src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.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.util.MessageManager;
  95 import jalview.viewmodel.AlignmentViewport;
  96 import jalview.ws.DBRefFetcher;
  97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  98 import jalview.ws.jws1.Discoverer;
  99 import jalview.ws.jws2.Jws2Discoverer;
 100 import jalview.ws.jws2.jabaws2.Jws2Instance;
 101 import jalview.ws.seqfetcher.DbSourceProxy;
 102
 103 import java.awt.BorderLayout;
 104 import java.awt.Component;
 105 import java.awt.Rectangle;
 106 import java.awt.Toolkit;
 107 import java.awt.datatransfer.Clipboard;
 108 import java.awt.datatransfer.DataFlavor;
 109 import java.awt.datatransfer.StringSelection;
 110 import java.awt.datatransfer.Transferable;
 111 import java.awt.dnd.DnDConstants;
 112 import java.awt.dnd.DropTargetDragEvent;
 113 import java.awt.dnd.DropTargetDropEvent;
 114 import java.awt.dnd.DropTargetEvent;
 115 import java.awt.dnd.DropTargetListener;
 116 import java.awt.event.ActionEvent;
 117 import java.awt.event.ActionListener;
 118 import java.awt.event.FocusAdapter;
 119 import java.awt.event.FocusEvent;
 120 import java.awt.event.ItemEvent;
 121 import java.awt.event.ItemListener;
 122 import java.awt.event.KeyAdapter;
 123 import java.awt.event.KeyEvent;
 124 import java.awt.event.MouseAdapter;
 125 import java.awt.event.MouseEvent;
 126 import java.awt.print.PageFormat;
 127 import java.awt.print.PrinterJob;
 128 import java.beans.PropertyChangeEvent;
 129 import java.io.File;
 130 import java.net.URL;
 131 import java.util.ArrayList;
 132 import java.util.Arrays;
 133 import java.util.Deque;
 134 import java.util.Enumeration;
 135 import java.util.Hashtable;
 136 import java.util.List;
 137 import java.util.Vector;
 138
 139 import javax.swing.JCheckBoxMenuItem;
 140 import javax.swing.JEditorPane;
 141 import javax.swing.JInternalFrame;
 142 import javax.swing.JLayeredPane;
 143 import javax.swing.JMenu;
 144 import javax.swing.JMenuItem;
 145 import javax.swing.JOptionPane;
 146 import javax.swing.JRadioButtonMenuItem;
 147 import javax.swing.JScrollPane;
 148 import javax.swing.SwingUtilities;
 149
 150 /**
 151  * DOCUMENT ME!
 152  *
 153  * @author $author$
 154  * @version $Revision$
 155  */
 156 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 157         IProgressIndicator, AlignViewControllerGuiI
 158 {
 159
 160   public static final int DEFAULT_WIDTH = 700;
 161
 162   public static final int DEFAULT_HEIGHT = 500;
 163
 164   /*
 165    * The currently displayed panel (selected tabbed view if more than one)
 166    */
 167   public AlignmentPanel alignPanel;
 168
 169   AlignViewport viewport;
 170
 171   public AlignViewControllerI avc;
 172
 173   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 174
 175   /**
 176    * Last format used to load or save alignments in this window
 177    */
 178   String currentFileFormat = null;
 179
 180   /**
 181    * Current filename for this alignment
 182    */
 183   String fileName = null;
 184
 185   /**
 186    * Creates a new AlignFrame object with specific width and height.
 187    *
 188    * @param al
 189    * @param width
 190    * @param height
 191    */
 192   public AlignFrame(AlignmentI al, int width, int height)
 193   {
 194     this(al, null, width, height);
 195   }
 196
 197   /**
 198    * Creates a new AlignFrame object with specific width, height and
 199    * sequenceSetId
 200    *
 201    * @param al
 202    * @param width
 203    * @param height
 204    * @param sequenceSetId
 205    */
 206   public AlignFrame(AlignmentI al, int width, int height,
 207           String sequenceSetId)
 208   {
 209     this(al, null, width, height, sequenceSetId);
 210   }
 211
 212   /**
 213    * Creates a new AlignFrame object with specific width, height and
 214    * sequenceSetId
 215    *
 216    * @param al
 217    * @param width
 218    * @param height
 219    * @param sequenceSetId
 220    * @param viewId
 221    */
 222   public AlignFrame(AlignmentI al, int width, int height,
 223           String sequenceSetId, String viewId)
 224   {
 225     this(al, null, width, height, sequenceSetId, viewId);
 226   }
 227
 228   /**
 229    * new alignment window with hidden columns
 230    *
 231    * @param al
 232    *          AlignmentI
 233    * @param hiddenColumns
 234    *          ColumnSelection or null
 235    * @param width
 236    *          Width of alignment frame
 237    * @param height
 238    *          height of frame.
 239    */
 240   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 241           int width, int height)
 242   {
 243     this(al, hiddenColumns, width, height, null);
 244   }
 245
 246   /**
 247    * Create alignment frame for al with hiddenColumns, a specific width and
 248    * height, and specific sequenceId
 249    *
 250    * @param al
 251    * @param hiddenColumns
 252    * @param width
 253    * @param height
 254    * @param sequenceSetId
 255    *          (may be null)
 256    */
 257   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 258           int width, int height, String sequenceSetId)
 259   {
 260     this(al, hiddenColumns, width, height, sequenceSetId, null);
 261   }
 262
 263   /**
 264    * Create alignment frame for al with hiddenColumns, a specific width and
 265    * height, and specific sequenceId
 266    *
 267    * @param al
 268    * @param hiddenColumns
 269    * @param width
 270    * @param height
 271    * @param sequenceSetId
 272    *          (may be null)
 273    * @param viewId
 274    *          (may be null)
 275    */
 276   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 277           int width, int height, String sequenceSetId, String viewId)
 278   {
 279     setSize(width, height);
 280
 281     if (al.getDataset() == null)
 282     {
 283       al.setDataset(null);
 284     }
 285
 286     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 287
 288     alignPanel = new AlignmentPanel(this, viewport);
 289
 290     addAlignmentPanel(alignPanel, true);
 291     init();
 292   }
 293
 294   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 295           ColumnSelection hiddenColumns, int width, int height)
 296   {
 297     setSize(width, height);
 298
 299     if (al.getDataset() == null)
 300     {
 301       al.setDataset(null);
 302     }
 303
 304     viewport = new AlignViewport(al, hiddenColumns);
 305
 306     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 307     {
 308       viewport.hideSequence(hiddenSeqs);
 309     }
 310     alignPanel = new AlignmentPanel(this, viewport);
 311     addAlignmentPanel(alignPanel, true);
 312     init();
 313   }
 314
 315   /**
 316    * Make a new AlignFrame from existing alignmentPanels
 317    *
 318    * @param ap
 319    *          AlignmentPanel
 320    * @param av
 321    *          AlignViewport
 322    */
 323   public AlignFrame(AlignmentPanel ap)
 324   {
 325     viewport = ap.av;
 326     alignPanel = ap;
 327     addAlignmentPanel(ap, false);
 328     init();
 329   }
 330
 331   /**
 332    * initalise the alignframe from the underlying viewport data and the
 333    * configurations
 334    */
 335   void init()
 336   {
 337     if (!Jalview.isHeadlessMode())
 338     {
 339       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 340     }
 341
 342     avc = new jalview.controller.AlignViewController(this, viewport,
 343             alignPanel);
 344     if (viewport.getAlignmentConservationAnnotation() == null)
 345     {
 346       BLOSUM62Colour.setEnabled(false);
 347       conservationMenuItem.setEnabled(false);
 348       modifyConservation.setEnabled(false);
 349       // PIDColour.setEnabled(false);
 350       // abovePIDThreshold.setEnabled(false);
 351       // modifyPID.setEnabled(false);
 352     }
 353
 354     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 355             "No sort");
 356
 357     if (sortby.equals("Id"))
 358     {
 359       sortIDMenuItem_actionPerformed(null);
 360     }
 361     else if (sortby.equals("Pairwise Identity"))
 362     {
 363       sortPairwiseMenuItem_actionPerformed(null);
 364     }
 365
 366     if (Desktop.desktop != null)
 367     {
 368       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 369       addServiceListeners();
