src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
   3  * Copyright (C) 2015 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  63 import jalview.io.AlignmentProperties;
  64 import jalview.io.AnnotationFile;
  65 import jalview.io.BioJsHTMLOutput;
  66 import jalview.io.FileLoader;
  67 import jalview.io.FormatAdapter;
  68 import jalview.io.HtmlSvgOutput;
  69 import jalview.io.IdentifyFile;
  70 import jalview.io.JalviewFileChooser;
  71 import jalview.io.JalviewFileView;
  72 import jalview.io.JnetAnnotationMaker;
  73 import jalview.io.NewickFile;
  74 import jalview.io.TCoffeeScoreFile;
  75 import jalview.jbgui.GAlignFrame;
  76 import jalview.schemes.Blosum62ColourScheme;
  77 import jalview.schemes.BuriedColourScheme;
  78 import jalview.schemes.ClustalxColourScheme;
  79 import jalview.schemes.ColourSchemeI;
  80 import jalview.schemes.ColourSchemeProperty;
  81 import jalview.schemes.HelixColourScheme;
  82 import jalview.schemes.HydrophobicColourScheme;
  83 import jalview.schemes.NucleotideColourScheme;
  84 import jalview.schemes.PIDColourScheme;
  85 import jalview.schemes.PurinePyrimidineColourScheme;
  86 import jalview.schemes.RNAHelicesColourChooser;
  87 import jalview.schemes.ResidueProperties;
  88 import jalview.schemes.StrandColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.schemes.TaylorColourScheme;
  91 import jalview.schemes.TurnColourScheme;
  92 import jalview.schemes.UserColourScheme;
  93 import jalview.schemes.ZappoColourScheme;
  94 import jalview.structure.StructureSelectionManager;
  95 import jalview.util.MessageManager;
  96 import jalview.viewmodel.AlignmentViewport;
  97 import jalview.ws.jws1.Discoverer;
  98 import jalview.ws.jws2.Jws2Discoverer;
  99 import jalview.ws.jws2.jabaws2.Jws2Instance;
 100 import jalview.ws.seqfetcher.DbSourceProxy;
 101
 102 import java.awt.BorderLayout;
 103 import java.awt.Component;
 104 import java.awt.Rectangle;
 105 import java.awt.Toolkit;
 106 import java.awt.datatransfer.Clipboard;
 107 import java.awt.datatransfer.DataFlavor;
 108 import java.awt.datatransfer.StringSelection;
 109 import java.awt.datatransfer.Transferable;
 110 import java.awt.dnd.DnDConstants;
 111 import java.awt.dnd.DropTargetDragEvent;
 112 import java.awt.dnd.DropTargetDropEvent;
 113 import java.awt.dnd.DropTargetEvent;
 114 import java.awt.dnd.DropTargetListener;
 115 import java.awt.event.ActionEvent;
 116 import java.awt.event.ActionListener;
 117 import java.awt.event.ItemEvent;
 118 import java.awt.event.ItemListener;
 119 import java.awt.event.KeyAdapter;
 120 import java.awt.event.KeyEvent;
 121 import java.awt.event.MouseAdapter;
 122 import java.awt.event.MouseEvent;
 123 import java.awt.print.PageFormat;
 124 import java.awt.print.PrinterJob;
 125 import java.beans.PropertyChangeEvent;
 126 import java.io.File;
 127 import java.net.URL;
 128 import java.util.ArrayList;
 129 import java.util.Arrays;
 130 import java.util.Deque;
 131 import java.util.Enumeration;
 132 import java.util.Hashtable;
 133 import java.util.List;
 134 import java.util.Set;
 135 import java.util.Vector;
 136
 137 import javax.swing.JCheckBoxMenuItem;
 138 import javax.swing.JEditorPane;
 139 import javax.swing.JInternalFrame;
 140 import javax.swing.JLayeredPane;
 141 import javax.swing.JMenu;
 142 import javax.swing.JMenuItem;
 143 import javax.swing.JOptionPane;
 144 import javax.swing.JRadioButtonMenuItem;
 145 import javax.swing.JScrollPane;
 146 import javax.swing.SwingUtilities;
 147
 148 /**
 149  * DOCUMENT ME!
 150  *
 151  * @author $author$
 152  * @version $Revision$
 153  */
 154 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 155         IProgressIndicator, AlignViewControllerGuiI
 156 {
 157
 158   public static final int DEFAULT_WIDTH = 700;
 159
 160   public static final int DEFAULT_HEIGHT = 500;
 161
 162   /*
 163    * The currently displayed panel (selected tabbed view if more than one)
 164    */
 165   public AlignmentPanel alignPanel;
 166
 167   AlignViewport viewport;
 168
 169   public AlignViewControllerI avc;
 170
 171   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 172
 173   /**
 174    * Last format used to load or save alignments in this window
 175    */
 176   String currentFileFormat = null;
 177
 178   /**
 179    * Current filename for this alignment
 180    */
 181   String fileName = null;
 182
 183   /**
 184    * Creates a new AlignFrame object with specific width and height.
 185    *
 186    * @param al
 187    * @param width
 188    * @param height
 189    */
 190   public AlignFrame(AlignmentI al, int width, int height)
 191   {
 192     this(al, null, width, height);
 193   }
 194
 195   /**
 196    * Creates a new AlignFrame object with specific width, height and
 197    * sequenceSetId
 198    *
 199    * @param al
 200    * @param width
 201    * @param height
 202    * @param sequenceSetId
 203    */
 204   public AlignFrame(AlignmentI al, int width, int height,
 205           String sequenceSetId)
 206   {
 207     this(al, null, width, height, sequenceSetId);
 208   }
 209
 210   /**
 211    * Creates a new AlignFrame object with specific width, height and
 212    * sequenceSetId
 213    *
 214    * @param al
 215    * @param width
 216    * @param height
 217    * @param sequenceSetId
 218    * @param viewId
 219    */
 220   public AlignFrame(AlignmentI al, int width, int height,
 221           String sequenceSetId, String viewId)
 222   {
 223     this(al, null, width, height, sequenceSetId, viewId);
 224   }
 225
 226   /**
 227    * new alignment window with hidden columns
 228    *
 229    * @param al
 230    *          AlignmentI
 231    * @param hiddenColumns
 232    *          ColumnSelection or null
 233    * @param width
 234    *          Width of alignment frame
 235    * @param height
 236    *          height of frame.
 237    */
 238   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 239           int width, int height)
 240   {
 241     this(al, hiddenColumns, width, height, null);
 242   }
 243
 244   /**
 245    * Create alignment frame for al with hiddenColumns, a specific width and
 246    * height, and specific sequenceId
 247    *
 248    * @param al
 249    * @param hiddenColumns
 250    * @param width
 251    * @param height
 252    * @param sequenceSetId
 253    *          (may be null)
 254    */
 255   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 256           int width, int height, String sequenceSetId)
 257   {
 258     this(al, hiddenColumns, width, height, sequenceSetId, null);
 259   }
 260
 261   /**
 262    * Create alignment frame for al with hiddenColumns, a specific width and
 263    * height, and specific sequenceId
 264    *
 265    * @param al
 266    * @param hiddenColumns
 267    * @param width
 268    * @param height
 269    * @param sequenceSetId
 270    *          (may be null)
 271    * @param viewId
 272    *          (may be null)
 273    */
 274   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 275           int width, int height, String sequenceSetId, String viewId)
 276   {
 277     setSize(width, height);
 278
 279     if (al.getDataset() == null)
 280     {
 281       al.setDataset(null);
 282     }
 283
 284     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 285
 286     alignPanel = new AlignmentPanel(this, viewport);
 287
 288     addAlignmentPanel(alignPanel, true);
 289     init();
 290   }
 291
 292   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 293           ColumnSelection hiddenColumns, int width, int height)
 294   {
 295     setSize(width, height);
 296
 297     if (al.getDataset() == null)
 298     {
 299       al.setDataset(null);
 300     }
 301
 302     viewport = new AlignViewport(al, hiddenColumns);
 303
 304     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 305     {
 306       viewport.hideSequence(hiddenSeqs);
 307     }
 308     alignPanel = new AlignmentPanel(this, viewport);
 309     addAlignmentPanel(alignPanel, true);
 310     init();
 311   }
 312
 313   /**
 314    * Make a new AlignFrame from existing alignmentPanels
 315    *
 316    * @param ap
 317    *          AlignmentPanel
 318    * @param av
 319    *          AlignViewport
 320    */
 321   public AlignFrame(AlignmentPanel ap)
 322   {
 323     viewport = ap.av;
 324     alignPanel = ap;
 325     addAlignmentPanel(ap, false);
 326     init();
 327   }
 328
 329   /**
 330    * initalise the alignframe from the underlying viewport data and the
 331    * configurations
 332    */
 333   void init()
 334   {
 335     if (!Jalview.isHeadlessMode())
 336     {
 337       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 338     }
 339
 340     avc = new jalview.controller.AlignViewController(this, viewport,
 341             alignPanel);
 342     if (viewport.getAlignmentConservationAnnotation() == null)
 343     {
 344       BLOSUM62Colour.setEnabled(false);
 345       conservationMenuItem.setEnabled(false);
 346       modifyConservation.setEnabled(false);
 347       // PIDColour.setEnabled(false);
 348       // abovePIDThreshold.setEnabled(false);
 349       // modifyPID.setEnabled(false);
 350     }
 351
 352     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 353             "No sort");
 354
 355     if (sortby.equals("Id"))
 356     {
 357       sortIDMenuItem_actionPerformed(null);
 358     }
 359     else if (sortby.equals("Pairwise Identity"))
 360     {
 361       sortPairwiseMenuItem_actionPerformed(null);
 362     }
 363
 364     if (Desktop.desktop != null)
 365     {
 366       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 367       addServiceListeners();
 368       setGUINucleotide(viewport.getAlignment().isNucleotide());
 369     }
 370
 371     this.alignPanel.av
 372             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 373
 374     setMenusFromViewport(viewport);
 375     buildSortByAnnotationScoresMenu();
 376     buildTreeMenu();
 377
 378     if (viewport.getWrapAlignment())
 379     {
 380       wrapMenuItem_actionPerformed(null);
 381     }
 382
 383     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 384     {
 385       this.overviewMenuItem_actionPerformed(null);
 386     }
 387
 388     addKeyListener();
 389
 390     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 391     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 392     final String menuLabel = MessageManager
 393             .getString("label.copy_format_from");
 394     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 395             new ViewSetProvider()
 396             {
 397
 398               @Override
 399               public AlignmentPanel[] getAllAlignmentPanels()
 400               {
 401                 origview.clear();
 402                 origview.add(alignPanel);
 403                 // make an array of all alignment panels except for this one
 404                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 405                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 406                 aps.remove(AlignFrame.this.alignPanel);
 407                 return aps.toArray(new AlignmentPanel[aps.size()]);
 408               }
 409             }, selviews, new ItemListener()
 410             {
 411
 412               @Override
 413               public void itemStateChanged(ItemEvent e)
 414               {
 415                 if (origview.size() > 0)
 416                 {
 417                   final AlignmentPanel ap = origview.get(0);
 418
 419                   /*
 420                    * Copy the ViewStyle of the selected panel to 'this one'.
 421                    * Don't change value of 'scaleProteinAsCdna' unless copying
 422                    * from a SplitFrame.
 423                    */
 424                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 425                           .getViewStyle();
 426                   boolean fromSplitFrame = selviews.get(0)
 427                           .getAlignViewport().getCodingComplement() != null;
 428                   if (!fromSplitFrame)
 429                   {
 430                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 431                             .getViewStyle().isScaleProteinAsCdna());
 432                   }
 433                   ap.getAlignViewport().setViewStyle(vs);
 434
 435                   /*
 436                    * Also rescale ViewStyle of SplitFrame complement if there is
 437                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 438                    * the whole ViewStyle (allow cDNA protein to have different
 439                    * fonts)
 440                    */
 441                   AlignViewportI complement = ap.getAlignViewport()
 442                           .getCodingComplement();
 443                   if (complement != null && vs.isScaleProteinAsCdna())
 444                   {
 445                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 446                     ((SplitFrame) af.getSplitViewContainer())
 447                             .adjustLayout();
 448                     af.setMenusForViewport();
 449                   }
 450
 451                   ap.updateLayout();
 452                   ap.setSelected(true);
 453                   ap.alignFrame.setMenusForViewport();
 454
 455                 }
 456               }
 457             });
 458     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 459             .indexOf("devel") > -1
 460             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 461                     .indexOf("test") > -1)
 462     {
 463       formatMenu.add(vsel);
 464     }
 465
 466   }
 467
 468   /**
 469    * Change the filename and format for the alignment, and enable the 'reload'
 470    * button functionality.
 471    *
 472    * @param file
 473    *          valid filename
 474    * @param format
 475    *          format of file
 476    */
 477   public void setFileName(String file, String format)
 478   {
 479     fileName = file;
 480     setFileFormat(format);
 481     reload.setEnabled(true);
 482   }
 483
 484   /**
 485    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 486    * events
 487    */
 488   void addKeyListener()
 489   {
 490     addKeyListener(new KeyAdapter()
 491     {
 492       @Override
 493       public void keyPressed(KeyEvent evt)
 494       {
 495         if (viewport.cursorMode
 496                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 497                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 498                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 499                 && Character.isDigit(evt.getKeyChar()))
 500         {
 501           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 502         }
 503
 504         switch (evt.getKeyCode())
 505         {
 506
 507         case 27: // escape key
 508           deselectAllSequenceMenuItem_actionPerformed(null);
 509
 510           break;
 511
 512         case KeyEvent.VK_DOWN:
 513           if (evt.isAltDown() || !viewport.cursorMode)
 514           {
 515             moveSelectedSequences(false);
 516           }
 517           if (viewport.cursorMode)
 518           {
 519             alignPanel.getSeqPanel().moveCursor(0, 1);
 520           }
 521           break;
 522
 523         case KeyEvent.VK_UP:
 524           if (evt.isAltDown() || !viewport.cursorMode)
 525           {
 526             moveSelectedSequences(true);
 527           }
 528           if (viewport.cursorMode)
 529           {
 530             alignPanel.getSeqPanel().moveCursor(0, -1);
 531           }
 532
 533           break;
 534
 535         case KeyEvent.VK_LEFT:
 536           if (evt.isAltDown() || !viewport.cursorMode)
 537           {
 538             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 539           }
 540           else
 541           {
 542             alignPanel.getSeqPanel().moveCursor(-1, 0);
 543           }
 544
 545           break;
 546
 547         case KeyEvent.VK_RIGHT:
 548           if (evt.isAltDown() || !viewport.cursorMode)
 549           {
 550             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 551           }
 552           else
 553           {
 554             alignPanel.getSeqPanel().moveCursor(1, 0);
 555           }
 556           break;
 557
 558         case KeyEvent.VK_SPACE:
 559           if (viewport.cursorMode)
 560           {
 561             alignPanel.getSeqPanel().insertGapAtCursor(
 562                     evt.isControlDown() || evt.isShiftDown()
 563                             || evt.isAltDown());
 564           }
 565           break;
 566
 567         // case KeyEvent.VK_A:
 568         // if (viewport.cursorMode)
 569         // {
 570         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 571         // //System.out.println("A");
 572         // }
 573         // break;
 574         /*
 575          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 576          * System.out.println("closing bracket"); } break;
 577          */
 578         case KeyEvent.VK_DELETE:
 579         case KeyEvent.VK_BACK_SPACE:
 580           if (!viewport.cursorMode)
 581           {
 582             cut_actionPerformed(null);
 583           }
 584           else
 585           {
 586             alignPanel.getSeqPanel().deleteGapAtCursor(
 587                     evt.isControlDown() || evt.isShiftDown()
 588                             || evt.isAltDown());
 589           }
 590
 591           break;
 592
 593         case KeyEvent.VK_S:
 594           if (viewport.cursorMode)
 595           {
 596             alignPanel.getSeqPanel().setCursorRow();
 597           }
 598           break;
 599         case KeyEvent.VK_C:
 600           if (viewport.cursorMode && !evt.isControlDown())
 601           {
 602             alignPanel.getSeqPanel().setCursorColumn();
 603           }
 604           break;
 605         case KeyEvent.VK_P:
 606           if (viewport.cursorMode)
 607           {
 608             alignPanel.getSeqPanel().setCursorPosition();
 609           }
 610           break;
 611
 612         case KeyEvent.VK_ENTER:
 613         case KeyEvent.VK_COMMA:
 614           if (viewport.cursorMode)
 615           {
 616             alignPanel.getSeqPanel().setCursorRowAndColumn();
 617           }
 618           break;
 619
 620         case KeyEvent.VK_Q:
 621           if (viewport.cursorMode)
 622           {
 623             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 624           }
 625           break;
 626         case KeyEvent.VK_M:
 627           if (viewport.cursorMode)
 628           {
 629             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 630           }
 631           break;
 632
 633         case KeyEvent.VK_F2:
 634           viewport.cursorMode = !viewport.cursorMode;
 635           statusBar.setText(MessageManager.formatMessage(
 636                   "label.keyboard_editing_mode",
 637                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 641             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 642           }
 643           alignPanel.getSeqPanel().seqCanvas.repaint();
 644           break;
 645
 646         case KeyEvent.VK_F1:
 647           try
 648           {
 649             Help.showHelpWindow();
 650           } catch (Exception ex)
 651           {
 652             ex.printStackTrace();
 653           }
 654           break;
 655         case KeyEvent.VK_H:
 656         {
 657           boolean toggleSeqs = !evt.isControlDown();
 658           boolean toggleCols = !evt.isShiftDown();
 659           toggleHiddenRegions(toggleSeqs, toggleCols);
 660           break;
 661         }
 662         case KeyEvent.VK_PAGE_UP:
 663           if (viewport.getWrapAlignment())
 664           {
 665             alignPanel.scrollUp(true);
 666           }
 667           else
 668           {
 669             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 670                     - viewport.endSeq + viewport.startSeq);
 671           }
 672           break;
 673         case KeyEvent.VK_PAGE_DOWN:
 674           if (viewport.getWrapAlignment())
 675           {
 676             alignPanel.scrollUp(false);
 677           }
 678           else
 679           {
 680             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 681                     + viewport.endSeq - viewport.startSeq);
 682           }
 683           break;
 684         }
 685       }
 686
 687       @Override
 688       public void keyReleased(KeyEvent evt)
 689       {
 690         switch (evt.getKeyCode())
 691         {
 692         case KeyEvent.VK_LEFT:
 693           if (evt.isAltDown() || !viewport.cursorMode)
 694           {
 695             viewport.firePropertyChange("alignment", null, viewport
 696                     .getAlignment().getSequences());
 697           }
 698           break;
 699
 700         case KeyEvent.VK_RIGHT:
 701           if (evt.isAltDown() || !viewport.cursorMode)
 702           {
 703             viewport.firePropertyChange("alignment", null, viewport
 704                     .getAlignment().getSequences());
 705           }
 706           break;
 707         }
 708       }
 709     });
 710   }
 711
 712   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 713   {
 714     ap.alignFrame = this;
 715     avc = new jalview.controller.AlignViewController(this, viewport,
 716             alignPanel);
 717
 718     alignPanels.add(ap);
 719
 720     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 721
 722     int aSize = alignPanels.size();
 723
 724     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 725
 726     if (aSize == 1 && ap.av.viewName == null)
 727     {
 728       this.getContentPane().add(ap, BorderLayout.CENTER);
 729     }
 730     else
 731     {
 732       if (aSize == 2)
 733       {
 734         setInitialTabVisible();
 735       }
 736
 737       expandViews.setEnabled(true);
 738       gatherViews.setEnabled(true);
 739       tabbedPane.addTab(ap.av.viewName, ap);
 740
 741       ap.setVisible(false);
 742     }
 743
 744     if (newPanel)
 745     {
 746       if (ap.av.isPadGaps())
 747       {
 748         ap.av.getAlignment().padGaps();
 749       }
 750       ap.av.updateConservation(ap);
 751       ap.av.updateConsensus(ap);
 752       ap.av.updateStrucConsensus(ap);
 753     }
 754   }
 755
 756   public void setInitialTabVisible()
 757   {
 758     expandViews.setEnabled(true);
 759     gatherViews.setEnabled(true);
 760     tabbedPane.setVisible(true);
 761     AlignmentPanel first = alignPanels.get(0);
 762     tabbedPane.addTab(first.av.viewName, first);
 763     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 764   }
 765
 766   public AlignViewport getViewport()
 767   {
 768     return viewport;
 769   }
 770
 771   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 772   private void addServiceListeners()
 773   {
 774     final java.beans.PropertyChangeListener thisListener;
 775     Desktop.instance.addJalviewPropertyChangeListener("services",
 776             thisListener = new java.beans.PropertyChangeListener()
 777             {
 778               @Override
 779               public void propertyChange(PropertyChangeEvent evt)
 780               {
 781                 // // System.out.println("Discoverer property change.");
 782                 // if (evt.getPropertyName().equals("services"))
 783                 {
 784                   SwingUtilities.invokeLater(new Runnable()
 785                   {
 786
 787                     @Override
 788                     public void run()
 789                     {
 790                       System.err
 791                               .println("Rebuild WS Menu for service change");
 792                       BuildWebServiceMenu();
 793                     }
 794
 795                   });
 796                 }
 797               }
 798             });
 799     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 800     {
 801       @Override
 802       public void internalFrameClosed(
 803               javax.swing.event.InternalFrameEvent evt)
 804       {
 805         // System.out.println("deregistering discoverer listener");
 806         Desktop.instance.removeJalviewPropertyChangeListener("services",
 807                 thisListener);
 808         closeMenuItem_actionPerformed(true);
 809       };
 810     });
 811     // Finally, build the menu once to get current service state
 812     new Thread(new Runnable()
 813     {
 814       @Override
 815       public void run()
 816       {
 817         BuildWebServiceMenu();
 818       }
 819     }).start();
 820   }
 821
 822   /**
 823    * Configure menu items that vary according to whether the alignment is
 824    * nucleotide or protein
 825    *
 826    * @param nucleotide
 827    */
 828   public void setGUINucleotide(boolean nucleotide)
 829   {
 830     showTranslation.setVisible(nucleotide);
 831     conservationMenuItem.setEnabled(!nucleotide);
 832     modifyConservation.setEnabled(!nucleotide);
 833     showGroupConservation.setEnabled(!nucleotide);
 834     rnahelicesColour.setEnabled(nucleotide);
 835     purinePyrimidineColour.setEnabled(nucleotide);
 836     showComplementMenuItem.setText(MessageManager
 837             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 838     setColourSelected(jalview.bin.Cache.getDefault(
 839             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 840                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 841   }
 842
 843   /**
 844    * set up menus for the current viewport. This may be called after any
 845    * operation that affects the data in the current view (selection changed,
 846    * etc) to update the menus to reflect the new state.
