {
1183         success = false;
1184       }
1185       else
1186       {
1187         try
1188         {
1189           java.io.PrintWriter out = new java.io.PrintWriter(
1190                   new java.io.FileWriter(file));
1191
1192           out.print(output);
1193           out.close();
1194           this.setTitle(file);
1195           statusBar.setText(MessageManager.formatMessage(
1196                   "label.successfully_saved_to_file_in_format",
1197                   new Object[] { fileName, format }));
1198         } catch (Exception ex)
1199         {
1200           success = false;
1201           ex.printStackTrace();
1202         }
1203       }
1204     }
1205
1206     if (!success)
1207     {
1208       JOptionPane.showInternalMessageDialog(this, MessageManager
1209               .formatMessage("label.couldnt_save_file",
1210                       new Object[] { fileName }), MessageManager
1211               .getString("label.error_saving_file"),
1212               JOptionPane.WARNING_MESSAGE);
1213     }
1214
1215     return success;
1216   }
1217
1218   private void warningMessage(String warning, String title)
1219   {
1220     if (new jalview.util.Platform().isHeadless())
1221     {
1222       System.err.println("Warning: " + title + "\nWarning: " + warning);
1223
1224     }
1225     else
1226     {
1227       JOptionPane.showInternalMessageDialog(this, warning, title,
1228               JOptionPane.WARNING_MESSAGE);
1229     }
1230     return;
1231   }
1232
1233   /**
1234    * DOCUMENT ME!
1235    *
1236    * @param e
1237    *          DOCUMENT ME!
1238    */
1239   @Override
1240   protected void outputText_actionPerformed(ActionEvent e)
1241   {
1242
1243     AlignmentExportData exportData = getAlignmentForExport(
1244             e.getActionCommand(), viewport, null);
1245     if (exportData.getSettings().isCancelled())
1246     {
1247       return;
1248     }
1249     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1250     cap.setForInput(null);
1251     try
1252     {
1253       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1254               .formatSequences(e.getActionCommand(),
1255                       exportData.getAlignment(),
1256                       exportData.getOmitHidden(),
1257                       exportData.getStartEndPostions(),
1258                       viewport.getColumnSelection()));
1259       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1260               "label.alignment_output_command",
1261               new Object[] { e.getActionCommand() }), 600, 500);
1262     } catch (OutOfMemoryError oom)
1263     {
1264       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1265       cap.dispose();
1266     }
1267
1268   }
1269
1270   public static AlignmentExportData getAlignmentForExport(
1271           String exportFormat, AlignViewportI viewport,
1272           AlignExportSettingI exportSettings)
1273   {
1274     AlignmentI alignmentToExport = null;
1275     AlignExportSettingI settings = exportSettings;
1276     String[] omitHidden = null;
1277     int[] alignmentStartEnd = new int[2];
1278
1279     HiddenSequences hiddenSeqs = viewport.getAlignment()
1280             .getHiddenSequences();
1281
1282     alignmentToExport = viewport.getAlignment();
1283     alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1284
1285     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1286     if (settings == null)
1287     {
1288       settings = new AlignExportSettings(hasHiddenSeqs,
1289               viewport.hasHiddenColumns(), exportFormat);
1290     }
1291     // settings.isExportAnnotations();
1292
1293     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1294     {
1295       omitHidden = viewport.getViewAsString(false);
1296     }
1297
1298     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1299     {
1300       alignmentToExport = hiddenSeqs.getFullAlignment();
1301     }
1302     else
1303     {
1304       alignmentToExport = viewport.getAlignment();
1305       alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1306               .getColumnSelection().getHiddenColumns());
1307     }
1308     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1309             omitHidden, alignmentStartEnd, settings);
1310     return ed;
1311   }
1312
1313   public static int[] getStartEnd(int[] aligmentStartEnd,
1314           List<int[]> hiddenCols)
1315   {
1316     int startPos = aligmentStartEnd[0];
1317     int endPos = aligmentStartEnd[1];
1318
1319     int[] lowestRange = new int[] { -1, -1 };
1320     int[] higestRange = new int[] { -1, -1 };
1321
1322     for (int[] hiddenCol : hiddenCols)
1323     {
1324       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1325       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1326     }
1327
1328     if (lowestRange[0] == -1 && lowestRange[1] == -1)
1329     {
1330       startPos = aligmentStartEnd[0];
1331     }
1332     else
1333     {
1334       startPos = lowestRange[1] + 1;
1335     }
1336
1337     if (higestRange[0] == -1 && higestRange[1] == -1)
1338     {
1339       endPos = aligmentStartEnd[1];
1340     }
1341     else
1342     {
1343       endPos = higestRange[0] - 1;
1344     }
1345
1346     // System.out.println("Export range : " + startPos + " - " + endPos);
1347     return new int[] { startPos, endPos };
1348   }
1349
1350   public static void main(String[] args)
1351   {
1352     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1353     hiddenCols.add(new int[] { 0, 0 });
1354     hiddenCols.add(new int[] { 6, 9 });
1355     hiddenCols.add(new int[] { 11, 12 });
1356     hiddenCols.add(new int[] { 33, 33 });
1357     hiddenCols.add(new int[] { 50, 50 });
1358
1359     int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1360     // System.out.println("Export range : " + x[0] + " - " + x[1]);
1361   }
1362
1363   /**
1364    * DOCUMENT ME!
1365    *
1366    * @param e
1367    *          DOCUMENT ME!
1368    */
1369   @Override
1370   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1371   {
1372     new HtmlSvgOutput(null, alignPanel);
1373   }
1374
1375   @Override
1376   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1377   {
1378     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1379     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1380   }
1381
1382   public void createImageMap(File file, String image)
1383   {
1384     alignPanel.makePNGImageMap(file, image);
1385   }
1386
1387   /**
1388    * DOCUMENT ME!
1389    *
1390    * @param e
1391    *          DOCUMENT ME!
1392    */
1393   @Override
1394   public void createPNG(File f)
1395   {
1396     alignPanel.makePNG(f);
1397   }
1398
1399   /**
1400    * DOCUMENT ME!
1401    *
1402    * @param e
1403    *          DOCUMENT ME!
1404    */
1405   @Override
1406   public void createEPS(File f)
1407   {
1408     alignPanel.makeEPS(f);
1409   }
1410
1411   @Override
1412   public void createSVG(File f)
1413   {
1414     alignPanel.makeSVG(f);
1415   }
1416
1417   @Override
1418   public void pageSetup_actionPerformed(ActionEvent e)
1419   {
1420     PrinterJob printJob = PrinterJob.getPrinterJob();
1421     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1422   }
1423
1424   /**
1425    * DOCUMENT ME!
1426    *
1427    * @param e
1428    *          DOCUMENT ME!
1429    */
1430   @Override
1431   public void printMenuItem_actionPerformed(ActionEvent e)
1432   {
1433     // Putting in a thread avoids Swing painting problems
1434     PrintThread thread = new PrintThread(alignPanel);
1435     thread.start();
1436   }
1437
1438   @Override
1439   public void exportFeatures_actionPerformed(ActionEvent e)
1440   {
1441     new AnnotationExporter().exportFeatures(alignPanel);
1442   }
1443
1444   @Override
1445   public void exportAnnotations_actionPerformed(ActionEvent e)
1446   {
1447     new AnnotationExporter().exportAnnotations(alignPanel);
1448   }
1449
1450   @Override
1451   public void associatedData_actionPerformed(ActionEvent e)
1452   {
1453     // Pick the tree file
1454     JalviewFileChooser chooser = new JalviewFileChooser(
1455             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1456     chooser.setFileView(new JalviewFileView());
1457     chooser.setDialogTitle(MessageManager
1458             .getString("label.load_jalview_annotations"));
1459     chooser.setToolTipText(MessageManager
1460             .getString("label.load_jalview_annotations"));
1461
1462     int value = chooser.showOpenDialog(null);
1463
1464     if (value == JalviewFileChooser.APPROVE_OPTION)
1465     {
1466       String choice = chooser.getSelectedFile().getPath();
1467       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1468       loadJalviewDataFile(choice, null, null, null);
1469     }
1470
1471   }
1472
1473   /**
1474    * Close the current view or all views in the alignment frame. If the frame
1475    * only contains one view then the alignment will be removed from memory.
1476    *
1477    * @param closeAllTabs
1478    */
1479   @Override
1480   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1481   {
1482     if (alignPanels != null && alignPanels.size() < 2)
1483     {
1484       closeAllTabs = true;
1485     }
1486
1487     try
1488     {
1489       if (alignPanels != null)
1490       {
1491         if (closeAllTabs)
1492         {
1493           if (this.isClosed())
1494           {
1495             // really close all the windows - otherwise wait till
1496             // setClosed(true) is called
1497             for (int i = 0; i < alignPanels.size(); i++)
1498             {
1499               AlignmentPanel ap = alignPanels.get(i);
1500               ap.closePanel();
1501             }
1502           }
1503         }
1504         else
1505         {
1506           closeView(alignPanel);
1507         }
1508       }
1509
1510       if (closeAllTabs)
1511       {
1512         /*
1513          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1514          * be called recursively, with the frame now in 'closed' state
1515          */
1516         this.setClosed(true);
1517       }
1518     } catch (Exception ex)
1519     {
1520       ex.printStackTrace();
1521     }
1522   }
1523
1524   /**
1525    * Close the specified panel and close up tabs appropriately.
1526    *
1527    * @param panelToClose
1528    */
1529   public void closeView(AlignmentPanel panelToClose)
1530   {
1531     int index = tabbedPane.getSelectedIndex();
1532     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1533     alignPanels.remove(panelToClose);
1534     panelToClose.closePanel();
1535     panelToClose = null;
1536
1537     tabbedPane.removeTabAt(closedindex);
1538     tabbedPane.validate();
1539
1540     if (index > closedindex || index == tabbedPane.getTabCount())
1541     {
1542       // modify currently selected tab index if necessary.
1543       index--;
1544     }
1545
1546     this.tabSelectionChanged(index);
1547   }
1548
1549   /**
1550    * DOCUMENT ME!
1551    */
1552   void updateEditMenuBar()
1553   {
1554
1555     if (viewport.getHistoryList().size() > 0)
1556     {
1557       undoMenuItem.setEnabled(true);
1558       CommandI command = viewport.getHistoryList().peek();
1559       undoMenuItem.setText(MessageManager.formatMessage(
1560               "label.undo_command",
1561               new Object[] { command.getDescription() }));
1562     }
1563     else
1564     {
1565       undoMenuItem.setEnabled(false);
1566       undoMenuItem.setText(MessageManager.getString("action.undo"));
1567     }
1568
1569     if (viewport.getRedoList().size() > 0)
1570     {
1571       redoMenuItem.setEnabled(true);
1572
1573       CommandI command = viewport.getRedoList().peek();
1574       redoMenuItem.setText(MessageManager.formatMessage(
1575               "label.redo_command",
1576               new Object[] { command.getDescription() }));
1577     }
1578     else
1579     {
1580       redoMenuItem.setEnabled(false);
1581       redoMenuItem.setText(MessageManager.getString("action.redo"));
1582     }
1583   }
1584
1585   @Override
1586   public void addHistoryItem(CommandI command)
1587   {
1588     if (command.getSize() > 0)
1589     {
1590       viewport.addToHistoryList(command);
1591       viewport.clearRedoList();
1592       updateEditMenuBar();
1593       viewport.updateHiddenColumns();
1594       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1595       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1596       // viewport.getColumnSelection()
1597       // .getHiddenColumns().size() > 0);
1598     }
1599   }
1600
1601   /**
1602    *
1603    * @return alignment objects for all views
1604    */
1605   AlignmentI[] getViewAlignments()
1606   {
1607     if (alignPanels != null)
1608     {
1609       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1610       int i = 0;
1611       for (AlignmentPanel ap : alignPanels)
1612       {
1613         als[i++] = ap.av.getAlignment();
1614       }
1615       return als;
1616     }
1617     if (viewport != null)
1618     {
1619       return new AlignmentI[] { viewport.getAlignment() };
1620     }
1621     return null;
1622   }
1623
1624   /**
1625    * DOCUMENT ME!
1626    *
1627    * @param e
1628    *          DOCUMENT ME!
1629    */
1630   @Override
1631   protected void undoMenuItem_actionPerformed(ActionEvent e)
1632   {
1633     if (viewport.getHistoryList().isEmpty())
1634     {
1635       return;
1636     }
1637     CommandI command = viewport.getHistoryList().pop();
1638     viewport.addToRedoList(command);
1639     command.undoCommand(getViewAlignments());
1640
1641     AlignmentViewport originalSource = getOriginatingSource(command);
1642     updateEditMenuBar();
1643
1644     if (originalSource != null)
1645     {
1646       if (originalSource != viewport)
1647       {
1648         Cache.log
1649                 .warn("Implementation worry: mismatch of viewport origin for undo");
1650       }
1651       originalSource.updateHiddenColumns();
1652       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1653       // null
1654       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1655       // viewport.getColumnSelection()
1656       // .getHiddenColumns().size() > 0);
1657       originalSource.firePropertyChange("alignment", null, originalSource
1658               .getAlignment().getSequences());
1659     }
1660   }
1661
1662   /**
1663    * DOCUMENT ME!
1664    *
1665    * @param e
1666    *          DOCUMENT ME!
1667    */
1668   @Override
1669   protected void redoMenuItem_actionPerformed(ActionEvent e)
1670   {
1671     if (viewport.getRedoList().size() < 1)
1672     {
1673       return;
1674     }
1675
1676     CommandI command = viewport.getRedoList().pop();
1677     viewport.addToHistoryList(command);
1678     command.doCommand(getViewAlignments());
1679
1680     AlignmentViewport originalSource = getOriginatingSource(command);
1681     updateEditMenuBar();
1682
1683     if (originalSource != null)
1684     {
1685
1686       if (originalSource != viewport)
1687       {
1688         Cache.log
1689                 .warn("Implementation worry: mismatch of viewport origin for redo");
1690       }
1691       originalSource.updateHiddenColumns();
1692       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1693       // null
1694       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1695       // viewport.getColumnSelection()
1696       // .getHiddenColumns().size() > 0);
1697       originalSource.firePropertyChange("alignment", null, originalSource
1698               .getAlignment().getSequences());
1699     }
1700   }
1701
1702   AlignmentViewport getOriginatingSource(CommandI command)
1703   {
1704     AlignmentViewport originalSource = null;
1705     // For sequence removal and addition, we need to fire
1706     // the property change event FROM the viewport where the
1707     // original alignment was altered
1708     AlignmentI al = null;
1709     if (command instanceof EditCommand)
1710     {
1711       EditCommand editCommand = (EditCommand) command;
1712       al = editCommand.getAlignment();
1713       List<Component> comps = PaintRefresher.components.get(viewport
1714               .getSequenceSetId());
1715
1716       for (Component comp : comps)
1717       {
1718         if (comp instanceof AlignmentPanel)
1719         {
1720           if (al == ((AlignmentPanel) comp).av.getAlignment())
1721           {
1722             originalSource = ((AlignmentPanel) comp).av;
1723             break;
1724           }
1725         }
1726       }
1727     }
1728
1729     if (originalSource == null)
1730     {
1731       // The original view is closed, we must validate
1732       // the current view against the closed view first
1733       if (al != null)
1734       {
1735         PaintRefresher.validateSequences(al, viewport.getAlignment());
1736       }
1737
1738       originalSource = viewport;
1739     }
1740
1741     return originalSource;
1742   }
1743
1744   /**
1745    * DOCUMENT ME!
1746    *
1747    * @param up
1748    *          DOCUMENT ME!