 370       setGUINucleotide(viewport.getAlignment().isNucleotide());
 371     }
 372
 373     this.alignPanel.av
 374             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 375
 376     setMenusFromViewport(viewport);
 377     buildSortByAnnotationScoresMenu();
 378     buildTreeMenu();
 379
 380     if (viewport.getWrapAlignment())
 381     {
 382       wrapMenuItem_actionPerformed(null);
 383     }
 384
 385     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 386     {
 387       this.overviewMenuItem_actionPerformed(null);
 388     }
 389
 390     addKeyListener();
 391
 392     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 393     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 394     final String menuLabel = MessageManager
 395             .getString("label.copy_format_from");
 396     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 397             new ViewSetProvider()
 398             {
 399
 400               @Override
 401               public AlignmentPanel[] getAllAlignmentPanels()
 402               {
 403                 origview.clear();
 404                 origview.add(alignPanel);
 405                 // make an array of all alignment panels except for this one
 406                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 407                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 408                 aps.remove(AlignFrame.this.alignPanel);
 409                 return aps.toArray(new AlignmentPanel[aps.size()]);
 410               }
 411             }, selviews, new ItemListener()
 412             {
 413
 414               @Override
 415               public void itemStateChanged(ItemEvent e)
 416               {
 417                 if (origview.size() > 0)
 418                 {
 419                   final AlignmentPanel ap = origview.get(0);
 420
 421                   /*
 422                    * Copy the ViewStyle of the selected panel to 'this one'.
 423                    * Don't change value of 'scaleProteinAsCdna' unless copying
 424                    * from a SplitFrame.
 425                    */
 426                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 427                           .getViewStyle();
 428                   boolean fromSplitFrame = selviews.get(0)
 429                           .getAlignViewport().getCodingComplement() != null;
 430                   if (!fromSplitFrame)
 431                   {
 432                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 433                             .getViewStyle().isScaleProteinAsCdna());
 434                   }
 435                   ap.getAlignViewport().setViewStyle(vs);
 436
 437                   /*
 438                    * Also rescale ViewStyle of SplitFrame complement if there is
 439                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 440                    * the whole ViewStyle (allow cDNA protein to have different
 441                    * fonts)
 442                    */
 443                   AlignViewportI complement = ap.getAlignViewport()
 444                           .getCodingComplement();
 445                   if (complement != null && vs.isScaleProteinAsCdna())
 446                   {
 447                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 448                     ((SplitFrame) af.getSplitViewContainer())
 449                             .adjustLayout();
 450                     af.setMenusForViewport();
 451                   }
 452
 453                   ap.updateLayout();
 454                   ap.setSelected(true);
 455                   ap.alignFrame.setMenusForViewport();
 456
 457                 }
 458               }
 459             });
 460     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 461             .indexOf("devel") > -1
 462             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 463                     .indexOf("test") > -1)
 464     {
 465       formatMenu.add(vsel);
 466     }
 467     addFocusListener(new FocusAdapter()
 468     {
 469       @Override
 470       public void focusGained(FocusEvent e)
 471       {
 472         Jalview.setCurrentAlignFrame(AlignFrame.this);
 473       }
 474     });
 475
 476   }
 477
 478   /**
 479    * Change the filename and format for the alignment, and enable the 'reload'
 480    * button functionality.
 481    *
 482    * @param file
 483    *          valid filename
 484    * @param format
 485    *          format of file
 486    */
 487   public void setFileName(String file, String format)
 488   {
 489     fileName = file;
 490     setFileFormat(format);
 491     reload.setEnabled(true);
 492   }
 493
 494   /**
 495    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 496    * events
 497    */
 498   void addKeyListener()
 499   {
 500     addKeyListener(new KeyAdapter()
 501     {
 502       @Override
 503       public void keyPressed(KeyEvent evt)
 504       {
 505         if (viewport.cursorMode
 506                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 507                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 508                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 509                 && Character.isDigit(evt.getKeyChar()))
 510         {
 511           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 512         }
 513
 514         switch (evt.getKeyCode())
 515         {
 516
 517         case 27: // escape key
 518           deselectAllSequenceMenuItem_actionPerformed(null);
 519
 520           break;
 521
 522         case KeyEvent.VK_DOWN:
 523           if (evt.isAltDown() || !viewport.cursorMode)
 524           {
 525             moveSelectedSequences(false);
 526           }
 527           if (viewport.cursorMode)
 528           {
 529             alignPanel.getSeqPanel().moveCursor(0, 1);
 530           }
 531           break;
 532
 533         case KeyEvent.VK_UP:
 534           if (evt.isAltDown() || !viewport.cursorMode)
 535           {
 536             moveSelectedSequences(true);
 537           }
 538           if (viewport.cursorMode)
 539           {
 540             alignPanel.getSeqPanel().moveCursor(0, -1);
 541           }
 542
 543           break;
 544
 545         case KeyEvent.VK_LEFT:
 546           if (evt.isAltDown() || !viewport.cursorMode)
 547           {
 548             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 549           }
 550           else
 551           {
 552             alignPanel.getSeqPanel().moveCursor(-1, 0);
 553           }
 554
 555           break;
 556
 557         case KeyEvent.VK_RIGHT:
 558           if (evt.isAltDown() || !viewport.cursorMode)
 559           {
 560             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 561           }
 562           else
 563           {
 564             alignPanel.getSeqPanel().moveCursor(1, 0);
 565           }
 566           break;
 567
 568         case KeyEvent.VK_SPACE:
 569           if (viewport.cursorMode)
 570           {
 571             alignPanel.getSeqPanel().insertGapAtCursor(
 572                     evt.isControlDown() || evt.isShiftDown()
 573                             || evt.isAltDown());
 574           }
 575           break;
 576
 577         // case KeyEvent.VK_A:
 578         // if (viewport.cursorMode)
 579         // {
 580         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 581         // //System.out.println("A");
 582         // }
 583         // break;
 584         /*
 585          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 586          * System.out.println("closing bracket"); } break;
 587          */
 588         case KeyEvent.VK_DELETE:
 589         case KeyEvent.VK_BACK_SPACE:
 590           if (!viewport.cursorMode)
 591           {
 592             cut_actionPerformed(null);
 593           }
 594           else
 595           {
 596             alignPanel.getSeqPanel().deleteGapAtCursor(
 597                     evt.isControlDown() || evt.isShiftDown()
 598                             || evt.isAltDown());
 599           }
 600
 601           break;
 602
 603         case KeyEvent.VK_S:
 604           if (viewport.cursorMode)
 605           {
 606             alignPanel.getSeqPanel().setCursorRow();
 607           }
 608           break;
 609         case KeyEvent.VK_C:
 610           if (viewport.cursorMode && !evt.isControlDown())
 611           {
 612             alignPanel.getSeqPanel().setCursorColumn();
 613           }
 614           break;
 615         case KeyEvent.VK_P:
 616           if (viewport.cursorMode)
 617           {
 618             alignPanel.getSeqPanel().setCursorPosition();
 619           }
 620           break;
 621
 622         case KeyEvent.VK_ENTER:
 623         case KeyEvent.VK_COMMA:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setCursorRowAndColumn();
 627           }
 628           break;
 629
 630         case KeyEvent.VK_Q:
 631           if (viewport.cursorMode)
 632           {
 633             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 634           }
 635           break;
 636         case KeyEvent.VK_M:
 637           if (viewport.cursorMode)
 638           {
 639             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 640           }
 641           break;
 642
 643         case KeyEvent.VK_F2:
 644           viewport.cursorMode = !viewport.cursorMode;
 645           statusBar.setText(MessageManager.formatMessage(
 646                   "label.keyboard_editing_mode",
 647                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 648           if (viewport.cursorMode)
 649           {
 650             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 651             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 652           }
 653           alignPanel.getSeqPanel().seqCanvas.repaint();
 654           break;
 655
 656         case KeyEvent.VK_F1:
 657           try
 658           {
 659             Help.showHelpWindow();
 660           } catch (Exception ex)
 661           {
 662             ex.printStackTrace();
 663           }
 664           break;
 665         case KeyEvent.VK_H:
 666         {
 667           boolean toggleSeqs = !evt.isControlDown();
 668           boolean toggleCols = !evt.isShiftDown();
 669           toggleHiddenRegions(toggleSeqs, toggleCols);
 670           break;
 671         }
 672         case KeyEvent.VK_PAGE_UP:
 673           if (viewport.getWrapAlignment())
 674           {
 675             alignPanel.scrollUp(true);
 676           }
 677           else
 678           {
 679             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 680                     - viewport.endSeq + viewport.startSeq);
 681           }
 682           break;
 683         case KeyEvent.VK_PAGE_DOWN:
 684           if (viewport.getWrapAlignment())
 685           {
 686             alignPanel.scrollUp(false);
 687           }
 688           else
 689           {
 690             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 691                     + viewport.endSeq - viewport.startSeq);
 692           }
 693           break;
 694         }
 695       }
 696
 697       @Override
 698       public void keyReleased(KeyEvent evt)
 699       {
 700         switch (evt.getKeyCode())
 701         {
 702         case KeyEvent.VK_LEFT:
 703           if (evt.isAltDown() || !viewport.cursorMode)
 704           {
 705             viewport.firePropertyChange("alignment", null, viewport
 706                     .getAlignment().getSequences());
 707           }
 708           break;
 709
 710         case KeyEvent.VK_RIGHT:
 711           if (evt.isAltDown() || !viewport.cursorMode)
 712           {
 713             viewport.firePropertyChange("alignment", null, viewport
 714                     .getAlignment().getSequences());
 715           }
 716           break;
 717         }
 718       }
 719     });
 720   }
 721
 722   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 723   {
 724     ap.alignFrame = this;
 725     avc = new jalview.controller.AlignViewController(this, viewport,
 726             alignPanel);
 727
 728     alignPanels.add(ap);
 729
 730     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 731
 732     int aSize = alignPanels.size();
 733
 734     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 735
 736     if (aSize == 1 && ap.av.viewName == null)
 737     {
 738       this.getContentPane().add(ap, BorderLayout.CENTER);
 739     }
 740     else
 741     {
 742       if (aSize == 2)
 743       {
 744         setInitialTabVisible();
 745       }
 746
 747       expandViews.setEnabled(true);
 748       gatherViews.setEnabled(true);
 749       tabbedPane.addTab(ap.av.viewName, ap);
 750
 751       ap.setVisible(false);
 752     }
 753
 754     if (newPanel)
 755     {
 756       if (ap.av.isPadGaps())
 757       {
 758         ap.av.getAlignment().padGaps();
 759       }
 760       ap.av.updateConservation(ap);
 761       ap.av.updateConsensus(ap);
 762       ap.av.updateStrucConsensus(ap);
 763     }
 764   }
 765
 766   public void setInitialTabVisible()
 767   {
 768     expandViews.setEnabled(true);
 769     gatherViews.setEnabled(true);
 770     tabbedPane.setVisible(true);
 771     AlignmentPanel first = alignPanels.get(0);
 772     tabbedPane.addTab(first.av.viewName, first);
 773     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 774   }
 775
 776   public AlignViewport getViewport()
 777   {
 778     return viewport;
 779   }
 780
 781   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 782   private void addServiceListeners()
 783   {
 784     final java.beans.PropertyChangeListener thisListener;
 785     Desktop.instance.addJalviewPropertyChangeListener("services",
 786             thisListener = new java.beans.PropertyChangeListener()
 787             {
 788               @Override
 789               public void propertyChange(PropertyChangeEvent evt)
 790               {
 791                 // // System.out.println("Discoverer property change.");
 792                 // if (evt.getPropertyName().equals("services"))
 793                 {
 794                   SwingUtilities.invokeLater(new Runnable()
 795                   {
 796
 797                     @Override
 798                     public void run()
 799                     {
 800                       System.err
 801                               .println("Rebuild WS Menu for service change");
 802                       BuildWebServiceMenu();
 803                     }
 804
 805                   });
 806                 }
 807               }
 808             });
 809     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 810     {
 811       @Override
 812       public void internalFrameClosed(
 813               javax.swing.event.InternalFrameEvent evt)
 814       {
 815         // System.out.println("deregistering discoverer listener");
 816         Desktop.instance.removeJalviewPropertyChangeListener("services",
 817                 thisListener);
 818         closeMenuItem_actionPerformed(true);
 819       };
 820     });
 821     // Finally, build the menu once to get current service state
 822     new Thread(new Runnable()
 823     {
 824       @Override
 825       public void run()
 826       {
 827         BuildWebServiceMenu();
 828       }
 829     }).start();
 830   }
 831
 832   /**
 833    * Configure menu items that vary according to whether the alignment is
 834    * nucleotide or protein
 835    *
 836    * @param nucleotide
 837    */
 838   public void setGUINucleotide(boolean nucleotide)
 839   {
 840     showTranslation.setVisible(nucleotide);
 841     showReverse.setVisible(nucleotide);
 842     showReverseComplement.setVisible(nucleotide);
 843     conservationMenuItem.setEnabled(!nucleotide);
 844     modifyConservation.setEnabled(!nucleotide);
 845     showGroupConservation.setEnabled(!nucleotide);
 846     rnahelicesColour.setEnabled(nucleotide);
 847     purinePyrimidineColour.setEnabled(nucleotide);
 848     showComplementMenuItem.setText(nucleotide ? MessageManager
 849             .getString("label.protein") : MessageManager
 850             .getString("label.nucleotide"));
 851     setColourSelected(jalview.bin.Cache.getDefault(
 852             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 853                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 854   }
 855
 856   /**
 857    * set up menus for the current viewport. This may be called after any
 858    * operation that affects the data in the current view (selection changed,
 859    * etc) to update the menus to reflect the new state.