 847    */
 848   public void setMenusForViewport()
 849   {
 850     setMenusFromViewport(viewport);
 851   }
 852
 853   /**
 854    * Need to call this method when tabs are selected for multiple views, or when
 855    * loading from Jalview2XML.java
 856    *
 857    * @param av
 858    *          AlignViewport
 859    */
 860   void setMenusFromViewport(AlignViewport av)
 861   {
 862     padGapsMenuitem.setSelected(av.isPadGaps());
 863     colourTextMenuItem.setSelected(av.isShowColourText());
 864     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 865     conservationMenuItem.setSelected(av.getConservationSelected());
 866     seqLimits.setSelected(av.getShowJVSuffix());
 867     idRightAlign.setSelected(av.isRightAlignIds());
 868     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 869     renderGapsMenuItem.setSelected(av.isRenderGaps());
 870     wrapMenuItem.setSelected(av.getWrapAlignment());
 871     scaleAbove.setVisible(av.getWrapAlignment());
 872     scaleLeft.setVisible(av.getWrapAlignment());
 873     scaleRight.setVisible(av.getWrapAlignment());
 874     annotationPanelMenuItem.setState(av.isShowAnnotation());
 875     /*
 876      * Show/hide annotations only enabled if annotation panel is shown
 877      */
 878     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 879     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 880     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 881     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 882     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 883     viewTextMenuItem.setSelected(av.getShowText());
 884     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 885     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 886     showGroupConservation.setSelected(av.isShowGroupConservation());
 887     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 888     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 889     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 890
 891     setColourSelected(ColourSchemeProperty.getColourName(av
 892             .getGlobalColourScheme()));
 893
 894     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 895     hiddenMarkers.setState(av.getShowHiddenMarkers());
 896     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 897     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 898     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 899     autoCalculate.setSelected(av.autoCalculateConsensus);
 900     sortByTree.setSelected(av.sortByTree);
 901     listenToViewSelections.setSelected(av.followSelection);
 902     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 903     rnahelicesColour
 904             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 905     setShowProductsEnabled();
 906     updateEditMenuBar();
 907   }
 908
 909   private IProgressIndicator progressBar;
 910
 911   /*
 912    * (non-Javadoc)
 913    *
 914    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 915    */
 916   @Override
 917   public void setProgressBar(String message, long id)
 918   {
 919     progressBar.setProgressBar(message, id);
 920   }
 921
 922   @Override
 923   public void registerHandler(final long id,
 924           final IProgressIndicatorHandler handler)
 925   {
 926     progressBar.registerHandler(id, handler);
 927   }
 928
 929   /**
 930    *
 931    * @return true if any progress bars are still active
 932    */
 933   @Override
 934   public boolean operationInProgress()
 935   {
 936     return progressBar.operationInProgress();
 937   }
 938
 939   @Override
 940   public void setStatus(String text)
 941   {
 942     statusBar.setText(text);
 943   }
 944
 945   /*
 946    * Added so Castor Mapping file can obtain Jalview Version
 947    */
 948   public String getVersion()
 949   {
 950     return jalview.bin.Cache.getProperty("VERSION");
 951   }
 952
 953   public FeatureRenderer getFeatureRenderer()
 954   {
 955     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 956   }
 957
 958   @Override
 959   public void fetchSequence_actionPerformed(ActionEvent e)
 960   {
 961     new SequenceFetcher(this);
 962   }
 963
 964   @Override
 965   public void addFromFile_actionPerformed(ActionEvent e)
 966   {
 967     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 968   }
 969
 970   @Override
 971   public void reload_actionPerformed(ActionEvent e)
 972   {
 973     if (fileName != null)
 974     {
 975       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 976       // originating file's format
 977       // TODO: work out how to recover feature settings for correct view(s) when
 978       // file is reloaded.
 979       if (currentFileFormat.equals("Jalview"))
 980       {
 981         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 982         for (int i = 0; i < frames.length; i++)
 983         {
 984           if (frames[i] instanceof AlignFrame && frames[i] != this
 985                   && ((AlignFrame) frames[i]).fileName != null
 986                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 987           {
 988             try
 989             {
 990               frames[i].setSelected(true);
 991               Desktop.instance.closeAssociatedWindows();
 992             } catch (java.beans.PropertyVetoException ex)
 993             {
 994             }
 995           }
 996
 997         }
 998         Desktop.instance.closeAssociatedWindows();
 999
1000         FileLoader loader = new FileLoader();
1001         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1002         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1003       }
1004       else
1005       {
1006         Rectangle bounds = this.getBounds();
1007
1008         FileLoader loader = new FileLoader();
1009         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1010         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1011                 protocol, currentFileFormat);
1012
1013         newframe.setBounds(bounds);
1014         if (featureSettings != null && featureSettings.isShowing())
1015         {
1016           final Rectangle fspos = featureSettings.frame.getBounds();
1017           // TODO: need a 'show feature settings' function that takes bounds -
1018           // need to refactor Desktop.addFrame
1019           newframe.featureSettings_actionPerformed(null);
1020           final FeatureSettings nfs = newframe.featureSettings;
1021           SwingUtilities.invokeLater(new Runnable()
1022           {
1023             @Override
1024             public void run()
1025             {
1026               nfs.frame.setBounds(fspos);
1027             }
1028           });
1029           this.featureSettings.close();
1030           this.featureSettings = null;
1031         }
1032         this.closeMenuItem_actionPerformed(true);
1033       }
1034     }
1035   }
1036
1037   @Override
1038   public void addFromText_actionPerformed(ActionEvent e)
1039   {
1040     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1041             .getAlignPanel());
1042   }
1043
1044   @Override
1045   public void addFromURL_actionPerformed(ActionEvent e)
1046   {
1047     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1048   }
1049
1050   @Override
1051   public void save_actionPerformed(ActionEvent e)
1052   {
1053     if (fileName == null
1054             || (currentFileFormat == null || !jalview.io.FormatAdapter
1055                     .isValidIOFormat(currentFileFormat, true))
1056             || fileName.startsWith("http"))
1057     {
1058       saveAs_actionPerformed(null);
1059     }
1060     else
1061     {
1062       saveAlignment(fileName, currentFileFormat);
1063     }
1064   }
1065
1066   /**
1067    * DOCUMENT ME!
1068    *
1069    * @param e
1070    *          DOCUMENT ME!
1071    */
1072   @Override
1073   public void saveAs_actionPerformed(ActionEvent e)
1074   {
1075     JalviewFileChooser chooser = new JalviewFileChooser(
1076             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1077             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1078             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1079             currentFileFormat, false);
1080
1081     chooser.setFileView(new JalviewFileView());
1082     chooser.setDialogTitle(MessageManager
1083             .getString("label.save_alignment_to_file"));
1084     chooser.setToolTipText(MessageManager.getString("action.save"));
1085
1086     int value = chooser.showSaveDialog(this);
1087
1088     if (value == JalviewFileChooser.APPROVE_OPTION)
1089     {
1090       currentFileFormat = chooser.getSelectedFormat();
1091       while (currentFileFormat == null)
1092       {
1093         JOptionPane
1094                 .showInternalMessageDialog(
1095                         Desktop.desktop,
1096                         MessageManager
1097                                 .getString("label.select_file_format_before_saving"),
1098                         MessageManager
1099                                 .getString("label.file_format_not_specified"),
1100                         JOptionPane.WARNING_MESSAGE);
1101         currentFileFormat = chooser.getSelectedFormat();
1102         value = chooser.showSaveDialog(this);
1103         if (value != JalviewFileChooser.APPROVE_OPTION)
1104         {
1105           return;
1106         }
1107       }
1108
1109       fileName = chooser.getSelectedFile().getPath();
1110
1111       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1112               currentFileFormat);
1113
1114       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1115       if (currentFileFormat.indexOf(" ") > -1)
1116       {
1117         currentFileFormat = currentFileFormat.substring(0,
1118                 currentFileFormat.indexOf(" "));
1119       }
1120       saveAlignment(fileName, currentFileFormat);
1121     }
1122   }
1123
1124   public boolean saveAlignment(String file, String format)
1125   {
1126     boolean success = true;
1127
1128     if (format.equalsIgnoreCase("Jalview"))
1129     {
1130       String shortName = title;
1131
1132       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1133       {
1134         shortName = shortName.substring(shortName
1135                 .lastIndexOf(java.io.File.separatorChar) + 1);
1136       }
1137
1138       success = new Jalview2XML().saveAlignment(this, file, shortName);
1139
1140       statusBar.setText(MessageManager.formatMessage(
1141               "label.successfully_saved_to_file_in_format", new Object[] {
1142                   fileName, format }));
1143
1144     }
1145     else
1146     {
1147       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1148       {
1149         warningMessage("Cannot save file " + fileName + " using format "
1150                 + format, "Alignment output format not supported");
1151         if (!Jalview.isHeadlessMode())
1152         {
1153           saveAs_actionPerformed(null);
1154         }
1155         return false;
1156       }
1157
1158       AlignmentExportData exportData = getAlignmentForExport(format,
1159               viewport, null);
1160       if (exportData.getSettings().isCancelled())
1161       {
1162         return false;
1163       }
1164       FormatAdapter f = new FormatAdapter(alignPanel,
1165               exportData.getSettings());
1166       String output = f.formatSequences(
1167               format,
1168               exportData.getAlignment(), // class cast exceptions will
1169               // occur in the distant future
1170               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1171               f.getCacheSuffixDefault(format),
1172               viewport.getColumnSelection());
1173
1174       if (output == null)
1175       {
1176         success = false;
1177       }
1178       else
1179       {
1180         try
1181         {
1182           java.io.PrintWriter out = new java.io.PrintWriter(
1183                   new java.io.FileWriter(file));
1184
1185           out.print(output);
1186           out.close();
1187           this.setTitle(file);
1188           statusBar.setText(MessageManager.formatMessage(
1189                   "label.successfully_saved_to_file_in_format",
1190                   new Object[] { fileName, format }));
1191         } catch (Exception ex)
1192         {
1193           success = false;
1194           ex.printStackTrace();
1195         }
1196       }
1197     }
1198
1199     if (!success)
1200     {
1201       JOptionPane.showInternalMessageDialog(this, MessageManager
1202               .formatMessage("label.couldnt_save_file",
1203                       new Object[] { fileName }), MessageManager
1204               .getString("label.error_saving_file"),
1205               JOptionPane.WARNING_MESSAGE);
1206     }
1207
1208     return success;
1209   }
1210
1211   private void warningMessage(String warning, String title)
1212   {
1213     if (new jalview.util.Platform().isHeadless())
1214     {
1215       System.err.println("Warning: " + title + "\nWarning: " + warning);
1216
1217     }
1218     else
1219     {
1220       JOptionPane.showInternalMessageDialog(this, warning, title,
1221               JOptionPane.WARNING_MESSAGE);
1222     }
1223     return;
1224   }
1225
1226   /**
1227    * DOCUMENT ME!
1228    *
1229    * @param e
1230    *          DOCUMENT ME!
1231    */
1232   @Override
1233   protected void outputText_actionPerformed(ActionEvent e)
1234   {
1235
1236     AlignmentExportData exportData = getAlignmentForExport(
1237             e.getActionCommand(), viewport, null);
1238     if (exportData.getSettings().isCancelled())
1239     {
1240       return;
1241     }
1242     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1243     cap.setForInput(null);
1244     try
1245     {
1246       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1247               .formatSequences(e.getActionCommand(),
1248                       exportData.getAlignment(),
1249                       exportData.getOmitHidden(),
1250                       exportData.getStartEndPostions(),
1251                       viewport.getColumnSelection()));
1252       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1253               "label.alignment_output_command",
1254               new Object[] { e.getActionCommand() }), 600, 500);
1255     } catch (OutOfMemoryError oom)
1256     {
1257       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1258       cap.dispose();
1259     }
1260
1261   }
1262
1263   public static AlignmentExportData getAlignmentForExport(
1264           String exportFormat, AlignViewportI viewport,
1265           AlignExportSettingI exportSettings)
1266   {
1267     AlignmentI alignmentToExport = null;
1268     AlignExportSettingI settings = exportSettings;
1269     String[] omitHidden = null;
1270     int[] alignmentStartEnd = new int[2];
1271
1272     HiddenSequences hiddenSeqs = viewport.getAlignment()
1273             .getHiddenSequences();
1274
1275     alignmentToExport = viewport.getAlignment();
1276     alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1277
1278     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1279     if (settings == null)
1280     {
1281       settings = new AlignExportSettings(hasHiddenSeqs,
1282               viewport.hasHiddenColumns(), exportFormat);
1283     }
1284     // settings.isExportAnnotations();
1285
1286     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1287     {
1288       omitHidden = viewport.getViewAsString(false);
1289     }
1290
1291     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1292     {
1293       alignmentToExport = hiddenSeqs.getFullAlignment();
1294     }
1295     else
1296     {
1297       alignmentToExport = viewport.getAlignment();
1298       alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1299               .getColumnSelection().getHiddenColumns());
1300     }
1301     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1302             omitHidden, alignmentStartEnd, settings);
1303     return ed;
1304   }
1305
1306   public static int[] getStartEnd(int[] aligmentStartEnd,
1307           List<int[]> hiddenCols)
1308   {
1309     int startPos = aligmentStartEnd[0];
1310     int endPos = aligmentStartEnd[1];
1311
1312     int[] lowestRange = new int[] { -1, -1 };
1313     int[] higestRange = new int[] { -1, -1 };
1314
1315     for (int[] hiddenCol : hiddenCols)
1316     {
1317       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1318       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1319     }
1320
1321     if (lowestRange[0] == -1 && lowestRange[1] == -1)
1322     {
1323       startPos = aligmentStartEnd[0];
1324     }
1325     else
1326     {
1327       startPos = lowestRange[1] + 1;
1328     }
1329
1330     if (higestRange[0] == -1 && higestRange[1] == -1)
1331     {
1332       endPos = aligmentStartEnd[1];
1333     }
1334     else
1335     {
1336       endPos = higestRange[0] - 1;
1337     }
1338
1339     // System.out.println("Export range : " + startPos + " - " + endPos);
1340     return new int[] { startPos, endPos };
1341   }
1342
1343   public static void main(String[] args)
1344   {
1345     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1346     hiddenCols.add(new int[] { 0, 0 });
1347     hiddenCols.add(new int[] { 6, 9 });
1348     hiddenCols.add(new int[] { 11, 12 });
1349     hiddenCols.add(new int[] { 33, 33 });
1350     hiddenCols.add(new int[] { 50, 50 });
1351
1352     int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1353     // System.out.println("Export range : " + x[0] + " - " + x[1]);
1354   }
1355
1356   /**
1357    * DOCUMENT ME!
1358    *
1359    * @param e
1360    *          DOCUMENT ME!
1361    */
1362   @Override
1363   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1364   {
1365     new HtmlSvgOutput(null, alignPanel);
1366   }
1367
1368   @Override
1369   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1370   {
1371     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1372     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1373   }
1374
1375   public void createImageMap(File file, String image)
1376   {
1377     alignPanel.makePNGImageMap(file, image);
1378   }
1379
1380   /**
1381    * DOCUMENT ME!
1382    *
1383    * @param e
1384    *          DOCUMENT ME!
1385    */
1386   @Override
1387   public void createPNG(File f)
1388   {
1389     alignPanel.makePNG(f);
1390   }
1391
1392   /**
1393    * DOCUMENT ME!
1394    *
1395    * @param e
1396    *          DOCUMENT ME!
1397    */
1398   @Override
1399   public void createEPS(File f)
1400   {
1401     alignPanel.makeEPS(f);
1402   }
1403
1404   public void createSVG(File f)
1405   {
1406     alignPanel.makeSVG(f);
1407   }
1408
1409   @Override
1410   public void pageSetup_actionPerformed(ActionEvent e)
1411   {
1412     PrinterJob printJob = PrinterJob.getPrinterJob();
1413     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1414   }
1415
1416   /**
1417    * DOCUMENT ME!
1418    *
1419    * @param e
1420    *          DOCUMENT ME!
1421    */
1422   @Override
1423   public void printMenuItem_actionPerformed(ActionEvent e)
1424   {
1425     // Putting in a thread avoids Swing painting problems
1426     PrintThread thread = new PrintThread(alignPanel);
1427     thread.start();
1428   }
1429
1430   @Override
1431   public void exportFeatures_actionPerformed(ActionEvent e)
1432   {
1433     new AnnotationExporter().exportFeatures(alignPanel);
1434   }
1435
1436   @Override
1437   public void exportAnnotations_actionPerformed(ActionEvent e)
1438   {
1439     new AnnotationExporter().exportAnnotations(alignPanel);
1440   }
1441
1442   @Override
1443   public void associatedData_actionPerformed(ActionEvent e)
1444   {
1445     // Pick the tree file
1446     JalviewFileChooser chooser = new JalviewFileChooser(
1447             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1448     chooser.setFileView(new JalviewFileView());
1449     chooser.setDialogTitle(MessageManager
1450             .getString("label.load_jalview_annotations"));
1451     chooser.setToolTipText(MessageManager
1452             .getString("label.load_jalview_annotations"));
1453
1454     int value = chooser.showOpenDialog(null);
1455
1456     if (value == JalviewFileChooser.APPROVE_OPTION)
1457     {
1458       String choice = chooser.getSelectedFile().getPath();
1459       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1460       loadJalviewDataFile(choice, null, null, null);
1461     }
1462
1463   }
1464
1465   /**
1466    * Close the current view or all views in the alignment frame. If the frame
1467    * only contains one view then the alignment will be removed from memory.
1468    *
1469    * @param closeAllTabs
1470    */
1471   @Override
1472   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1473   {
1474     if (alignPanels != null && alignPanels.size() < 2)
1475     {
1476       closeAllTabs = true;
1477     }
1478
1479     try
1480     {
1481       if (alignPanels != null)
1482       {
1483         if (closeAllTabs)
1484         {
1485           if (this.isClosed())
1486           {
1487             // really close all the windows - otherwise wait till
1488             // setClosed(true) is called
1489             for (int i = 0; i < alignPanels.size(); i++)
1490             {
1491               AlignmentPanel ap = alignPanels.get(i);
1492               ap.closePanel();
1493             }
1494           }
1495         }
1496         else
1497         {
1498           closeView(alignPanel);
1499         }
1500       }
1501
1502       if (closeAllTabs)
1503       {
1504         /*
1505          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1506          * be called recursively, with the frame now in 'closed' state
1507          */
1508         this.setClosed(true);
1509       }
1510     } catch (Exception ex)
1511     {
1512       ex.printStackTrace();
1513     }
1514   }
1515
1516   /**
1517    * Close the specified panel and close up tabs appropriately.