1749    */
1750   public void moveSelectedSequences(boolean up)
1751   {
1752     SequenceGroup sg = viewport.getSelectionGroup();
1753
1754     if (sg == null)
1755     {
1756       return;
1757     }
1758     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1759             viewport.getHiddenRepSequences(), up);
1760     alignPanel.paintAlignment(true);
1761   }
1762
1763   synchronized void slideSequences(boolean right, int size)
1764   {
1765     List<SequenceI> sg = new ArrayList<SequenceI>();
1766     if (viewport.cursorMode)
1767     {
1768       sg.add(viewport.getAlignment().getSequenceAt(
1769               alignPanel.getSeqPanel().seqCanvas.cursorY));
1770     }
1771     else if (viewport.getSelectionGroup() != null
1772             && viewport.getSelectionGroup().getSize() != viewport
1773                     .getAlignment().getHeight())
1774     {
1775       sg = viewport.getSelectionGroup().getSequences(
1776               viewport.getHiddenRepSequences());
1777     }
1778
1779     if (sg.size() < 1)
1780     {
1781       return;
1782     }
1783
1784     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1785
1786     for (SequenceI seq : viewport.getAlignment().getSequences())
1787     {
1788       if (!sg.contains(seq))
1789       {
1790         invertGroup.add(seq);
1791       }
1792     }
1793
1794     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1795
1796     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1797     for (int i = 0; i < invertGroup.size(); i++)
1798     {
1799       seqs2[i] = invertGroup.get(i);
1800     }
1801
1802     SlideSequencesCommand ssc;
1803     if (right)
1804     {
1805       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1806               size, viewport.getGapCharacter());
1807     }
1808     else
1809     {
1810       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1811               size, viewport.getGapCharacter());
1812     }
1813
1814     int groupAdjustment = 0;
1815     if (ssc.getGapsInsertedBegin() && right)
1816     {
1817       if (viewport.cursorMode)
1818       {
1819         alignPanel.getSeqPanel().moveCursor(size, 0);
1820       }
1821       else
1822       {
1823         groupAdjustment = size;
1824       }
1825     }
1826     else if (!ssc.getGapsInsertedBegin() && !right)
1827     {
1828       if (viewport.cursorMode)
1829       {
1830         alignPanel.getSeqPanel().moveCursor(-size, 0);
1831       }
1832       else
1833       {
1834         groupAdjustment = -size;
1835       }
1836     }
1837
1838     if (groupAdjustment != 0)
1839     {
1840       viewport.getSelectionGroup().setStartRes(
1841               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1842       viewport.getSelectionGroup().setEndRes(
1843               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1844     }
1845
1846     /*
1847      * just extend the last slide command if compatible; but not if in
1848      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1849      */
1850     boolean appendHistoryItem = false;
1851     Deque<CommandI> historyList = viewport.getHistoryList();
1852     boolean inSplitFrame = getSplitViewContainer() != null;
1853     if (!inSplitFrame && historyList != null && historyList.size() > 0
1854             && historyList.peek() instanceof SlideSequencesCommand)
1855     {
1856       appendHistoryItem = ssc
1857               .appendSlideCommand((SlideSequencesCommand) historyList
1858                       .peek());
1859     }
1860
1861     if (!appendHistoryItem)
1862     {
1863       addHistoryItem(ssc);
1864     }
1865
1866     repaint();
1867   }
1868
1869   /**
1870    * DOCUMENT ME!
1871    *
1872    * @param e
1873    *          DOCUMENT ME!
1874    */
1875   @Override
1876   protected void copy_actionPerformed(ActionEvent e)
1877   {
1878     System.gc();
1879     if (viewport.getSelectionGroup() == null)
1880     {
1881       return;
1882     }
1883     // TODO: preserve the ordering of displayed alignment annotation in any
1884     // internal paste (particularly sequence associated annotation)
1885     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1886     String[] omitHidden = null;
1887
1888     if (viewport.hasHiddenColumns())
1889     {
1890       omitHidden = viewport.getViewAsString(true);
1891     }
1892
1893     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1894             omitHidden, null);
1895
1896     StringSelection ss = new StringSelection(output);
1897
1898     try
1899     {
1900       jalview.gui.Desktop.internalCopy = true;
1901       // Its really worth setting the clipboard contents
1902       // to empty before setting the large StringSelection!!
1903       Toolkit.getDefaultToolkit().getSystemClipboard()
1904               .setContents(new StringSelection(""), null);
1905
1906       Toolkit.getDefaultToolkit().getSystemClipboard()
1907               .setContents(ss, Desktop.instance);
1908     } catch (OutOfMemoryError er)
1909     {
1910       new OOMWarning("copying region", er);
1911       return;
1912     }
1913
1914     ArrayList<int[]> hiddenColumns = null;
1915     if (viewport.hasHiddenColumns())
1916     {
1917       hiddenColumns = new ArrayList<int[]>();
1918       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1919               .getSelectionGroup().getEndRes();
1920       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1921       {
1922         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1923         {
1924           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1925               region[1] - hiddenOffset });
1926         }
1927       }
1928     }
1929
1930     Desktop.jalviewClipboard = new Object[] { seqs,
1931         viewport.getAlignment().getDataset(), hiddenColumns };
1932     statusBar.setText(MessageManager.formatMessage(
1933             "label.copied_sequences_to_clipboard", new Object[] { Integer
1934                     .valueOf(seqs.length).toString() }));
1935   }
1936
1937   /**
1938    * DOCUMENT ME!
1939    *
1940    * @param e
1941    *          DOCUMENT ME!
1942    */
1943   @Override
1944   protected void pasteNew_actionPerformed(ActionEvent e)
1945   {
1946     paste(true);
1947   }
1948
1949   /**
1950    * DOCUMENT ME!
1951    *
1952    * @param e
1953    *          DOCUMENT ME!
1954    */
1955   @Override
1956   protected void pasteThis_actionPerformed(ActionEvent e)
1957   {
1958     paste(false);
1959   }
1960
1961   /**
1962    * Paste contents of Jalview clipboard
1963    *
1964    * @param newAlignment
1965    *          true to paste to a new alignment, otherwise add to this.
1966    */
1967   void paste(boolean newAlignment)
1968   {
1969     boolean externalPaste = true;
1970     try
1971     {
1972       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1973       Transferable contents = c.getContents(this);
1974
1975       if (contents == null)
1976       {
1977         return;
1978       }
1979
1980       String str, format;
1981       try
1982       {
1983         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1984         if (str.length() < 1)
1985         {
1986           return;
1987         }
1988
1989         format = new IdentifyFile().identify(str, "Paste");
1990
1991       } catch (OutOfMemoryError er)
1992       {
1993         new OOMWarning("Out of memory pasting sequences!!", er);
1994         return;
1995       }
1996
1997       SequenceI[] sequences;
1998       boolean annotationAdded = false;
1999       AlignmentI alignment = null;
2000
2001       if (Desktop.jalviewClipboard != null)
2002       {
2003         // The clipboard was filled from within Jalview, we must use the
2004         // sequences
2005         // And dataset from the copied alignment
2006         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2007         // be doubly sure that we create *new* sequence objects.
2008         sequences = new SequenceI[newseq.length];
2009         for (int i = 0; i < newseq.length; i++)
2010         {
2011           sequences[i] = new Sequence(newseq[i]);
2012         }
2013         alignment = new Alignment(sequences);
2014         externalPaste = false;
2015       }
2016       else
2017       {
2018         // parse the clipboard as an alignment.
2019         alignment = new FormatAdapter().readFile(str, "Paste", format);
2020         sequences = alignment.getSequencesArray();
2021       }
2022
2023       int alwidth = 0;
2024       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2025       int fgroup = -1;
2026
2027       if (newAlignment)
2028       {
2029
2030         if (Desktop.jalviewClipboard != null)
2031         {
2032           // dataset is inherited
2033           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2034         }
2035         else
2036         {
2037           // new dataset is constructed
2038           alignment.setDataset(null);
2039         }
2040         alwidth = alignment.getWidth() + 1;
2041       }
2042       else
2043       {
2044         AlignmentI pastedal = alignment; // preserve pasted alignment object
2045         // Add pasted sequences and dataset into existing alignment.
2046         alignment = viewport.getAlignment();
2047         alwidth = alignment.getWidth() + 1;
2048         // decide if we need to import sequences from an existing dataset
2049         boolean importDs = Desktop.jalviewClipboard != null
2050                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2051         // importDs==true instructs us to copy over new dataset sequences from
2052         // an existing alignment
2053         Vector newDs = (importDs) ? new Vector() : null; // used to create
2054         // minimum dataset set
2055
2056         for (int i = 0; i < sequences.length; i++)
2057         {
2058           if (importDs)
2059           {
2060             newDs.addElement(null);
2061           }
2062           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2063           // paste
2064           if (importDs && ds != null)
2065           {
2066             if (!newDs.contains(ds))
2067             {
2068               newDs.setElementAt(ds, i);
2069               ds = new Sequence(ds);
2070               // update with new dataset sequence
2071               sequences[i].setDatasetSequence(ds);
2072             }
2073             else
2074             {
2075               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2076             }
2077           }
2078           else
2079           {
2080             // copy and derive new dataset sequence
2081             sequences[i] = sequences[i].deriveSequence();
2082             alignment.getDataset().addSequence(
2083                     sequences[i].getDatasetSequence());
2084             // TODO: avoid creation of duplicate dataset sequences with a
2085             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2086           }
2087           alignment.addSequence(sequences[i]); // merges dataset
2088         }
2089         if (newDs != null)
2090         {
2091           newDs.clear(); // tidy up
2092         }
2093         if (alignment.getAlignmentAnnotation() != null)
2094         {
2095           for (AlignmentAnnotation alan : alignment
2096                   .getAlignmentAnnotation())
2097           {
2098             if (alan.graphGroup > fgroup)
2099             {
2100               fgroup = alan.graphGroup;
2101             }
2102           }
2103         }
2104         if (pastedal.getAlignmentAnnotation() != null)
2105         {
2106           // Add any annotation attached to alignment.
2107           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2108           for (int i = 0; i < alann.length; i++)
2109           {
2110             annotationAdded = true;
2111             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2112             {
2113               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2114               if (newann.graphGroup > -1)
2115               {
2116                 if (newGraphGroups.size() <= newann.graphGroup
2117                         || newGraphGroups.get(newann.graphGroup) == null)
2118                 {
2119                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2120                   {
2121                     newGraphGroups.add(q, null);
2122                   }
2123                   newGraphGroups.set(newann.graphGroup, new Integer(
2124                           ++fgroup));
2125                 }
2126                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2127                         .intValue();
2128               }
2129
2130               newann.padAnnotation(alwidth);
2131               alignment.addAnnotation(newann);
2132             }
2133           }
2134         }
2135       }
2136       if (!newAlignment)
2137       {
2138         // /////
2139         // ADD HISTORY ITEM
2140         //
2141         addHistoryItem(new EditCommand(
2142                 MessageManager.getString("label.add_sequences"),
2143                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2144       }
2145       // Add any annotations attached to sequences
2146       for (int i = 0; i < sequences.length; i++)
2147       {
2148         if (sequences[i].getAnnotation() != null)
2149         {
2150           AlignmentAnnotation newann;
2151           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2152           {
2153             annotationAdded = true;
2154             newann = sequences[i].getAnnotation()[a];
2155             newann.adjustForAlignment();
2156             newann.padAnnotation(alwidth);
2157             if (newann.graphGroup > -1)
2158             {
2159               if (newann.graphGroup > -1)
2160               {
2161                 if (newGraphGroups.size() <= newann.graphGroup
2162                         || newGraphGroups.get(newann.graphGroup) == null)
2163                 {
2164                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2165                   {
2166                     newGraphGroups.add(q, null);
2167                   }
2168                   newGraphGroups.set(newann.graphGroup, new Integer(
2169                           ++fgroup));
2170                 }
2171                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2172                         .intValue();
2173               }
2174             }
2175             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2176             // was
2177             // duplicated
2178             // earlier
2179             alignment
2180                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2181           }
2182         }
2183       }
2184       if (!newAlignment)
2185       {
2186
2187         // propagate alignment changed.
2188         viewport.setEndSeq(alignment.getHeight());
2189         if (annotationAdded)
2190         {
2191           // Duplicate sequence annotation in all views.
2192           AlignmentI[] alview = this.getViewAlignments();
2193           for (int i = 0; i < sequences.length; i++)
2194           {
2195             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2196             if (sann == null)
2197             {
2198               continue;
2199             }
2200             for (int avnum = 0; avnum < alview.length; avnum++)
2201             {
2202               if (alview[avnum] != alignment)
2203               {
2204                 // duplicate in a view other than the one with input focus
2205                 int avwidth = alview[avnum].getWidth() + 1;
2206                 // this relies on sann being preserved after we
2207                 // modify the sequence's annotation array for each duplication
2208                 for (int a = 0; a < sann.length; a++)
2209                 {
2210                   AlignmentAnnotation newann = new AlignmentAnnotation(
2211                           sann[a]);
2212                   sequences[i].addAlignmentAnnotation(newann);
2213                   newann.padAnnotation(avwidth);
2214                   alview[avnum].addAnnotation(newann); // annotation was
2215                   // duplicated earlier
2216                   // TODO JAL-1145 graphGroups are not updated for sequence
2217                   // annotation added to several views. This may cause
2218                   // strangeness
2219                   alview[avnum].setAnnotationIndex(newann, a);
2220                 }
2221               }
2222             }
2223           }
2224           buildSortByAnnotationScoresMenu();
2225         }
2226         viewport.firePropertyChange("alignment", null,
2227                 alignment.getSequences());
2228         if (alignPanels != null)
2229         {
2230           for (AlignmentPanel ap : alignPanels)
2231           {
2232             ap.validateAnnotationDimensions(false);
2233           }
2234         }
2235         else
2236         {
2237           alignPanel.validateAnnotationDimensions(false);
2238         }
2239
2240       }
2241       else
2242       {
2243         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2244                 DEFAULT_HEIGHT);
2245         String newtitle = new String("Copied sequences");
2246
2247         if (Desktop.jalviewClipboard != null
2248                 && Desktop.jalviewClipboard[2] != null)
2249         {
2250           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2251           for (int[] region : hc)
2252           {
2253             af.viewport.hideColumns(region[0], region[1]);
2254           }
2255         }
2256
2257         // >>>This is a fix for the moment, until a better solution is
2258         // found!!<<<
2259         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2260                 .transferSettings(
2261                         alignPanel.getSeqPanel().seqCanvas
2262                                 .getFeatureRenderer());
2263
2264         // TODO: maintain provenance of an alignment, rather than just make the
2265         // title a concatenation of operations.
2266         if (!externalPaste)
2267         {
2268           if (title.startsWith("Copied sequences"))
2269           {
2270             newtitle = title;
2271           }
2272           else
2273           {
2274             newtitle = newtitle.concat("- from " + title);
2275           }
2276         }
2277         else
2278         {
2279           newtitle = new String("Pasted sequences");
2280         }
2281
2282         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2283                 DEFAULT_HEIGHT);
2284
2285       }
2286
2287     } catch (Exception ex)
2288     {
2289       ex.printStackTrace();
2290       System.out.println("Exception whilst pasting: " + ex);
2291       // could be anything being pasted in here
2292     }
2293
2294   }
2295
2296   @Override
2297   protected void expand_newalign(ActionEvent e)
2298   {
2299     try
2300     {
2301       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2302               .getAlignment(), -1);
2303       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2304               DEFAULT_HEIGHT);
2305       String newtitle = new String("Flanking alignment");
2306
2307       if (Desktop.jalviewClipboard != null
2308               && Desktop.jalviewClipboard[2] != null)
2309       {
2310         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2311         for (int region[] : hc)
2312         {
2313           af.viewport.hideColumns(region[0], region[1]);
2314         }
2315       }
2316
2317       // >>>This is a fix for the moment, until a better solution is
2318       // found!!<<<
2319       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2320               .transferSettings(
2321                       alignPanel.getSeqPanel().seqCanvas
2322                               .getFeatureRenderer());
2323
2324       // TODO: maintain provenance of an alignment, rather than just make the
2325       // title a concatenation of operations.
2326       {
2327         if (title.startsWith("Copied sequences"))
2328         {
2329           newtitle = title;
2330         }
2331         else
2332         {
2333           newtitle = newtitle.concat("- from " + title);
2334         }
2335       }
2336
2337       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2338
2339     } catch (Exception ex)
2340     {
2341       ex.printStackTrace();
2342       System.out.println("Exception whilst pasting: " + ex);
2343       // could be anything being pasted in here
2344     } catch (OutOfMemoryError oom)
2345     {
2346       new OOMWarning("Viewing flanking region of alignment", oom);
2347     }
2348   }
2349
2350   /**
2351    * DOCUMENT ME!
2352    *
2353    * @param e
2354    *          DOCUMENT ME!
2355    */
2356   @Override
2357   protected void cut_actionPerformed(ActionEvent e)
2358   {
2359     copy_actionPerformed(null);
2360     delete_actionPerformed(null);
2361   }
2362
2363   /**
2364    * DOCUMENT ME!
2365    *
2366    * @param e
2367    *          DOCUMENT ME!
2368    */
2369   @Override
2370   protected void delete_actionPerformed(ActionEvent evt)
2371   {
2372
2373     SequenceGroup sg = viewport.getSelectionGroup();
2374     if (sg == null)
2375     {
2376       return;
2377     }
2378
2379     /*
2380      * If the cut affects all sequences, warn, remove highlighted columns
2381      */
2382     if (sg.getSize() == viewport.getAlignment().getHeight())
2383     {
2384       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2385               .getAlignment().getWidth()) ? true : false;
2386       if (isEntireAlignWidth)
2387       {
2388         int confirm = JOptionPane.showConfirmDialog(this,
2389                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2390                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2391                 JOptionPane.OK_CANCEL_OPTION);
2392
2393         if (confirm == JOptionPane.CANCEL_OPTION
2394                 || confirm == JOptionPane.CLOSED_OPTION)
2395         {
2396           return;
2397         }
2398       }
2399       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2400               sg.getEndRes() + 1);
2401     }
2402     SequenceI[] cut = sg.getSequences()
2403             .toArray(new SequenceI[sg.getSize()]);
2404
2405     addHistoryItem(new EditCommand(
2406             MessageManager.getString("label.cut_sequences"), Action.CUT,
2407             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2408             viewport.getAlignment()));
2409
2410     viewport.setSelectionGroup(null);
2411     viewport.sendSelection();
2412     viewport.getAlignment().deleteGroup(sg);
2413
2414     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2415             .getSequences());
2416     if (viewport.getAlignment().getHeight() < 1)
2417     {
2418       try
2419       {
2420         this.setClosed(true);
2421       } catch (Exception ex)
2422       {
2423       }
2424     }
2425   }
2426
2427   /**
2428    * DOCUMENT ME!