 860    */
 861   @Override
 862   public void setMenusForViewport()
 863   {
 864     setMenusFromViewport(viewport);
 865   }
 866
 867   /**
 868    * Need to call this method when tabs are selected for multiple views, or when
 869    * loading from Jalview2XML.java
 870    *
 871    * @param av
 872    *          AlignViewport
 873    */
 874   void setMenusFromViewport(AlignViewport av)
 875   {
 876     padGapsMenuitem.setSelected(av.isPadGaps());
 877     colourTextMenuItem.setSelected(av.isShowColourText());
 878     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 879     conservationMenuItem.setSelected(av.getConservationSelected());
 880     seqLimits.setSelected(av.getShowJVSuffix());
 881     idRightAlign.setSelected(av.isRightAlignIds());
 882     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 883     renderGapsMenuItem.setSelected(av.isRenderGaps());
 884     wrapMenuItem.setSelected(av.getWrapAlignment());
 885     scaleAbove.setVisible(av.getWrapAlignment());
 886     scaleLeft.setVisible(av.getWrapAlignment());
 887     scaleRight.setVisible(av.getWrapAlignment());
 888     annotationPanelMenuItem.setState(av.isShowAnnotation());
 889     /*
 890      * Show/hide annotations only enabled if annotation panel is shown
 891      */
 892     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 893     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 894     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 895     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 897     viewTextMenuItem.setSelected(av.getShowText());
 898     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 899     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 900     showGroupConservation.setSelected(av.isShowGroupConservation());
 901     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 902     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 903     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 904
 905     setColourSelected(ColourSchemeProperty.getColourName(av
 906             .getGlobalColourScheme()));
 907
 908     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 909     hiddenMarkers.setState(av.getShowHiddenMarkers());
 910     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 911     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 912     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 913     autoCalculate.setSelected(av.autoCalculateConsensus);
 914     sortByTree.setSelected(av.sortByTree);
 915     listenToViewSelections.setSelected(av.followSelection);
 916     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 917     rnahelicesColour
 918             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 919
 920     showProducts.setEnabled(canShowProducts());
 921     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 922
 923     updateEditMenuBar();
 924   }
 925
 926   /**
 927    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 928    *
 929    * @param b
 930    */
 931   public void setGroovyEnabled(boolean b)
 932   {
 933     runGroovy.setEnabled(b);
 934   }
 935
 936   private IProgressIndicator progressBar;
 937
 938   /*
 939    * (non-Javadoc)
 940    *
 941    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 942    */
 943   @Override
 944   public void setProgressBar(String message, long id)
 945   {
 946     progressBar.setProgressBar(message, id);
 947   }
 948
 949   @Override
 950   public void registerHandler(final long id,
 951           final IProgressIndicatorHandler handler)
 952   {
 953     progressBar.registerHandler(id, handler);
 954   }
 955
 956   /**
 957    *
 958    * @return true if any progress bars are still active
 959    */
 960   @Override
 961   public boolean operationInProgress()
 962   {
 963     return progressBar.operationInProgress();
 964   }
 965
 966   @Override
 967   public void setStatus(String text)
 968   {
 969     statusBar.setText(text);
 970   }
 971
 972   /*
 973    * Added so Castor Mapping file can obtain Jalview Version
 974    */
 975   public String getVersion()
 976   {
 977     return jalview.bin.Cache.getProperty("VERSION");
 978   }
 979
 980   public FeatureRenderer getFeatureRenderer()
 981   {
 982     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 983   }
 984
 985   @Override
 986   public void fetchSequence_actionPerformed(ActionEvent e)
 987   {
 988     new jalview.gui.SequenceFetcher(this);
 989   }
 990
 991   @Override
 992   public void addFromFile_actionPerformed(ActionEvent e)
 993   {
 994     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 995   }
 996
 997   @Override
 998   public void reload_actionPerformed(ActionEvent e)
 999   {
1000     if (fileName != null)
1001     {
1002       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003       // originating file's format
1004       // TODO: work out how to recover feature settings for correct view(s) when
1005       // file is reloaded.
1006       if (currentFileFormat.equals("Jalview"))
1007       {
1008         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009         for (int i = 0; i < frames.length; i++)
1010         {
1011           if (frames[i] instanceof AlignFrame && frames[i] != this
1012                   && ((AlignFrame) frames[i]).fileName != null
1013                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1014           {
1015             try
1016             {
1017               frames[i].setSelected(true);
1018               Desktop.instance.closeAssociatedWindows();
1019             } catch (java.beans.PropertyVetoException ex)
1020             {
1021             }
1022           }
1023
1024         }
1025         Desktop.instance.closeAssociatedWindows();
1026
1027         FileLoader loader = new FileLoader();
1028         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1029         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1030       }
1031       else
1032       {
1033         Rectangle bounds = this.getBounds();
1034
1035         FileLoader loader = new FileLoader();
1036         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1037         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1038                 protocol, currentFileFormat);
1039
1040         newframe.setBounds(bounds);
1041         if (featureSettings != null && featureSettings.isShowing())
1042         {
1043           final Rectangle fspos = featureSettings.frame.getBounds();
1044           // TODO: need a 'show feature settings' function that takes bounds -
1045           // need to refactor Desktop.addFrame
1046           newframe.featureSettings_actionPerformed(null);
1047           final FeatureSettings nfs = newframe.featureSettings;
1048           SwingUtilities.invokeLater(new Runnable()
1049           {
1050             @Override
1051             public void run()
1052             {
1053               nfs.frame.setBounds(fspos);
1054             }
1055           });
1056           this.featureSettings.close();
1057           this.featureSettings = null;
1058         }
1059         this.closeMenuItem_actionPerformed(true);
1060       }
1061     }
1062   }
1063
1064   @Override
1065   public void addFromText_actionPerformed(ActionEvent e)
1066   {
1067     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1068             .getAlignPanel());
1069   }
1070
1071   @Override
1072   public void addFromURL_actionPerformed(ActionEvent e)
1073   {
1074     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1075   }
1076
1077   @Override
1078   public void save_actionPerformed(ActionEvent e)
1079   {
1080     if (fileName == null
1081             || (currentFileFormat == null || !jalview.io.FormatAdapter
1082                     .isValidIOFormat(currentFileFormat, true))
1083             || fileName.startsWith("http"))
1084     {
1085       saveAs_actionPerformed(null);
1086     }
1087     else
1088     {
1089       saveAlignment(fileName, currentFileFormat);
1090     }
1091   }
1092
1093   /**
1094    * DOCUMENT ME!