1518    *
1519    * @param panelToClose
1520    */
1521   public void closeView(AlignmentPanel panelToClose)
1522   {
1523     int index = tabbedPane.getSelectedIndex();
1524     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1525     alignPanels.remove(panelToClose);
1526     panelToClose.closePanel();
1527     panelToClose = null;
1528
1529     tabbedPane.removeTabAt(closedindex);
1530     tabbedPane.validate();
1531
1532     if (index > closedindex || index == tabbedPane.getTabCount())
1533     {
1534       // modify currently selected tab index if necessary.
1535       index--;
1536     }
1537
1538     this.tabSelectionChanged(index);
1539   }
1540
1541   /**
1542    * DOCUMENT ME!
1543    */
1544   void updateEditMenuBar()
1545   {
1546
1547     if (viewport.getHistoryList().size() > 0)
1548     {
1549       undoMenuItem.setEnabled(true);
1550       CommandI command = viewport.getHistoryList().peek();
1551       undoMenuItem.setText(MessageManager.formatMessage(
1552               "label.undo_command",
1553               new Object[] { command.getDescription() }));
1554     }
1555     else
1556     {
1557       undoMenuItem.setEnabled(false);
1558       undoMenuItem.setText(MessageManager.getString("action.undo"));
1559     }
1560
1561     if (viewport.getRedoList().size() > 0)
1562     {
1563       redoMenuItem.setEnabled(true);
1564
1565       CommandI command = viewport.getRedoList().peek();
1566       redoMenuItem.setText(MessageManager.formatMessage(
1567               "label.redo_command",
1568               new Object[] { command.getDescription() }));
1569     }
1570     else
1571     {
1572       redoMenuItem.setEnabled(false);
1573       redoMenuItem.setText(MessageManager.getString("action.redo"));
1574     }
1575   }
1576
1577   public void addHistoryItem(CommandI command)
1578   {
1579     if (command.getSize() > 0)
1580     {
1581       viewport.addToHistoryList(command);
1582       viewport.clearRedoList();
1583       updateEditMenuBar();
1584       viewport.updateHiddenColumns();
1585       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1586       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1587       // viewport.getColumnSelection()
1588       // .getHiddenColumns().size() > 0);
1589     }
1590   }
1591
1592   /**
1593    *
1594    * @return alignment objects for all views
1595    */
1596   AlignmentI[] getViewAlignments()
1597   {
1598     if (alignPanels != null)
1599     {
1600       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1601       int i = 0;
1602       for (AlignmentPanel ap : alignPanels)
1603       {
1604         als[i++] = ap.av.getAlignment();
1605       }
1606       return als;
1607     }
1608     if (viewport != null)
1609     {
1610       return new AlignmentI[] { viewport.getAlignment() };
1611     }
1612     return null;
1613   }
1614
1615   /**
1616    * DOCUMENT ME!
1617    *
1618    * @param e
1619    *          DOCUMENT ME!
1620    */
1621   @Override
1622   protected void undoMenuItem_actionPerformed(ActionEvent e)
1623   {
1624     if (viewport.getHistoryList().isEmpty())
1625     {
1626       return;
1627     }
1628     CommandI command = viewport.getHistoryList().pop();
1629     viewport.addToRedoList(command);
1630     command.undoCommand(getViewAlignments());
1631
1632     AlignmentViewport originalSource = getOriginatingSource(command);
1633     updateEditMenuBar();
1634
1635     if (originalSource != null)
1636     {
1637       if (originalSource != viewport)
1638       {
1639         Cache.log
1640                 .warn("Implementation worry: mismatch of viewport origin for undo");
1641       }
1642       originalSource.updateHiddenColumns();
1643       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1644       // null
1645       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1646       // viewport.getColumnSelection()
1647       // .getHiddenColumns().size() > 0);
1648       originalSource.firePropertyChange("alignment", null, originalSource
1649               .getAlignment().getSequences());
1650     }
1651   }
1652
1653   /**
1654    * DOCUMENT ME!
1655    *
1656    * @param e
1657    *          DOCUMENT ME!
1658    */
1659   @Override
1660   protected void redoMenuItem_actionPerformed(ActionEvent e)
1661   {
1662     if (viewport.getRedoList().size() < 1)
1663     {
1664       return;
1665     }
1666
1667     CommandI command = viewport.getRedoList().pop();
1668     viewport.addToHistoryList(command);
1669     command.doCommand(getViewAlignments());
1670
1671     AlignmentViewport originalSource = getOriginatingSource(command);
1672     updateEditMenuBar();
1673
1674     if (originalSource != null)
1675     {
1676
1677       if (originalSource != viewport)
1678       {
1679         Cache.log
1680                 .warn("Implementation worry: mismatch of viewport origin for redo");
1681       }
1682       originalSource.updateHiddenColumns();
1683       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1684       // null
1685       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1686       // viewport.getColumnSelection()
1687       // .getHiddenColumns().size() > 0);
1688       originalSource.firePropertyChange("alignment", null, originalSource
1689               .getAlignment().getSequences());
1690     }
1691   }
1692
1693   AlignmentViewport getOriginatingSource(CommandI command)
1694   {
1695     AlignmentViewport originalSource = null;
1696     // For sequence removal and addition, we need to fire
1697     // the property change event FROM the viewport where the
1698     // original alignment was altered
1699     AlignmentI al = null;
1700     if (command instanceof EditCommand)
1701     {
1702       EditCommand editCommand = (EditCommand) command;
1703       al = editCommand.getAlignment();
1704       List<Component> comps = PaintRefresher.components.get(viewport
1705               .getSequenceSetId());
1706
1707       for (Component comp : comps)
1708       {
1709         if (comp instanceof AlignmentPanel)
1710         {
1711           if (al == ((AlignmentPanel) comp).av.getAlignment())
1712           {
1713             originalSource = ((AlignmentPanel) comp).av;
1714             break;
1715           }
1716         }
1717       }
1718     }
1719
1720     if (originalSource == null)
1721     {
1722       // The original view is closed, we must validate
1723       // the current view against the closed view first
1724       if (al != null)
1725       {
1726         PaintRefresher.validateSequences(al, viewport.getAlignment());
1727       }
1728
1729       originalSource = viewport;
1730     }
1731
1732     return originalSource;
1733   }
1734
1735   /**
1736    * DOCUMENT ME!
1737    *
1738    * @param up
1739    *          DOCUMENT ME!
1740    */
1741   public void moveSelectedSequences(boolean up)
1742   {
1743     SequenceGroup sg = viewport.getSelectionGroup();
1744
1745     if (sg == null)
1746     {
1747       return;
1748     }
1749     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1750             viewport.getHiddenRepSequences(), up);
1751     alignPanel.paintAlignment(true);
1752   }
1753
1754   synchronized void slideSequences(boolean right, int size)
1755   {
1756     List<SequenceI> sg = new ArrayList<SequenceI>();
1757     if (viewport.cursorMode)
1758     {
1759       sg.add(viewport.getAlignment().getSequenceAt(
1760               alignPanel.getSeqPanel().seqCanvas.cursorY));
1761     }
1762     else if (viewport.getSelectionGroup() != null
1763             && viewport.getSelectionGroup().getSize() != viewport
1764                     .getAlignment().getHeight())
1765     {
1766       sg = viewport.getSelectionGroup().getSequences(
1767               viewport.getHiddenRepSequences());
1768     }
1769
1770     if (sg.size() < 1)
1771     {
1772       return;
1773     }
1774
1775     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1776
1777     for (SequenceI seq : viewport.getAlignment().getSequences())
1778     {
1779       if (!sg.contains(seq))
1780       {
1781         invertGroup.add(seq);
1782       }
1783     }
1784
1785     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1786
1787     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1788     for (int i = 0; i < invertGroup.size(); i++)
1789     {
1790       seqs2[i] = invertGroup.get(i);
1791     }
1792
1793     SlideSequencesCommand ssc;
1794     if (right)
1795     {
1796       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1797               size, viewport.getGapCharacter());
1798     }
1799     else
1800     {
1801       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1802               size, viewport.getGapCharacter());
1803     }
1804
1805     int groupAdjustment = 0;
1806     if (ssc.getGapsInsertedBegin() && right)
1807     {
1808       if (viewport.cursorMode)
1809       {
1810         alignPanel.getSeqPanel().moveCursor(size, 0);
1811       }
1812       else
1813       {
1814         groupAdjustment = size;
1815       }
1816     }
1817     else if (!ssc.getGapsInsertedBegin() && !right)
1818     {
1819       if (viewport.cursorMode)
1820       {
1821         alignPanel.getSeqPanel().moveCursor(-size, 0);
1822       }
1823       else
1824       {
1825         groupAdjustment = -size;
1826       }
1827     }
1828
1829     if (groupAdjustment != 0)
1830     {
1831       viewport.getSelectionGroup().setStartRes(
1832               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1833       viewport.getSelectionGroup().setEndRes(
1834               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1835     }
1836
1837     /*
1838      * just extend the last slide command if compatible; but not if in
1839      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1840      */
1841     boolean appendHistoryItem = false;
1842     Deque<CommandI> historyList = viewport.getHistoryList();
1843     boolean inSplitFrame = getSplitViewContainer() != null;
1844     if (!inSplitFrame && historyList != null && historyList.size() > 0
1845             && historyList.peek() instanceof SlideSequencesCommand)
1846     {
1847       appendHistoryItem = ssc
1848               .appendSlideCommand((SlideSequencesCommand) historyList
1849                       .peek());
1850     }
1851
1852     if (!appendHistoryItem)
1853     {
1854       addHistoryItem(ssc);
1855     }
1856
1857     repaint();
1858   }
1859
1860   /**
1861    * DOCUMENT ME!
1862    *
1863    * @param e
1864    *          DOCUMENT ME!
1865    */
1866   @Override
1867   protected void copy_actionPerformed(ActionEvent e)
1868   {
1869     System.gc();
1870     if (viewport.getSelectionGroup() == null)
1871     {
1872       return;
1873     }
1874     // TODO: preserve the ordering of displayed alignment annotation in any
1875     // internal paste (particularly sequence associated annotation)
1876     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1877     String[] omitHidden = null;
1878
1879     if (viewport.hasHiddenColumns())
1880     {
1881       omitHidden = viewport.getViewAsString(true);
1882     }
1883
1884     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1885             omitHidden, null);
1886
1887     StringSelection ss = new StringSelection(output);
1888
1889     try
1890     {
1891       jalview.gui.Desktop.internalCopy = true;
1892       // Its really worth setting the clipboard contents
1893       // to empty before setting the large StringSelection!!
1894       Toolkit.getDefaultToolkit().getSystemClipboard()
1895               .setContents(new StringSelection(""), null);
1896
1897       Toolkit.getDefaultToolkit().getSystemClipboard()
1898               .setContents(ss, Desktop.instance);
1899     } catch (OutOfMemoryError er)
1900     {
1901       new OOMWarning("copying region", er);
1902       return;
1903     }
1904
1905     ArrayList<int[]> hiddenColumns = null;
1906     if (viewport.hasHiddenColumns())
1907     {
1908       hiddenColumns = new ArrayList<int[]>();
1909       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1910               .getSelectionGroup().getEndRes();
1911       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1912       {
1913         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1914         {
1915           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1916               region[1] - hiddenOffset });
1917         }
1918       }
1919     }
1920
1921     Desktop.jalviewClipboard = new Object[] { seqs,
1922         viewport.getAlignment().getDataset(), hiddenColumns };
1923     statusBar.setText(MessageManager.formatMessage(
1924             "label.copied_sequences_to_clipboard", new Object[] { Integer
1925                     .valueOf(seqs.length).toString() }));
1926   }
1927
1928   /**
1929    * DOCUMENT ME!
1930    *
1931    * @param e
1932    *          DOCUMENT ME!
1933    */
1934   @Override
1935   protected void pasteNew_actionPerformed(ActionEvent e)
1936   {
1937     paste(true);
1938   }
1939
1940   /**
1941    * DOCUMENT ME!
1942    *
1943    * @param e
1944    *          DOCUMENT ME!
1945    */
1946   @Override
1947   protected void pasteThis_actionPerformed(ActionEvent e)
1948   {
1949     paste(false);
1950   }
1951
1952   /**
1953    * Paste contents of Jalview clipboard
1954    *
1955    * @param newAlignment
1956    *          true to paste to a new alignment, otherwise add to this.
1957    */
1958   void paste(boolean newAlignment)
1959   {
1960     boolean externalPaste = true;
1961     try
1962     {
1963       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1964       Transferable contents = c.getContents(this);
1965
1966       if (contents == null)
1967       {
1968         return;
1969       }
1970
1971       String str, format;
1972       try
1973       {
1974         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1975         if (str.length() < 1)
1976         {
1977           return;
1978         }
1979
1980         format = new IdentifyFile().Identify(str, "Paste");
1981
1982       } catch (OutOfMemoryError er)
1983       {
1984         new OOMWarning("Out of memory pasting sequences!!", er);
1985         return;
1986       }
1987
1988       SequenceI[] sequences;
1989       boolean annotationAdded = false;
1990       AlignmentI alignment = null;
1991
1992       if (Desktop.jalviewClipboard != null)
1993       {
1994         // The clipboard was filled from within Jalview, we must use the
1995         // sequences
1996         // And dataset from the copied alignment
1997         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1998         // be doubly sure that we create *new* sequence objects.
1999         sequences = new SequenceI[newseq.length];
2000         for (int i = 0; i < newseq.length; i++)
2001         {
2002           sequences[i] = new Sequence(newseq[i]);
2003         }
2004         alignment = new Alignment(sequences);
2005         externalPaste = false;
2006       }
2007       else
2008       {
2009         // parse the clipboard as an alignment.
2010         alignment = new FormatAdapter().readFile(str, "Paste", format);
2011         sequences = alignment.getSequencesArray();
2012       }
2013
2014       int alwidth = 0;
2015       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2016       int fgroup = -1;
2017
2018       if (newAlignment)
2019       {
2020
2021         if (Desktop.jalviewClipboard != null)
2022         {
2023           // dataset is inherited
2024           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2025         }
2026         else
2027         {
2028           // new dataset is constructed
2029           alignment.setDataset(null);
2030         }
2031         alwidth = alignment.getWidth() + 1;
2032       }
2033       else
2034       {
2035         AlignmentI pastedal = alignment; // preserve pasted alignment object
2036         // Add pasted sequences and dataset into existing alignment.
2037         alignment = viewport.getAlignment();
2038         alwidth = alignment.getWidth() + 1;
2039         // decide if we need to import sequences from an existing dataset
2040         boolean importDs = Desktop.jalviewClipboard != null
2041                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2042         // importDs==true instructs us to copy over new dataset sequences from
2043         // an existing alignment
2044         Vector newDs = (importDs) ? new Vector() : null; // used to create
2045         // minimum dataset set
2046
2047         for (int i = 0; i < sequences.length; i++)
2048         {
2049           if (importDs)
2050           {
2051             newDs.addElement(null);
2052           }
2053           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2054           // paste
2055           if (importDs && ds != null)
2056           {
2057             if (!newDs.contains(ds))
2058             {
2059               newDs.setElementAt(ds, i);
2060               ds = new Sequence(ds);
2061               // update with new dataset sequence
2062               sequences[i].setDatasetSequence(ds);
2063             }
2064             else
2065             {
2066               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2067             }
2068           }
2069           else
2070           {
2071             // copy and derive new dataset sequence
2072             sequences[i] = sequences[i].deriveSequence();
2073             alignment.getDataset().addSequence(
2074                     sequences[i].getDatasetSequence());
2075             // TODO: avoid creation of duplicate dataset sequences with a
2076             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2077           }
2078           alignment.addSequence(sequences[i]); // merges dataset
2079         }
2080         if (newDs != null)
2081         {
2082           newDs.clear(); // tidy up
2083         }
2084         if (alignment.getAlignmentAnnotation() != null)
2085         {
2086           for (AlignmentAnnotation alan : alignment
2087                   .getAlignmentAnnotation())
2088           {
2089             if (alan.graphGroup > fgroup)
2090             {
2091               fgroup = alan.graphGroup;
2092             }
2093           }
2094         }
2095         if (pastedal.getAlignmentAnnotation() != null)
2096         {
2097           // Add any annotation attached to alignment.
2098           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2099           for (int i = 0; i < alann.length; i++)
2100           {
2101             annotationAdded = true;
2102             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2103             {
2104               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2105               if (newann.graphGroup > -1)
2106               {
2107                 if (newGraphGroups.size() <= newann.graphGroup
2108                         || newGraphGroups.get(newann.graphGroup) == null)
2109                 {
2110                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2111                   {
2112                     newGraphGroups.add(q, null);
2113                   }
2114                   newGraphGroups.set(newann.graphGroup, new Integer(
2115                           ++fgroup));
2116                 }
2117                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2118                         .intValue();
2119               }
2120
2121               newann.padAnnotation(alwidth);
2122               alignment.addAnnotation(newann);
2123             }
2124           }
2125         }
2126       }
2127       if (!newAlignment)
2128       {
2129         // /////
2130         // ADD HISTORY ITEM
2131         //
2132         addHistoryItem(new EditCommand(
2133                 MessageManager.getString("label.add_sequences"),
2134                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2135       }
2136       // Add any annotations attached to sequences
2137       for (int i = 0; i < sequences.length; i++)
2138       {
2139         if (sequences[i].getAnnotation() != null)
2140         {
2141           AlignmentAnnotation newann;
2142           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2143           {
2144             annotationAdded = true;
2145             newann = sequences[i].getAnnotation()[a];
2146             newann.adjustForAlignment();
2147             newann.padAnnotation(alwidth);
2148             if (newann.graphGroup > -1)
2149             {
2150               if (newann.graphGroup > -1)
2151               {
2152                 if (newGraphGroups.size() <= newann.graphGroup
2153                         || newGraphGroups.get(newann.graphGroup) == null)
2154                 {
2155                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2156                   {
2157                     newGraphGroups.add(q, null);
2158                   }
2159                   newGraphGroups.set(newann.graphGroup, new Integer(
2160                           ++fgroup));
2161                 }
2162                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2163                         .intValue();
2164               }
2165             }
2166             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2167             // was
2168             // duplicated
2169             // earlier
2170             alignment
2171                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2172           }
2173         }
2174       }
2175       if (!newAlignment)
2176       {
2177
2178         // propagate alignment changed.
2179         viewport.setEndSeq(alignment.getHeight());
2180         if (annotationAdded)
2181         {
2182           // Duplicate sequence annotation in all views.
2183           AlignmentI[] alview = this.getViewAlignments();
2184           for (int i = 0; i < sequences.length; i++)
2185           {
2186             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2187             if (sann == null)
2188             {
2189               continue;
2190             }
2191             for (int avnum = 0; avnum < alview.length; avnum++)
2192             {
2193               if (alview[avnum] != alignment)
2194               {
2195                 // duplicate in a view other than the one with input focus
2196                 int avwidth = alview[avnum].getWidth() + 1;
2197                 // this relies on sann being preserved after we
2198                 // modify the sequence's annotation array for each duplication
2199                 for (int a = 0; a < sann.length; a++)
2200                 {
2201                   AlignmentAnnotation newann = new AlignmentAnnotation(
2202                           sann[a]);
2203                   sequences[i].addAlignmentAnnotation(newann);
2204                   newann.padAnnotation(avwidth);
2205                   alview[avnum].addAnnotation(newann); // annotation was
2206                   // duplicated earlier
2207                   // TODO JAL-1145 graphGroups are not updated for sequence
2208                   // annotation added to several views. This may cause
2209                   // strangeness
2210                   alview[avnum].setAnnotationIndex(newann, a);
2211                 }
2212               }
2213             }
2214           }
2215           buildSortByAnnotationScoresMenu();
2216         }
2217         viewport.firePropertyChange("alignment", null,
2218                 alignment.getSequences());
2219         if (alignPanels != null)
2220         {
2221           for (AlignmentPanel ap : alignPanels)
2222           {
2223             ap.validateAnnotationDimensions(false);
2224           }
2225         }
2226         else
2227         {
2228           alignPanel.validateAnnotationDimensions(false);
2229         }
2230
2231       }
2232       else
2233       {
2234         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2235                 DEFAULT_HEIGHT);
2236         String newtitle = new String("Copied sequences");
2237
2238         if (Desktop.jalviewClipboard != null
2239                 && Desktop.jalviewClipboard[2] != null)
2240         {
2241           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2242           for (int[] region : hc)
2243           {
2244             af.viewport.hideColumns(region[0], region[1]);
2245           }
2246         }
2247
2248         // >>>This is a fix for the moment, until a better solution is
2249         // found!!<<<
2250         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2251                 .transferSettings(
2252                         alignPanel.getSeqPanel().seqCanvas
2253                                 .getFeatureRenderer());
2254
2255         // TODO: maintain provenance of an alignment, rather than just make the
2256         // title a concatenation of operations.