2429    *
2430    * @param e
2431    *          DOCUMENT ME!
2432    */
2433   @Override
2434   protected void deleteGroups_actionPerformed(ActionEvent e)
2435   {
2436     if (avc.deleteGroups())
2437     {
2438       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2439       alignPanel.updateAnnotation();
2440       alignPanel.paintAlignment(true);
2441     }
2442   }
2443
2444   /**
2445    * DOCUMENT ME!
2446    *
2447    * @param e
2448    *          DOCUMENT ME!
2449    */
2450   @Override
2451   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2452   {
2453     SequenceGroup sg = new SequenceGroup();
2454
2455     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2456     {
2457       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2458     }
2459
2460     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2461     viewport.setSelectionGroup(sg);
2462     viewport.sendSelection();
2463     alignPanel.paintAlignment(true);
2464     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2465   }
2466
2467   /**
2468    * DOCUMENT ME!
2469    *
2470    * @param e
2471    *          DOCUMENT ME!
2472    */
2473   @Override
2474   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2475   {
2476     if (viewport.cursorMode)
2477     {
2478       alignPanel.getSeqPanel().keyboardNo1 = null;
2479       alignPanel.getSeqPanel().keyboardNo2 = null;
2480     }
2481     viewport.setSelectionGroup(null);
2482     viewport.getColumnSelection().clear();
2483     viewport.setSelectionGroup(null);
2484     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2485     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2486     alignPanel.paintAlignment(true);
2487     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2488     viewport.sendSelection();
2489   }
2490
2491   /**
2492    * DOCUMENT ME!
2493    *
2494    * @param e
2495    *          DOCUMENT ME!
2496    */
2497   @Override
2498   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2499   {
2500     SequenceGroup sg = viewport.getSelectionGroup();
2501
2502     if (sg == null)
2503     {
2504       selectAllSequenceMenuItem_actionPerformed(null);
2505
2506       return;
2507     }
2508
2509     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2510     {
2511       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2512     }
2513
2514     alignPanel.paintAlignment(true);
2515     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2516     viewport.sendSelection();
2517   }
2518
2519   @Override
2520   public void invertColSel_actionPerformed(ActionEvent e)
2521   {
2522     viewport.invertColumnSelection();
2523     alignPanel.paintAlignment(true);
2524     viewport.sendSelection();
2525   }
2526
2527   /**
2528    * DOCUMENT ME!
2529    *
2530    * @param e
2531    *          DOCUMENT ME!
2532    */
2533   @Override
2534   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2535   {
2536     trimAlignment(true);
2537   }
2538
2539   /**
2540    * DOCUMENT ME!
2541    *
2542    * @param e
2543    *          DOCUMENT ME!
2544    */
2545   @Override
2546   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2547   {
2548     trimAlignment(false);
2549   }
2550
2551   void trimAlignment(boolean trimLeft)
2552   {
2553     ColumnSelection colSel = viewport.getColumnSelection();
2554     int column;
2555
2556     if (!colSel.isEmpty())
2557     {
2558       if (trimLeft)
2559       {
2560         column = colSel.getMin();
2561       }
2562       else
2563       {
2564         column = colSel.getMax();
2565       }
2566
2567       SequenceI[] seqs;
2568       if (viewport.getSelectionGroup() != null)
2569       {
2570         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2571                 viewport.getHiddenRepSequences());
2572       }
2573       else
2574       {
2575         seqs = viewport.getAlignment().getSequencesArray();
2576       }
2577
2578       TrimRegionCommand trimRegion;
2579       if (trimLeft)
2580       {
2581         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2582                 column, viewport.getAlignment());
2583         viewport.setStartRes(0);
2584       }
2585       else
2586       {
2587         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2588                 column, viewport.getAlignment());
2589       }
2590
2591       statusBar.setText(MessageManager.formatMessage(
2592               "label.removed_columns",
2593               new String[] { Integer.valueOf(trimRegion.getSize())
2594                       .toString() }));
2595
2596       addHistoryItem(trimRegion);
2597
2598       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2599       {
2600         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2601                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2602         {
2603           viewport.getAlignment().deleteGroup(sg);
2604         }
2605       }
2606
2607       viewport.firePropertyChange("alignment", null, viewport
2608               .getAlignment().getSequences());
2609     }
2610   }
2611
2612   /**
2613    * DOCUMENT ME!
2614    *
2615    * @param e
2616    *          DOCUMENT ME!
2617    */
2618   @Override
2619   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2620   {
2621     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2622
2623     SequenceI[] seqs;
2624     if (viewport.getSelectionGroup() != null)
2625     {
2626       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2627               viewport.getHiddenRepSequences());
2628       start = viewport.getSelectionGroup().getStartRes();
2629       end = viewport.getSelectionGroup().getEndRes();
2630     }
2631     else
2632     {
2633       seqs = viewport.getAlignment().getSequencesArray();
2634     }
2635
2636     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2637             "Remove Gapped Columns", seqs, start, end,
2638             viewport.getAlignment());
2639
2640     addHistoryItem(removeGapCols);
2641
2642     statusBar.setText(MessageManager.formatMessage(
2643             "label.removed_empty_columns",
2644             new Object[] { Integer.valueOf(removeGapCols.getSize())
2645                     .toString() }));
2646
2647     // This is to maintain viewport position on first residue
2648     // of first sequence
2649     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2650     int startRes = seq.findPosition(viewport.startRes);
2651     // ShiftList shifts;
2652     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2653     // edit.alColumnChanges=shifts.getInverse();
2654     // if (viewport.hasHiddenColumns)
2655     // viewport.getColumnSelection().compensateForEdits(shifts);
2656     viewport.setStartRes(seq.findIndex(startRes) - 1);
2657     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2658             .getSequences());
2659
2660   }
2661
2662   /**
2663    * DOCUMENT ME!
2664    *
2665    * @param e
2666    *          DOCUMENT ME!
2667    */
2668   @Override
2669   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2670   {
2671     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2672
2673     SequenceI[] seqs;
2674     if (viewport.getSelectionGroup() != null)
2675     {
2676       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2677               viewport.getHiddenRepSequences());
2678       start = viewport.getSelectionGroup().getStartRes();
2679       end = viewport.getSelectionGroup().getEndRes();
2680     }
2681     else
2682     {
2683       seqs = viewport.getAlignment().getSequencesArray();
2684     }
2685
2686     // This is to maintain viewport position on first residue
2687     // of first sequence
2688     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2689     int startRes = seq.findPosition(viewport.startRes);
2690
2691     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2692             viewport.getAlignment()));
2693
2694     viewport.setStartRes(seq.findIndex(startRes) - 1);
2695
2696     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2697             .getSequences());
2698
2699   }
2700
2701   /**
2702    * DOCUMENT ME!
2703    *
2704    * @param e
2705    *          DOCUMENT ME!
2706    */
2707   @Override
2708   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2709   {
2710     viewport.setPadGaps(padGapsMenuitem.isSelected());
2711     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2712             .getSequences());
2713   }
2714
2715   /**
2716    * DOCUMENT ME!
2717    *
2718    * @param e
2719    *          DOCUMENT ME!
2720    */
2721   @Override
2722   public void findMenuItem_actionPerformed(ActionEvent e)
2723   {
2724     new Finder();
2725   }
2726
2727   /**
2728    * Create a new view of the current alignment.
2729    */
2730   @Override
2731   public void newView_actionPerformed(ActionEvent e)
2732   {
2733     newView(null, true);
2734   }
2735
2736   /**
2737    * Creates and shows a new view of the current alignment.
2738    *
2739    * @param viewTitle
2740    *          title of newly created view; if null, one will be generated
2741    * @param copyAnnotation
2742    *          if true then duplicate all annnotation, groups and settings
2743    * @return new alignment panel, already displayed.
2744    */
2745   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2746   {
2747     /*
2748      * Create a new AlignmentPanel (with its own, new Viewport)
2749      */
2750     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2751             true);
2752     if (!copyAnnotation)
2753     {
2754       /*
2755        * remove all groups and annotation except for the automatic stuff
2756        */
2757       newap.av.getAlignment().deleteAllGroups();
2758       newap.av.getAlignment().deleteAllAnnotations(false);
2759     }
2760
2761     newap.av.setGatherViewsHere(false);
2762
2763     if (viewport.viewName == null)
2764     {
2765       viewport.viewName = MessageManager
2766               .getString("label.view_name_original");
2767     }
2768
2769     /*
2770      * Views share the same edits undo and redo stacks
2771      */
2772     newap.av.setHistoryList(viewport.getHistoryList());
2773     newap.av.setRedoList(viewport.getRedoList());
2774
2775     /*
2776      * Views share the same mappings; need to deregister any new mappings
2777      * created by copyAlignPanel, and register the new reference to the shared
2778      * mappings
2779      */
2780     newap.av.replaceMappings(viewport.getAlignment());
2781
2782     newap.av.viewName = getNewViewName(viewTitle);
2783
2784     addAlignmentPanel(newap, true);
2785     newap.alignmentChanged();
2786
2787     if (alignPanels.size() == 2)
2788     {
2789       viewport.setGatherViewsHere(true);
2790     }
2791     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2792     return newap;
2793   }
2794
2795   /**
2796    * Make a new name for the view, ensuring it is unique within the current
2797    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2798    * these now use viewId. Unique view names are still desirable for usability.)
2799    *
2800    * @param viewTitle
2801    * @return
2802    */
2803   protected String getNewViewName(String viewTitle)
2804   {
2805     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2806     boolean addFirstIndex = false;
2807     if (viewTitle == null || viewTitle.trim().length() == 0)
2808     {
2809       viewTitle = MessageManager.getString("action.view");
2810       addFirstIndex = true;
2811     }
2812     else
2813     {
2814       index = 1;// we count from 1 if given a specific name
2815     }
2816     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2817
2818     List<Component> comps = PaintRefresher.components.get(viewport
2819             .getSequenceSetId());
2820
2821     List<String> existingNames = getExistingViewNames(comps);
2822
2823     while (existingNames.contains(newViewName))
2824     {
2825       newViewName = viewTitle + " " + (++index);
2826     }
2827     return newViewName;
2828   }
2829
2830   /**
2831    * Returns a list of distinct view names found in the given list of
2832    * components. View names are held on the viewport of an AlignmentPanel.
2833    *
2834    * @param comps
2835    * @return
2836    */
2837   protected List<String> getExistingViewNames(List<Component> comps)
2838   {
2839     List<String> existingNames = new ArrayList<String>();
2840     for (Component comp : comps)
2841     {
2842       if (comp instanceof AlignmentPanel)
2843       {
2844         AlignmentPanel ap = (AlignmentPanel) comp;
2845         if (!existingNames.contains(ap.av.viewName))
2846         {
2847           existingNames.add(ap.av.viewName);
2848         }
2849       }
2850     }
2851     return existingNames;
2852   }
2853
2854   /**
2855    * Explode tabbed views into separate windows.
2856    */
2857   @Override
2858   public void expandViews_actionPerformed(ActionEvent e)
2859   {
2860     Desktop.instance.explodeViews(this);
2861   }
2862
2863   /**
2864    * Gather views in separate windows back into a tabbed presentation.
2865    */
2866   @Override
2867   public void gatherViews_actionPerformed(ActionEvent e)
2868   {
2869     Desktop.instance.gatherViews(this);
2870   }
2871
2872   /**
2873    * DOCUMENT ME!
2874    *
2875    * @param e
2876    *          DOCUMENT ME!
2877    */
2878   @Override
2879   public void font_actionPerformed(ActionEvent e)
2880   {
2881     new FontChooser(alignPanel);
2882   }
2883
2884   /**
2885    * DOCUMENT ME!
2886    *
2887    * @param e
2888    *          DOCUMENT ME!
2889    */
2890   @Override
2891   protected void seqLimit_actionPerformed(ActionEvent e)
2892   {
2893     viewport.setShowJVSuffix(seqLimits.isSelected());
2894
2895     alignPanel.getIdPanel().getIdCanvas()
2896             .setPreferredSize(alignPanel.calculateIdWidth());
2897     alignPanel.paintAlignment(true);
2898   }
2899
2900   @Override
2901   public void idRightAlign_actionPerformed(ActionEvent e)
2902   {
2903     viewport.setRightAlignIds(idRightAlign.isSelected());
2904     alignPanel.paintAlignment(true);
2905   }
2906
2907   @Override
2908   public void centreColumnLabels_actionPerformed(ActionEvent e)
2909   {
2910     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2911     alignPanel.paintAlignment(true);
2912   }
2913
2914   /*
2915    * (non-Javadoc)
2916    *
2917    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2918    */
2919   @Override
2920   protected void followHighlight_actionPerformed()
2921   {
2922     /*
2923      * Set the 'follow' flag on the Viewport (and scroll to position if now
2924      * true).
2925      */
2926     final boolean state = this.followHighlightMenuItem.getState();
2927     viewport.setFollowHighlight(state);
2928     if (state)
2929     {
2930       alignPanel.scrollToPosition(
2931               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2932     }
2933   }
2934
2935   /**
2936    * DOCUMENT ME!
2937    *
2938    * @param e
2939    *          DOCUMENT ME!
2940    */
2941   @Override
2942   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2943   {
2944     viewport.setColourText(colourTextMenuItem.isSelected());
2945     alignPanel.paintAlignment(true);
2946   }
2947
2948   /**
2949    * DOCUMENT ME!
2950    *
2951    * @param e
2952    *          DOCUMENT ME!
2953    */
2954   @Override
2955   public void wrapMenuItem_actionPerformed(ActionEvent e)
2956   {
2957     scaleAbove.setVisible(wrapMenuItem.isSelected());
2958     scaleLeft.setVisible(wrapMenuItem.isSelected());
2959     scaleRight.setVisible(wrapMenuItem.isSelected());
2960     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2961     alignPanel.updateLayout();
2962   }
2963
2964   @Override
2965   public void showAllSeqs_actionPerformed(ActionEvent e)
2966   {
2967     viewport.showAllHiddenSeqs();
2968   }
2969
2970   @Override
2971   public void showAllColumns_actionPerformed(ActionEvent e)
2972   {
2973     viewport.showAllHiddenColumns();
2974     repaint();
2975     viewport.sendSelection();
2976   }
2977
2978   @Override
2979   public void hideSelSequences_actionPerformed(ActionEvent e)
2980   {
2981     viewport.hideAllSelectedSeqs();
2982     // alignPanel.paintAlignment(true);
2983   }
2984
2985   /**
2986    * called by key handler and the hide all/show all menu items
2987    *
2988    * @param toggleSeqs
2989    * @param toggleCols
2990    */
2991   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2992   {
2993
2994     boolean hide = false;
2995     SequenceGroup sg = viewport.getSelectionGroup();
2996     if (!toggleSeqs && !toggleCols)
2997     {
2998       // Hide everything by the current selection - this is a hack - we do the
2999       // invert and then hide
3000       // first check that there will be visible columns after the invert.
3001       if ((viewport.getColumnSelection() != null
3002               && viewport.getColumnSelection().getSelected() != null && viewport
3003               .getColumnSelection().getSelected().size() > 0)
3004               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3005                       .getEndRes()))
3006       {
3007         // now invert the sequence set, if required - empty selection implies
3008         // that no hiding is required.
3009         if (sg != null)
3010         {
3011           invertSequenceMenuItem_actionPerformed(null);
3012           sg = viewport.getSelectionGroup();
3013           toggleSeqs = true;
3014
3015         }
3016         viewport.expandColSelection(sg, true);
3017         // finally invert the column selection and get the new sequence
3018         // selection.