1095    *
1096    * @param e
1097    *          DOCUMENT ME!
1098    */
1099   @Override
1100   public void saveAs_actionPerformed(ActionEvent e)
1101   {
1102     JalviewFileChooser chooser = new JalviewFileChooser(
1103             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1104             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1105             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1106             currentFileFormat, false);
1107
1108     chooser.setFileView(new JalviewFileView());
1109     chooser.setDialogTitle(MessageManager
1110             .getString("label.save_alignment_to_file"));
1111     chooser.setToolTipText(MessageManager.getString("action.save"));
1112
1113     int value = chooser.showSaveDialog(this);
1114
1115     if (value == JalviewFileChooser.APPROVE_OPTION)
1116     {
1117       currentFileFormat = chooser.getSelectedFormat();
1118       while (currentFileFormat == null)
1119       {
1120         JOptionPane
1121                 .showInternalMessageDialog(
1122                         Desktop.desktop,
1123                         MessageManager
1124                                 .getString("label.select_file_format_before_saving"),
1125                         MessageManager
1126                                 .getString("label.file_format_not_specified"),
1127                         JOptionPane.WARNING_MESSAGE);
1128         currentFileFormat = chooser.getSelectedFormat();
1129         value = chooser.showSaveDialog(this);
1130         if (value != JalviewFileChooser.APPROVE_OPTION)
1131         {
1132           return;
1133         }
1134       }
1135
1136       fileName = chooser.getSelectedFile().getPath();
1137
1138       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1139               currentFileFormat);
1140
1141       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1142       if (currentFileFormat.indexOf(" ") > -1)
1143       {
1144         currentFileFormat = currentFileFormat.substring(0,
1145                 currentFileFormat.indexOf(" "));
1146       }
1147       saveAlignment(fileName, currentFileFormat);
1148     }
1149   }
1150
1151   public boolean saveAlignment(String file, String format)
1152   {
1153     boolean success = true;
1154
1155     if (format.equalsIgnoreCase("Jalview"))
1156     {
1157       String shortName = title;
1158
1159       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1160       {
1161         shortName = shortName.substring(shortName
1162                 .lastIndexOf(java.io.File.separatorChar) + 1);
1163       }
1164
1165       success = new Jalview2XML().saveAlignment(this, file, shortName);
1166
1167       statusBar.setText(MessageManager.formatMessage(
1168               "label.successfully_saved_to_file_in_format", new Object[] {
1169                   fileName, format }));
1170
1171     }
1172     else
1173     {
1174       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1175       {
1176         warningMessage("Cannot save file " + fileName + " using format "
1177                 + format, "Alignment output format not supported");
1178         if (!Jalview.isHeadlessMode())
1179         {
1180           saveAs_actionPerformed(null);
1181         }
1182         return false;
1183       }
1184
1185       AlignmentExportData exportData = getAlignmentForExport(format,
1186               viewport, null);
1187       if (exportData.getSettings().isCancelled())
1188       {
1189         return false;
1190       }
1191       FormatAdapter f = new FormatAdapter(alignPanel,
1192               exportData.getSettings());
1193       String output = f.formatSequences(
1194               format,
1195               exportData.getAlignment(), // class cast exceptions will
1196               // occur in the distant future
1197               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1198               f.getCacheSuffixDefault(format),
1199               viewport.getColumnSelection());
1200
1201       if (output == null)
1202       {
1203         success = false;
1204       }
1205       else
1206       {
1207         try
1208         {
1209           java.io.PrintWriter out = new java.io.PrintWriter(
1210                   new java.io.FileWriter(file));
1211
1212           out.print(output);
1213           out.close();
1214           this.setTitle(file);
1215           statusBar.setText(MessageManager.formatMessage(
1216                   "label.successfully_saved_to_file_in_format",
1217                   new Object[] { fileName, format }));
1218         } catch (Exception ex)
1219         {
1220           success = false;
1221           ex.printStackTrace();
1222         }
1223       }
1224     }
1225
1226     if (!success)
1227     {
1228       JOptionPane.showInternalMessageDialog(this, MessageManager
1229               .formatMessage("label.couldnt_save_file",
1230                       new Object[] { fileName }), MessageManager
1231               .getString("label.error_saving_file"),
1232               JOptionPane.WARNING_MESSAGE);
1233     }
1234
1235     return success;
1236   }
1237
1238   private void warningMessage(String warning, String title)
1239   {
1240     if (new jalview.util.Platform().isHeadless())
1241     {
1242       System.err.println("Warning: " + title + "\nWarning: " + warning);
1243
1244     }
1245     else
1246     {
1247       JOptionPane.showInternalMessageDialog(this, warning, title,
1248               JOptionPane.WARNING_MESSAGE);
1249     }
1250     return;
1251   }
1252
1253   /**
1254    * DOCUMENT ME!
1255    *
1256    * @param e
1257    *          DOCUMENT ME!
1258    */
1259   @Override
1260   protected void outputText_actionPerformed(ActionEvent e)
1261   {
1262
1263     AlignmentExportData exportData = getAlignmentForExport(
1264             e.getActionCommand(), viewport, null);
1265     if (exportData.getSettings().isCancelled())
1266     {
1267       return;
1268     }
1269     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1270     cap.setForInput(null);
1271     try
1272     {
1273       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1274               .formatSequences(e.getActionCommand(),
1275                       exportData.getAlignment(),
1276                       exportData.getOmitHidden(),
1277                       exportData.getStartEndPostions(),
1278                       viewport.getColumnSelection()));
1279       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1280               "label.alignment_output_command",
1281               new Object[] { e.getActionCommand() }), 600, 500);
1282     } catch (OutOfMemoryError oom)
1283     {
1284       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1285       cap.dispose();
1286     }
1287
1288   }
1289
1290   public static AlignmentExportData getAlignmentForExport(
1291           String exportFormat, AlignViewportI viewport,
1292           AlignExportSettingI exportSettings)
1293   {
1294     AlignmentI alignmentToExport = null;
1295     AlignExportSettingI settings = exportSettings;
1296     String[] omitHidden = null;
1297
1298     HiddenSequences hiddenSeqs = viewport.getAlignment()
1299             .getHiddenSequences();
1300
1301     alignmentToExport = viewport.getAlignment();
1302
1303     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1304     if (settings == null)
1305     {
1306       settings = new AlignExportSettings(hasHiddenSeqs,
1307               viewport.hasHiddenColumns(), exportFormat);
1308     }
1309     // settings.isExportAnnotations();
1310
1311     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1312     {
1313       omitHidden = viewport.getViewAsString(false,
1314               settings.isExportHiddenSequences());
1315     }
1316
1317     int[] alignmentStartEnd = new int[2];
1318     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1319     {
1320       alignmentToExport = hiddenSeqs.getFullAlignment();
1321     }
1322     else
1323     {
1324       alignmentToExport = viewport.getAlignment();
1325     }
1326     alignmentStartEnd = alignmentToExport
1327             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1328                     .getHiddenColumns());
1329     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1330             omitHidden, alignmentStartEnd, settings);
1331     return ed;
1332   }
1333
1334   /**
1335    * DOCUMENT ME!
1336    *
1337    * @param e
1338    *          DOCUMENT ME!