2257         if (!externalPaste)
2258         {
2259           if (title.startsWith("Copied sequences"))
2260           {
2261             newtitle = title;
2262           }
2263           else
2264           {
2265             newtitle = newtitle.concat("- from " + title);
2266           }
2267         }
2268         else
2269         {
2270           newtitle = new String("Pasted sequences");
2271         }
2272
2273         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2274                 DEFAULT_HEIGHT);
2275
2276       }
2277
2278     } catch (Exception ex)
2279     {
2280       ex.printStackTrace();
2281       System.out.println("Exception whilst pasting: " + ex);
2282       // could be anything being pasted in here
2283     }
2284
2285   }
2286
2287   @Override
2288   protected void expand_newalign(ActionEvent e)
2289   {
2290     try
2291     {
2292       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2293               .getAlignment(), -1);
2294       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2295               DEFAULT_HEIGHT);
2296       String newtitle = new String("Flanking alignment");
2297
2298       if (Desktop.jalviewClipboard != null
2299               && Desktop.jalviewClipboard[2] != null)
2300       {
2301         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2302         for (int region[] : hc)
2303         {
2304           af.viewport.hideColumns(region[0], region[1]);
2305         }
2306       }
2307
2308       // >>>This is a fix for the moment, until a better solution is
2309       // found!!<<<
2310       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2311               .transferSettings(
2312                       alignPanel.getSeqPanel().seqCanvas
2313                               .getFeatureRenderer());
2314
2315       // TODO: maintain provenance of an alignment, rather than just make the
2316       // title a concatenation of operations.
2317       {
2318         if (title.startsWith("Copied sequences"))
2319         {
2320           newtitle = title;
2321         }
2322         else
2323         {
2324           newtitle = newtitle.concat("- from " + title);
2325         }
2326       }
2327
2328       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2329
2330     } catch (Exception ex)
2331     {
2332       ex.printStackTrace();
2333       System.out.println("Exception whilst pasting: " + ex);
2334       // could be anything being pasted in here
2335     } catch (OutOfMemoryError oom)
2336     {
2337       new OOMWarning("Viewing flanking region of alignment", oom);
2338     }
2339   }
2340
2341   /**
2342    * DOCUMENT ME!
2343    *
2344    * @param e
2345    *          DOCUMENT ME!
2346    */
2347   @Override
2348   protected void cut_actionPerformed(ActionEvent e)
2349   {
2350     copy_actionPerformed(null);
2351     delete_actionPerformed(null);
2352   }
2353
2354   /**
2355    * DOCUMENT ME!
2356    *
2357    * @param e
2358    *          DOCUMENT ME!
2359    */
2360   @Override
2361   protected void delete_actionPerformed(ActionEvent evt)
2362   {
2363
2364     SequenceGroup sg = viewport.getSelectionGroup();
2365     if (sg == null)
2366     {
2367       return;
2368     }
2369
2370     /*
2371      * If the cut affects all sequences, warn, remove highlighted columns
2372      */
2373     if (sg.getSize() == viewport.getAlignment().getHeight())
2374     {
2375       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2376               .getAlignment().getWidth()) ? true : false;
2377       if (isEntireAlignWidth)
2378       {
2379         int confirm = JOptionPane.showConfirmDialog(this,
2380                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2381                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2382                 JOptionPane.OK_CANCEL_OPTION);
2383
2384         if (confirm == JOptionPane.CANCEL_OPTION
2385                 || confirm == JOptionPane.CLOSED_OPTION)
2386         {
2387           return;
2388         }
2389       }
2390       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2391               sg.getEndRes() + 1);
2392     }
2393     SequenceI[] cut = sg.getSequences()
2394             .toArray(new SequenceI[sg.getSize()]);
2395
2396     addHistoryItem(new EditCommand(
2397             MessageManager.getString("label.cut_sequences"), Action.CUT,
2398             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2399             viewport.getAlignment()));
2400
2401     viewport.setSelectionGroup(null);
2402     viewport.sendSelection();
2403     viewport.getAlignment().deleteGroup(sg);
2404
2405     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2406             .getSequences());
2407     if (viewport.getAlignment().getHeight() < 1)
2408     {
2409       try
2410       {
2411         this.setClosed(true);
2412       } catch (Exception ex)
2413       {
2414       }
2415     }
2416   }
2417
2418
2419   /**
2420    * DOCUMENT ME!
2421    *
2422    * @param e
2423    *          DOCUMENT ME!
2424    */
2425   @Override
2426   protected void deleteGroups_actionPerformed(ActionEvent e)
2427   {
2428     if (avc.deleteGroups())
2429     {
2430       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2431       alignPanel.updateAnnotation();
2432       alignPanel.paintAlignment(true);
2433     }
2434   }
2435
2436   /**
2437    * DOCUMENT ME!
2438    *
2439    * @param e
2440    *          DOCUMENT ME!
2441    */
2442   @Override
2443   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2444   {
2445     SequenceGroup sg = new SequenceGroup();
2446
2447     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2448     {
2449       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2450     }
2451
2452     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2453     viewport.setSelectionGroup(sg);
2454     viewport.sendSelection();
2455     alignPanel.paintAlignment(true);
2456     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2457   }
2458
2459   /**
2460    * DOCUMENT ME!
2461    *
2462    * @param e
2463    *          DOCUMENT ME!
2464    */
2465   @Override
2466   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2467   {
2468     if (viewport.cursorMode)
2469     {
2470       alignPanel.getSeqPanel().keyboardNo1 = null;
2471       alignPanel.getSeqPanel().keyboardNo2 = null;
2472     }
2473     viewport.setSelectionGroup(null);
2474     viewport.getColumnSelection().clear();
2475     viewport.setSelectionGroup(null);
2476     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2477     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2478     alignPanel.paintAlignment(true);
2479     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2480     viewport.sendSelection();
2481   }
2482
2483   /**
2484    * DOCUMENT ME!
2485    *
2486    * @param e
2487    *          DOCUMENT ME!
2488    */
2489   @Override
2490   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2491   {
2492     SequenceGroup sg = viewport.getSelectionGroup();
2493
2494     if (sg == null)
2495     {
2496       selectAllSequenceMenuItem_actionPerformed(null);
2497
2498       return;
2499     }
2500
2501     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2502     {
2503       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2504     }
2505
2506     alignPanel.paintAlignment(true);
2507     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2508     viewport.sendSelection();
2509   }
2510
2511   @Override
2512   public void invertColSel_actionPerformed(ActionEvent e)
2513   {
2514     viewport.invertColumnSelection();
2515     alignPanel.paintAlignment(true);
2516     viewport.sendSelection();
2517   }
2518
2519   /**
2520    * DOCUMENT ME!
2521    *
2522    * @param e
2523    *          DOCUMENT ME!
2524    */
2525   @Override
2526   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2527   {
2528     trimAlignment(true);
2529   }
2530
2531   /**
2532    * DOCUMENT ME!
2533    *
2534    * @param e
2535    *          DOCUMENT ME!
2536    */
2537   @Override
2538   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2539   {
2540     trimAlignment(false);
2541   }
2542
2543   void trimAlignment(boolean trimLeft)
2544   {
2545     ColumnSelection colSel = viewport.getColumnSelection();
2546     int column;
2547
2548     if (colSel.size() > 0)
2549     {
2550       if (trimLeft)
2551       {
2552         column = colSel.getMin();
2553       }
2554       else
2555       {
2556         column = colSel.getMax();
2557       }
2558
2559       SequenceI[] seqs;
2560       if (viewport.getSelectionGroup() != null)
2561       {
2562         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2563                 viewport.getHiddenRepSequences());
2564       }
2565       else
2566       {
2567         seqs = viewport.getAlignment().getSequencesArray();
2568       }
2569
2570       TrimRegionCommand trimRegion;
2571       if (trimLeft)
2572       {
2573         trimRegion = new TrimRegionCommand("Remove Left",
2574                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2575                 viewport.getAlignment(), viewport.getColumnSelection(),
2576                 viewport.getSelectionGroup());
2577         viewport.setStartRes(0);
2578       }
2579       else
2580       {
2581         trimRegion = new TrimRegionCommand("Remove Right",
2582                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2583                 viewport.getAlignment(), viewport.getColumnSelection(),
2584                 viewport.getSelectionGroup());
2585       }
2586
2587       statusBar.setText(MessageManager.formatMessage(
2588               "label.removed_columns",
2589               new String[] { Integer.valueOf(trimRegion.getSize())
2590                       .toString() }));
2591
2592       addHistoryItem(trimRegion);
2593
2594       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2595       {
2596         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2597                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2598         {
2599           viewport.getAlignment().deleteGroup(sg);
2600         }
2601       }
2602
2603       viewport.firePropertyChange("alignment", null, viewport
2604               .getAlignment().getSequences());
2605     }
2606   }
2607
2608   /**
2609    * DOCUMENT ME!
2610    *
2611    * @param e
2612    *          DOCUMENT ME!
2613    */
2614   @Override
2615   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2616   {
2617     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2618
2619     SequenceI[] seqs;
2620     if (viewport.getSelectionGroup() != null)
2621     {
2622       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2623               viewport.getHiddenRepSequences());
2624       start = viewport.getSelectionGroup().getStartRes();
2625       end = viewport.getSelectionGroup().getEndRes();
2626     }
2627     else
2628     {
2629       seqs = viewport.getAlignment().getSequencesArray();
2630     }
2631
2632     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2633             "Remove Gapped Columns", seqs, start, end,
2634             viewport.getAlignment());
2635
2636     addHistoryItem(removeGapCols);
2637
2638     statusBar.setText(MessageManager.formatMessage(
2639             "label.removed_empty_columns",
2640             new Object[] { Integer.valueOf(removeGapCols.getSize())
2641                     .toString() }));
2642
2643     // This is to maintain viewport position on first residue
2644     // of first sequence
2645     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2646     int startRes = seq.findPosition(viewport.startRes);
2647     // ShiftList shifts;
2648     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2649     // edit.alColumnChanges=shifts.getInverse();
2650     // if (viewport.hasHiddenColumns)
2651     // viewport.getColumnSelection().compensateForEdits(shifts);
2652     viewport.setStartRes(seq.findIndex(startRes) - 1);
2653     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2654             .getSequences());
2655
2656   }
2657
2658   /**
2659    * DOCUMENT ME!
2660    *
2661    * @param e
2662    *          DOCUMENT ME!
2663    */
2664   @Override
2665   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2666   {
2667     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2668
2669     SequenceI[] seqs;
2670     if (viewport.getSelectionGroup() != null)
2671     {
2672       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2673               viewport.getHiddenRepSequences());
2674       start = viewport.getSelectionGroup().getStartRes();
2675       end = viewport.getSelectionGroup().getEndRes();
2676     }
2677     else
2678     {
2679       seqs = viewport.getAlignment().getSequencesArray();
2680     }
2681
2682     // This is to maintain viewport position on first residue
2683     // of first sequence
2684     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2685     int startRes = seq.findPosition(viewport.startRes);
2686
2687     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2688             viewport.getAlignment()));
2689
2690     viewport.setStartRes(seq.findIndex(startRes) - 1);
2691
2692     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2693             .getSequences());
2694
2695   }
2696
2697   /**
2698    * DOCUMENT ME!
2699    *
2700    * @param e
2701    *          DOCUMENT ME!
2702    */
2703   @Override
2704   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2705   {
2706     viewport.setPadGaps(padGapsMenuitem.isSelected());
2707     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2708             .getSequences());
2709   }
2710
2711   /**
2712    * DOCUMENT ME!
2713    *
2714    * @param e
2715    *          DOCUMENT ME!
2716    */
2717   @Override
2718   public void findMenuItem_actionPerformed(ActionEvent e)
2719   {
2720     new Finder();
2721   }
2722
2723   /**
2724    * Create a new view of the current alignment.
2725    */
2726   @Override
2727   public void newView_actionPerformed(ActionEvent e)
2728   {
2729     newView(null, true);
2730   }
2731
2732   /**
2733    * Creates and shows a new view of the current alignment.
2734    *
2735    * @param viewTitle
2736    *          title of newly created view; if null, one will be generated
2737    * @param copyAnnotation
2738    *          if true then duplicate all annnotation, groups and settings
2739    * @return new alignment panel, already displayed.
2740    */
2741   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2742   {
2743     /*
2744      * Create a new AlignmentPanel (with its own, new Viewport)
2745      */
2746     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2747             true);
2748     if (!copyAnnotation)
2749     {
2750       /*
2751        * remove all groups and annotation except for the automatic stuff
2752        */
2753       newap.av.getAlignment().deleteAllGroups();
2754       newap.av.getAlignment().deleteAllAnnotations(false);
2755     }
2756
2757     newap.av.setGatherViewsHere(false);
2758
2759     if (viewport.viewName == null)
2760     {
2761       viewport.viewName = MessageManager
2762               .getString("label.view_name_original");
2763     }
2764
2765     /*
2766      * Views share the same edits undo and redo stacks
2767      */
2768     newap.av.setHistoryList(viewport.getHistoryList());
2769     newap.av.setRedoList(viewport.getRedoList());
2770
2771     /*
2772      * Views share the same mappings; need to deregister any new mappings
2773      * created by copyAlignPanel, and register the new reference to the shared
2774      * mappings
2775      */
2776     newap.av.replaceMappings(viewport.getAlignment());
2777
2778     newap.av.viewName = getNewViewName(viewTitle);
2779
2780     addAlignmentPanel(newap, true);
2781     newap.alignmentChanged();
2782
2783     if (alignPanels.size() == 2)
2784     {
2785       viewport.setGatherViewsHere(true);
2786     }
2787     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2788     return newap;
2789   }
2790
2791   /**
2792    * Make a new name for the view, ensuring it is unique within the current
2793    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2794    * these now use viewId. Unique view names are still desirable for usability.)
2795    *
2796    * @param viewTitle
2797    * @return
2798    */
2799   protected String getNewViewName(String viewTitle)
2800   {
2801     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2802     boolean addFirstIndex = false;
2803     if (viewTitle == null || viewTitle.trim().length() == 0)
2804     {
2805       viewTitle = MessageManager.getString("action.view");
2806       addFirstIndex = true;
2807     }
2808     else
2809     {
2810       index = 1;// we count from 1 if given a specific name
2811     }
2812     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2813
2814     List<Component> comps = PaintRefresher.components.get(viewport
2815             .getSequenceSetId());
2816
2817     List<String> existingNames = getExistingViewNames(comps);
2818
2819     while (existingNames.contains(newViewName))
2820     {
2821       newViewName = viewTitle + " " + (++index);
2822     }
2823     return newViewName;
2824   }
2825
2826   /**
2827    * Returns a list of distinct view names found in the given list of
2828    * components. View names are held on the viewport of an AlignmentPanel.
2829    *
2830    * @param comps
2831    * @return
2832    */
2833   protected List<String> getExistingViewNames(List<Component> comps)
2834   {
2835     List<String> existingNames = new ArrayList<String>();
2836     for (Component comp : comps)
2837     {
2838       if (comp instanceof AlignmentPanel)
2839       {
2840         AlignmentPanel ap = (AlignmentPanel) comp;
2841         if (!existingNames.contains(ap.av.viewName))
2842         {
2843           existingNames.add(ap.av.viewName);
2844         }
2845       }
2846     }
2847     return existingNames;
2848   }
2849
2850   /**
2851    * Explode tabbed views into separate windows.
2852    */
2853   @Override
2854   public void expandViews_actionPerformed(ActionEvent e)
2855   {
2856     Desktop.instance.explodeViews(this);
2857   }
2858
2859   /**
2860    * Gather views in separate windows back into a tabbed presentation.
2861    */
2862   @Override
2863   public void gatherViews_actionPerformed(ActionEvent e)
2864   {
2865     Desktop.instance.gatherViews(this);
2866   }
2867
2868   /**
2869    * DOCUMENT ME!
2870    *
2871    * @param e
2872    *          DOCUMENT ME!
2873    */
2874   @Override
2875   public void font_actionPerformed(ActionEvent e)
2876   {
2877     new FontChooser(alignPanel);
2878   }
2879
2880   /**
2881    * DOCUMENT ME!
2882    *
2883    * @param e
2884    *          DOCUMENT ME!
2885    */
2886   @Override
2887   protected void seqLimit_actionPerformed(ActionEvent e)
2888   {
2889     viewport.setShowJVSuffix(seqLimits.isSelected());
2890
2891     alignPanel.getIdPanel().getIdCanvas()
2892             .setPreferredSize(alignPanel.calculateIdWidth());
2893     alignPanel.paintAlignment(true);
2894   }
2895
2896   @Override
2897   public void idRightAlign_actionPerformed(ActionEvent e)
2898   {
2899     viewport.setRightAlignIds(idRightAlign.isSelected());
2900     alignPanel.paintAlignment(true);
2901   }
2902
2903   @Override
2904   public void centreColumnLabels_actionPerformed(ActionEvent e)
2905   {
2906     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2907     alignPanel.paintAlignment(true);
2908   }
2909
2910   /*
2911    * (non-Javadoc)
2912    *
2913    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2914    */
2915   @Override
2916   protected void followHighlight_actionPerformed()
2917   {
2918     /*
2919      * Set the 'follow' flag on the Viewport (and scroll to position if now
2920      * true).
2921      */
2922     final boolean state = this.followHighlightMenuItem.getState();
2923     viewport.setFollowHighlight(state);
2924     if (state)
2925     {
2926       alignPanel.scrollToPosition(
2927               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2928     }
2929   }
2930
2931   /**
2932    * DOCUMENT ME!
2933    *
2934    * @param e
2935    *          DOCUMENT ME!
2936    */
2937   @Override
2938   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2939   {
2940     viewport.setColourText(colourTextMenuItem.isSelected());
2941     alignPanel.paintAlignment(true);
2942   }
2943
2944   /**
2945    * DOCUMENT ME!
2946    *
2947    * @param e
2948    *          DOCUMENT ME!
2949    */
2950   @Override
2951   public void wrapMenuItem_actionPerformed(ActionEvent e)
2952   {
2953     scaleAbove.setVisible(wrapMenuItem.isSelected());
2954     scaleLeft.setVisible(wrapMenuItem.isSelected());
2955     scaleRight.setVisible(wrapMenuItem.isSelected());
2956     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2957     alignPanel.updateLayout();
2958   }
2959
2960   @Override
2961   public void showAllSeqs_actionPerformed(ActionEvent e)
2962   {
2963     viewport.showAllHiddenSeqs();
2964   }
2965
2966   @Override
2967   public void showAllColumns_actionPerformed(ActionEvent e)
2968   {
2969     viewport.showAllHiddenColumns();
2970     repaint();
2971   }
2972
2973   @Override
2974   public void hideSelSequences_actionPerformed(ActionEvent e)
2975   {
2976     viewport.hideAllSelectedSeqs();
2977     // alignPanel.paintAlignment(true);
2978   }
2979
2980   /**
2981    * called by key handler and the hide all/show all menu items
2982    *
2983    * @param toggleSeqs
2984    * @param toggleCols
2985    */
2986   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2987   {
2988
2989     boolean hide = false;
2990     SequenceGroup sg = viewport.getSelectionGroup();
2991     if (!toggleSeqs && !toggleCols)
2992     {
2993       // Hide everything by the current selection - this is a hack - we do the
2994       // invert and then hide
2995       // first check that there will be visible columns after the invert.
2996       if ((viewport.getColumnSelection() != null
2997               && viewport.getColumnSelection().getSelected() != null && viewport
2998               .getColumnSelection().getSelected().size() > 0)
2999               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3000                       .getEndRes()))
3001       {
3002         // now invert the sequence set, if required - empty selection implies
3003         // that no hiding is required.
3004         if (sg != null)
3005         {
3006           invertSequenceMenuItem_actionPerformed(null);
3007           sg = viewport.getSelectionGroup();
3008           toggleSeqs = true;
3009
3010         }
3011         viewport.expandColSelection(sg, true);
3012         // finally invert the column selection and get the new sequence
3013         // selection.