3019         invertColSel_actionPerformed(null);
3020         toggleCols = true;
3021       }
3022     }
3023
3024     if (toggleSeqs)
3025     {
3026       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3027       {
3028         hideSelSequences_actionPerformed(null);
3029         hide = true;
3030       }
3031       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3032               .size() > 0))
3033       {
3034         showAllSeqs_actionPerformed(null);
3035       }
3036     }
3037
3038     if (toggleCols)
3039     {
3040       if (viewport.getColumnSelection().getSelected().size() > 0)
3041       {
3042         hideSelColumns_actionPerformed(null);
3043         if (!toggleSeqs)
3044         {
3045           viewport.setSelectionGroup(sg);
3046         }
3047       }
3048       else if (!hide)
3049       {
3050         showAllColumns_actionPerformed(null);
3051       }
3052     }
3053   }
3054
3055   /*
3056    * (non-Javadoc)
3057    *
3058    * @see
3059    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3060    * event.ActionEvent)
3061    */
3062   @Override
3063   public void hideAllButSelection_actionPerformed(ActionEvent e)
3064   {
3065     toggleHiddenRegions(false, false);
3066     viewport.sendSelection();
3067   }
3068
3069   /*
3070    * (non-Javadoc)
3071    *
3072    * @see
3073    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3074    * .ActionEvent)
3075    */
3076   @Override
3077   public void hideAllSelection_actionPerformed(ActionEvent e)
3078   {
3079     SequenceGroup sg = viewport.getSelectionGroup();
3080     viewport.expandColSelection(sg, false);
3081     viewport.hideAllSelectedSeqs();
3082     viewport.hideSelectedColumns();
3083     alignPanel.paintAlignment(true);
3084     viewport.sendSelection();
3085   }
3086
3087   /*
3088    * (non-Javadoc)
3089    *
3090    * @see
3091    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3092    * ActionEvent)
3093    */
3094   @Override
3095   public void showAllhidden_actionPerformed(ActionEvent e)
3096   {
3097     viewport.showAllHiddenColumns();
3098     viewport.showAllHiddenSeqs();
3099     alignPanel.paintAlignment(true);
3100     viewport.sendSelection();
3101   }
3102
3103   @Override
3104   public void hideSelColumns_actionPerformed(ActionEvent e)
3105   {
3106     viewport.hideSelectedColumns();
3107     alignPanel.paintAlignment(true);
3108     viewport.sendSelection();
3109   }
3110
3111   @Override
3112   public void hiddenMarkers_actionPerformed(ActionEvent e)
3113   {
3114     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3115     repaint();
3116   }
3117
3118   /**
3119    * DOCUMENT ME!
3120    *
3121    * @param e
3122    *          DOCUMENT ME!
3123    */
3124   @Override
3125   protected void scaleAbove_actionPerformed(ActionEvent e)
3126   {
3127     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3128     alignPanel.paintAlignment(true);
3129   }
3130
3131   /**
3132    * DOCUMENT ME!
3133    *
3134    * @param e
3135    *          DOCUMENT ME!
3136    */
3137   @Override
3138   protected void scaleLeft_actionPerformed(ActionEvent e)
3139   {
3140     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3141     alignPanel.paintAlignment(true);
3142   }
3143
3144   /**
3145    * DOCUMENT ME!
3146    *
3147    * @param e
3148    *          DOCUMENT ME!
3149    */
3150   @Override
3151   protected void scaleRight_actionPerformed(ActionEvent e)
3152   {
3153     viewport.setScaleRightWrapped(scaleRight.isSelected());
3154     alignPanel.paintAlignment(true);
3155   }
3156
3157   /**
3158    * DOCUMENT ME!
3159    *
3160    * @param e
3161    *          DOCUMENT ME!
3162    */
3163   @Override
3164   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3165   {
3166     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3167     alignPanel.paintAlignment(true);
3168   }
3169
3170   /**
3171    * DOCUMENT ME!
3172    *
3173    * @param e
3174    *          DOCUMENT ME!
3175    */
3176   @Override
3177   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3178   {
3179     viewport.setShowText(viewTextMenuItem.isSelected());
3180     alignPanel.paintAlignment(true);
3181   }
3182
3183   /**
3184    * DOCUMENT ME!
3185    *
3186    * @param e
3187    *          DOCUMENT ME!
3188    */
3189   @Override
3190   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3191   {
3192     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3193     alignPanel.paintAlignment(true);
3194   }
3195
3196   public FeatureSettings featureSettings;
3197
3198   @Override
3199   public FeatureSettingsControllerI getFeatureSettingsUI()
3200   {
3201     return featureSettings;
3202   }
3203
3204   @Override
3205   public void featureSettings_actionPerformed(ActionEvent e)
3206   {
3207     if (featureSettings != null)
3208     {
3209       featureSettings.close();
3210       featureSettings = null;
3211     }
3212     if (!showSeqFeatures.isSelected())
3213     {
3214       // make sure features are actually displayed
3215       showSeqFeatures.setSelected(true);
3216       showSeqFeatures_actionPerformed(null);
3217     }
3218     featureSettings = new FeatureSettings(this);
3219   }
3220
3221   /**
3222    * Set or clear 'Show Sequence Features'
3223    *
3224    * @param evt
3225    *          DOCUMENT ME!
3226    */
3227   @Override
3228   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3229   {
3230     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3231     alignPanel.paintAlignment(true);
3232     if (alignPanel.getOverviewPanel() != null)
3233     {
3234       alignPanel.getOverviewPanel().updateOverviewImage();
3235     }
3236   }
3237
3238   /**
3239    * Set or clear 'Show Sequence Features'
3240    *
3241    * @param evt
3242    *          DOCUMENT ME!
3243    */
3244   @Override
3245   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3246   {
3247     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3248             .isSelected());
3249     if (viewport.isShowSequenceFeaturesHeight())
3250     {
3251       // ensure we're actually displaying features
3252       viewport.setShowSequenceFeatures(true);
3253       showSeqFeatures.setSelected(true);
3254     }
3255     alignPanel.paintAlignment(true);
3256     if (alignPanel.getOverviewPanel() != null)
3257     {
3258       alignPanel.getOverviewPanel().updateOverviewImage();
3259     }
3260   }
3261
3262   /**
3263    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3264    * the annotations panel as a whole.
3265    *
3266    * The options to show/hide all annotations should be enabled when the panel
3267    * is shown, and disabled when the panel is hidden.
3268    *
3269    * @param e
3270    */
3271   @Override
3272   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3273   {
3274     final boolean setVisible = annotationPanelMenuItem.isSelected();
3275     viewport.setShowAnnotation(setVisible);
3276     this.showAllSeqAnnotations.setEnabled(setVisible);
3277     this.hideAllSeqAnnotations.setEnabled(setVisible);
3278     this.showAllAlAnnotations.setEnabled(setVisible);
3279     this.hideAllAlAnnotations.setEnabled(setVisible);
3280     alignPanel.updateLayout();
3281   }
3282
3283   @Override
3284   public void alignmentProperties()
3285   {
3286     JEditorPane editPane = new JEditorPane("text/html", "");
3287     editPane.setEditable(false);
3288     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3289             .formatAsHtml();
3290     editPane.setText(MessageManager.formatMessage("label.html_content",
3291             new Object[] { contents.toString() }));
3292     JInternalFrame frame = new JInternalFrame();
3293     frame.getContentPane().add(new JScrollPane(editPane));
3294
3295     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3296             "label.alignment_properties", new Object[] { getTitle() }),
3297             500, 400);
3298   }
3299
3300   /**
3301    * DOCUMENT ME!
3302    *
3303    * @param e
3304    *          DOCUMENT ME!
3305    */
3306   @Override
3307   public void overviewMenuItem_actionPerformed(ActionEvent e)
3308   {
3309     if (alignPanel.overviewPanel != null)
3310     {
3311       return;
3312     }
3313
3314     JInternalFrame frame = new JInternalFrame();
3315     OverviewPanel overview = new OverviewPanel(alignPanel);
3316     frame.setContentPane(overview);
3317     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3318             "label.overview_params", new Object[] { this.getTitle() }),
3319             frame.getWidth(), frame.getHeight());
3320     frame.pack();
3321     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3322     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3323     {
3324       @Override
3325       public void internalFrameClosed(
3326               javax.swing.event.InternalFrameEvent evt)
3327       {
3328         alignPanel.setOverviewPanel(null);
3329       };
3330     });
3331
3332     alignPanel.setOverviewPanel(overview);
3333   }
3334
3335   @Override
3336   public void textColour_actionPerformed(ActionEvent e)
3337   {
3338     new TextColourChooser().chooseColour(alignPanel, null);
3339   }
3340
3341   /**
3342    * DOCUMENT ME!
3343    *
3344    * @param e
3345    *          DOCUMENT ME!
3346    */
3347   @Override
3348   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3349   {
3350     changeColour(null);
3351   }
3352
3353   /**
3354    * DOCUMENT ME!
3355    *
3356    * @param e
3357    *          DOCUMENT ME!
3358    */
3359   @Override
3360   public void clustalColour_actionPerformed(ActionEvent e)
3361   {
3362     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3363             viewport.getHiddenRepSequences()));
3364   }
3365
3366   /**
3367    * DOCUMENT ME!
3368    *
3369    * @param e
3370    *          DOCUMENT ME!
3371    */
3372   @Override
3373   public void zappoColour_actionPerformed(ActionEvent e)
3374   {
3375     changeColour(new ZappoColourScheme());
3376   }
3377
3378   /**
3379    * DOCUMENT ME!
3380    *
3381    * @param e
3382    *          DOCUMENT ME!
3383    */
3384   @Override
3385   public void taylorColour_actionPerformed(ActionEvent e)
3386   {
3387     changeColour(new TaylorColourScheme());
3388   }
3389
3390   /**
3391    * DOCUMENT ME!
3392    *
3393    * @param e
3394    *          DOCUMENT ME!
3395    */
3396   @Override
3397   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3398   {
3399     changeColour(new HydrophobicColourScheme());
3400   }
3401
3402   /**
3403    * DOCUMENT ME!
3404    *
3405    * @param e
3406    *          DOCUMENT ME!
3407    */
3408   @Override
3409   public void helixColour_actionPerformed(ActionEvent e)
3410   {
3411     changeColour(new HelixColourScheme());
3412   }
3413
3414   /**
3415    * DOCUMENT ME!
3416    *
3417    * @param e
3418    *          DOCUMENT ME!
3419    */
3420   @Override
3421   public void strandColour_actionPerformed(ActionEvent e)
3422   {
3423     changeColour(new StrandColourScheme());
3424   }
3425
3426   /**
3427    * DOCUMENT ME!
3428    *
3429    * @param e
3430    *          DOCUMENT ME!
3431    */
3432   @Override
3433   public void turnColour_actionPerformed(ActionEvent e)
3434   {
3435     changeColour(new TurnColourScheme());
3436   }
3437
3438   /**
3439    * DOCUMENT ME!
3440    *
3441    * @param e
3442    *          DOCUMENT ME!
3443    */
3444   @Override
3445   public void buriedColour_actionPerformed(ActionEvent e)
3446   {
3447     changeColour(new BuriedColourScheme());
3448   }
3449
3450   /**
3451    * DOCUMENT ME!
3452    *
3453    * @param e
3454    *          DOCUMENT ME!
3455    */
3456   @Override
3457   public void nucleotideColour_actionPerformed(ActionEvent e)
3458   {
3459     changeColour(new NucleotideColourScheme());
3460   }
3461
3462   @Override
3463   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3464   {
3465     changeColour(new PurinePyrimidineColourScheme());
3466   }
3467
3468   /*
3469    * public void covariationColour_actionPerformed(ActionEvent e) {
3470    * changeColour(new
3471    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3472    * ()[0])); }
3473    */
3474   @Override
3475   public void annotationColour_actionPerformed(ActionEvent e)
3476   {
3477     new AnnotationColourChooser(viewport, alignPanel);
3478   }
3479
3480   @Override
3481   public void annotationColumn_actionPerformed(ActionEvent e)
3482   {
3483     new AnnotationColumnChooser(viewport, alignPanel);
3484   }
3485
3486   @Override
3487   public void rnahelicesColour_actionPerformed(ActionEvent e)
3488   {
3489     new RNAHelicesColourChooser(viewport, alignPanel);
3490   }
3491
3492   /**
3493    * DOCUMENT ME!
3494    *
3495    * @param e
3496    *          DOCUMENT ME!
3497    */
3498   @Override
3499   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3500   {
3501     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3502   }
3503
3504   /**
3505    * DOCUMENT ME!
3506    *
3507    * @param cs
3508    *          DOCUMENT ME!
3509    */
3510   @Override
3511   public void changeColour(ColourSchemeI cs)
3512   {
3513     // TODO: pull up to controller method
3514
3515     if (cs != null)
3516     {
3517       // Make sure viewport is up to date w.r.t. any sliders
3518       if (viewport.getAbovePIDThreshold())
3519       {
3520         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3521                 "Background");
3522         viewport.setThreshold(threshold);
3523       }
3524
3525       if (viewport.getConservationSelected())
3526       {
3527         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3528                 cs, "Background"));
3529       }
3530       if (cs instanceof TCoffeeColourScheme)
3531       {
3532         tcoffeeColour.setEnabled(true);
3533         tcoffeeColour.setSelected(true);
3534       }
3535     }
3536
3537     viewport.setGlobalColourScheme(cs);
3538
3539     alignPanel.paintAlignment(true);
3540   }
3541
3542   /**
3543    * DOCUMENT ME!
3544    *
3545    * @param e
3546    *          DOCUMENT ME!
3547    */
3548   @Override
3549   protected void modifyPID_actionPerformed(ActionEvent e)
3550   {
3551     if (viewport.getAbovePIDThreshold()
3552             && viewport.getGlobalColourScheme() != null)
3553     {
3554       SliderPanel.setPIDSliderSource(alignPanel,
3555               viewport.getGlobalColourScheme(), "Background");
3556       SliderPanel.showPIDSlider();
3557     }
3558   }
3559
3560   /**
3561    * DOCUMENT ME!
3562    *
3563    * @param e
3564    *          DOCUMENT ME!
3565    */
3566   @Override
3567   protected void modifyConservation_actionPerformed(ActionEvent e)
3568   {
3569     if (viewport.getConservationSelected()
3570             && viewport.getGlobalColourScheme() != null)
3571     {
3572       SliderPanel.setConservationSlider(alignPanel,
3573               viewport.getGlobalColourScheme(), "Background");
3574       SliderPanel.showConservationSlider();
3575     }
3576   }
3577
3578   /**
3579    * DOCUMENT ME!
3580    *
3581    * @param e
3582    *          DOCUMENT ME!
3583    */
3584   @Override
3585   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3586   {
3587     viewport.setConservationSelected(conservationMenuItem.isSelected());
3588
3589     viewport.setAbovePIDThreshold(false);
3590     abovePIDThreshold.setSelected(false);
3591
3592     changeColour(viewport.getGlobalColourScheme());
3593
3594     modifyConservation_actionPerformed(null);
3595   }
3596
3597   /**
3598    * DOCUMENT ME!
3599    *
3600    * @param e
3601    *          DOCUMENT ME!
3602    */
3603   @Override
3604   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3605   {
3606     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3607
3608     conservationMenuItem.setSelected(false);
3609     viewport.setConservationSelected(false);
3610
3611     changeColour(viewport.getGlobalColourScheme());
3612
3613     modifyPID_actionPerformed(null);
3614   }
3615
3616   /**
3617    * DOCUMENT ME!
3618    *
3619    * @param e
3620    *          DOCUMENT ME!
3621    */
3622   @Override
3623   public void userDefinedColour_actionPerformed(ActionEvent e)
3624   {
3625     if (e.getActionCommand().equals(
3626             MessageManager.getString("action.user_defined")))
3627     {
3628       new UserDefinedColours(alignPanel, null);
3629     }
3630     else
3631     {
3632       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3633               .getUserColourSchemes().get(e.getActionCommand());
3634
3635       changeColour(udc);
3636     }
3637   }
3638
3639   public void updateUserColourMenu()
3640   {
3641
3642     Component[] menuItems = colourMenu.getMenuComponents();
3643     int iSize = menuItems.length;
3644     for (int i = 0; i < iSize; i++)
3645     {
3646       if (menuItems[i].getName() != null
3647               && menuItems[i].getName().equals("USER_DEFINED"))
3648       {
3649         colourMenu.remove(menuItems[i]);
3650         iSize--;
3651       }
3652     }
3653     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3654     {
3655       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3656               .getUserColourSchemes().keys();
3657
3658       while (userColours.hasMoreElements())
3659       {
3660         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3661                 userColours.nextElement().toString());
3662         radioItem.setName("USER_DEFINED");
3663         radioItem.addMouseListener(new MouseAdapter()
3664         {
3665           @Override
3666           public void mousePressed(MouseEvent evt)
3667           {
3668             if (evt.isControlDown()
3669                     || SwingUtilities.isRightMouseButton(evt))
3670             {
3671               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3672
3673               int option = JOptionPane.showInternalConfirmDialog(
3674                       jalview.gui.Desktop.desktop,
3675                       MessageManager
3676                               .getString("label.remove_from_default_list"),
3677                       MessageManager
3678                               .getString("label.remove_user_defined_colour"),
3679                       JOptionPane.YES_NO_OPTION);
3680               if (option == JOptionPane.YES_OPTION)
3681               {
3682                 jalview.gui.UserDefinedColours
3683                         .removeColourFromDefaults(radioItem.getText());
3684                 colourMenu.remove(radioItem);
3685               }
3686               else
3687               {
3688                 radioItem.addActionListener(new ActionListener()
3689                 {
3690                   @Override
3691                   public void actionPerformed(ActionEvent evt)
3692                   {
3693                     userDefinedColour_actionPerformed(evt);
3694                   }
3695                 });
3696               }
3697             }
3698           }
3699         });
3700         radioItem.addActionListener(new ActionListener()
3701         {
3702           @Override
3703           public void actionPerformed(ActionEvent evt)
3704           {
3705             userDefinedColour_actionPerformed(evt);
3706           }
3707         });
3708
3709         colourMenu.insert(radioItem, 15);
3710         colours.add(radioItem);
3711       }
3712     }
3713   }
3714
3715   /**
3716    * DOCUMENT ME!