1339    */
1340   @Override
1341   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1342   {
1343     new HtmlSvgOutput(null, alignPanel);
1344   }
1345
1346   @Override
1347   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1348   {
1349     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1350     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1351   }
1352
1353   public void createImageMap(File file, String image)
1354   {
1355     alignPanel.makePNGImageMap(file, image);
1356   }
1357
1358   /**
1359    * DOCUMENT ME!
1360    *
1361    * @param e
1362    *          DOCUMENT ME!
1363    */
1364   @Override
1365   public void createPNG(File f)
1366   {
1367     alignPanel.makePNG(f);
1368   }
1369
1370   /**
1371    * DOCUMENT ME!
1372    *
1373    * @param e
1374    *          DOCUMENT ME!
1375    */
1376   @Override
1377   public void createEPS(File f)
1378   {
1379     alignPanel.makeEPS(f);
1380   }
1381
1382   @Override
1383   public void createSVG(File f)
1384   {
1385     alignPanel.makeSVG(f);
1386   }
1387
1388   @Override
1389   public void pageSetup_actionPerformed(ActionEvent e)
1390   {
1391     PrinterJob printJob = PrinterJob.getPrinterJob();
1392     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1393   }
1394
1395   /**
1396    * DOCUMENT ME!
1397    *
1398    * @param e
1399    *          DOCUMENT ME!
1400    */
1401   @Override
1402   public void printMenuItem_actionPerformed(ActionEvent e)
1403   {
1404     // Putting in a thread avoids Swing painting problems
1405     PrintThread thread = new PrintThread(alignPanel);
1406     thread.start();
1407   }
1408
1409   @Override
1410   public void exportFeatures_actionPerformed(ActionEvent e)
1411   {
1412     new AnnotationExporter().exportFeatures(alignPanel);
1413   }
1414
1415   @Override
1416   public void exportAnnotations_actionPerformed(ActionEvent e)
1417   {
1418     new AnnotationExporter().exportAnnotations(alignPanel);
1419   }
1420
1421   @Override
1422   public void associatedData_actionPerformed(ActionEvent e)
1423   {
1424     // Pick the tree file
1425     JalviewFileChooser chooser = new JalviewFileChooser(
1426             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1427     chooser.setFileView(new JalviewFileView());
1428     chooser.setDialogTitle(MessageManager
1429             .getString("label.load_jalview_annotations"));
1430     chooser.setToolTipText(MessageManager
1431             .getString("label.load_jalview_annotations"));
1432
1433     int value = chooser.showOpenDialog(null);
1434
1435     if (value == JalviewFileChooser.APPROVE_OPTION)
1436     {
1437       String choice = chooser.getSelectedFile().getPath();
1438       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1439       loadJalviewDataFile(choice, null, null, null);
1440     }
1441
1442   }
1443
1444   /**
1445    * Close the current view or all views in the alignment frame. If the frame
1446    * only contains one view then the alignment will be removed from memory.
1447    *
1448    * @param closeAllTabs
1449    */
1450   @Override
1451   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1452   {
1453     if (alignPanels != null && alignPanels.size() < 2)
1454     {
1455       closeAllTabs = true;
1456     }
1457
1458     try
1459     {
1460       if (alignPanels != null)
1461       {
1462         if (closeAllTabs)
1463         {
1464           if (this.isClosed())
1465           {
1466             // really close all the windows - otherwise wait till
1467             // setClosed(true) is called
1468             for (int i = 0; i < alignPanels.size(); i++)
1469             {
1470               AlignmentPanel ap = alignPanels.get(i);
1471               ap.closePanel();
1472             }
1473           }
1474         }
1475         else
1476         {
1477           closeView(alignPanel);
1478         }
1479       }
1480
1481       if (closeAllTabs)
1482       {
1483         /*
1484          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1485          * be called recursively, with the frame now in 'closed' state
1486          */
1487         this.setClosed(true);
1488       }
1489     } catch (Exception ex)
1490     {
1491       ex.printStackTrace();
1492     }
1493   }
1494
1495   /**
1496    * Close the specified panel and close up tabs appropriately.
1497    *
1498    * @param panelToClose
1499    */
1500   public void closeView(AlignmentPanel panelToClose)
1501   {
1502     int index = tabbedPane.getSelectedIndex();
1503     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1504     alignPanels.remove(panelToClose);
1505     panelToClose.closePanel();
1506     panelToClose = null;
1507
1508     tabbedPane.removeTabAt(closedindex);
1509     tabbedPane.validate();
1510
1511     if (index > closedindex || index == tabbedPane.getTabCount())
1512     {
1513       // modify currently selected tab index if necessary.
1514       index--;
1515     }
1516
1517     this.tabSelectionChanged(index);
1518   }
1519
1520   /**
1521    * DOCUMENT ME!
1522    */
1523   void updateEditMenuBar()
1524   {
1525
1526     if (viewport.getHistoryList().size() > 0)
1527     {
1528       undoMenuItem.setEnabled(true);
1529       CommandI command = viewport.getHistoryList().peek();
1530       undoMenuItem.setText(MessageManager.formatMessage(
1531               "label.undo_command",
1532               new Object[] { command.getDescription() }));
1533     }
1534     else
1535     {
1536       undoMenuItem.setEnabled(false);
1537       undoMenuItem.setText(MessageManager.getString("action.undo"));
1538     }
1539
1540     if (viewport.getRedoList().size() > 0)
1541     {
1542       redoMenuItem.setEnabled(true);
1543
1544       CommandI command = viewport.getRedoList().peek();
1545       redoMenuItem.setText(MessageManager.formatMessage(
1546               "label.redo_command",
1547               new Object[] { command.getDescription() }));
1548     }
1549     else
1550     {
1551       redoMenuItem.setEnabled(false);
1552       redoMenuItem.setText(MessageManager.getString("action.redo"));
1553     }
1554   }
1555
1556   @Override
1557   public void addHistoryItem(CommandI command)
1558   {
1559     if (command.getSize() > 0)
1560     {
1561       viewport.addToHistoryList(command);
1562       viewport.clearRedoList();
1563       updateEditMenuBar();
1564       viewport.updateHiddenColumns();
1565       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1566       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1567       // viewport.getColumnSelection()
1568       // .getHiddenColumns().size() > 0);
1569     }
1570   }
1571
1572   /**
1573    *
1574    * @return alignment objects for all views
1575    */
1576   AlignmentI[] getViewAlignments()
1577   {
1578     if (alignPanels != null)
1579     {
1580       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1581       int i = 0;
1582       for (AlignmentPanel ap : alignPanels)
1583       {
1584         als[i++] = ap.av.getAlignment();
1585       }
1586       return als;
1587     }
1588     if (viewport != null)
1589     {
1590       return new AlignmentI[] { viewport.getAlignment() };
1591     }
1592     return null;
1593   }
1594
1595   /**
1596    * DOCUMENT ME!
1597    *
1598    * @param e
1599    *          DOCUMENT ME!