3014         invertColSel_actionPerformed(null);
3015         toggleCols = true;
3016       }
3017     }
3018
3019     if (toggleSeqs)
3020     {
3021       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3022       {
3023         hideSelSequences_actionPerformed(null);
3024         hide = true;
3025       }
3026       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3027               .size() > 0))
3028       {
3029         showAllSeqs_actionPerformed(null);
3030       }
3031     }
3032
3033     if (toggleCols)
3034     {
3035       if (viewport.getColumnSelection().getSelected().size() > 0)
3036       {
3037         hideSelColumns_actionPerformed(null);
3038         if (!toggleSeqs)
3039         {
3040           viewport.setSelectionGroup(sg);
3041         }
3042       }
3043       else if (!hide)
3044       {
3045         showAllColumns_actionPerformed(null);
3046       }
3047     }
3048   }
3049
3050   /*
3051    * (non-Javadoc)
3052    *
3053    * @see
3054    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3055    * event.ActionEvent)
3056    */
3057   @Override
3058   public void hideAllButSelection_actionPerformed(ActionEvent e)
3059   {
3060     toggleHiddenRegions(false, false);
3061   }
3062
3063   /*
3064    * (non-Javadoc)
3065    *
3066    * @see
3067    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3068    * .ActionEvent)
3069    */
3070   @Override
3071   public void hideAllSelection_actionPerformed(ActionEvent e)
3072   {
3073     SequenceGroup sg = viewport.getSelectionGroup();
3074     viewport.expandColSelection(sg, false);
3075     viewport.hideAllSelectedSeqs();
3076     viewport.hideSelectedColumns();
3077     alignPanel.paintAlignment(true);
3078   }
3079
3080   /*
3081    * (non-Javadoc)
3082    *
3083    * @see
3084    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3085    * ActionEvent)
3086    */
3087   @Override
3088   public void showAllhidden_actionPerformed(ActionEvent e)
3089   {
3090     viewport.showAllHiddenColumns();
3091     viewport.showAllHiddenSeqs();
3092     alignPanel.paintAlignment(true);
3093   }
3094
3095   @Override
3096   public void hideSelColumns_actionPerformed(ActionEvent e)
3097   {
3098     viewport.hideSelectedColumns();
3099     alignPanel.paintAlignment(true);
3100   }
3101
3102   @Override
3103   public void hiddenMarkers_actionPerformed(ActionEvent e)
3104   {
3105     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3106     repaint();
3107   }
3108
3109   /**
3110    * DOCUMENT ME!
3111    *
3112    * @param e
3113    *          DOCUMENT ME!
3114    */
3115   @Override
3116   protected void scaleAbove_actionPerformed(ActionEvent e)
3117   {
3118     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3119     alignPanel.paintAlignment(true);
3120   }
3121
3122   /**
3123    * DOCUMENT ME!
3124    *
3125    * @param e
3126    *          DOCUMENT ME!
3127    */
3128   @Override
3129   protected void scaleLeft_actionPerformed(ActionEvent e)
3130   {
3131     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3132     alignPanel.paintAlignment(true);
3133   }
3134
3135   /**
3136    * DOCUMENT ME!
3137    *
3138    * @param e
3139    *          DOCUMENT ME!
3140    */
3141   @Override
3142   protected void scaleRight_actionPerformed(ActionEvent e)
3143   {
3144     viewport.setScaleRightWrapped(scaleRight.isSelected());
3145     alignPanel.paintAlignment(true);
3146   }
3147
3148   /**
3149    * DOCUMENT ME!
3150    *
3151    * @param e
3152    *          DOCUMENT ME!
3153    */
3154   @Override
3155   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3156   {
3157     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3158     alignPanel.paintAlignment(true);
3159   }
3160
3161   /**
3162    * DOCUMENT ME!
3163    *
3164    * @param e
3165    *          DOCUMENT ME!
3166    */
3167   @Override
3168   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3169   {
3170     viewport.setShowText(viewTextMenuItem.isSelected());
3171     alignPanel.paintAlignment(true);
3172   }
3173
3174   /**
3175    * DOCUMENT ME!
3176    *
3177    * @param e
3178    *          DOCUMENT ME!
3179    */
3180   @Override
3181   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3182   {
3183     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3184     alignPanel.paintAlignment(true);
3185   }
3186
3187   public FeatureSettings featureSettings;
3188
3189   @Override
3190   public FeatureSettingsControllerI getFeatureSettingsUI()
3191   {
3192     return featureSettings;
3193   }
3194
3195   @Override
3196   public void featureSettings_actionPerformed(ActionEvent e)
3197   {
3198     if (featureSettings != null)
3199     {
3200       featureSettings.close();
3201       featureSettings = null;
3202     }
3203     if (!showSeqFeatures.isSelected())
3204     {
3205       // make sure features are actually displayed
3206       showSeqFeatures.setSelected(true);
3207       showSeqFeatures_actionPerformed(null);
3208     }
3209     featureSettings = new FeatureSettings(this);
3210   }
3211
3212   /**
3213    * Set or clear 'Show Sequence Features'
3214    *
3215    * @param evt
3216    *          DOCUMENT ME!
3217    */
3218   @Override
3219   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3220   {
3221     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3222     alignPanel.paintAlignment(true);
3223     if (alignPanel.getOverviewPanel() != null)
3224     {
3225       alignPanel.getOverviewPanel().updateOverviewImage();
3226     }
3227   }
3228
3229   /**
3230    * Set or clear 'Show Sequence Features'
3231    *
3232    * @param evt
3233    *          DOCUMENT ME!
3234    */
3235   @Override
3236   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3237   {
3238     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3239             .isSelected());
3240     if (viewport.isShowSequenceFeaturesHeight())
3241     {
3242       // ensure we're actually displaying features
3243       viewport.setShowSequenceFeatures(true);
3244       showSeqFeatures.setSelected(true);
3245     }
3246     alignPanel.paintAlignment(true);
3247     if (alignPanel.getOverviewPanel() != null)
3248     {
3249       alignPanel.getOverviewPanel().updateOverviewImage();
3250     }
3251   }
3252
3253   /**
3254    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3255    * the annotations panel as a whole.
3256    *
3257    * The options to show/hide all annotations should be enabled when the panel
3258    * is shown, and disabled when the panel is hidden.
3259    *
3260    * @param e
3261    */
3262   @Override
3263   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3264   {
3265     final boolean setVisible = annotationPanelMenuItem.isSelected();
3266     viewport.setShowAnnotation(setVisible);
3267     this.showAllSeqAnnotations.setEnabled(setVisible);
3268     this.hideAllSeqAnnotations.setEnabled(setVisible);
3269     this.showAllAlAnnotations.setEnabled(setVisible);
3270     this.hideAllAlAnnotations.setEnabled(setVisible);
3271     alignPanel.updateLayout();
3272   }
3273
3274   @Override
3275   public void alignmentProperties()
3276   {
3277     JEditorPane editPane = new JEditorPane("text/html", "");
3278     editPane.setEditable(false);
3279     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3280             .formatAsHtml();
3281     editPane.setText(MessageManager.formatMessage("label.html_content",
3282             new Object[] { contents.toString() }));
3283     JInternalFrame frame = new JInternalFrame();
3284     frame.getContentPane().add(new JScrollPane(editPane));
3285
3286     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3287             "label.alignment_properties", new Object[] { getTitle() }),
3288             500, 400);
3289   }
3290
3291   /**
3292    * DOCUMENT ME!
3293    *
3294    * @param e
3295    *          DOCUMENT ME!
3296    */
3297   @Override
3298   public void overviewMenuItem_actionPerformed(ActionEvent e)
3299   {
3300     if (alignPanel.overviewPanel != null)
3301     {
3302       return;
3303     }
3304
3305     JInternalFrame frame = new JInternalFrame();
3306     OverviewPanel overview = new OverviewPanel(alignPanel);
3307     frame.setContentPane(overview);
3308     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3309             "label.overview_params", new Object[] { this.getTitle() }),
3310             frame.getWidth(), frame.getHeight());
3311     frame.pack();
3312     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3313     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3314     {
3315       @Override
3316       public void internalFrameClosed(
3317               javax.swing.event.InternalFrameEvent evt)
3318       {
3319         alignPanel.setOverviewPanel(null);
3320       };
3321     });
3322
3323     alignPanel.setOverviewPanel(overview);
3324   }
3325
3326   @Override
3327   public void textColour_actionPerformed(ActionEvent e)
3328   {
3329     new TextColourChooser().chooseColour(alignPanel, null);
3330   }
3331
3332   /**
3333    * DOCUMENT ME!
3334    *
3335    * @param e
3336    *          DOCUMENT ME!
3337    */
3338   @Override
3339   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3340   {
3341     changeColour(null);
3342   }
3343
3344   /**
3345    * DOCUMENT ME!
3346    *
3347    * @param e
3348    *          DOCUMENT ME!
3349    */
3350   @Override
3351   public void clustalColour_actionPerformed(ActionEvent e)
3352   {
3353     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3354             viewport.getHiddenRepSequences()));
3355   }
3356
3357   /**
3358    * DOCUMENT ME!
3359    *
3360    * @param e
3361    *          DOCUMENT ME!
3362    */
3363   @Override
3364   public void zappoColour_actionPerformed(ActionEvent e)
3365   {
3366     changeColour(new ZappoColourScheme());
3367   }
3368
3369   /**
3370    * DOCUMENT ME!
3371    *
3372    * @param e
3373    *          DOCUMENT ME!
3374    */
3375   @Override
3376   public void taylorColour_actionPerformed(ActionEvent e)
3377   {
3378     changeColour(new TaylorColourScheme());
3379   }
3380
3381   /**
3382    * DOCUMENT ME!
3383    *
3384    * @param e
3385    *          DOCUMENT ME!
3386    */
3387   @Override
3388   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3389   {
3390     changeColour(new HydrophobicColourScheme());
3391   }
3392
3393   /**
3394    * DOCUMENT ME!
3395    *
3396    * @param e
3397    *          DOCUMENT ME!
3398    */
3399   @Override
3400   public void helixColour_actionPerformed(ActionEvent e)
3401   {
3402     changeColour(new HelixColourScheme());
3403   }
3404
3405   /**
3406    * DOCUMENT ME!
3407    *
3408    * @param e
3409    *          DOCUMENT ME!
3410    */
3411   @Override
3412   public void strandColour_actionPerformed(ActionEvent e)
3413   {
3414     changeColour(new StrandColourScheme());
3415   }
3416
3417   /**
3418    * DOCUMENT ME!
3419    *
3420    * @param e
3421    *          DOCUMENT ME!
3422    */
3423   @Override
3424   public void turnColour_actionPerformed(ActionEvent e)
3425   {
3426     changeColour(new TurnColourScheme());
3427   }
3428
3429   /**
3430    * DOCUMENT ME!
3431    *
3432    * @param e
3433    *          DOCUMENT ME!
3434    */
3435   @Override
3436   public void buriedColour_actionPerformed(ActionEvent e)
3437   {
3438     changeColour(new BuriedColourScheme());
3439   }
3440
3441   /**
3442    * DOCUMENT ME!
3443    *
3444    * @param e
3445    *          DOCUMENT ME!
3446    */
3447   @Override
3448   public void nucleotideColour_actionPerformed(ActionEvent e)
3449   {
3450     changeColour(new NucleotideColourScheme());
3451   }
3452
3453   @Override
3454   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3455   {
3456     changeColour(new PurinePyrimidineColourScheme());
3457   }
3458
3459   /*
3460    * public void covariationColour_actionPerformed(ActionEvent e) {
3461    * changeColour(new
3462    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3463    * ()[0])); }
3464    */
3465   @Override
3466   public void annotationColour_actionPerformed(ActionEvent e)
3467   {
3468     new AnnotationColourChooser(viewport, alignPanel);
3469   }
3470
3471   @Override
3472   public void annotationColumn_actionPerformed(ActionEvent e)
3473   {
3474     new AnnotationColumnChooser(viewport, alignPanel);
3475   }
3476
3477   @Override
3478   public void rnahelicesColour_actionPerformed(ActionEvent e)
3479   {
3480     new RNAHelicesColourChooser(viewport, alignPanel);
3481   }
3482
3483   /**
3484    * DOCUMENT ME!
3485    *
3486    * @param e
3487    *          DOCUMENT ME!
3488    */
3489   @Override
3490   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3491   {
3492     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3493   }
3494
3495   /**
3496    * DOCUMENT ME!
3497    *
3498    * @param cs
3499    *          DOCUMENT ME!
3500    */
3501   public void changeColour(ColourSchemeI cs)
3502   {
3503     // TODO: pull up to controller method
3504
3505     if (cs != null)
3506     {
3507       // Make sure viewport is up to date w.r.t. any sliders
3508       if (viewport.getAbovePIDThreshold())
3509       {
3510         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3511                 "Background");
3512         viewport.setThreshold(threshold);
3513       }
3514
3515       if (viewport.getConservationSelected())
3516       {
3517         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3518                 cs, "Background"));
3519       }
3520     }
3521
3522     viewport.setGlobalColourScheme(cs);
3523
3524     alignPanel.paintAlignment(true);
3525   }
3526
3527   /**
3528    * DOCUMENT ME!
3529    *
3530    * @param e
3531    *          DOCUMENT ME!
3532    */
3533   @Override
3534   protected void modifyPID_actionPerformed(ActionEvent e)
3535   {
3536     if (viewport.getAbovePIDThreshold()
3537             && viewport.getGlobalColourScheme() != null)
3538     {
3539       SliderPanel.setPIDSliderSource(alignPanel,
3540               viewport.getGlobalColourScheme(), "Background");
3541       SliderPanel.showPIDSlider();
3542     }
3543   }
3544
3545   /**
3546    * DOCUMENT ME!
3547    *
3548    * @param e
3549    *          DOCUMENT ME!
3550    */
3551   @Override
3552   protected void modifyConservation_actionPerformed(ActionEvent e)
3553   {
3554     if (viewport.getConservationSelected()
3555             && viewport.getGlobalColourScheme() != null)
3556     {
3557       SliderPanel.setConservationSlider(alignPanel,
3558               viewport.getGlobalColourScheme(), "Background");
3559       SliderPanel.showConservationSlider();
3560     }
3561   }
3562
3563   /**
3564    * DOCUMENT ME!
3565    *
3566    * @param e
3567    *          DOCUMENT ME!
3568    */
3569   @Override
3570   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3571   {
3572     viewport.setConservationSelected(conservationMenuItem.isSelected());
3573
3574     viewport.setAbovePIDThreshold(false);
3575     abovePIDThreshold.setSelected(false);
3576
3577     changeColour(viewport.getGlobalColourScheme());
3578
3579     modifyConservation_actionPerformed(null);
3580   }
3581
3582   /**
3583    * DOCUMENT ME!
3584    *
3585    * @param e
3586    *          DOCUMENT ME!
3587    */
3588   @Override
3589   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3590   {
3591     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3592
3593     conservationMenuItem.setSelected(false);
3594     viewport.setConservationSelected(false);
3595
3596     changeColour(viewport.getGlobalColourScheme());
3597
3598     modifyPID_actionPerformed(null);
3599   }
3600
3601   /**
3602    * DOCUMENT ME!
3603    *
3604    * @param e
3605    *          DOCUMENT ME!
3606    */
3607   @Override
3608   public void userDefinedColour_actionPerformed(ActionEvent e)
3609   {
3610     if (e.getActionCommand().equals(
3611             MessageManager.getString("action.user_defined")))
3612     {
3613       new UserDefinedColours(alignPanel, null);
3614     }
3615     else
3616     {
3617       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3618               .getUserColourSchemes().get(e.getActionCommand());
3619
3620       changeColour(udc);
3621     }
3622   }
3623
3624   public void updateUserColourMenu()
3625   {
3626
3627     Component[] menuItems = colourMenu.getMenuComponents();
3628     int iSize = menuItems.length;
3629     for (int i = 0; i < iSize; i++)
3630     {
3631       if (menuItems[i].getName() != null
3632               && menuItems[i].getName().equals("USER_DEFINED"))
3633       {
3634         colourMenu.remove(menuItems[i]);
3635         iSize--;
3636       }
3637     }
3638     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3639     {
3640       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3641               .getUserColourSchemes().keys();
3642
3643       while (userColours.hasMoreElements())
3644       {
3645         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3646                 userColours.nextElement().toString());
3647         radioItem.setName("USER_DEFINED");
3648         radioItem.addMouseListener(new MouseAdapter()
3649         {
3650           @Override
3651           public void mousePressed(MouseEvent evt)
3652           {
3653             if (evt.isControlDown()
3654                     || SwingUtilities.isRightMouseButton(evt))
3655             {
3656               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3657
3658               int option = JOptionPane.showInternalConfirmDialog(
3659                       jalview.gui.Desktop.desktop,
3660                       MessageManager
3661                               .getString("label.remove_from_default_list"),
3662                       MessageManager
3663                               .getString("label.remove_user_defined_colour"),
3664                       JOptionPane.YES_NO_OPTION);
3665               if (option == JOptionPane.YES_OPTION)
3666               {
3667                 jalview.gui.UserDefinedColours
3668                         .removeColourFromDefaults(radioItem.getText());
3669                 colourMenu.remove(radioItem);
3670               }
3671               else
3672               {
3673                 radioItem.addActionListener(new ActionListener()
3674                 {
3675                   @Override
3676                   public void actionPerformed(ActionEvent evt)
3677                   {
3678                     userDefinedColour_actionPerformed(evt);
3679                   }
3680                 });
3681               }
3682             }
3683           }
3684         });
3685         radioItem.addActionListener(new ActionListener()
3686         {
3687           @Override
3688           public void actionPerformed(ActionEvent evt)
3689           {
3690             userDefinedColour_actionPerformed(evt);
3691           }
3692         });
3693
3694         colourMenu.insert(radioItem, 15);
3695         colours.add(radioItem);
3696       }
3697     }
3698   }
3699
3700   /**
3701    * DOCUMENT ME!
3702    *
3703    * @param e
3704    *          DOCUMENT ME!
3705    */
3706   @Override
3707   public void PIDColour_actionPerformed(ActionEvent e)
3708   {
3709     changeColour(new PIDColourScheme());
3710   }
3711
3712   /**
3713    * DOCUMENT ME!
3714    *
3715    * @param e
3716    *          DOCUMENT ME!
3717    */
3718   @Override
3719   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3720   {
3721     changeColour(new Blosum62ColourScheme());
3722   }
3723
3724   /**
3725    * DOCUMENT ME!
3726    *
3727    * @param e
3728    *          DOCUMENT ME!
3729    */
3730   @Override
3731   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3732   {
3733     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3734     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3735             .getAlignment().getSequenceAt(0), null);
3736     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3737             viewport.getAlignment()));
3738     alignPanel.paintAlignment(true);
3739   }
3740
3741   /**
3742    * DOCUMENT ME!
3743    *
3744    * @param e
3745    *          DOCUMENT ME!
3746    */
3747   @Override
3748   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3749   {
3750     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751     AlignmentSorter.sortByID(viewport.getAlignment());
3752     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3753             viewport.getAlignment()));
3754     alignPanel.paintAlignment(true);
3755   }
3756
3757   /**
3758    * DOCUMENT ME!
3759    *
3760    * @param e
3761    *          DOCUMENT ME!
3762    */
3763   @Override
3764   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3765   {
3766     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3767     AlignmentSorter.sortByLength(viewport.getAlignment());
3768     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3769             viewport.getAlignment()));
3770     alignPanel.paintAlignment(true);
3771   }
3772
3773   /**
3774    * DOCUMENT ME!
3775    *
3776    * @param e
3777    *          DOCUMENT ME!
3778    */
3779   @Override
3780   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3781   {
3782     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3783     AlignmentSorter.sortByGroup(viewport.getAlignment());
3784     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3785             viewport.getAlignment()));
3786
3787     alignPanel.paintAlignment(true);
3788   }
3789
3790   /**
3791    * DOCUMENT ME!
3792    *
3793    * @param e
3794    *          DOCUMENT ME!
3795    */
3796   @Override
3797   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3798   {
3799     new RedundancyPanel(alignPanel, this);
3800   }
3801
3802   /**
3803    * DOCUMENT ME!
3804    *
3805    * @param e
3806    *          DOCUMENT ME!
3807    */
3808   @Override
3809   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3810   {
3811     if ((viewport.getSelectionGroup() == null)
3812             || (viewport.getSelectionGroup().getSize() < 2))
3813     {
3814       JOptionPane.showInternalMessageDialog(this, MessageManager
3815               .getString("label.you_must_select_least_two_sequences"),
3816               MessageManager.getString("label.invalid_selection"),
3817               JOptionPane.WARNING_MESSAGE);
3818     }
3819     else
3820     {
3821       JInternalFrame frame = new JInternalFrame();
3822       frame.setContentPane(new PairwiseAlignPanel(viewport));
3823       Desktop.addInternalFrame(frame,
3824               MessageManager.getString("action.pairwise_alignment"), 600,
3825               500);
3826     }
3827   }
3828
3829   /**
3830    * DOCUMENT ME!
3831    *
3832    * @param e
3833    *          DOCUMENT ME!