3717    *
3718    * @param e
3719    *          DOCUMENT ME!
3720    */
3721   @Override
3722   public void PIDColour_actionPerformed(ActionEvent e)
3723   {
3724     changeColour(new PIDColourScheme());
3725   }
3726
3727   /**
3728    * DOCUMENT ME!
3729    *
3730    * @param e
3731    *          DOCUMENT ME!
3732    */
3733   @Override
3734   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3735   {
3736     changeColour(new Blosum62ColourScheme());
3737   }
3738
3739   /**
3740    * DOCUMENT ME!
3741    *
3742    * @param e
3743    *          DOCUMENT ME!
3744    */
3745   @Override
3746   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3747   {
3748     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3749     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3750             .getAlignment().getSequenceAt(0), null);
3751     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3752             viewport.getAlignment()));
3753     alignPanel.paintAlignment(true);
3754   }
3755
3756   /**
3757    * DOCUMENT ME!
3758    *
3759    * @param e
3760    *          DOCUMENT ME!
3761    */
3762   @Override
3763   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3764   {
3765     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3766     AlignmentSorter.sortByID(viewport.getAlignment());
3767     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3768             viewport.getAlignment()));
3769     alignPanel.paintAlignment(true);
3770   }
3771
3772   /**
3773    * DOCUMENT ME!
3774    *
3775    * @param e
3776    *          DOCUMENT ME!
3777    */
3778   @Override
3779   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3780   {
3781     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3782     AlignmentSorter.sortByLength(viewport.getAlignment());
3783     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3784             viewport.getAlignment()));
3785     alignPanel.paintAlignment(true);
3786   }
3787
3788   /**
3789    * DOCUMENT ME!
3790    *
3791    * @param e
3792    *          DOCUMENT ME!
3793    */
3794   @Override
3795   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3796   {
3797     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3798     AlignmentSorter.sortByGroup(viewport.getAlignment());
3799     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3800             viewport.getAlignment()));
3801
3802     alignPanel.paintAlignment(true);
3803   }
3804
3805   /**
3806    * DOCUMENT ME!
3807    *
3808    * @param e
3809    *          DOCUMENT ME!
3810    */
3811   @Override
3812   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3813   {
3814     new RedundancyPanel(alignPanel, this);
3815   }
3816
3817   /**
3818    * DOCUMENT ME!
3819    *
3820    * @param e
3821    *          DOCUMENT ME!
3822    */
3823   @Override
3824   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3825   {
3826     if ((viewport.getSelectionGroup() == null)
3827             || (viewport.getSelectionGroup().getSize() < 2))
3828     {
3829       JOptionPane.showInternalMessageDialog(this, MessageManager
3830               .getString("label.you_must_select_least_two_sequences"),
3831               MessageManager.getString("label.invalid_selection"),
3832               JOptionPane.WARNING_MESSAGE);
3833     }
3834     else
3835     {
3836       JInternalFrame frame = new JInternalFrame();
3837       frame.setContentPane(new PairwiseAlignPanel(viewport));
3838       Desktop.addInternalFrame(frame,
3839               MessageManager.getString("action.pairwise_alignment"), 600,
3840               500);
3841     }
3842   }
3843
3844   /**
3845    * DOCUMENT ME!
3846    *
3847    * @param e
3848    *          DOCUMENT ME!
3849    */
3850   @Override
3851   public void PCAMenuItem_actionPerformed(ActionEvent e)
3852   {
3853     if (((viewport.getSelectionGroup() != null)
3854             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3855             .getSelectionGroup().getSize() > 0))
3856             || (viewport.getAlignment().getHeight() < 4))
3857     {
3858       JOptionPane
3859               .showInternalMessageDialog(
3860                       this,
3861                       MessageManager
3862                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3863                       MessageManager
3864                               .getString("label.sequence_selection_insufficient"),
3865                       JOptionPane.WARNING_MESSAGE);
3866
3867       return;
3868     }
3869
3870     new PCAPanel(alignPanel);
3871   }
3872
3873   @Override
3874   public void autoCalculate_actionPerformed(ActionEvent e)
3875   {
3876     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3877     if (viewport.autoCalculateConsensus)
3878     {
3879       viewport.firePropertyChange("alignment", null, viewport
3880               .getAlignment().getSequences());
3881     }
3882   }
3883
3884   @Override
3885   public void sortByTreeOption_actionPerformed(ActionEvent e)
3886   {
3887     viewport.sortByTree = sortByTree.isSelected();
3888   }
3889
3890   @Override
3891   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3892   {
3893     viewport.followSelection = listenToViewSelections.isSelected();
3894   }
3895
3896   /**
3897    * DOCUMENT ME!
3898    *
3899    * @param e
3900    *          DOCUMENT ME!
3901    */
3902   @Override
3903   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3904   {
3905     newTreePanel("AV", "PID", "Average distance tree using PID");
3906   }
3907
3908   /**
3909    * DOCUMENT ME!
3910    *
3911    * @param e
3912    *          DOCUMENT ME!
3913    */
3914   @Override
3915   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3916   {
3917     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3918   }
3919
3920   /**
3921    * DOCUMENT ME!
3922    *
3923    * @param e
3924    *          DOCUMENT ME!
3925    */
3926   @Override
3927   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3928   {
3929     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3930   }
3931
3932   /**
3933    * DOCUMENT ME!
3934    *
3935    * @param e
3936    *          DOCUMENT ME!
3937    */
3938   @Override
3939   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3940   {
3941     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3942   }
3943
3944   /**
3945    * DOCUMENT ME!
3946    *
3947    * @param type
3948    *          DOCUMENT ME!
3949    * @param pwType
3950    *          DOCUMENT ME!
3951    * @param title
3952    *          DOCUMENT ME!
3953    */
3954   void newTreePanel(String type, String pwType, String title)
3955   {
3956     TreePanel tp;
3957
3958     if (viewport.getSelectionGroup() != null
3959             && viewport.getSelectionGroup().getSize() > 0)
3960     {
3961       if (viewport.getSelectionGroup().getSize() < 3)
3962       {
3963         JOptionPane
3964                 .showMessageDialog(
3965                         Desktop.desktop,
3966                         MessageManager
3967                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3968                         MessageManager
3969                                 .getString("label.not_enough_sequences"),
3970                         JOptionPane.WARNING_MESSAGE);
3971         return;
3972       }
3973
3974       SequenceGroup sg = viewport.getSelectionGroup();
3975
3976       /* Decide if the selection is a column region */
3977       for (SequenceI _s : sg.getSequences())
3978       {
3979         if (_s.getLength() < sg.getEndRes())
3980         {
3981           JOptionPane
3982                   .showMessageDialog(
3983                           Desktop.desktop,
3984                           MessageManager
3985                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3986                           MessageManager
3987                                   .getString("label.sequences_selection_not_aligned"),
3988                           JOptionPane.WARNING_MESSAGE);
3989
3990           return;
3991         }
3992       }
3993
3994       title = title + " on region";
3995       tp = new TreePanel(alignPanel, type, pwType);
3996     }
3997     else
3998     {
3999       // are the visible sequences aligned?
4000       if (!viewport.getAlignment().isAligned(false))
4001       {
4002         JOptionPane
4003                 .showMessageDialog(
4004                         Desktop.desktop,
4005                         MessageManager
4006                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4007                         MessageManager
4008                                 .getString("label.sequences_not_aligned"),
4009                         JOptionPane.WARNING_MESSAGE);
4010
4011         return;
4012       }
4013
4014       if (viewport.getAlignment().getHeight() < 2)
4015       {
4016         return;
4017       }
4018
4019       tp = new TreePanel(alignPanel, type, pwType);
4020     }
4021
4022     title += " from ";
4023
4024     if (viewport.viewName != null)
4025     {
4026       title += viewport.viewName + " of ";
4027     }
4028
4029     title += this.title;
4030
4031     Desktop.addInternalFrame(tp, title, 600, 500);
4032   }
4033
4034   /**
4035    * DOCUMENT ME!
4036    *
4037    * @param title
4038    *          DOCUMENT ME!
4039    * @param order
4040    *          DOCUMENT ME!
4041    */
4042   public void addSortByOrderMenuItem(String title,
4043           final AlignmentOrder order)
4044   {
4045     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4046             "action.by_title_param", new Object[] { title }));
4047     sort.add(item);
4048     item.addActionListener(new java.awt.event.ActionListener()
4049     {
4050       @Override
4051       public void actionPerformed(ActionEvent e)
4052       {
4053         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4054
4055         // TODO: JBPNote - have to map order entries to curent SequenceI
4056         // pointers
4057         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4058
4059         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4060                 .getAlignment()));
4061
4062         alignPanel.paintAlignment(true);
4063       }
4064     });
4065   }
4066
4067   /**
4068    * Add a new sort by annotation score menu item
4069    *
4070    * @param sort
4071    *          the menu to add the option to
4072    * @param scoreLabel
4073    *          the label used to retrieve scores for each sequence on the
4074    *          alignment
4075    */
4076   public void addSortByAnnotScoreMenuItem(JMenu sort,
4077           final String scoreLabel)
4078   {
4079     final JMenuItem item = new JMenuItem(scoreLabel);
4080     sort.add(item);
4081     item.addActionListener(new java.awt.event.ActionListener()
4082     {
4083       @Override
4084       public void actionPerformed(ActionEvent e)
4085       {
4086         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4087         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4088                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4089         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4090                 viewport.getAlignment()));
4091         alignPanel.paintAlignment(true);
4092       }
4093     });
4094   }
4095
4096   /**
4097    * last hash for alignment's annotation array - used to minimise cost of
4098    * rebuild.
4099    */
4100   protected int _annotationScoreVectorHash;
4101
4102   /**
4103    * search the alignment and rebuild the sort by annotation score submenu the
4104    * last alignment annotation vector hash is stored to minimize cost of
4105    * rebuilding in subsequence calls.
4106    *
4107    */
4108   @Override
4109   public void buildSortByAnnotationScoresMenu()
4110   {
4111     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4112     {
4113       return;
4114     }
4115
4116     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4117     {
4118       sortByAnnotScore.removeAll();
4119       // almost certainly a quicker way to do this - but we keep it simple
4120       Hashtable scoreSorts = new Hashtable();
4121       AlignmentAnnotation aann[];
4122       for (SequenceI sqa : viewport.getAlignment().getSequences())
4123       {
4124         aann = sqa.getAnnotation();
4125         for (int i = 0; aann != null && i < aann.length; i++)
4126         {
4127           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4128           {
4129             scoreSorts.put(aann[i].label, aann[i].label);
4130           }
4131         }
4132       }
4133       Enumeration labels = scoreSorts.keys();
4134       while (labels.hasMoreElements())
4135       {
4136         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4137                 (String) labels.nextElement());
4138       }
4139       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4140       scoreSorts.clear();
4141
4142       _annotationScoreVectorHash = viewport.getAlignment()
4143               .getAlignmentAnnotation().hashCode();
4144     }
4145   }
4146
4147   /**
4148    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4149    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4150    * call. Listeners are added to remove the menu item when the treePanel is
4151    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4152    * modified.
4153    *
4154    * @param treePanel
4155    *          Displayed tree window.
4156    * @param title
4157    *          SortBy menu item title.
4158    */
4159   @Override
4160   public void buildTreeMenu()
4161   {
4162     calculateTree.removeAll();
4163     // build the calculate menu
4164
4165     for (final String type : new String[] { "NJ", "AV" })
4166     {
4167       String treecalcnm = MessageManager.getString("label.tree_calc_"
4168               + type.toLowerCase());
4169       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4170       {
4171         JMenuItem tm = new JMenuItem();
4172         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4173         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4174         {
4175           String smn = MessageManager.getStringOrReturn(
4176                   "label.score_model_", sm.getName());
4177           final String title = MessageManager.formatMessage(
4178                   "label.treecalc_title", treecalcnm, smn);
4179           tm.setText(title);//
4180           tm.addActionListener(new java.awt.event.ActionListener()
4181           {
4182             @Override
4183             public void actionPerformed(ActionEvent e)
4184             {
4185               newTreePanel(type, pwtype, title);
4186             }
4187           });
4188           calculateTree.add(tm);
4189         }
4190
4191       }
4192     }
4193     sortByTreeMenu.removeAll();
4194
4195     List<Component> comps = PaintRefresher.components.get(viewport
4196             .getSequenceSetId());
4197     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4198     for (Component comp : comps)
4199     {
4200       if (comp instanceof TreePanel)
4201       {
4202         treePanels.add((TreePanel) comp);
4203       }
4204     }
4205
4206     if (treePanels.size() < 1)
4207     {
4208       sortByTreeMenu.setVisible(false);
4209       return;
4210     }
4211
4212     sortByTreeMenu.setVisible(true);
4213
4214     for (final TreePanel tp : treePanels)
4215     {
4216       final JMenuItem item = new JMenuItem(tp.getTitle());
4217       item.addActionListener(new java.awt.event.ActionListener()
4218       {
4219         @Override
4220         public void actionPerformed(ActionEvent e)
4221         {
4222           tp.sortByTree_actionPerformed();
4223           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4224
4225         }
4226       });
4227
4228       sortByTreeMenu.add(item);
4229     }
4230   }
4231
4232   public boolean sortBy(AlignmentOrder alorder, String undoname)
4233   {
4234     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4235     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4236     if (undoname != null)
4237     {
4238       addHistoryItem(new OrderCommand(undoname, oldOrder,
4239               viewport.getAlignment()));
4240     }
4241     alignPanel.paintAlignment(true);
4242     return true;
4243   }
4244
4245   /**
4246    * Work out whether the whole set of sequences or just the selected set will
4247    * be submitted for multiple alignment.
4248    *
4249    */
4250   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4251   {
4252     // Now, check we have enough sequences
4253     AlignmentView msa = null;
4254
4255     if ((viewport.getSelectionGroup() != null)
4256             && (viewport.getSelectionGroup().getSize() > 1))
4257     {
4258       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4259       // some common interface!
4260       /*
4261        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4262        * SequenceI[sz = seqs.getSize(false)];
4263        *
4264        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4265        * seqs.getSequenceAt(i); }
4266        */
4267       msa = viewport.getAlignmentView(true);
4268     }
4269     else if (viewport.getSelectionGroup() != null
4270             && viewport.getSelectionGroup().getSize() == 1)
4271     {
4272       int option = JOptionPane.showConfirmDialog(this,
4273               MessageManager.getString("warn.oneseq_msainput_selection"),
4274               MessageManager.getString("label.invalid_selection"),
4275               JOptionPane.OK_CANCEL_OPTION);
4276       if (option == JOptionPane.OK_OPTION)
4277       {
4278         msa = viewport.getAlignmentView(false);
4279       }
4280     }
4281     else
4282     {
4283       msa = viewport.getAlignmentView(false);
4284     }
4285     return msa;
4286   }
4287
4288   /**
4289    * Decides what is submitted to a secondary structure prediction service: the
4290    * first sequence in the alignment, or in the current selection, or, if the
4291    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4292    * region or the whole alignment. (where the first sequence in the set is the
4293    * one that the prediction will be for).
4294    */
4295   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4296   {
4297     AlignmentView seqs = null;
4298
4299     if ((viewport.getSelectionGroup() != null)
4300             && (viewport.getSelectionGroup().getSize() > 0))
4301     {
4302       seqs = viewport.getAlignmentView(true);
4303     }
4304     else
4305     {
4306       seqs = viewport.getAlignmentView(false);
4307     }
4308     // limit sequences - JBPNote in future - could spawn multiple prediction
4309     // jobs
4310     // TODO: viewport.getAlignment().isAligned is a global state - the local
4311     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4312     if (!viewport.getAlignment().isAligned(false))
4313     {
4314       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4315       // TODO: if seqs.getSequences().length>1 then should really have warned
4316       // user!
4317
4318     }
4319     return seqs;
4320   }
4321
4322   /**
4323    * DOCUMENT ME!
4324    *
4325    * @param e
4326    *          DOCUMENT ME!