1600    */
1601   @Override
1602   protected void undoMenuItem_actionPerformed(ActionEvent e)
1603   {
1604     if (viewport.getHistoryList().isEmpty())
1605     {
1606       return;
1607     }
1608     CommandI command = viewport.getHistoryList().pop();
1609     viewport.addToRedoList(command);
1610     command.undoCommand(getViewAlignments());
1611
1612     AlignmentViewport originalSource = getOriginatingSource(command);
1613     updateEditMenuBar();
1614
1615     if (originalSource != null)
1616     {
1617       if (originalSource != viewport)
1618       {
1619         Cache.log
1620                 .warn("Implementation worry: mismatch of viewport origin for undo");
1621       }
1622       originalSource.updateHiddenColumns();
1623       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1624       // null
1625       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1626       // viewport.getColumnSelection()
1627       // .getHiddenColumns().size() > 0);
1628       originalSource.firePropertyChange("alignment", null, originalSource
1629               .getAlignment().getSequences());
1630     }
1631   }
1632
1633   /**
1634    * DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   @Override
1640   protected void redoMenuItem_actionPerformed(ActionEvent e)
1641   {
1642     if (viewport.getRedoList().size() < 1)
1643     {
1644       return;
1645     }
1646
1647     CommandI command = viewport.getRedoList().pop();
1648     viewport.addToHistoryList(command);
1649     command.doCommand(getViewAlignments());
1650
1651     AlignmentViewport originalSource = getOriginatingSource(command);
1652     updateEditMenuBar();
1653
1654     if (originalSource != null)
1655     {
1656
1657       if (originalSource != viewport)
1658       {
1659         Cache.log
1660                 .warn("Implementation worry: mismatch of viewport origin for redo");
1661       }
1662       originalSource.updateHiddenColumns();
1663       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1664       // null
1665       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1666       // viewport.getColumnSelection()
1667       // .getHiddenColumns().size() > 0);
1668       originalSource.firePropertyChange("alignment", null, originalSource
1669               .getAlignment().getSequences());
1670     }
1671   }
1672
1673   AlignmentViewport getOriginatingSource(CommandI command)
1674   {
1675     AlignmentViewport originalSource = null;
1676     // For sequence removal and addition, we need to fire
1677     // the property change event FROM the viewport where the
1678     // original alignment was altered
1679     AlignmentI al = null;
1680     if (command instanceof EditCommand)
1681     {
1682       EditCommand editCommand = (EditCommand) command;
1683       al = editCommand.getAlignment();
1684       List<Component> comps = PaintRefresher.components.get(viewport
1685               .getSequenceSetId());
1686
1687       for (Component comp : comps)
1688       {
1689         if (comp instanceof AlignmentPanel)
1690         {
1691           if (al == ((AlignmentPanel) comp).av.getAlignment())
1692           {
1693             originalSource = ((AlignmentPanel) comp).av;
1694             break;
1695           }
1696         }
1697       }
1698     }
1699
1700     if (originalSource == null)
1701     {
1702       // The original view is closed, we must validate
1703       // the current view against the closed view first
1704       if (al != null)
1705       {
1706         PaintRefresher.validateSequences(al, viewport.getAlignment());
1707       }
1708
1709       originalSource = viewport;
1710     }
1711
1712     return originalSource;
1713   }
1714
1715   /**
1716    * DOCUMENT ME!
1717    *
1718    * @param up
1719    *          DOCUMENT ME!
1720    */
1721   public void moveSelectedSequences(boolean up)
1722   {
1723     SequenceGroup sg = viewport.getSelectionGroup();
1724
1725     if (sg == null)
1726     {
1727       return;
1728     }
1729     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1730             viewport.getHiddenRepSequences(), up);
1731     alignPanel.paintAlignment(true);
1732   }
1733
1734   synchronized void slideSequences(boolean right, int size)
1735   {
1736     List<SequenceI> sg = new ArrayList<SequenceI>();
1737     if (viewport.cursorMode)
1738     {
1739       sg.add(viewport.getAlignment().getSequenceAt(
1740               alignPanel.getSeqPanel().seqCanvas.cursorY));
1741     }
1742     else if (viewport.getSelectionGroup() != null
1743             && viewport.getSelectionGroup().getSize() != viewport
1744                     .getAlignment().getHeight())
1745     {
1746       sg = viewport.getSelectionGroup().getSequences(
1747               viewport.getHiddenRepSequences());
1748     }
1749
1750     if (sg.size() < 1)
1751     {
1752       return;
1753     }
1754
1755     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1756
1757     for (SequenceI seq : viewport.getAlignment().getSequences())
1758     {
1759       if (!sg.contains(seq))
1760       {
1761         invertGroup.add(seq);
1762       }
1763     }
1764
1765     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1766
1767     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1768     for (int i = 0; i < invertGroup.size(); i++)
1769     {
1770       seqs2[i] = invertGroup.get(i);
1771     }
1772
1773     SlideSequencesCommand ssc;
1774     if (right)
1775     {
1776       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1777               size, viewport.getGapCharacter());
1778     }
1779     else
1780     {
1781       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1782               size, viewport.getGapCharacter());
1783     }
1784
1785     int groupAdjustment = 0;
1786     if (ssc.getGapsInsertedBegin() && right)
1787     {
1788       if (viewport.cursorMode)
1789       {
1790         alignPanel.getSeqPanel().moveCursor(size, 0);
1791       }
1792       else
1793       {
1794         groupAdjustment = size;
1795       }
1796     }
1797     else if (!ssc.getGapsInsertedBegin() && !right)
1798     {
1799       if (viewport.cursorMode)
1800       {
1801         alignPanel.getSeqPanel().moveCursor(-size, 0);
1802       }
1803       else
1804       {
1805         groupAdjustment = -size;
1806       }
1807     }
1808
1809     if (groupAdjustment != 0)
1810     {
1811       viewport.getSelectionGroup().setStartRes(
1812               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1813       viewport.getSelectionGroup().setEndRes(
1814               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1815     }
1816
1817     /*
1818      * just extend the last slide command if compatible; but not if in
1819      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1820      */
1821     boolean appendHistoryItem = false;
1822     Deque<CommandI> historyList = viewport.getHistoryList();
1823     boolean inSplitFrame = getSplitViewContainer() != null;
1824     if (!inSplitFrame && historyList != null && historyList.size() > 0
1825             && historyList.peek() instanceof SlideSequencesCommand)
1826     {
1827       appendHistoryItem = ssc
1828               .appendSlideCommand((SlideSequencesCommand) historyList
1829                       .peek());
1830     }
1831
1832     if (!appendHistoryItem)
1833     {
1834       addHistoryItem(ssc);
1835     }
1836
1837     repaint();
1838   }
1839
1840   /**
1841    * DOCUMENT ME!
1842    *
1843    * @param e
1844    *          DOCUMENT ME!
1845    */
1846   @Override
1847   protected void copy_actionPerformed(ActionEvent e)
1848   {
1849     System.gc();
1850     if (viewport.getSelectionGroup() == null)
1851     {
1852       return;
1853     }
1854     // TODO: preserve the ordering of displayed alignment annotation in any
1855     // internal paste (particularly sequence associated annotation)
1856     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1857     String[] omitHidden = null;
1858
1859     if (viewport.hasHiddenColumns())
1860     {
1861       omitHidden = viewport.getViewAsString(true);
1862     }
1863
1864     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1865             omitHidden, null);
1866
1867     StringSelection ss = new StringSelection(output);
1868
1869     try
1870     {
1871       jalview.gui.Desktop.internalCopy = true;
1872       // Its really worth setting the clipboard contents
1873       // to empty before setting the large StringSelection!!