3834    */
3835   @Override
3836   public void PCAMenuItem_actionPerformed(ActionEvent e)
3837   {
3838     if (((viewport.getSelectionGroup() != null)
3839             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3840             .getSelectionGroup().getSize() > 0))
3841             || (viewport.getAlignment().getHeight() < 4))
3842     {
3843       JOptionPane
3844               .showInternalMessageDialog(
3845                       this,
3846                       MessageManager
3847                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3848                       MessageManager
3849                               .getString("label.sequence_selection_insufficient"),
3850                       JOptionPane.WARNING_MESSAGE);
3851
3852       return;
3853     }
3854
3855     new PCAPanel(alignPanel);
3856   }
3857
3858   @Override
3859   public void autoCalculate_actionPerformed(ActionEvent e)
3860   {
3861     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3862     if (viewport.autoCalculateConsensus)
3863     {
3864       viewport.firePropertyChange("alignment", null, viewport
3865               .getAlignment().getSequences());
3866     }
3867   }
3868
3869   @Override
3870   public void sortByTreeOption_actionPerformed(ActionEvent e)
3871   {
3872     viewport.sortByTree = sortByTree.isSelected();
3873   }
3874
3875   @Override
3876   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3877   {
3878     viewport.followSelection = listenToViewSelections.isSelected();
3879   }
3880
3881   /**
3882    * DOCUMENT ME!
3883    *
3884    * @param e
3885    *          DOCUMENT ME!
3886    */
3887   @Override
3888   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3889   {
3890     newTreePanel("AV", "PID", "Average distance tree using PID");
3891   }
3892
3893   /**
3894    * DOCUMENT ME!
3895    *
3896    * @param e
3897    *          DOCUMENT ME!
3898    */
3899   @Override
3900   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3901   {
3902     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3903   }
3904
3905   /**
3906    * DOCUMENT ME!
3907    *
3908    * @param e
3909    *          DOCUMENT ME!
3910    */
3911   @Override
3912   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3913   {
3914     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3915   }
3916
3917   /**
3918    * DOCUMENT ME!
3919    *
3920    * @param e
3921    *          DOCUMENT ME!
3922    */
3923   @Override
3924   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3925   {
3926     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3927   }
3928
3929   /**
3930    * DOCUMENT ME!
3931    *
3932    * @param type
3933    *          DOCUMENT ME!
3934    * @param pwType
3935    *          DOCUMENT ME!
3936    * @param title
3937    *          DOCUMENT ME!
3938    */
3939   void newTreePanel(String type, String pwType, String title)
3940   {
3941     TreePanel tp;
3942
3943     if (viewport.getSelectionGroup() != null
3944             && viewport.getSelectionGroup().getSize() > 0)
3945     {
3946       if (viewport.getSelectionGroup().getSize() < 3)
3947       {
3948         JOptionPane
3949                 .showMessageDialog(
3950                         Desktop.desktop,
3951                         MessageManager
3952                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3953                         MessageManager
3954                                 .getString("label.not_enough_sequences"),
3955                         JOptionPane.WARNING_MESSAGE);
3956         return;
3957       }
3958
3959       SequenceGroup sg = viewport.getSelectionGroup();
3960
3961       /* Decide if the selection is a column region */
3962       for (SequenceI _s : sg.getSequences())
3963       {
3964         if (_s.getLength() < sg.getEndRes())
3965         {
3966           JOptionPane
3967                   .showMessageDialog(
3968                           Desktop.desktop,
3969                           MessageManager
3970                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3971                           MessageManager
3972                                   .getString("label.sequences_selection_not_aligned"),
3973                           JOptionPane.WARNING_MESSAGE);
3974
3975           return;
3976         }
3977       }
3978
3979       title = title + " on region";
3980       tp = new TreePanel(alignPanel, type, pwType);
3981     }
3982     else
3983     {
3984       // are the visible sequences aligned?
3985       if (!viewport.getAlignment().isAligned(false))
3986       {
3987         JOptionPane
3988                 .showMessageDialog(
3989                         Desktop.desktop,
3990                         MessageManager
3991                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3992                         MessageManager
3993                                 .getString("label.sequences_not_aligned"),
3994                         JOptionPane.WARNING_MESSAGE);
3995
3996         return;
3997       }
3998
3999       if (viewport.getAlignment().getHeight() < 2)
4000       {
4001         return;
4002       }
4003
4004       tp = new TreePanel(alignPanel, type, pwType);
4005     }
4006
4007     title += " from ";
4008
4009     if (viewport.viewName != null)
4010     {
4011       title += viewport.viewName + " of ";
4012     }
4013
4014     title += this.title;
4015
4016     Desktop.addInternalFrame(tp, title, 600, 500);
4017   }
4018
4019   /**
4020    * DOCUMENT ME!
4021    *
4022    * @param title
4023    *          DOCUMENT ME!
4024    * @param order
4025    *          DOCUMENT ME!
4026    */
4027   public void addSortByOrderMenuItem(String title,
4028           final AlignmentOrder order)
4029   {
4030     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4031             "action.by_title_param", new Object[] { title }));
4032     sort.add(item);
4033     item.addActionListener(new java.awt.event.ActionListener()
4034     {
4035       @Override
4036       public void actionPerformed(ActionEvent e)
4037       {
4038         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4039
4040         // TODO: JBPNote - have to map order entries to curent SequenceI
4041         // pointers
4042         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4043
4044         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4045                 .getAlignment()));
4046
4047         alignPanel.paintAlignment(true);
4048       }
4049     });
4050   }
4051
4052   /**
4053    * Add a new sort by annotation score menu item
4054    *
4055    * @param sort
4056    *          the menu to add the option to
4057    * @param scoreLabel
4058    *          the label used to retrieve scores for each sequence on the
4059    *          alignment
4060    */
4061   public void addSortByAnnotScoreMenuItem(JMenu sort,
4062           final String scoreLabel)
4063   {
4064     final JMenuItem item = new JMenuItem(scoreLabel);
4065     sort.add(item);
4066     item.addActionListener(new java.awt.event.ActionListener()
4067     {
4068       @Override
4069       public void actionPerformed(ActionEvent e)
4070       {
4071         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4072         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4073                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4074         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4075                 viewport.getAlignment()));
4076         alignPanel.paintAlignment(true);
4077       }
4078     });
4079   }
4080
4081   /**
4082    * last hash for alignment's annotation array - used to minimise cost of
4083    * rebuild.
4084    */
4085   protected int _annotationScoreVectorHash;
4086
4087   /**
4088    * search the alignment and rebuild the sort by annotation score submenu the
4089    * last alignment annotation vector hash is stored to minimize cost of
4090    * rebuilding in subsequence calls.
4091    *
4092    */
4093   @Override
4094   public void buildSortByAnnotationScoresMenu()
4095   {
4096     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4097     {
4098       return;
4099     }
4100
4101     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4102     {
4103       sortByAnnotScore.removeAll();
4104       // almost certainly a quicker way to do this - but we keep it simple
4105       Hashtable scoreSorts = new Hashtable();
4106       AlignmentAnnotation aann[];
4107       for (SequenceI sqa : viewport.getAlignment().getSequences())
4108       {
4109         aann = sqa.getAnnotation();
4110         for (int i = 0; aann != null && i < aann.length; i++)
4111         {
4112           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4113           {
4114             scoreSorts.put(aann[i].label, aann[i].label);
4115           }
4116         }
4117       }
4118       Enumeration labels = scoreSorts.keys();
4119       while (labels.hasMoreElements())
4120       {
4121         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4122                 (String) labels.nextElement());
4123       }
4124       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4125       scoreSorts.clear();
4126
4127       _annotationScoreVectorHash = viewport.getAlignment()
4128               .getAlignmentAnnotation().hashCode();
4129     }
4130   }
4131
4132   /**
4133    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4134    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4135    * call. Listeners are added to remove the menu item when the treePanel is
4136    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4137    * modified.
4138    *
4139    * @param treePanel
4140    *          Displayed tree window.
4141    * @param title
4142    *          SortBy menu item title.
4143    */
4144   @Override
4145   public void buildTreeMenu()
4146   {
4147     calculateTree.removeAll();
4148     // build the calculate menu
4149
4150     for (final String type : new String[] { "NJ", "AV" })
4151     {
4152       String treecalcnm = MessageManager.getString("label.tree_calc_"
4153               + type.toLowerCase());
4154       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4155       {
4156         JMenuItem tm = new JMenuItem();
4157         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4158         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4159         {
4160           String smn = MessageManager.getStringOrReturn(
4161                   "label.score_model_", sm.getName());
4162           final String title = MessageManager.formatMessage(
4163                   "label.treecalc_title", treecalcnm, smn);
4164           tm.setText(title);//
4165           tm.addActionListener(new java.awt.event.ActionListener()
4166           {
4167             @Override
4168             public void actionPerformed(ActionEvent e)
4169             {
4170               newTreePanel(type, pwtype, title);
4171             }
4172           });
4173           calculateTree.add(tm);
4174         }
4175
4176       }
4177     }
4178     sortByTreeMenu.removeAll();
4179
4180     List<Component> comps = PaintRefresher.components.get(viewport
4181             .getSequenceSetId());
4182     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4183     for (Component comp : comps)
4184     {
4185       if (comp instanceof TreePanel)
4186       {
4187         treePanels.add((TreePanel) comp);
4188       }
4189     }
4190
4191     if (treePanels.size() < 1)
4192     {
4193       sortByTreeMenu.setVisible(false);
4194       return;
4195     }
4196
4197     sortByTreeMenu.setVisible(true);
4198
4199     for (final TreePanel tp : treePanels)
4200     {
4201       final JMenuItem item = new JMenuItem(tp.getTitle());
4202       item.addActionListener(new java.awt.event.ActionListener()
4203       {
4204         @Override
4205         public void actionPerformed(ActionEvent e)
4206         {
4207           tp.sortByTree_actionPerformed();
4208           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4209
4210         }
4211       });
4212
4213       sortByTreeMenu.add(item);
4214     }
4215   }
4216
4217   public boolean sortBy(AlignmentOrder alorder, String undoname)
4218   {
4219     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4220     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4221     if (undoname != null)
4222     {
4223       addHistoryItem(new OrderCommand(undoname, oldOrder,
4224               viewport.getAlignment()));
4225     }
4226     alignPanel.paintAlignment(true);
4227     return true;
4228   }
4229
4230   /**
4231    * Work out whether the whole set of sequences or just the selected set will
4232    * be submitted for multiple alignment.
4233    *
4234    */
4235   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4236   {
4237     // Now, check we have enough sequences
4238     AlignmentView msa = null;
4239
4240     if ((viewport.getSelectionGroup() != null)
4241             && (viewport.getSelectionGroup().getSize() > 1))
4242     {
4243       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4244       // some common interface!
4245       /*
4246        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4247        * SequenceI[sz = seqs.getSize(false)];
4248        *
4249        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4250        * seqs.getSequenceAt(i); }
4251        */
4252       msa = viewport.getAlignmentView(true);
4253     }
4254     else if (viewport.getSelectionGroup() != null
4255             && viewport.getSelectionGroup().getSize() == 1)
4256     {
4257       int option = JOptionPane.showConfirmDialog(this,
4258               MessageManager.getString("warn.oneseq_msainput_selection"),
4259               MessageManager.getString("label.invalid_selection"),
4260               JOptionPane.OK_CANCEL_OPTION);
4261       if (option == JOptionPane.OK_OPTION)
4262       {
4263         msa = viewport.getAlignmentView(false);
4264       }
4265     }
4266     else
4267     {
4268       msa = viewport.getAlignmentView(false);
4269     }
4270     return msa;
4271   }
4272
4273   /**
4274    * Decides what is submitted to a secondary structure prediction service: the
4275    * first sequence in the alignment, or in the current selection, or, if the
4276    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4277    * region or the whole alignment. (where the first sequence in the set is the
4278    * one that the prediction will be for).
4279    */
4280   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4281   {
4282     AlignmentView seqs = null;
4283
4284     if ((viewport.getSelectionGroup() != null)
4285             && (viewport.getSelectionGroup().getSize() > 0))
4286     {
4287       seqs = viewport.getAlignmentView(true);
4288     }
4289     else
4290     {
4291       seqs = viewport.getAlignmentView(false);
4292     }
4293     // limit sequences - JBPNote in future - could spawn multiple prediction
4294     // jobs
4295     // TODO: viewport.getAlignment().isAligned is a global state - the local
4296     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4297     if (!viewport.getAlignment().isAligned(false))
4298     {
4299       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4300       // TODO: if seqs.getSequences().length>1 then should really have warned
4301       // user!
4302
4303     }
4304     return seqs;
4305   }
4306
4307   /**
4308    * DOCUMENT ME!
4309    *
4310    * @param e
4311    *          DOCUMENT ME!
4312    */
4313   @Override
4314   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4315   {
4316     // Pick the tree file
4317     JalviewFileChooser chooser = new JalviewFileChooser(
4318             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4319     chooser.setFileView(new JalviewFileView());
4320     chooser.setDialogTitle(MessageManager
4321             .getString("label.select_newick_like_tree_file"));
4322     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4323
4324     int value = chooser.showOpenDialog(null);
4325
4326     if (value == JalviewFileChooser.APPROVE_OPTION)
4327     {
4328       String choice = chooser.getSelectedFile().getPath();
4329       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4330       jalview.io.NewickFile fin = null;
4331       try
4332       {
4333         fin = new jalview.io.NewickFile(choice, "File");
4334         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4335       } catch (Exception ex)
4336       {
4337         JOptionPane
4338                 .showMessageDialog(
4339                         Desktop.desktop,
4340                         ex.getMessage(),
4341                         MessageManager
4342                                 .getString("label.problem_reading_tree_file"),
4343                         JOptionPane.WARNING_MESSAGE);
4344         ex.printStackTrace();
4345       }
4346       if (fin != null && fin.hasWarningMessage())
4347       {
4348         JOptionPane.showMessageDialog(Desktop.desktop, fin
4349                 .getWarningMessage(), MessageManager
4350                 .getString("label.possible_problem_with_tree_file"),
4351                 JOptionPane.WARNING_MESSAGE);
4352       }
4353     }
4354   }
4355
4356   @Override
4357   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4358   {
4359     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4360   }
4361
4362   public TreePanel ShowNewickTree(NewickFile nf, String title)
4363   {
4364     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4365   }
4366
4367   public TreePanel ShowNewickTree(NewickFile nf, String title,
4368           AlignmentView input)
4369   {
4370     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4371   }
4372
4373   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4374           int h, int x, int y)
4375   {
4376     return ShowNewickTree(nf, title, null, w, h, x, y);
4377   }
4378
4379   /**
4380    * Add a treeviewer for the tree extracted from a newick file object to the
4381    * current alignment view
4382    *
4383    * @param nf
4384    *          the tree
4385    * @param title
4386    *          tree viewer title
4387    * @param input
4388    *          Associated alignment input data (or null)
4389    * @param w
4390    *          width
4391    * @param h
4392    *          height
4393    * @param x
4394    *          position
4395    * @param y
4396    *          position
4397    * @return TreePanel handle
4398    */
4399   public TreePanel ShowNewickTree(NewickFile nf, String title,
4400           AlignmentView input, int w, int h, int x, int y)
4401   {
4402     TreePanel tp = null;
4403
4404     try
4405     {
4406       nf.parse();
4407
4408       if (nf.getTree() != null)
4409       {
4410         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4411
4412         tp.setSize(w, h);
4413
4414         if (x > 0 && y > 0)
4415         {
4416           tp.setLocation(x, y);
4417         }
4418
4419         Desktop.addInternalFrame(tp, title, w, h);
4420       }
4421     } catch (Exception ex)
4422     {
4423       ex.printStackTrace();
4424     }
4425
4426     return tp;
4427   }
4428
4429   private boolean buildingMenu = false;
4430
4431   /**
4432    * Generates menu items and listener event actions for web service clients
4433    *
4434    */
4435   public void BuildWebServiceMenu()
4436   {
4437     while (buildingMenu)
4438     {
4439       try
4440       {
4441         System.err.println("Waiting for building menu to finish.");
4442         Thread.sleep(10);
4443       } catch (Exception e)
4444       {
4445       }
4446     }
4447     final AlignFrame me = this;
4448     buildingMenu = true;
4449     new Thread(new Runnable()
4450     {
4451       @Override
4452       public void run()
4453       {
4454         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4455         try
4456         {
4457           // System.err.println("Building ws menu again "
4458           // + Thread.currentThread());
4459           // TODO: add support for context dependent disabling of services based
4460           // on
4461           // alignment and current selection
4462           // TODO: add additional serviceHandle parameter to specify abstract
4463           // handler
4464           // class independently of AbstractName
4465           // TODO: add in rediscovery GUI function to restart discoverer
4466           // TODO: group services by location as well as function and/or
4467           // introduce
4468           // object broker mechanism.
4469           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4470           final IProgressIndicator af = me;
4471           final JMenu msawsmenu = new JMenu("Alignment");
4472           final JMenu secstrmenu = new JMenu(
4473                   "Secondary Structure Prediction");
4474           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4475           final JMenu analymenu = new JMenu("Analysis");
4476           final JMenu dismenu = new JMenu("Protein Disorder");
4477           // final JMenu msawsmenu = new
4478           // JMenu(MessageManager.getString("label.alignment"));
4479           // final JMenu secstrmenu = new
4480           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4481           // final JMenu seqsrchmenu = new
4482           // JMenu(MessageManager.getString("label.sequence_database_search"));
4483           // final JMenu analymenu = new
4484           // JMenu(MessageManager.getString("label.analysis"));
4485           // final JMenu dismenu = new
4486           // JMenu(MessageManager.getString("label.protein_disorder"));
4487           // JAL-940 - only show secondary structure prediction services from
4488           // the legacy server
4489           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4490               // &&
4491           Discoverer.services != null && (Discoverer.services.size() > 0))
4492           {
4493             // TODO: refactor to allow list of AbstractName/Handler bindings to
4494             // be
4495             // stored or retrieved from elsewhere
4496             // No MSAWS used any more:
4497             // Vector msaws = null; // (Vector)
4498             // Discoverer.services.get("MsaWS");
4499             Vector secstrpr = (Vector) Discoverer.services
4500                     .get("SecStrPred");
4501             if (secstrpr != null)
4502             {
4503               // Add any secondary structure prediction services
4504               for (int i = 0, j = secstrpr.size(); i < j; i++)
4505               {
4506                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4507                         .get(i);
4508                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4509                         .getServiceClient(sh);
4510                 int p = secstrmenu.getItemCount();
4511                 impl.attachWSMenuEntry(secstrmenu, me);
4512                 int q = secstrmenu.getItemCount();
4513                 for (int litm = p; litm < q; litm++)
4514                 {
4515                   legacyItems.add(secstrmenu.getItem(litm));
4516                 }
4517               }
4518             }
4519           }
4520
4521           // Add all submenus in the order they should appear on the web
4522           // services menu
4523           wsmenu.add(msawsmenu);
4524           wsmenu.add(secstrmenu);
4525           wsmenu.add(dismenu);
4526           wsmenu.add(analymenu);
4527           // No search services yet
4528           // wsmenu.add(seqsrchmenu);
4529
4530           javax.swing.SwingUtilities.invokeLater(new Runnable()
4531           {
4532             @Override
4533             public void run()
4534             {
4535               try
4536               {
4537                 webService.removeAll();
4538                 // first, add discovered services onto the webservices menu
4539                 if (wsmenu.size() > 0)
4540                 {
4541                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4542                   {
4543                     webService.add(wsmenu.get(i));
4544                   }
4545                 }
4546                 else
4547                 {
4548                   webService.add(me.webServiceNoServices);
4549                 }
4550                 // TODO: move into separate menu builder class.
4551                 boolean new_sspred = false;
4552                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4553                 {
4554                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4555                   if (jws2servs != null)
4556                   {
4557                     if (jws2servs.hasServices())
4558                     {
4559                       jws2servs.attachWSMenuEntry(webService, me);
4560                       for (Jws2Instance sv : jws2servs.getServices())
4561                       {
4562                         if (sv.description.toLowerCase().contains("jpred"))
4563                         {
4564                           for (JMenuItem jmi : legacyItems)
4565                           {
4566                             jmi.setVisible(false);
4567                           }
4568                         }
4569                       }
4570
4571                     }
4572                     if (jws2servs.isRunning())
4573                     {
4574                       JMenuItem tm = new JMenuItem(
4575                               "Still discovering JABA Services");
4576                       tm.setEnabled(false);
4577                       webService.add(tm);
4578                     }
4579                   }
4580                 }
4581                 build_urlServiceMenu(me.webService);
4582                 build_fetchdbmenu(webService);
4583                 for (JMenu item : wsmenu)
4584                 {
4585                   if (item.getItemCount() == 0)
4586                   {
4587                     item.setEnabled(false);
4588                   }
4589                   else
4590                   {
4591                     item.setEnabled(true);
4592                   }
4593                 }
4594               } catch (Exception e)
4595               {
4596                 Cache.log
4597                         .debug("Exception during web service menu building process.",
4598                                 e);
4599               }
4600             }
4601           });
4602         } catch (Exception e)
4603         {
4604         }
4605         buildingMenu = false;
4606       }
4607     }).start();
4608
4609   }
4610
4611   /**
4612    * construct any groupURL type service menu entries.