4327    */
4328   @Override
4329   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4330   {
4331     // Pick the tree file
4332     JalviewFileChooser chooser = new JalviewFileChooser(
4333             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4334     chooser.setFileView(new JalviewFileView());
4335     chooser.setDialogTitle(MessageManager
4336             .getString("label.select_newick_like_tree_file"));
4337     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4338
4339     int value = chooser.showOpenDialog(null);
4340
4341     if (value == JalviewFileChooser.APPROVE_OPTION)
4342     {
4343       String choice = chooser.getSelectedFile().getPath();
4344       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4345       jalview.io.NewickFile fin = null;
4346       try
4347       {
4348         fin = new jalview.io.NewickFile(choice, "File");
4349         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4350       } catch (Exception ex)
4351       {
4352         JOptionPane
4353                 .showMessageDialog(
4354                         Desktop.desktop,
4355                         ex.getMessage(),
4356                         MessageManager
4357                                 .getString("label.problem_reading_tree_file"),
4358                         JOptionPane.WARNING_MESSAGE);
4359         ex.printStackTrace();
4360       }
4361       if (fin != null && fin.hasWarningMessage())
4362       {
4363         JOptionPane.showMessageDialog(Desktop.desktop, fin
4364                 .getWarningMessage(), MessageManager
4365                 .getString("label.possible_problem_with_tree_file"),
4366                 JOptionPane.WARNING_MESSAGE);
4367       }
4368     }
4369   }
4370
4371   @Override
4372   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4373   {
4374     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4375   }
4376
4377   public TreePanel ShowNewickTree(NewickFile nf, String title)
4378   {
4379     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4380   }
4381
4382   public TreePanel ShowNewickTree(NewickFile nf, String title,
4383           AlignmentView input)
4384   {
4385     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4386   }
4387
4388   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4389           int h, int x, int y)
4390   {
4391     return ShowNewickTree(nf, title, null, w, h, x, y);
4392   }
4393
4394   /**
4395    * Add a treeviewer for the tree extracted from a newick file object to the
4396    * current alignment view
4397    *
4398    * @param nf
4399    *          the tree
4400    * @param title
4401    *          tree viewer title
4402    * @param input
4403    *          Associated alignment input data (or null)
4404    * @param w
4405    *          width
4406    * @param h
4407    *          height
4408    * @param x
4409    *          position
4410    * @param y
4411    *          position
4412    * @return TreePanel handle
4413    */
4414   public TreePanel ShowNewickTree(NewickFile nf, String title,
4415           AlignmentView input, int w, int h, int x, int y)
4416   {
4417     TreePanel tp = null;
4418
4419     try
4420     {
4421       nf.parse();
4422
4423       if (nf.getTree() != null)
4424       {
4425         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4426
4427         tp.setSize(w, h);
4428
4429         if (x > 0 && y > 0)
4430         {
4431           tp.setLocation(x, y);
4432         }
4433
4434         Desktop.addInternalFrame(tp, title, w, h);
4435       }
4436     } catch (Exception ex)
4437     {
4438       ex.printStackTrace();
4439     }
4440
4441     return tp;
4442   }
4443
4444   private boolean buildingMenu = false;
4445
4446   /**
4447    * Generates menu items and listener event actions for web service clients
4448    *
4449    */
4450   public void BuildWebServiceMenu()
4451   {
4452     while (buildingMenu)
4453     {
4454       try
4455       {
4456         System.err.println("Waiting for building menu to finish.");
4457         Thread.sleep(10);
4458       } catch (Exception e)
4459       {
4460       }
4461     }
4462     final AlignFrame me = this;
4463     buildingMenu = true;
4464     new Thread(new Runnable()
4465     {
4466       @Override
4467       public void run()
4468       {
4469         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4470         try
4471         {
4472           // System.err.println("Building ws menu again "
4473           // + Thread.currentThread());
4474           // TODO: add support for context dependent disabling of services based
4475           // on
4476           // alignment and current selection
4477           // TODO: add additional serviceHandle parameter to specify abstract
4478           // handler
4479           // class independently of AbstractName
4480           // TODO: add in rediscovery GUI function to restart discoverer
4481           // TODO: group services by location as well as function and/or
4482           // introduce
4483           // object broker mechanism.
4484           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4485           final IProgressIndicator af = me;
4486           final JMenu msawsmenu = new JMenu("Alignment");
4487           final JMenu secstrmenu = new JMenu(
4488                   "Secondary Structure Prediction");
4489           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4490           final JMenu analymenu = new JMenu("Analysis");
4491           final JMenu dismenu = new JMenu("Protein Disorder");
4492           // final JMenu msawsmenu = new
4493           // JMenu(MessageManager.getString("label.alignment"));
4494           // final JMenu secstrmenu = new
4495           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4496           // final JMenu seqsrchmenu = new
4497           // JMenu(MessageManager.getString("label.sequence_database_search"));
4498           // final JMenu analymenu = new
4499           // JMenu(MessageManager.getString("label.analysis"));
4500           // final JMenu dismenu = new
4501           // JMenu(MessageManager.getString("label.protein_disorder"));
4502           // JAL-940 - only show secondary structure prediction services from
4503           // the legacy server
4504           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4505               // &&
4506           Discoverer.services != null && (Discoverer.services.size() > 0))
4507           {
4508             // TODO: refactor to allow list of AbstractName/Handler bindings to
4509             // be
4510             // stored or retrieved from elsewhere
4511             // No MSAWS used any more:
4512             // Vector msaws = null; // (Vector)
4513             // Discoverer.services.get("MsaWS");
4514             Vector secstrpr = (Vector) Discoverer.services
4515                     .get("SecStrPred");
4516             if (secstrpr != null)
4517             {
4518               // Add any secondary structure prediction services
4519               for (int i = 0, j = secstrpr.size(); i < j; i++)
4520               {
4521                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4522                         .get(i);
4523                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4524                         .getServiceClient(sh);
4525                 int p = secstrmenu.getItemCount();
4526                 impl.attachWSMenuEntry(secstrmenu, me);
4527                 int q = secstrmenu.getItemCount();
4528                 for (int litm = p; litm < q; litm++)
4529                 {
4530                   legacyItems.add(secstrmenu.getItem(litm));
4531                 }
4532               }
4533             }
4534           }
4535
4536           // Add all submenus in the order they should appear on the web
4537           // services menu
4538           wsmenu.add(msawsmenu);
4539           wsmenu.add(secstrmenu);
4540           wsmenu.add(dismenu);
4541           wsmenu.add(analymenu);
4542           // No search services yet
4543           // wsmenu.add(seqsrchmenu);
4544
4545           javax.swing.SwingUtilities.invokeLater(new Runnable()
4546           {
4547             @Override
4548             public void run()
4549             {
4550               try
4551               {
4552                 webService.removeAll();
4553                 // first, add discovered services onto the webservices menu
4554                 if (wsmenu.size() > 0)
4555                 {
4556                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4557                   {
4558                     webService.add(wsmenu.get(i));
4559                   }
4560                 }
4561                 else
4562                 {
4563                   webService.add(me.webServiceNoServices);
4564                 }
4565                 // TODO: move into separate menu builder class.
4566                 boolean new_sspred = false;
4567                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4568                 {
4569                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4570                   if (jws2servs != null)
4571                   {
4572                     if (jws2servs.hasServices())
4573                     {
4574                       jws2servs.attachWSMenuEntry(webService, me);
4575                       for (Jws2Instance sv : jws2servs.getServices())
4576                       {
4577                         if (sv.description.toLowerCase().contains("jpred"))
4578                         {
4579                           for (JMenuItem jmi : legacyItems)
4580                           {
4581                             jmi.setVisible(false);
4582                           }
4583                         }
4584                       }
4585
4586                     }
4587                     if (jws2servs.isRunning())
4588                     {
4589                       JMenuItem tm = new JMenuItem(
4590                               "Still discovering JABA Services");
4591                       tm.setEnabled(false);
4592                       webService.add(tm);
4593                     }
4594                   }
4595                 }
4596                 build_urlServiceMenu(me.webService);
4597                 build_fetchdbmenu(webService);
4598                 for (JMenu item : wsmenu)
4599                 {
4600                   if (item.getItemCount() == 0)
4601                   {
4602                     item.setEnabled(false);
4603                   }
4604                   else
4605                   {
4606                     item.setEnabled(true);
4607                   }
4608                 }
4609               } catch (Exception e)
4610               {
4611                 Cache.log
4612                         .debug("Exception during web service menu building process.",
4613                                 e);
4614               }
4615             }
4616           });
4617         } catch (Exception e)
4618         {
4619         }
4620         buildingMenu = false;
4621       }
4622     }).start();
4623
4624   }
4625
4626   /**
4627    * construct any groupURL type service menu entries.
4628    *
4629    * @param webService
4630    */
4631   private void build_urlServiceMenu(JMenu webService)
4632   {
4633     // TODO: remove this code when 2.7 is released
4634     // DEBUG - alignmentView
4635     /*
4636      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4637      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4638      *
4639      * @Override public void actionPerformed(ActionEvent e) {
4640      * jalview.datamodel.AlignmentView
4641      * .testSelectionViews(af.viewport.getAlignment(),
4642      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4643      *
4644      * }); webService.add(testAlView);
4645      */
4646     // TODO: refactor to RestClient discoverer and merge menu entries for
4647     // rest-style services with other types of analysis/calculation service
4648     // SHmmr test client - still being implemented.
4649     // DEBUG - alignmentView
4650
4651     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4652             .getRestClients())
4653     {
4654       client.attachWSMenuEntry(
4655               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4656               this);
4657     }
4658   }
4659
4660   /**
4661    * Searches selected sequences for xRef products and builds the Show
4662    * Cross-References menu (formerly called Show Products)
4663    *
4664    * @return true if Show Cross-references menu should be enabled.
4665    */
4666   public boolean canShowProducts()
4667   {
4668     SequenceI[] selection = viewport.getSequenceSelection();
4669     AlignmentI dataset = viewport.getAlignment().getDataset();
4670     boolean showp = false;
4671     try
4672     {
4673       showProducts.removeAll();
4674       final boolean dna = viewport.getAlignment().isNucleotide();
4675       String[] ptypes = (selection == null || selection.length == 0) ? null
4676               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4677
4678       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4679       {
4680         showp = true;
4681         final AlignFrame af = this;
4682         final String source = ptypes[t];
4683         JMenuItem xtype = new JMenuItem(ptypes[t]);
4684         xtype.addActionListener(new ActionListener()
4685         {
4686
4687           @Override
4688           public void actionPerformed(ActionEvent e)
4689           {
4690             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4691           }
4692
4693         });
4694         showProducts.add(xtype);
4695       }
4696       showProducts.setVisible(showp);
4697       showProducts.setEnabled(showp);
4698     } catch (Exception e)
4699     {
4700       jalview.bin.Cache.log
4701               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4702                       e);
4703       return false;
4704     }
4705     return showp;
4706   }
4707
4708   protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4709           final String source)
4710   {
4711     Runnable foo = new Runnable()
4712     {
4713
4714       @Override
4715       public void run()
4716       {
4717         final long sttime = System.currentTimeMillis();
4718         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4719                 "status.searching_for_sequences_from",
4720                 new Object[] { source }), sttime);
4721         try
4722         {
4723           /*
4724            * 'peer' sequences are any to add to this alignment, for example
4725            * alternative protein products for my protein's gene
4726            */
4727           List<SequenceI> addedPeers = new ArrayList<SequenceI>();
4728           AlignmentI alignment = AlignFrame.this.getViewport()
4729                   .getAlignment();
4730           Alignment xrefs = CrossRef.findXrefSequences(sel, dna, source,
4731                   alignment, addedPeers);
4732           if (xrefs != null)
4733           {
4734             /*
4735              * figure out colour scheme if any to apply to features
4736              */
4737             ASequenceFetcher sftch = new SequenceFetcher();
4738             List<DbSourceProxy> proxies = sftch.getSourceProxy(source);
4739             FeatureSettingsI featureColourScheme = null;
4740             for (DbSourceProxy proxy : proxies)
4741             {
4742               FeatureSettingsI preferredColours = proxy
4743                       .getFeatureColourScheme();
4744               if (preferredColours != null)
4745               {
4746                 featureColourScheme = preferredColours;
4747                 break;
4748               }
4749             }
4750             Alignment al = makeCrossReferencesAlignment(
4751                     alignment.getDataset(), xrefs);
4752
4753             /*
4754              * Copy dna-to-protein mappings to new alignment
4755              */
4756             // TODO 1: no mappings are set up for EMBL product
4757             // TODO 2: if they were, should add them to protein alignment, not
4758             // dna
4759             // List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4760             // for (AlignedCodonFrame acf : cf)
4761             // {
4762             // al.addCodonFrame(acf);
4763             // }
4764             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4765                     DEFAULT_HEIGHT);
4766             String newtitle = String.format("%s %s %s",
4767                     MessageManager.getString(dna ? "label.proteins"
4768                             : "label.nucleotides"), MessageManager
4769                             .getString("label.for"), getTitle());
4770             newFrame.setTitle(newtitle);
4771
4772             boolean asSplitFrame = Cache.getDefault(
4773                     Preferences.ENABLE_SPLIT_FRAME, true);
4774             if (asSplitFrame)
4775             {
4776               /*
4777                * Make a copy of this alignment (sharing the same dataset
4778                * sequences). If we are DNA, drop introns and update mappings
4779                */
4780               AlignmentI copyAlignment = null;
4781               final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4782                       .getSequenceSelection();
4783               List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4784               if (dna)
4785               {
4786                 copyAlignment = AlignmentUtils.makeCdsAlignment(
4787                         sequenceSelection, cf);
4788                 al.getCodonFrames().clear();
4789                 al.getCodonFrames().addAll(cf);
4790               }
4791               else
4792               {
4793                 copyAlignment = new Alignment(new Alignment(
4794                         sequenceSelection));
4795                 copyAlignment.getCodonFrames().addAll(cf);
4796               }
4797               StructureSelectionManager ssm = StructureSelectionManager
4798                       .getStructureSelectionManager(Desktop.instance);
4799               ssm.registerMappings(cf);
4800
4801               /*
4802                * add in any extra 'peer' sequences discovered
4803                * (e.g. alternative protein products)
4804                */
4805               for (SequenceI peer : addedPeers)
4806               {
4807                 copyAlignment.addSequence(peer);
4808               }
4809
4810               /*
4811                * align protein to dna
4812                */
4813               // TODO needs debugging
4814               // if (dna)
4815               // {
4816               // al.alignAs(copyAlignment);
4817               // }
4818               // else
4819               // {
4820               // copyAlignment.alignAs(al);
4821               // }
4822
4823               AlignFrame copyThis = new AlignFrame(copyAlignment,
4824                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4825               copyThis.setTitle(AlignFrame.this.getTitle());
4826
4827               boolean showSequenceFeatures = viewport
4828                       .isShowSequenceFeatures();
4829               newFrame.setShowSeqFeatures(showSequenceFeatures);
4830               copyThis.setShowSeqFeatures(showSequenceFeatures);
4831               FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4832                       .getFeatureRenderer();
4833
4834               /*
4835                * copy feature rendering settings to split frame
4836                */
4837               newFrame.alignPanel.getSeqPanel().seqCanvas
4838                       .getFeatureRenderer().transferSettings(
4839                               myFeatureStyling);
4840               copyThis.alignPanel.getSeqPanel().seqCanvas
4841                       .getFeatureRenderer().transferSettings(
4842                               myFeatureStyling);
4843
4844               /*
4845                * apply 'database source' feature configuration
4846                * if any was found
4847                */
4848               newFrame.getViewport()
4849                       .applyFeaturesStyle(featureColourScheme);
4850               copyThis.getViewport()
4851                       .applyFeaturesStyle(featureColourScheme);
4852
4853               SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4854                       dna ? newFrame : copyThis);
4855               newFrame.setVisible(true);
4856               copyThis.setVisible(true);
4857               String linkedTitle = MessageManager
4858                       .getString("label.linked_view_title");
4859               Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4860               sf.adjustDivider();
4861             }
4862             else
4863             {
4864               Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4865                       DEFAULT_HEIGHT);
4866             }
4867           }
4868           else
4869           {
4870             System.err.println("No Sequences generated for xRef type "
4871                     + source);
4872           }
4873         } catch (Exception e)
4874         {
4875           jalview.bin.Cache.log.error(
4876                   "Exception when finding crossreferences", e);
4877         } catch (OutOfMemoryError e)
4878         {
4879           new OOMWarning("whilst fetching crossreferences", e);
4880         } catch (Error e)
4881         {
4882           jalview.bin.Cache.log.error("Error when finding crossreferences",
4883                   e);
4884         }
4885         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4886                 "status.finished_searching_for_sequences_from",
4887                 new Object[] { source }), sttime);
4888       }
4889
4890       /**
4891        * @param alignment
4892        * @param prods
4893        * @return
4894        */
4895       protected Alignment makeCrossReferencesAlignment(Alignment dataset,
4896               Alignment prods)
4897       {
4898         SequenceI[] sprods = new SequenceI[prods.getHeight()];
4899         for (int s = 0; s < sprods.length; s++)
4900         {
4901           sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4902           if (dataset.getSequences() == null
4903                   || !dataset.getSequences().contains(
4904                           sprods[s].getDatasetSequence()))
4905           {
4906             dataset.addSequence(sprods[s].getDatasetSequence());
4907           }
4908           sprods[s].updatePDBIds();
4909         }
4910         Alignment al = new Alignment(sprods);
4911         al.setDataset(dataset);
4912         return al;
4913       }
4914
4915     };
4916     Thread frunner = new Thread(foo);
4917     frunner.start();
4918   }
4919
4920   public boolean canShowTranslationProducts(SequenceI[] selection,
4921           AlignmentI alignment)
4922   {
4923     // old way
4924     try
4925     {
4926       return (jalview.analysis.Dna.canTranslate(selection,
4927               viewport.getViewAsVisibleContigs(true)));
4928     } catch (Exception e)
4929     {
4930       jalview.bin.Cache.log
4931               .warn("canTranslate threw an exception - please report to help@jalview.org",
4932                       e);
4933       return false;
4934     }
4935   }
4936
4937   /**
4938    * Construct and display a new frame containing the translation of this
4939    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4940    */
4941   @Override
4942   public void showTranslation_actionPerformed(ActionEvent e)
4943   {
4944     AlignmentI al = null;
4945     try
4946     {
4947       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4948
4949       al = dna.translateCdna();
4950     } catch (Exception ex)
4951     {
4952       jalview.bin.Cache.log.error(
4953               "Exception during translation. Please report this !", ex);
4954       final String msg = MessageManager
4955               .getString("label.error_when_translating_sequences_submit_bug_report");
4956       final String errorTitle = MessageManager
4957               .getString("label.implementation_error")
4958               + MessageManager.getString("translation_failed");
4959       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4960               JOptionPane.ERROR_MESSAGE);
4961       return;
4962     }
4963     if (al == null || al.getHeight() == 0)
4964     {
4965       final String msg = MessageManager
4966               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4967       final String errorTitle = MessageManager
4968               .getString("label.translation_failed");
4969       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4970               JOptionPane.WARNING_MESSAGE);
4971     }
4972     else
4973     {
4974       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4975       af.setFileFormat(this.currentFileFormat);
4976       final String newTitle = MessageManager.formatMessage(
4977               "label.translation_of_params",
4978               new Object[] { this.getTitle() });
4979       af.setTitle(newTitle);
4980       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4981       {
4982         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4983         viewport.openSplitFrame(af, new Alignment(seqs));
4984       }
4985       else
4986       {
4987         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4988                 DEFAULT_HEIGHT);
4989       }
4990     }
4991   }
4992
4993   /**
4994    * Set the file format
4995    *
4996    * @param fileFormat
4997    */
4998   public void setFileFormat(String fileFormat)
4999   {
5000     this.currentFileFormat = fileFormat;
5001   }
5002
5003   /**
5004    * Try to load a features file onto the alignment.