4613    *
4614    * @param webService
4615    */
4616   private void build_urlServiceMenu(JMenu webService)
4617   {
4618     // TODO: remove this code when 2.7 is released
4619     // DEBUG - alignmentView
4620     /*
4621      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4622      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4623      *
4624      * @Override public void actionPerformed(ActionEvent e) {
4625      * jalview.datamodel.AlignmentView
4626      * .testSelectionViews(af.viewport.getAlignment(),
4627      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4628      *
4629      * }); webService.add(testAlView);
4630      */
4631     // TODO: refactor to RestClient discoverer and merge menu entries for
4632     // rest-style services with other types of analysis/calculation service
4633     // SHmmr test client - still being implemented.
4634     // DEBUG - alignmentView
4635
4636     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4637             .getRestClients())
4638     {
4639       client.attachWSMenuEntry(
4640               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4641               this);
4642     }
4643   }
4644
4645   /*
4646    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4647    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4648    * getProperty("LAST_DIRECTORY"));
4649    *
4650    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4651    * to Vamsas file"); chooser.setToolTipText("Export");
4652    *
4653    * int value = chooser.showSaveDialog(this);
4654    *
4655    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4656    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4657    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4658    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4659    */
4660   /**
4661    * prototype of an automatically enabled/disabled analysis function
4662    *
4663    */
4664   protected void setShowProductsEnabled()
4665   {
4666     SequenceI[] selection = viewport.getSequenceSelection();
4667     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4668             viewport.getAlignment().getDataset()))
4669     {
4670       showProducts.setEnabled(true);
4671
4672     }
4673     else
4674     {
4675       showProducts.setEnabled(false);
4676     }
4677   }
4678
4679   /**
4680    * search selection for sequence xRef products and build the show products
4681    * menu.
4682    *
4683    * @param selection
4684    * @param dataset
4685    * @return true if showProducts menu should be enabled.
4686    */
4687   public boolean canShowProducts(SequenceI[] selection,
4688           boolean isRegionSelection, Alignment dataset)
4689   {
4690     boolean showp = false;
4691     try
4692     {
4693       showProducts.removeAll();
4694       final boolean dna = viewport.getAlignment().isNucleotide();
4695       final Alignment ds = dataset;
4696       String[] ptypes = (selection == null || selection.length == 0) ? null
4697               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4698       // Object[] prods =
4699       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4700       // selection, dataset, true);
4701       final SequenceI[] sel = selection;
4702       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4703       {
4704         showp = true;
4705         final boolean isRegSel = isRegionSelection;
4706         final AlignFrame af = this;
4707         final String source = ptypes[t];
4708         JMenuItem xtype = new JMenuItem(ptypes[t]);
4709         xtype.addActionListener(new ActionListener()
4710         {
4711
4712           @Override
4713           public void actionPerformed(ActionEvent e)
4714           {
4715             // TODO: new thread for this call with vis-delay
4716             af.showProductsFor(af.viewport.getSequenceSelection(),
4717                     isRegSel, dna, source);
4718           }
4719
4720         });
4721         showProducts.add(xtype);
4722       }
4723       showProducts.setVisible(showp);
4724       showProducts.setEnabled(showp);
4725     } catch (Exception e)
4726     {
4727       jalview.bin.Cache.log
4728               .warn("canTranslate threw an exception - please report to help@jalview.org",
4729                       e);
4730       return false;
4731     }
4732     return showp;
4733   }
4734
4735   protected void showProductsFor(final SequenceI[] sel,
4736           final boolean isRegSel, final boolean dna, final String source)
4737   {
4738     Runnable foo = new Runnable()
4739     {
4740
4741       @Override
4742       public void run()
4743       {
4744         final long sttime = System.currentTimeMillis();
4745         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4746                 "status.searching_for_sequences_from",
4747                 new Object[] { source }), sttime);
4748         try
4749         {
4750           // update our local dataset reference
4751           Alignment ds = AlignFrame.this.getViewport().getAlignment()
4752                   .getDataset();
4753           Alignment prods = CrossRef
4754                   .findXrefSequences(sel, dna, source, ds);
4755           if (prods != null)
4756           {
4757             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4758             for (int s = 0; s < sprods.length; s++)
4759             {
4760               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4761               if (ds.getSequences() == null
4762                       || !ds.getSequences().contains(
4763                               sprods[s].getDatasetSequence()))
4764               {
4765                 ds.addSequence(sprods[s].getDatasetSequence());
4766               }
4767               sprods[s].updatePDBIds();
4768             }
4769             Alignment al = new Alignment(sprods);
4770             al.setDataset(ds);
4771
4772             /*
4773              * Copy dna-to-protein mappings to new alignment
4774              */
4775             // TODO 1: no mappings are set up for EMBL product
4776             // TODO 2: if they were, should add them to protein alignment, not
4777             // dna
4778             Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4779             for (AlignedCodonFrame acf : cf)
4780             {
4781               al.addCodonFrame(acf);
4782             }
4783             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4784                     DEFAULT_HEIGHT);
4785             String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4786                     + " for " + ((isRegSel) ? "selected region of " : "")
4787                     + getTitle();
4788             naf.setTitle(newtitle);
4789
4790             // temporary flag until SplitFrame is released
4791             boolean asSplitFrame = Cache.getDefault(
4792                     Preferences.ENABLE_SPLIT_FRAME, true);
4793             if (asSplitFrame)
4794             {
4795               /*
4796                * Make a copy of this alignment (sharing the same dataset
4797                * sequences). If we are DNA, drop introns and update mappings
4798                */
4799               AlignmentI copyAlignment = null;
4800               final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4801                       .getSequenceSelection();
4802               if (dna)
4803               {
4804                 copyAlignment = AlignmentUtils.makeExonAlignment(
4805                         sequenceSelection, cf);
4806                 al.getCodonFrames().clear();
4807                 al.getCodonFrames().addAll(cf);
4808                 final StructureSelectionManager ssm = StructureSelectionManager
4809                         .getStructureSelectionManager(Desktop.instance);
4810                 ssm.registerMappings(cf);
4811               }
4812               else
4813               {
4814                 copyAlignment = new Alignment(new Alignment(
4815                         sequenceSelection));
4816               }
4817               AlignFrame copyThis = new AlignFrame(copyAlignment,
4818                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4819               copyThis.setTitle(AlignFrame.this.getTitle());
4820               // SplitFrame with dna above, protein below
4821               SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4822                       dna ? naf : copyThis);
4823               naf.setVisible(true);
4824               copyThis.setVisible(true);
4825               String linkedTitle = MessageManager
4826                       .getString("label.linked_view_title");
4827               Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4828             }
4829             else
4830             {
4831               Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4832                       DEFAULT_HEIGHT);
4833             }
4834           }
4835           else
4836           {
4837             System.err.println("No Sequences generated for xRef type "
4838                     + source);
4839           }
4840         } catch (Exception e)
4841         {
4842           jalview.bin.Cache.log.error(
4843                   "Exception when finding crossreferences", e);
4844         } catch (OutOfMemoryError e)
4845         {
4846           new OOMWarning("whilst fetching crossreferences", e);
4847         } catch (Error e)
4848         {
4849           jalview.bin.Cache.log.error("Error when finding crossreferences",
4850                   e);
4851         }
4852         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4853                 "status.finished_searching_for_sequences_from",
4854                 new Object[] { source }), sttime);
4855       }
4856
4857     };
4858     Thread frunner = new Thread(foo);
4859     frunner.start();
4860   }
4861
4862   public boolean canShowTranslationProducts(SequenceI[] selection,
4863           AlignmentI alignment)
4864   {
4865     // old way
4866     try
4867     {
4868       return (jalview.analysis.Dna.canTranslate(selection,
4869               viewport.getViewAsVisibleContigs(true)));
4870     } catch (Exception e)
4871     {
4872       jalview.bin.Cache.log
4873               .warn("canTranslate threw an exception - please report to help@jalview.org",
4874                       e);
4875       return false;
4876     }
4877   }
4878
4879   /**
4880    * Construct and display a new frame containing the translation of this
4881    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4882    */
4883   @Override
4884   public void showTranslation_actionPerformed(ActionEvent e)
4885   {
4886     AlignmentI al = null;
4887     try
4888     {
4889       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4890
4891       al = dna.translateCdna();
4892     } catch (Exception ex)
4893     {
4894       jalview.bin.Cache.log.error(
4895               "Exception during translation. Please report this !", ex);
4896       final String msg = MessageManager
4897               .getString("label.error_when_translating_sequences_submit_bug_report");
4898       final String errorTitle = MessageManager
4899               .getString("label.implementation_error")
4900               + MessageManager.getString("translation_failed");
4901       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4902               JOptionPane.ERROR_MESSAGE);
4903       return;
4904     }
4905     if (al == null || al.getHeight() == 0)
4906     {
4907       final String msg = MessageManager
4908               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4909       final String errorTitle = MessageManager
4910               .getString("label.translation_failed");
4911       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4912               JOptionPane.WARNING_MESSAGE);
4913     }
4914     else
4915     {
4916       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4917       af.setFileFormat(this.currentFileFormat);
4918       final String newTitle = MessageManager.formatMessage(
4919               "label.translation_of_params",
4920               new Object[] { this.getTitle() });
4921       af.setTitle(newTitle);
4922       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4923       {
4924         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4925         viewport.openSplitFrame(af, new Alignment(seqs));
4926       }
4927       else
4928       {
4929         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4930                 DEFAULT_HEIGHT);
4931       }
4932     }
4933   }
4934
4935   /**
4936    * Set the file format
4937    *
4938    * @param fileFormat
4939    */
4940   public void setFileFormat(String fileFormat)
4941   {
4942     this.currentFileFormat = fileFormat;
4943   }
4944
4945   /**
4946    * Try to load a features file onto the alignment.
4947    *
4948    * @param file
4949    *          contents or path to retrieve file
4950    * @param type
4951    *          access mode of file (see jalview.io.AlignFile)
4952    * @return true if features file was parsed correctly.
4953    */
4954   public boolean parseFeaturesFile(String file, String type)
4955   {
4956     return avc.parseFeaturesFile(file, type,
4957             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4958
4959   }
4960
4961   @Override
4962   public void refreshFeatureUI(boolean enableIfNecessary)
4963   {
4964     // note - currently this is only still here rather than in the controller
4965     // because of the featureSettings hard reference that is yet to be
4966     // abstracted
4967     if (enableIfNecessary)
4968     {
4969       viewport.setShowSequenceFeatures(true);
4970       showSeqFeatures.setSelected(true);
4971     }
4972
4973   }
4974
4975   @Override
4976   public void dragEnter(DropTargetDragEvent evt)
4977   {
4978   }
4979
4980   @Override
4981   public void dragExit(DropTargetEvent evt)
4982   {
4983   }
4984
4985   @Override
4986   public void dragOver(DropTargetDragEvent evt)
4987   {
4988   }
4989
4990   @Override
4991   public void dropActionChanged(DropTargetDragEvent evt)
4992   {
4993   }
4994
4995   @Override
4996   public void drop(DropTargetDropEvent evt)
4997   {
4998     Transferable t = evt.getTransferable();
4999     java.util.List files = null;
5000
5001     try
5002     {
5003       DataFlavor uriListFlavor = new DataFlavor(
5004               "text/uri-list;class=java.lang.String");
5005       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5006       {
5007         // Works on Windows and MacOSX
5008         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5009         files = (java.util.List) t
5010                 .getTransferData(DataFlavor.javaFileListFlavor);
5011       }
5012       else if (t.isDataFlavorSupported(uriListFlavor))
5013       {
5014         // This is used by Unix drag system
5015         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5016         String data = (String) t.getTransferData(uriListFlavor);
5017         files = new java.util.ArrayList(1);
5018         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5019                 data, "\r\n"); st.hasMoreTokens();)
5020         {
5021           String s = st.nextToken();
5022           if (s.startsWith("#"))
5023           {
5024             // the line is a comment (as per the RFC 2483)
5025             continue;
5026           }
5027
5028           java.net.URI uri = new java.net.URI(s);
5029           // check to see if we can handle this kind of URI
5030           if (uri.getScheme().toLowerCase().startsWith("http"))
5031           {
5032             files.add(uri.toString());
5033           }
5034           else
5035           {
5036             // otherwise preserve old behaviour: catch all for file objects
5037             java.io.File file = new java.io.File(uri);
5038             files.add(file.toString());
5039           }
5040         }
5041       }
5042     } catch (Exception e)
5043     {
5044       e.printStackTrace();
5045     }
5046     if (files != null)
5047     {
5048       try
5049       {
5050         // check to see if any of these files have names matching sequences in
5051         // the alignment
5052         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5053                 .getAlignment().getSequencesArray());
5054         /**
5055          * Object[] { String,SequenceI}
5056          */
5057         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5058         ArrayList<String> filesnotmatched = new ArrayList<String>();
5059         for (int i = 0; i < files.size(); i++)
5060         {
5061           String file = files.get(i).toString();
5062           String pdbfn = "";
5063           String protocol = FormatAdapter.checkProtocol(file);
5064           if (protocol == jalview.io.FormatAdapter.FILE)
5065           {
5066             File fl = new File(file);
5067             pdbfn = fl.getName();
5068           }
5069           else if (protocol == jalview.io.FormatAdapter.URL)
5070           {
5071             URL url = new URL(file);
5072             pdbfn = url.getFile();
5073           }
5074           if (pdbfn.length() > 0)
5075           {
5076             // attempt to find a match in the alignment
5077             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5078             int l = 0, c = pdbfn.indexOf(".");
5079             while (mtch == null && c != -1)
5080             {
5081               do
5082               {
5083                 l = c;
5084               } while ((c = pdbfn.indexOf(".", l)) > l);
5085               if (l > -1)
5086               {
5087                 pdbfn = pdbfn.substring(0, l);
5088               }
5089               mtch = idm.findAllIdMatches(pdbfn);
5090             }
5091             if (mtch != null)
5092             {
5093               String type = null;
5094               try
5095               {
5096                 type = new IdentifyFile().Identify(file, protocol);
5097               } catch (Exception ex)
5098               {
5099                 type = null;
5100               }
5101               if (type != null)
5102               {
5103                 if (type.equalsIgnoreCase("PDB"))
5104                 {
5105                   filesmatched.add(new Object[] { file, protocol, mtch });
5106                   continue;
5107                 }
5108               }
5109             }
5110             // File wasn't named like one of the sequences or wasn't a PDB file.
5111             filesnotmatched.add(file);
5112           }
5113         }
5114         int assocfiles = 0;
5115         if (filesmatched.size() > 0)
5116         {
5117           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5118                   || JOptionPane
5119                           .showConfirmDialog(
5120                                   this,
5121                                   MessageManager
5122                                           .formatMessage(
5123                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5124                                                   new Object[] { Integer
5125                                                           .valueOf(
5126                                                                   filesmatched
5127                                                                           .size())
5128                                                           .toString() }),
5129                                   MessageManager
5130                                           .getString("label.automatically_associate_pdb_files_by_name"),
5131                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5132
5133           {
5134             for (Object[] fm : filesmatched)
5135             {
5136               // try and associate
5137               // TODO: may want to set a standard ID naming formalism for
5138               // associating PDB files which have no IDs.
5139               for (SequenceI toassoc : (SequenceI[]) fm[2])
5140               {
5141                 PDBEntry pe = new AssociatePdbFileWithSeq()
5142                         .associatePdbWithSeq((String) fm[0],
5143                                 (String) fm[1], toassoc, false,
5144                                 Desktop.instance);
5145                 if (pe != null)
5146                 {
5147                   System.err.println("Associated file : "
5148                           + ((String) fm[0]) + " with "
5149                           + toassoc.getDisplayId(true));
5150                   assocfiles++;
5151                 }
5152               }
5153               alignPanel.paintAlignment(true);
5154             }
5155           }
5156         }
5157         if (filesnotmatched.size() > 0)
5158         {
5159           if (assocfiles > 0
5160                   && (Cache.getDefault(
5161                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5162                           .showConfirmDialog(
5163                                   this,
5164                                   "<html>"
5165                                           + MessageManager
5166                                                   .formatMessage(
5167                                                           "label.ignore_unmatched_dropped_files_info",
5168                                                           new Object[] { Integer
5169                                                                   .valueOf(
5170                                                                           filesnotmatched
5171                                                                                   .size())
5172                                                                   .toString() })
5173                                           + "</html>",
5174                                   MessageManager
5175                                           .getString("label.ignore_unmatched_dropped_files"),
5176                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5177           {
5178             return;
5179           }
5180           for (String fn : filesnotmatched)
5181           {
5182             loadJalviewDataFile(fn, null, null, null);
5183           }
5184
5185         }
5186       } catch (Exception ex)
5187       {
5188         ex.printStackTrace();
5189       }
5190     }
5191   }
5192
5193   /**
5194    * Attempt to load a "dropped" file or URL string: First by testing whether
5195    * it's and Annotation file, then a JNet file, and finally a features file. If
5196    * all are false then the user may have dropped an alignment file onto this
5197    * AlignFrame.
5198    *
5199    * @param file
5200    *          either a filename or a URL string.
5201    */
5202   public void loadJalviewDataFile(String file, String protocol,
5203           String format, SequenceI assocSeq)
5204   {
5205     try
5206     {
5207       if (protocol == null)
5208       {
5209         protocol = jalview.io.FormatAdapter.checkProtocol(file);
5210       }
5211       // if the file isn't identified, or not positively identified as some
5212       // other filetype (PFAM is default unidentified alignment file type) then
5213       // try to parse as annotation.
5214       boolean isAnnotation = (format == null || format
5215               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5216               .annotateAlignmentView(viewport, file, protocol) : false;
5217
5218       if (!isAnnotation)
5219       {
5220         // first see if its a T-COFFEE score file
5221         TCoffeeScoreFile tcf = null;
5222         try
5223         {
5224           tcf = new TCoffeeScoreFile(file, protocol);
5225           if (tcf.isValid())
5226           {
5227             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5228             {
5229               tcoffeeColour.setEnabled(true);
5230               tcoffeeColour.setSelected(true);
5231               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5232               isAnnotation = true;
5233               statusBar
5234                       .setText(MessageManager
5235                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5236             }
5237             else
5238             {
5239               // some problem - if no warning its probable that the ID matching
5240               // process didn't work
5241               JOptionPane
5242                       .showMessageDialog(
5243                               Desktop.desktop,
5244                               tcf.getWarningMessage() == null ? MessageManager
5245                                       .getString("label.check_file_matches_sequence_ids_alignment")
5246                                       : tcf.getWarningMessage(),
5247                               MessageManager
5248                                       .getString("label.problem_reading_tcoffee_score_file"),
5249                               JOptionPane.WARNING_MESSAGE);
5250             }
5251           }
5252           else
5253           {
5254             tcf = null;
5255           }
5256         } catch (Exception x)
5257         {
5258           Cache.log
5259                   .debug("Exception when processing data source as T-COFFEE score file",
5260                           x);
5261           tcf = null;
5262         }
5263         if (tcf == null)
5264         {
5265           // try to see if its a JNet 'concise' style annotation file *before*
5266           // we
5267           // try to parse it as a features file
5268           if (format == null)
5269           {
5270             format = new IdentifyFile().Identify(file, protocol);
5271           }
5272           if (format.equalsIgnoreCase("JnetFile"))
5273           {
5274             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5275                     file, protocol);
5276             new JnetAnnotationMaker();
5277             JnetAnnotationMaker.add_annotation(predictions,
5278                     viewport.getAlignment(), 0, false);
5279             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5280             viewport.getAlignment().setSeqrep(repseq);
5281             ColumnSelection cs = new ColumnSelection();
5282             cs.hideInsertionsFor(repseq);
5283             viewport.setColumnSelection(cs);
5284             isAnnotation = true;
5285           }
5286           else
5287           {
5288             /*
5289              * if (format.equalsIgnoreCase("PDB")) {
5290              *
5291              * String pdbfn = ""; // try to match up filename with sequence id
5292              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5293              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5294              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5295              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5296              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5297              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5298              * // attempt to find a match in the alignment SequenceI mtch =
5299              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5300              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5301              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5302              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5303              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5304              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5305              * { System.err.println("Associated file : " + file + " with " +
5306              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5307              * TODO: maybe need to load as normal otherwise return; } }
5308              */
5309             // try to parse it as a features file
5310             boolean isGroupsFile = parseFeaturesFile(file, protocol);
5311             // if it wasn't a features file then we just treat it as a general
5312             // alignment file to load into the current view.