5005    *
5006    * @param file
5007    *          contents or path to retrieve file
5008    * @param type
5009    *          access mode of file (see jalview.io.AlignFile)
5010    * @return true if features file was parsed correctly.
5011    */
5012   public boolean parseFeaturesFile(String file, String type)
5013   {
5014     return avc.parseFeaturesFile(file, type,
5015             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5016
5017   }
5018
5019   @Override
5020   public void refreshFeatureUI(boolean enableIfNecessary)
5021   {
5022     // note - currently this is only still here rather than in the controller
5023     // because of the featureSettings hard reference that is yet to be
5024     // abstracted
5025     if (enableIfNecessary)
5026     {
5027       viewport.setShowSequenceFeatures(true);
5028       showSeqFeatures.setSelected(true);
5029     }
5030
5031   }
5032
5033   @Override
5034   public void dragEnter(DropTargetDragEvent evt)
5035   {
5036   }
5037
5038   @Override
5039   public void dragExit(DropTargetEvent evt)
5040   {
5041   }
5042
5043   @Override
5044   public void dragOver(DropTargetDragEvent evt)
5045   {
5046   }
5047
5048   @Override
5049   public void dropActionChanged(DropTargetDragEvent evt)
5050   {
5051   }
5052
5053   @Override
5054   public void drop(DropTargetDropEvent evt)
5055   {
5056     Transferable t = evt.getTransferable();
5057     java.util.List files = null;
5058
5059     try
5060     {
5061       DataFlavor uriListFlavor = new DataFlavor(
5062               "text/uri-list;class=java.lang.String");
5063       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5064       {
5065         // Works on Windows and MacOSX
5066         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5067         files = (java.util.List) t
5068                 .getTransferData(DataFlavor.javaFileListFlavor);
5069       }
5070       else if (t.isDataFlavorSupported(uriListFlavor))
5071       {
5072         // This is used by Unix drag system
5073         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5074         String data = (String) t.getTransferData(uriListFlavor);
5075         files = new java.util.ArrayList(1);
5076         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5077                 data, "\r\n"); st.hasMoreTokens();)
5078         {
5079           String s = st.nextToken();
5080           if (s.startsWith("#"))
5081           {
5082             // the line is a comment (as per the RFC 2483)
5083             continue;
5084           }
5085
5086           java.net.URI uri = new java.net.URI(s);
5087           // check to see if we can handle this kind of URI
5088           if (uri.getScheme().toLowerCase().startsWith("http"))
5089           {
5090             files.add(uri.toString());
5091           }
5092           else
5093           {
5094             // otherwise preserve old behaviour: catch all for file objects
5095             java.io.File file = new java.io.File(uri);
5096             files.add(file.toString());
5097           }
5098         }
5099       }
5100     } catch (Exception e)
5101     {
5102       e.printStackTrace();
5103     }
5104     if (files != null)
5105     {
5106       try
5107       {
5108         // check to see if any of these files have names matching sequences in
5109         // the alignment
5110         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5111                 .getAlignment().getSequencesArray());
5112         /**
5113          * Object[] { String,SequenceI}
5114          */
5115         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5116         ArrayList<String> filesnotmatched = new ArrayList<String>();
5117         for (int i = 0; i < files.size(); i++)
5118         {
5119           String file = files.get(i).toString();
5120           String pdbfn = "";
5121           String protocol = FormatAdapter.checkProtocol(file);
5122           if (protocol == jalview.io.FormatAdapter.FILE)
5123           {
5124             File fl = new File(file);
5125             pdbfn = fl.getName();
5126           }
5127           else if (protocol == jalview.io.FormatAdapter.URL)
5128           {
5129             URL url = new URL(file);
5130             pdbfn = url.getFile();
5131           }
5132           if (pdbfn.length() > 0)
5133           {
5134             // attempt to find a match in the alignment
5135             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5136             int l = 0, c = pdbfn.indexOf(".");
5137             while (mtch == null && c != -1)
5138             {
5139               do
5140               {
5141                 l = c;
5142               } while ((c = pdbfn.indexOf(".", l)) > l);
5143               if (l > -1)
5144               {
5145                 pdbfn = pdbfn.substring(0, l);
5146               }
5147               mtch = idm.findAllIdMatches(pdbfn);
5148             }
5149             if (mtch != null)
5150             {
5151               String type = null;
5152               try
5153               {
5154                 type = new IdentifyFile().identify(file, protocol);
5155               } catch (Exception ex)
5156               {
5157                 type = null;
5158               }
5159               if (type != null)
5160               {
5161                 if (type.equalsIgnoreCase("PDB"))
5162                 {
5163                   filesmatched.add(new Object[] { file, protocol, mtch });
5164                   continue;
5165                 }
5166               }
5167             }
5168             // File wasn't named like one of the sequences or wasn't a PDB file.
5169             filesnotmatched.add(file);
5170           }
5171         }
5172         int assocfiles = 0;
5173         if (filesmatched.size() > 0)
5174         {
5175           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5176                   || JOptionPane
5177                           .showConfirmDialog(
5178                                   this,
5179                                   MessageManager
5180                                           .formatMessage(
5181                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5182                                                   new Object[] { Integer
5183                                                           .valueOf(
5184                                                                   filesmatched
5185                                                                           .size())
5186                                                           .toString() }),
5187                                   MessageManager
5188                                           .getString("label.automatically_associate_pdb_files_by_name"),
5189                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5190
5191           {
5192             for (Object[] fm : filesmatched)
5193             {
5194               // try and associate
5195               // TODO: may want to set a standard ID naming formalism for
5196               // associating PDB files which have no IDs.
5197               for (SequenceI toassoc : (SequenceI[]) fm[2])
5198               {
5199                 PDBEntry pe = new AssociatePdbFileWithSeq()
5200                         .associatePdbWithSeq((String) fm[0],
5201                                 (String) fm[1], toassoc, false,
5202                                 Desktop.instance);
5203                 if (pe != null)
5204                 {
5205                   System.err.println("Associated file : "
5206                           + ((String) fm[0]) + " with "
5207                           + toassoc.getDisplayId(true));
5208                   assocfiles++;
5209                 }
5210               }
5211               alignPanel.paintAlignment(true);
5212             }
5213           }
5214         }
5215         if (filesnotmatched.size() > 0)
5216         {
5217           if (assocfiles > 0
5218                   && (Cache.getDefault(
5219                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5220                           .showConfirmDialog(
5221                                   this,
5222                                   "<html>"
5223                                           + MessageManager
5224                                                   .formatMessage(
5225                                                           "label.ignore_unmatched_dropped_files_info",
5226                                                           new Object[] { Integer
5227                                                                   .valueOf(
5228                                                                           filesnotmatched
5229                                                                                   .size())
5230                                                                   .toString() })
5231                                           + "</html>",
5232                                   MessageManager
5233                                           .getString("label.ignore_unmatched_dropped_files"),
5234                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5235           {
5236             return;
5237           }
5238           for (String fn : filesnotmatched)
5239           {
5240             loadJalviewDataFile(fn, null, null, null);
5241           }
5242
5243         }
5244       } catch (Exception ex)
5245       {
5246         ex.printStackTrace();
5247       }
5248     }
5249   }
5250
5251   /**
5252    * Attempt to load a "dropped" file or URL string: First by testing whether
5253    * it's an Annotation file, then a JNet file, and finally a features file. If
5254    * all are false then the user may have dropped an alignment file onto this
5255    * AlignFrame.
5256    *
5257    * @param file
5258    *          either a filename or a URL string.
5259    */
5260   public void loadJalviewDataFile(String file, String protocol,
5261           String format, SequenceI assocSeq)
5262   {
5263     try
5264     {
5265       if (protocol == null)
5266       {
5267         protocol = FormatAdapter.checkProtocol(file);
5268       }
5269       // if the file isn't identified, or not positively identified as some
5270       // other filetype (PFAM is default unidentified alignment file type) then
5271       // try to parse as annotation.
5272       boolean isAnnotation = (format == null || format
5273               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5274               .annotateAlignmentView(viewport, file, protocol) : false;
5275
5276       if (!isAnnotation)
5277       {
5278         // first see if its a T-COFFEE score file
5279         TCoffeeScoreFile tcf = null;
5280         try
5281         {
5282           tcf = new TCoffeeScoreFile(file, protocol);
5283           if (tcf.isValid())
5284           {
5285             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5286             {
5287               tcoffeeColour.setEnabled(true);
5288               tcoffeeColour.setSelected(true);
5289               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5290               isAnnotation = true;
5291               statusBar
5292                       .setText(MessageManager
5293                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5294             }
5295             else
5296             {
5297               // some problem - if no warning its probable that the ID matching
5298               // process didn't work
5299               JOptionPane
5300                       .showMessageDialog(
5301                               Desktop.desktop,
5302                               tcf.getWarningMessage() == null ? MessageManager
5303                                       .getString("label.check_file_matches_sequence_ids_alignment")
5304                                       : tcf.getWarningMessage(),
5305                               MessageManager
5306                                       .getString("label.problem_reading_tcoffee_score_file"),
5307                               JOptionPane.WARNING_MESSAGE);
5308             }
5309           }
5310           else
5311           {
5312             tcf = null;
5313           }
5314         } catch (Exception x)
5315         {
5316           Cache.log
5317                   .debug("Exception when processing data source as T-COFFEE score file",
5318                           x);
5319           tcf = null;
5320         }
5321         if (tcf == null)
5322         {
5323           // try to see if its a JNet 'concise' style annotation file *before*
5324           // we
5325           // try to parse it as a features file
5326           if (format == null)
5327           {
5328             format = new IdentifyFile().identify(file, protocol);
5329           }
5330           if (format.equalsIgnoreCase("JnetFile"))
5331           {
5332             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5333                     file, protocol);
5334             new JnetAnnotationMaker();
5335             JnetAnnotationMaker.add_annotation(predictions,
5336                     viewport.getAlignment(), 0, false);
5337             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5338             viewport.getAlignment().setSeqrep(repseq);
5339             ColumnSelection cs = new ColumnSelection();
5340             cs.hideInsertionsFor(repseq);
5341             viewport.setColumnSelection(cs);
5342             isAnnotation = true;
5343           }
5344           else if (IdentifyFile.FeaturesFile.equals(format))
5345           {
5346             if (parseFeaturesFile(file, protocol))
5347             {
5348               alignPanel.paintAlignment(true);
5349             }
5350           }
5351           else
5352           {
5353             new FileLoader().LoadFile(viewport, file, protocol, format);
5354           }
5355         }
5356       }
5357       if (isAnnotation)
5358       {
5359
5360         alignPanel.adjustAnnotationHeight();
5361         viewport.updateSequenceIdColours();
5362         buildSortByAnnotationScoresMenu();
5363         alignPanel.paintAlignment(true);
5364       }
5365     } catch (Exception ex)
5366     {
5367       ex.printStackTrace();
5368     } catch (OutOfMemoryError oom)
5369     {
5370       try
5371       {
5372         System.gc();
5373       } catch (Exception x)
5374       {
5375       }
5376       new OOMWarning(
5377               "loading data "
5378                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5379                               : "using " + protocol + " from " + file)
5380                               : ".")
5381                       + (format != null ? "(parsing as '" + format
5382                               + "' file)" : ""), oom, Desktop.desktop);
5383     }
5384   }
5385
5386   /**
5387    * Method invoked by the ChangeListener on the tabbed pane, in other words
5388    * when a different tabbed pane is selected by the user or programmatically.
5389    */
5390   @Override
5391   public void tabSelectionChanged(int index)
5392   {
5393     if (index > -1)
5394     {
5395       alignPanel = alignPanels.get(index);
5396       viewport = alignPanel.av;
5397       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5398       setMenusFromViewport(viewport);
5399     }
5400
5401     /*
5402      * If there is a frame linked to this one in a SplitPane, switch it to the
5403      * same view tab index. No infinite recursion of calls should happen, since
5404      * tabSelectionChanged() should not get invoked on setting the selected
5405      * index to an unchanged value. Guard against setting an invalid index
5406      * before the new view peer tab has been created.
5407      */
5408     final AlignViewportI peer = viewport.getCodingComplement();
5409     if (peer != null)
5410     {
5411       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5412       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5413       {
5414         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5415       }
5416     }
5417   }
5418
5419   /**
5420    * On right mouse click on view tab, prompt for and set new view name.
5421    */
5422   @Override
5423   public void tabbedPane_mousePressed(MouseEvent e)
5424   {
5425     if (SwingUtilities.isRightMouseButton(e))
5426     {
5427       String msg = MessageManager.getString("label.enter_view_name");
5428       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5429               JOptionPane.QUESTION_MESSAGE);
5430
5431       if (reply != null)
5432       {
5433         viewport.viewName = reply;
5434         // TODO warn if reply is in getExistingViewNames()?
5435         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5436       }
5437     }
5438   }
5439
5440   public AlignViewport getCurrentView()
5441   {
5442     return viewport;
5443   }
5444
5445   /**
5446    * Open the dialog for regex description parsing.
5447    */
5448   @Override
5449   protected void extractScores_actionPerformed(ActionEvent e)
5450   {
5451     ParseProperties pp = new jalview.analysis.ParseProperties(
5452             viewport.getAlignment());
5453     // TODO: verify regex and introduce GUI dialog for version 2.5
5454     // if (pp.getScoresFromDescription("col", "score column ",
5455     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5456     // true)>0)
5457     if (pp.getScoresFromDescription("description column",
5458             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5459     {
5460       buildSortByAnnotationScoresMenu();
5461     }
5462   }
5463
5464   /*
5465    * (non-Javadoc)
5466    *
5467    * @see
5468    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5469    * )
5470    */
5471   @Override
5472   protected void showDbRefs_actionPerformed(ActionEvent e)
5473   {
5474     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5475   }
5476
5477   /*
5478    * (non-Javadoc)
5479    *
5480    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5481    * ActionEvent)
5482    */
5483   @Override
5484   protected void showNpFeats_actionPerformed(ActionEvent e)
5485   {
5486     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5487   }
5488
5489   /**
5490    * find the viewport amongst the tabs in this alignment frame and close that
5491    * tab
5492    *
5493    * @param av
5494    */
5495   public boolean closeView(AlignViewportI av)
5496   {
5497     if (viewport == av)
5498     {
5499       this.closeMenuItem_actionPerformed(false);
5500       return true;
5501     }
5502     Component[] comp = tabbedPane.getComponents();
5503     for (int i = 0; comp != null && i < comp.length; i++)
5504     {
5505       if (comp[i] instanceof AlignmentPanel)
5506       {
5507         if (((AlignmentPanel) comp[i]).av == av)
5508         {
5509           // close the view.
5510           closeView((AlignmentPanel) comp[i]);
5511           return true;
5512         }
5513       }
5514     }
5515     return false;
5516   }
5517
5518   protected void build_fetchdbmenu(JMenu webService)
5519   {
5520     // Temporary hack - DBRef Fetcher always top level ws entry.