5313             if (!isGroupsFile)
5314             {
5315               new FileLoader().LoadFile(viewport, file, protocol, format);
5316             }
5317             else
5318             {
5319               alignPanel.paintAlignment(true);
5320             }
5321           }
5322         }
5323       }
5324       if (isAnnotation)
5325       {
5326
5327         alignPanel.adjustAnnotationHeight();
5328         viewport.updateSequenceIdColours();
5329         buildSortByAnnotationScoresMenu();
5330         alignPanel.paintAlignment(true);
5331       }
5332     } catch (Exception ex)
5333     {
5334       ex.printStackTrace();
5335     } catch (OutOfMemoryError oom)
5336     {
5337       try
5338       {
5339         System.gc();
5340       } catch (Exception x)
5341       {
5342       }
5343       ;
5344       new OOMWarning(
5345               "loading data "
5346                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5347                               : "using " + protocol + " from " + file)
5348                               : ".")
5349                       + (format != null ? "(parsing as '" + format
5350                               + "' file)" : ""), oom, Desktop.desktop);
5351     }
5352   }
5353
5354   /**
5355    * Method invoked by the ChangeListener on the tabbed pane, in other words
5356    * when a different tabbed pane is selected by the user or programmatically.
5357    */
5358   @Override
5359   public void tabSelectionChanged(int index)
5360   {
5361     if (index > -1)
5362     {
5363       alignPanel = alignPanels.get(index);
5364       viewport = alignPanel.av;
5365       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5366       setMenusFromViewport(viewport);
5367     }
5368
5369     /*
5370      * If there is a frame linked to this one in a SplitPane, switch it to the
5371      * same view tab index. No infinite recursion of calls should happen, since
5372      * tabSelectionChanged() should not get invoked on setting the selected
5373      * index to an unchanged value. Guard against setting an invalid index
5374      * before the new view peer tab has been created.
5375      */
5376     final AlignViewportI peer = viewport.getCodingComplement();
5377     if (peer != null)
5378     {
5379       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5380       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5381       {
5382         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5383       }
5384     }
5385   }
5386
5387   /**
5388    * On right mouse click on view tab, prompt for and set new view name.
5389    */
5390   @Override
5391   public void tabbedPane_mousePressed(MouseEvent e)
5392   {
5393     if (SwingUtilities.isRightMouseButton(e))
5394     {
5395       String msg = MessageManager.getString("label.enter_view_name");
5396       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5397               JOptionPane.QUESTION_MESSAGE);
5398
5399       if (reply != null)
5400       {
5401         viewport.viewName = reply;
5402         // TODO warn if reply is in getExistingViewNames()?
5403         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5404       }
5405     }
5406   }
5407
5408   public AlignViewport getCurrentView()
5409   {
5410     return viewport;
5411   }
5412
5413   /**
5414    * Open the dialog for regex description parsing.
5415    */
5416   @Override
5417   protected void extractScores_actionPerformed(ActionEvent e)
5418   {
5419     ParseProperties pp = new jalview.analysis.ParseProperties(
5420             viewport.getAlignment());
5421     // TODO: verify regex and introduce GUI dialog for version 2.5
5422     // if (pp.getScoresFromDescription("col", "score column ",
5423     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5424     // true)>0)
5425     if (pp.getScoresFromDescription("description column",
5426             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5427     {
5428       buildSortByAnnotationScoresMenu();
5429     }
5430   }
5431
5432   /*
5433    * (non-Javadoc)
5434    *
5435    * @see
5436    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5437    * )
5438    */
5439   @Override
5440   protected void showDbRefs_actionPerformed(ActionEvent e)
5441   {
5442     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5443   }
5444
5445   /*
5446    * (non-Javadoc)
5447    *
5448    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5449    * ActionEvent)
5450    */
5451   @Override
5452   protected void showNpFeats_actionPerformed(ActionEvent e)
5453   {
5454     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5455   }
5456
5457   /**
5458    * find the viewport amongst the tabs in this alignment frame and close that
5459    * tab
5460    *
5461    * @param av
5462    */
5463   public boolean closeView(AlignViewportI av)
5464   {
5465     if (viewport == av)
5466     {
5467       this.closeMenuItem_actionPerformed(false);
5468       return true;
5469     }
5470     Component[] comp = tabbedPane.getComponents();
5471     for (int i = 0; comp != null && i < comp.length; i++)
5472     {
5473       if (comp[i] instanceof AlignmentPanel)
5474       {
5475         if (((AlignmentPanel) comp[i]).av == av)
5476         {
5477           // close the view.
5478           closeView((AlignmentPanel) comp[i]);
5479           return true;
5480         }
5481       }
5482     }
5483     return false;
5484   }
5485
5486   protected void build_fetchdbmenu(JMenu webService)
5487   {
5488     // Temporary hack - DBRef Fetcher always top level ws entry.
5489     // TODO We probably want to store a sequence database checklist in
5490     // preferences and have checkboxes.. rather than individual sources selected
5491     // here
5492     final JMenu rfetch = new JMenu(
5493             MessageManager.getString("action.fetch_db_references"));
5494     rfetch.setToolTipText(MessageManager
5495             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5496     webService.add(rfetch);
5497
5498     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5499             MessageManager.getString("option.trim_retrieved_seqs"));
5500     trimrs.setToolTipText(MessageManager
5501             .getString("label.trim_retrieved_sequences"));
5502     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5503     trimrs.addActionListener(new ActionListener()
5504     {
5505       @Override
5506       public void actionPerformed(ActionEvent e)
5507       {
5508         trimrs.setSelected(trimrs.isSelected());
5509         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5510                 Boolean.valueOf(trimrs.isSelected()).toString());
5511       };
5512     });
5513     rfetch.add(trimrs);
5514     JMenuItem fetchr = new JMenuItem(
5515             MessageManager.getString("label.standard_databases"));
5516     fetchr.setToolTipText(MessageManager
5517             .getString("label.fetch_embl_uniprot"));
5518     fetchr.addActionListener(new ActionListener()
5519     {
5520
5521       @Override
5522       public void actionPerformed(ActionEvent e)
5523       {
5524         new Thread(new Runnable()
5525         {
5526
5527           @Override
5528           public void run()
5529           {
5530             new jalview.ws.DBRefFetcher(alignPanel.av
5531                     .getSequenceSelection(), alignPanel.alignFrame)
5532                     .fetchDBRefs(false);
5533           }
5534         }).start();
5535
5536       }
5537
5538     });
5539     rfetch.add(fetchr);
5540     final AlignFrame me = this;
5541     new Thread(new Runnable()
5542     {
5543       @Override
5544       public void run()
5545       {
5546         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5547                 .getSequenceFetcherSingleton(me);
5548         javax.swing.SwingUtilities.invokeLater(new Runnable()
5549         {
5550           @Override
5551           public void run()
5552           {
5553             String[] dbclasses = sf.getOrderedSupportedSources();
5554             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5555             // jalview.util.QuickSort.sort(otherdb, otherdb);
5556             List<DbSourceProxy> otherdb;
5557             JMenu dfetch = new JMenu();
5558             JMenu ifetch = new JMenu();
5559             JMenuItem fetchr = null;
5560             int comp = 0, icomp = 0, mcomp = 15;
5561             String mname = null;
5562             int dbi = 0;
5563             for (String dbclass : dbclasses)
5564             {
5565               otherdb = sf.getSourceProxy(dbclass);
5566               // add a single entry for this class, or submenu allowing 'fetch
5567               // all' or pick one
5568               if (otherdb == null || otherdb.size() < 1)
5569               {
5570                 continue;
5571               }
5572               // List<DbSourceProxy> dbs=otherdb;
5573               // otherdb=new ArrayList<DbSourceProxy>();
5574               // for (DbSourceProxy db:dbs)
5575               // {
5576               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5577               // }
5578               if (mname == null)
5579               {
5580                 mname = "From " + dbclass;
5581               }
5582               if (otherdb.size() == 1)
5583               {
5584                 final DbSourceProxy[] dassource = otherdb
5585                         .toArray(new DbSourceProxy[0]);
5586                 DbSourceProxy src = otherdb.get(0);
5587                 fetchr = new JMenuItem(src.getDbSource());
5588                 fetchr.addActionListener(new ActionListener()
5589                 {
5590
5591                   @Override
5592                   public void actionPerformed(ActionEvent e)
5593                   {
5594                     new Thread(new Runnable()
5595                     {
5596
5597                       @Override
5598                       public void run()
5599                       {
5600                         new jalview.ws.DBRefFetcher(alignPanel.av
5601                                 .getSequenceSelection(),
5602                                 alignPanel.alignFrame, dassource)
5603                                 .fetchDBRefs(false);
5604                       }
5605                     }).start();
5606                   }
5607
5608                 });
5609                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5610                         MessageManager.formatMessage(
5611                                 "label.fetch_retrieve_from",
5612                                 new Object[] { src.getDbName() })));
5613                 dfetch.add(fetchr);
5614                 comp++;
5615               }
5616               else
5617               {
5618                 final DbSourceProxy[] dassource = otherdb
5619                         .toArray(new DbSourceProxy[0]);
5620                 // fetch all entry
5621                 DbSourceProxy src = otherdb.get(0);
5622                 fetchr = new JMenuItem(MessageManager.formatMessage(
5623                         "label.fetch_all_param",
5624                         new Object[] { src.getDbSource() }));
5625                 fetchr.addActionListener(new ActionListener()
5626                 {
5627                   @Override
5628                   public void actionPerformed(ActionEvent e)
5629                   {
5630                     new Thread(new Runnable()
5631                     {
5632
5633                       @Override
5634                       public void run()
5635                       {
5636                         new jalview.ws.DBRefFetcher(alignPanel.av
5637                                 .getSequenceSelection(),
5638                                 alignPanel.alignFrame, dassource)
5639                                 .fetchDBRefs(false);
5640                       }
5641                     }).start();
5642                   }
5643                 });
5644
5645                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5646                         MessageManager.formatMessage(
5647                                 "label.fetch_retrieve_from_all_sources",
5648                                 new Object[] {
5649                                     Integer.valueOf(otherdb.size())
5650                                             .toString(), src.getDbSource(),
5651                                     src.getDbName() })));
5652                 dfetch.add(fetchr);
5653                 comp++;
5654                 // and then build the rest of the individual menus
5655                 ifetch = new JMenu(MessageManager.formatMessage(
5656                         "label.source_from_db_source",
5657                         new Object[] { src.getDbSource() }));
5658                 icomp = 0;
5659                 String imname = null;
5660                 int i = 0;
5661                 for (DbSourceProxy sproxy : otherdb)
5662                 {
5663                   String dbname = sproxy.getDbName();
5664                   String sname = dbname.length() > 5 ? dbname.substring(0,
5665                           5) + "..." : dbname;
5666                   String msname = dbname.length() > 10 ? dbname.substring(
5667                           0, 10) + "..." : dbname;
5668                   if (imname == null)
5669                   {
5670                     imname = MessageManager.formatMessage(
5671                             "label.from_msname", new Object[] { sname });
5672                   }
5673                   fetchr = new JMenuItem(msname);
5674                   final DbSourceProxy[] dassrc = { sproxy };
5675                   fetchr.addActionListener(new ActionListener()
5676                   {
5677
5678                     @Override
5679                     public void actionPerformed(ActionEvent e)
5680                     {
5681                       new Thread(new Runnable()
5682                       {
5683
5684                         @Override
5685                         public void run()
5686                         {
5687                           new jalview.ws.DBRefFetcher(alignPanel.av
5688                                   .getSequenceSelection(),
5689                                   alignPanel.alignFrame, dassrc)
5690                                   .fetchDBRefs(false);
5691                         }
5692                       }).start();
5693                     }
5694
5695                   });
5696                   fetchr.setToolTipText("<html>"
5697                           + MessageManager.formatMessage(
5698                                   "label.fetch_retrieve_from", new Object[]
5699                                   { dbname }));
5700                   ifetch.add(fetchr);
5701                   ++i;
5702                   if (++icomp >= mcomp || i == (otherdb.size()))
5703                   {
5704                     ifetch.setText(MessageManager.formatMessage(
5705                             "label.source_to_target", imname, sname));
5706                     dfetch.add(ifetch);
5707                     ifetch = new JMenu();
5708                     imname = null;
5709                     icomp = 0;
5710                     comp++;
5711                   }
5712                 }
5713               }
5714               ++dbi;
5715               if (comp >= mcomp || dbi >= (dbclasses.length))
5716               {
5717                 dfetch.setText(MessageManager.formatMessage(
5718                         "label.source_to_target", mname, dbclass));
5719                 rfetch.add(dfetch);
5720                 dfetch = new JMenu();
5721                 mname = null;
5722                 comp = 0;
5723               }
5724             }
5725           }
5726         });
5727       }
5728     }).start();
5729
5730   }
5731
5732   /**
5733    * Left justify the whole alignment.
5734    */
5735   @Override
5736   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5737   {
5738     AlignmentI al = viewport.getAlignment();
5739     al.justify(false);
5740     viewport.firePropertyChange("alignment", null, al);
5741   }
5742
5743   /**
5744    * Right justify the whole alignment.
5745    */
5746   @Override
5747   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5748   {
5749     AlignmentI al = viewport.getAlignment();
5750     al.justify(true);
5751     viewport.firePropertyChange("alignment", null, al);
5752   }
5753
5754   public void setShowSeqFeatures(boolean b)
5755   {
5756     showSeqFeatures.setSelected(b);
5757     viewport.setShowSequenceFeatures(b);
5758   }
5759
5760   /*
5761    * (non-Javadoc)
5762    *
5763    * @see
5764    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5765    * awt.event.ActionEvent)
5766    */
5767   @Override
5768   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5769   {
5770     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5771     alignPanel.paintAlignment(true);
5772   }
5773
5774   /*
5775    * (non-Javadoc)
5776    *
5777    * @see
5778    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5779    * .ActionEvent)
5780    */
5781   @Override
5782   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5783   {
5784     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5785     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5786
5787   }
5788
5789   /*
5790    * (non-Javadoc)
5791    *
5792    * @see
5793    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5794    * .event.ActionEvent)
5795    */
5796   @Override
5797   protected void showGroupConservation_actionPerformed(ActionEvent e)
5798   {
5799     viewport.setShowGroupConservation(showGroupConservation.getState());
5800     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5801   }
5802
5803   /*
5804    * (non-Javadoc)
5805    *
5806    * @see
5807    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5808    * .event.ActionEvent)
5809    */
5810   @Override
5811   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5812   {
5813     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5814     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5815   }
5816
5817   /*
5818    * (non-Javadoc)
5819    *
5820    * @see
5821    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5822    * .event.ActionEvent)
5823    */
5824   @Override
5825   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5826   {
5827     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5828     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5829   }
5830
5831   @Override
5832   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5833   {
5834     showSequenceLogo.setState(true);
5835     viewport.setShowSequenceLogo(true);
5836     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5837     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5838   }
5839
5840   @Override
5841   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5842   {
5843     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5844   }
5845
5846   /*
5847    * (non-Javadoc)
5848    *
5849    * @see
5850    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5851    * .event.ActionEvent)
5852    */
5853   @Override
5854   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5855   {
5856     if (avc.makeGroupsFromSelection())
5857     {
5858       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5859       alignPanel.updateAnnotation();
5860       alignPanel.paintAlignment(true);
5861     }
5862   }
5863
5864   public void clearAlignmentSeqRep()
5865   {
5866     // TODO refactor alignmentseqrep to controller
5867     if (viewport.getAlignment().hasSeqrep())
5868     {
5869       viewport.getAlignment().setSeqrep(null);
5870       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5871       alignPanel.updateAnnotation();
5872       alignPanel.paintAlignment(true);
5873     }
5874   }
5875
5876   @Override
5877   protected void createGroup_actionPerformed(ActionEvent e)
5878   {
5879     if (avc.createGroup())
5880     {
5881       alignPanel.alignmentChanged();
5882     }
5883   }
5884
5885   @Override
5886   protected void unGroup_actionPerformed(ActionEvent e)
5887   {
5888     if (avc.unGroup())
5889     {
5890       alignPanel.alignmentChanged();
5891     }
5892   }
5893
5894   /**
5895    * make the given alignmentPanel the currently selected tab
5896    *
5897    * @param alignmentPanel
5898    */
5899   public void setDisplayedView(AlignmentPanel alignmentPanel)
5900   {
5901     if (!viewport.getSequenceSetId().equals(
5902             alignmentPanel.av.getSequenceSetId()))
5903     {
5904       throw new Error(
5905               MessageManager
5906                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5907     }
5908     if (tabbedPane != null
5909             && tabbedPane.getTabCount() > 0
5910             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5911                     .getSelectedIndex())
5912     {
5913       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5914     }
5915   }
5916
5917   /**
5918    * Action on selection of menu options to Show or Hide annotations.
5919    *
5920    * @param visible
5921    * @param forSequences
5922    *          update sequence-related annotations
5923    * @param forAlignment
5924    *          update non-sequence-related annotations
5925    */
5926   @Override
5927   protected void setAnnotationsVisibility(boolean visible,
5928           boolean forSequences, boolean forAlignment)
5929   {
5930     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5931             .getAlignmentAnnotation())
5932     {
5933       /*
5934        * don't display non-positional annotations on an alignment
5935        */
5936       if (aa.annotations == null)
5937       {
5938         continue;
5939       }
5940       boolean apply = (aa.sequenceRef == null && forAlignment)
5941               || (aa.sequenceRef != null && forSequences);
5942       if (apply)
5943       {
5944         aa.visible = visible;
5945       }
5946     }
5947     alignPanel.validateAnnotationDimensions(true);
5948     alignPanel.alignmentChanged();
5949   }
5950
5951   /**
5952    * Store selected annotation sort order for the view and repaint.
5953    */
5954   @Override
5955   protected void sortAnnotations_actionPerformed()
5956   {
5957     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5958     this.alignPanel.av
5959             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5960     alignPanel.paintAlignment(true);
5961   }
5962
5963   /**
5964    *
5965    * @return alignment panels in this alignment frame
5966    */
5967   public List<? extends AlignmentViewPanel> getAlignPanels()
5968   {
5969     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5970   }
5971
5972   /**
5973    * Open a new alignment window, with the cDNA associated with this (protein)
5974    * alignment, aligned as is the protein.
5975    */
5976   protected void viewAsCdna_actionPerformed()
5977   {
5978     // TODO no longer a menu action - refactor as required
5979     final AlignmentI alignment = getViewport().getAlignment();
5980     Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5981     if (mappings == null)
5982     {
5983       return;
5984     }
5985     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5986     for (SequenceI aaSeq : alignment.getSequences())
5987     {
5988       for (AlignedCodonFrame acf : mappings)
5989       {
5990         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5991         if (dnaSeq != null)
5992         {
5993           /*
5994            * There is a cDNA mapping for this protein sequence - add to new
5995            * alignment. It will share the same dataset sequence as other mapped
5996            * cDNA (no new mappings need to be created).
5997            */
5998           final Sequence newSeq = new Sequence(dnaSeq);
5999           newSeq.setDatasetSequence(dnaSeq);
6000           cdnaSeqs.add(newSeq);
6001         }
6002       }
6003     }
6004     if (cdnaSeqs.size() == 0)
6005     {
6006       // show a warning dialog no mapped cDNA
6007       return;
6008     }
6009     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6010             .size()]));
6011     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6012             AlignFrame.DEFAULT_HEIGHT);
6013     cdna.alignAs(alignment);
6014     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6015             + this.title;
6016     Desktop.addInternalFrame(alignFrame, newtitle,
6017             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6018   }
6019
6020   /**
6021    * Set visibility of dna/protein complement view (available when shown in a
6022    * split frame).
6023    *
6024    * @param show
6025    */
6026   @Override
6027   protected void showComplement_actionPerformed(boolean show)
6028   {
6029     SplitContainerI sf = getSplitViewContainer();
6030     if (sf != null)
6031     {
6032       sf.setComplementVisible(this, show);
6033     }
6034   }
6035 }
6036
6037 class PrintThread extends Thread
6038 {
6039   AlignmentPanel ap;
6040
6041   public PrintThread(AlignmentPanel ap)
6042   {
6043     this.ap = ap;
6044   }
6045
6046   static PageFormat pf;
6047
6048   @Override
6049   public void run()
6050   {
6051     PrinterJob printJob = PrinterJob.getPrinterJob();
6052
6053     if (pf != null)
6054     {
6055       printJob.setPrintable(ap, pf);
6056     }
6057     else
6058     {
6059       printJob.setPrintable(ap);
6060     }
6061
6062     if (printJob.printDialog())
6063     {
6064       try
6065       {
6066         printJob.print();
6067       } catch (Exception PrintException)
6068       {
6069         PrintException.printStackTrace();
6070       }
6071     }
6072   }
6073 }