5521     // TODO We probably want to store a sequence database checklist in
5522     // preferences and have checkboxes.. rather than individual sources selected
5523     // here
5524     final JMenu rfetch = new JMenu(
5525             MessageManager.getString("action.fetch_db_references"));
5526     rfetch.setToolTipText(MessageManager
5527             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5528     webService.add(rfetch);
5529
5530     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5531             MessageManager.getString("option.trim_retrieved_seqs"));
5532     trimrs.setToolTipText(MessageManager
5533             .getString("label.trim_retrieved_sequences"));
5534     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5535     trimrs.addActionListener(new ActionListener()
5536     {
5537       @Override
5538       public void actionPerformed(ActionEvent e)
5539       {
5540         trimrs.setSelected(trimrs.isSelected());
5541         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5542                 Boolean.valueOf(trimrs.isSelected()).toString());
5543       };
5544     });
5545     rfetch.add(trimrs);
5546     JMenuItem fetchr = new JMenuItem(
5547             MessageManager.getString("label.standard_databases"));
5548     fetchr.setToolTipText(MessageManager
5549             .getString("label.fetch_embl_uniprot"));
5550     fetchr.addActionListener(new ActionListener()
5551     {
5552
5553       @Override
5554       public void actionPerformed(ActionEvent e)
5555       {
5556         new Thread(new Runnable()
5557         {
5558
5559           @Override
5560           public void run()
5561           {
5562             boolean isNuclueotide = alignPanel.alignFrame.getViewport()
5563                     .getAlignment().isNucleotide();
5564             new jalview.ws.DBRefFetcher(alignPanel.av
5565                     .getSequenceSelection(), alignPanel.alignFrame, null,
5566                     alignPanel.alignFrame.featureSettings, isNuclueotide)
5567                     .fetchDBRefs(false);
5568           }
5569         }).start();
5570
5571       }
5572
5573     });
5574     rfetch.add(fetchr);
5575     final AlignFrame me = this;
5576     new Thread(new Runnable()
5577     {
5578       @Override
5579       public void run()
5580       {
5581         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5582                 .getSequenceFetcherSingleton(me);
5583         javax.swing.SwingUtilities.invokeLater(new Runnable()
5584         {
5585           @Override
5586           public void run()
5587           {
5588             String[] dbclasses = sf.getOrderedSupportedSources();
5589             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5590             // jalview.util.QuickSort.sort(otherdb, otherdb);
5591             List<DbSourceProxy> otherdb;
5592             JMenu dfetch = new JMenu();
5593             JMenu ifetch = new JMenu();
5594             JMenuItem fetchr = null;
5595             int comp = 0, icomp = 0, mcomp = 15;
5596             String mname = null;
5597             int dbi = 0;
5598             for (String dbclass : dbclasses)
5599             {
5600               otherdb = sf.getSourceProxy(dbclass);
5601               // add a single entry for this class, or submenu allowing 'fetch
5602               // all' or pick one
5603               if (otherdb == null || otherdb.size() < 1)
5604               {
5605                 continue;
5606               }
5607               // List<DbSourceProxy> dbs=otherdb;
5608               // otherdb=new ArrayList<DbSourceProxy>();
5609               // for (DbSourceProxy db:dbs)
5610               // {
5611               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5612               // }
5613               if (mname == null)
5614               {
5615                 mname = "From " + dbclass;
5616               }
5617               if (otherdb.size() == 1)
5618               {
5619                 final DbSourceProxy[] dassource = otherdb
5620                         .toArray(new DbSourceProxy[0]);
5621                 DbSourceProxy src = otherdb.get(0);
5622                 fetchr = new JMenuItem(src.getDbSource());
5623                 fetchr.addActionListener(new ActionListener()
5624                 {
5625
5626                   @Override
5627                   public void actionPerformed(ActionEvent e)
5628                   {
5629                     new Thread(new Runnable()
5630                     {
5631
5632                       @Override
5633                       public void run()
5634                       {
5635                         boolean isNuclueotide = alignPanel.alignFrame
5636                                 .getViewport().getAlignment()
5637                                 .isNucleotide();
5638                         new jalview.ws.DBRefFetcher(alignPanel.av
5639                                 .getSequenceSelection(),
5640                                 alignPanel.alignFrame, dassource,
5641                                 alignPanel.alignFrame.featureSettings,
5642                                 isNuclueotide).fetchDBRefs(false);
5643                       }
5644                     }).start();
5645                   }
5646
5647                 });
5648                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5649                         MessageManager.formatMessage(
5650                                 "label.fetch_retrieve_from",
5651                                 new Object[] { src.getDbName() })));
5652                 dfetch.add(fetchr);
5653                 comp++;
5654               }
5655               else
5656               {
5657                 final DbSourceProxy[] dassource = otherdb
5658                         .toArray(new DbSourceProxy[0]);
5659                 // fetch all entry
5660                 DbSourceProxy src = otherdb.get(0);
5661                 fetchr = new JMenuItem(MessageManager.formatMessage(
5662                         "label.fetch_all_param",
5663                         new Object[] { src.getDbSource() }));
5664                 fetchr.addActionListener(new ActionListener()
5665                 {
5666                   @Override
5667                   public void actionPerformed(ActionEvent e)
5668                   {
5669                     new Thread(new Runnable()
5670                     {
5671
5672                       @Override
5673                       public void run()
5674                       {
5675                         boolean isNuclueotide = alignPanel.alignFrame
5676                                 .getViewport().getAlignment()
5677                                 .isNucleotide();
5678                         new jalview.ws.DBRefFetcher(alignPanel.av
5679                                 .getSequenceSelection(),
5680                                 alignPanel.alignFrame, dassource,
5681                                 alignPanel.alignFrame.featureSettings,
5682                                 isNuclueotide).fetchDBRefs(false);
5683                       }
5684                     }).start();
5685                   }
5686                 });
5687
5688                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5689                         MessageManager.formatMessage(
5690                                 "label.fetch_retrieve_from_all_sources",
5691                                 new Object[] {
5692                                     Integer.valueOf(otherdb.size())
5693                                             .toString(), src.getDbSource(),
5694                                     src.getDbName() })));
5695                 dfetch.add(fetchr);
5696                 comp++;
5697                 // and then build the rest of the individual menus
5698                 ifetch = new JMenu(MessageManager.formatMessage(
5699                         "label.source_from_db_source",
5700                         new Object[] { src.getDbSource() }));
5701                 icomp = 0;
5702                 String imname = null;
5703                 int i = 0;
5704                 for (DbSourceProxy sproxy : otherdb)
5705                 {
5706                   String dbname = sproxy.getDbName();
5707                   String sname = dbname.length() > 5 ? dbname.substring(0,
5708                           5) + "..." : dbname;
5709                   String msname = dbname.length() > 10 ? dbname.substring(
5710                           0, 10) + "..." : dbname;
5711                   if (imname == null)
5712                   {
5713                     imname = MessageManager.formatMessage(
5714                             "label.from_msname", new Object[] { sname });
5715                   }
5716                   fetchr = new JMenuItem(msname);
5717                   final DbSourceProxy[] dassrc = { sproxy };
5718                   fetchr.addActionListener(new ActionListener()
5719                   {
5720
5721                     @Override
5722                     public void actionPerformed(ActionEvent e)
5723                     {
5724                       new Thread(new Runnable()
5725                       {
5726
5727                         @Override
5728                         public void run()
5729                         {
5730                           boolean isNuclueotide = alignPanel.alignFrame
5731                                   .getViewport().getAlignment()
5732                                   .isNucleotide();
5733                           new jalview.ws.DBRefFetcher(alignPanel.av
5734                                   .getSequenceSelection(),
5735                                   alignPanel.alignFrame, dassrc,
5736                                   alignPanel.alignFrame.featureSettings,
5737                                   isNuclueotide).fetchDBRefs(false);
5738                         }
5739                       }).start();
5740                     }
5741
5742                   });
5743                   fetchr.setToolTipText("<html>"
5744                           + MessageManager.formatMessage(
5745                                   "label.fetch_retrieve_from", new Object[]
5746                                   { dbname }));
5747                   ifetch.add(fetchr);
5748                   ++i;
5749                   if (++icomp >= mcomp || i == (otherdb.size()))
5750                   {
5751                     ifetch.setText(MessageManager.formatMessage(
5752                             "label.source_to_target", imname, sname));
5753                     dfetch.add(ifetch);
5754                     ifetch = new JMenu();
5755                     imname = null;
5756                     icomp = 0;
5757                     comp++;
5758                   }
5759                 }
5760               }
5761               ++dbi;
5762               if (comp >= mcomp || dbi >= (dbclasses.length))
5763               {
5764                 dfetch.setText(MessageManager.formatMessage(
5765                         "label.source_to_target", mname, dbclass));
5766                 rfetch.add(dfetch);
5767                 dfetch = new JMenu();
5768                 mname = null;
5769                 comp = 0;
5770               }
5771             }
5772           }
5773         });
5774       }
5775     }).start();
5776
5777   }
5778
5779   /**
5780    * Left justify the whole alignment.
5781    */
5782   @Override
5783   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5784   {
5785     AlignmentI al = viewport.getAlignment();
5786     al.justify(false);
5787     viewport.firePropertyChange("alignment", null, al);
5788   }
5789
5790   /**
5791    * Right justify the whole alignment.
5792    */
5793   @Override
5794   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5795   {
5796     AlignmentI al = viewport.getAlignment();
5797     al.justify(true);
5798     viewport.firePropertyChange("alignment", null, al);
5799   }
5800
5801   @Override
5802   public void setShowSeqFeatures(boolean b)
5803   {
5804     showSeqFeatures.setSelected(b);
5805     viewport.setShowSequenceFeatures(b);
5806   }
5807
5808   /*
5809    * (non-Javadoc)
5810    *
5811    * @see
5812    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5813    * awt.event.ActionEvent)
5814    */
5815   @Override
5816   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5817   {
5818     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5819     alignPanel.paintAlignment(true);
5820   }
5821
5822   /*
5823    * (non-Javadoc)
5824    *
5825    * @see
5826    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5827    * .ActionEvent)
5828    */
5829   @Override
5830   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5831   {
5832     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5833     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5834
5835   }
5836
5837   /*
5838    * (non-Javadoc)
5839    *
5840    * @see
5841    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5842    * .event.ActionEvent)
5843    */
5844   @Override
5845   protected void showGroupConservation_actionPerformed(ActionEvent e)
5846   {
5847     viewport.setShowGroupConservation(showGroupConservation.getState());
5848     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5849   }
5850
5851   /*
5852    * (non-Javadoc)
5853    *
5854    * @see
5855    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5856    * .event.ActionEvent)
5857    */
5858   @Override
5859   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5860   {
5861     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5862     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5863   }
5864
5865   /*
5866    * (non-Javadoc)
5867    *
5868    * @see
5869    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5870    * .event.ActionEvent)
5871    */
5872   @Override
5873   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5874   {
5875     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5876     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5877   }
5878
5879   @Override
5880   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5881   {
5882     showSequenceLogo.setState(true);
5883     viewport.setShowSequenceLogo(true);
5884     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5885     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5886   }
5887
5888   @Override
5889   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5890   {
5891     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5892   }
5893
5894   /*
5895    * (non-Javadoc)
5896    *
5897    * @see
5898    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5899    * .event.ActionEvent)
5900    */
5901   @Override
5902   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5903   {
5904     if (avc.makeGroupsFromSelection())
5905     {
5906       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5907       alignPanel.updateAnnotation();
5908       alignPanel.paintAlignment(true);
5909     }
5910   }
5911
5912   public void clearAlignmentSeqRep()
5913   {
5914     // TODO refactor alignmentseqrep to controller
5915     if (viewport.getAlignment().hasSeqrep())
5916     {
5917       viewport.getAlignment().setSeqrep(null);
5918       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5919       alignPanel.updateAnnotation();
5920       alignPanel.paintAlignment(true);
5921     }
5922   }
5923
5924   @Override
5925   protected void createGroup_actionPerformed(ActionEvent e)
5926   {
5927     if (avc.createGroup())
5928     {
5929       alignPanel.alignmentChanged();
5930     }
5931   }
5932
5933   @Override
5934   protected void unGroup_actionPerformed(ActionEvent e)
5935   {
5936     if (avc.unGroup())
5937     {
5938       alignPanel.alignmentChanged();
5939     }
5940   }
5941
5942   /**
5943    * make the given alignmentPanel the currently selected tab
5944    *
5945    * @param alignmentPanel
5946    */
5947   public void setDisplayedView(AlignmentPanel alignmentPanel)
5948   {
5949     if (!viewport.getSequenceSetId().equals(
5950             alignmentPanel.av.getSequenceSetId()))
5951     {
5952       throw new Error(
5953               MessageManager
5954                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5955     }
5956     if (tabbedPane != null
5957             && tabbedPane.getTabCount() > 0
5958             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5959                     .getSelectedIndex())
5960     {
5961       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5962     }
5963   }
5964
5965   /**
5966    * Action on selection of menu options to Show or Hide annotations.
5967    *
5968    * @param visible
5969    * @param forSequences
5970    *          update sequence-related annotations
5971    * @param forAlignment
5972    *          update non-sequence-related annotations
5973    */
5974   @Override
5975   protected void setAnnotationsVisibility(boolean visible,
5976           boolean forSequences, boolean forAlignment)
5977   {
5978     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5979             .getAlignmentAnnotation())
5980     {
5981       /*
5982        * don't display non-positional annotations on an alignment
5983        */
5984       if (aa.annotations == null)
5985       {
5986         continue;
5987       }
5988       boolean apply = (aa.sequenceRef == null && forAlignment)
5989               || (aa.sequenceRef != null && forSequences);
5990       if (apply)
5991       {
5992         aa.visible = visible;
5993       }
5994     }
5995     alignPanel.validateAnnotationDimensions(true);
5996     alignPanel.alignmentChanged();
5997   }
5998
5999   /**
6000    * Store selected annotation sort order for the view and repaint.
6001    */
6002   @Override
6003   protected void sortAnnotations_actionPerformed()
6004   {
6005     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6006     this.alignPanel.av
6007             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6008     alignPanel.paintAlignment(true);
6009   }
6010
6011   /**
6012    *
6013    * @return alignment panels in this alignment frame
6014    */
6015   public List<? extends AlignmentViewPanel> getAlignPanels()
6016   {
6017     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6018   }
6019
6020   /**
6021    * Open a new alignment window, with the cDNA associated with this (protein)
6022    * alignment, aligned as is the protein.
6023    */
6024   protected void viewAsCdna_actionPerformed()
6025   {
6026     // TODO no longer a menu action - refactor as required
6027     final AlignmentI alignment = getViewport().getAlignment();
6028     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6029     if (mappings == null)
6030     {
6031       return;
6032     }
6033     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6034     for (SequenceI aaSeq : alignment.getSequences())
6035     {
6036       for (AlignedCodonFrame acf : mappings)
6037       {
6038         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6039         if (dnaSeq != null)
6040         {
6041           /*
6042            * There is a cDNA mapping for this protein sequence - add to new
6043            * alignment. It will share the same dataset sequence as other mapped
6044            * cDNA (no new mappings need to be created).
6045            */
6046           final Sequence newSeq = new Sequence(dnaSeq);
6047           newSeq.setDatasetSequence(dnaSeq);
6048           cdnaSeqs.add(newSeq);
6049         }
6050       }
6051     }
6052     if (cdnaSeqs.size() == 0)
6053     {
6054       // show a warning dialog no mapped cDNA
6055       return;
6056     }
6057     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6058             .size()]));
6059     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6060             AlignFrame.DEFAULT_HEIGHT);
6061     cdna.alignAs(alignment);
6062     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6063             + this.title;
6064     Desktop.addInternalFrame(alignFrame, newtitle,
6065             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6066   }
6067
6068   /**
6069    * Set visibility of dna/protein complement view (available when shown in a
6070    * split frame).
6071    *
6072    * @param show
6073    */
6074   @Override
6075   protected void showComplement_actionPerformed(boolean show)
6076   {
6077     SplitContainerI sf = getSplitViewContainer();
6078     if (sf != null)
6079     {
6080       sf.setComplementVisible(this, show);
6081     }
6082   }
6083
6084   /**
6085    * Generate the reverse (optionally complemented) of the selected sequences,
6086    * and add them to the alignment
6087    */
6088   @Override
6089   protected void showReverse_actionPerformed(boolean complement)
6090   {
6091     AlignmentI al = null;
6092     try
6093     {
6094       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6095
6096       al = dna.reverseCdna(complement);
6097       viewport.addAlignment(al, "");
6098     } catch (Exception ex)
6099     {
6100       System.err.println(ex.getMessage());
6101       return;
6102     }
6103   }
6104 }
6105
6106 class PrintThread extends Thread
6107 {
6108   AlignmentPanel ap;
6109
6110   public PrintThread(AlignmentPanel ap)
6111   {
6112     this.ap = ap;
6113   }
6114
6115   static PageFormat pf;
6116
6117   @Override
6118   public void run()
6119   {
6120     PrinterJob printJob = PrinterJob.getPrinterJob();
6121
6122     if (pf != null)
6123     {
6124       printJob.setPrintable(ap, pf);
6125     }
6126     else
6127     {
6128       printJob.setPrintable(ap);
6129     }
6130
6131     if (printJob.printDialog())
6132     {
6133       try
6134       {
6135         printJob.print();
6136       } catch (Exception PrintException)
6137       {
6138         PrintException.printStackTrace();
6139       }
6140     }
6141   }
6142 }