1874       Toolkit.getDefaultToolkit().getSystemClipboard()
1875               .setContents(new StringSelection(""), null);
1876
1877       Toolkit.getDefaultToolkit().getSystemClipboard()
1878               .setContents(ss, Desktop.instance);
1879     } catch (OutOfMemoryError er)
1880     {
1881       new OOMWarning("copying region", er);
1882       return;
1883     }
1884
1885     ArrayList<int[]> hiddenColumns = null;
1886     if (viewport.hasHiddenColumns())
1887     {
1888       hiddenColumns = new ArrayList<int[]>();
1889       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1890               .getSelectionGroup().getEndRes();
1891       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1892       {
1893         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1894         {
1895           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1896               region[1] - hiddenOffset });
1897         }
1898       }
1899     }
1900
1901     Desktop.jalviewClipboard = new Object[] { seqs,
1902         viewport.getAlignment().getDataset(), hiddenColumns };
1903     statusBar.setText(MessageManager.formatMessage(
1904             "label.copied_sequences_to_clipboard", new Object[] { Integer
1905                     .valueOf(seqs.length).toString() }));
1906   }
1907
1908   /**
1909    * DOCUMENT ME!
1910    *
1911    * @param e
1912    *          DOCUMENT ME!
1913    */
1914   @Override
1915   protected void pasteNew_actionPerformed(ActionEvent e)
1916   {
1917     paste(true);
1918   }
1919
1920   /**
1921    * DOCUMENT ME!
1922    *
1923    * @param e
1924    *          DOCUMENT ME!
1925    */
1926   @Override
1927   protected void pasteThis_actionPerformed(ActionEvent e)
1928   {
1929     paste(false);
1930   }
1931
1932   /**
1933    * Paste contents of Jalview clipboard
1934    *
1935    * @param newAlignment
1936    *          true to paste to a new alignment, otherwise add to this.
1937    */
1938   void paste(boolean newAlignment)
1939   {
1940     boolean externalPaste = true;
1941     try
1942     {
1943       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1944       Transferable contents = c.getContents(this);
1945
1946       if (contents == null)
1947       {
1948         return;
1949       }
1950
1951       String str, format;
1952       try
1953       {
1954         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1955         if (str.length() < 1)
1956         {
1957           return;
1958         }
1959
1960         format = new IdentifyFile().identify(str, "Paste");
1961
1962       } catch (OutOfMemoryError er)
1963       {
1964         new OOMWarning("Out of memory pasting sequences!!", er);
1965         return;
1966       }
1967
1968       SequenceI[] sequences;
1969       boolean annotationAdded = false;
1970       AlignmentI alignment = null;
1971
1972       if (Desktop.jalviewClipboard != null)
1973       {
1974         // The clipboard was filled from within Jalview, we must use the
1975         // sequences
1976         // And dataset from the copied alignment
1977         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1978         // be doubly sure that we create *new* sequence objects.
1979         sequences = new SequenceI[newseq.length];
1980         for (int i = 0; i < newseq.length; i++)
1981         {
1982           sequences[i] = new Sequence(newseq[i]);
1983         }
1984         alignment = new Alignment(sequences);
1985         externalPaste = false;
1986       }
1987       else
1988       {
1989         // parse the clipboard as an alignment.
1990         alignment = new FormatAdapter().readFile(str, "Paste", format);
1991         sequences = alignment.getSequencesArray();
1992       }
1993
1994       int alwidth = 0;
1995       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1996       int fgroup = -1;
1997
1998       if (newAlignment)
1999       {
2000
2001         if (Desktop.jalviewClipboard != null)
2002         {
2003           // dataset is inherited
2004           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2005         }
2006         else
2007         {
2008           // new dataset is constructed
2009           alignment.setDataset(null);
2010         }
2011         alwidth = alignment.getWidth() + 1;
2012       }
2013       else
2014       {
2015         AlignmentI pastedal = alignment; // preserve pasted alignment object
2016         // Add pasted sequences and dataset into existing alignment.
2017         alignment = viewport.getAlignment();
2018         alwidth = alignment.getWidth() + 1;
2019         // decide if we need to import sequences from an existing dataset
2020         boolean importDs = Desktop.jalviewClipboard != null
2021                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2022         // importDs==true instructs us to copy over new dataset sequences from
2023         // an existing alignment
2024         Vector newDs = (importDs) ? new Vector() : null; // used to create
2025         // minimum dataset set
2026
2027         for (int i = 0; i < sequences.length; i++)
2028         {
2029           if (importDs)
2030           {
2031             newDs.addElement(null);
2032           }
2033           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2034           // paste
2035           if (importDs && ds != null)
2036           {
2037             if (!newDs.contains(ds))
2038             {
2039               newDs.setElementAt(ds, i);
2040               ds = new Sequence(ds);
2041               // update with new dataset sequence
2042               sequences[i].setDatasetSequence(ds);
2043             }
2044             else
2045             {
2046               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2047             }
2048           }
2049           else
2050           {
2051             // copy and derive new dataset sequence
2052             sequences[i] = sequences[i].deriveSequence();
2053             alignment.getDataset().addSequence(
2054                     sequences[i].getDatasetSequence());
2055             // TODO: avoid creation of duplicate dataset sequences with a
2056             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2057           }
2058           alignment.addSequence(sequences[i]); // merges dataset
2059         }
2060         if (newDs != null)
2061         {
2062           newDs.clear(); // tidy up
2063         }
2064         if (alignment.getAlignmentAnnotation() != null)
2065         {
2066           for (AlignmentAnnotation alan : alignment
2067                   .getAlignmentAnnotation())
2068           {
2069             if (alan.graphGroup > fgroup)
2070             {
2071               fgroup = alan.graphGroup;
2072             }
2073           }
2074         }
2075         if (pastedal.getAlignmentAnnotation() != null)
2076         {
2077           // Add any annotation attached to alignment.
2078           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2079           for (int i = 0; i < alann.length; i++)
2080           {
2081             annotationAdded = true;
2082             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2083             {
2084               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2085               if (newann.graphGroup > -1)
2086               {
2087                 if (newGraphGroups.size() <= newann.graphGroup
2088                         || newGraphGroups.get(newann.graphGroup) == null)
2089                 {
2090                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2091                   {
2092                     newGraphGroups.add(q, null);
2093                   }
2094                   newGraphGroups.set(newann.graphGroup, new Integer(
2095                           ++fgroup));
2096                 }
2097                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2098                         .intValue();
2099               }
2100
2101               newann.padAnnotation(alwidth);
2102               alignment.addAnnotation(newann);
2103             }
2104           }
2105         }
2106       }
2107       if (!newAlignment)
2108       {
2109         // /////
2110         // ADD HISTORY ITEM
2111         //
2112         addHistoryItem(new EditCommand(
2113                 MessageManager.getString("label.add_sequences"),
2114                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2115       }
2116       // Add any annotations attached to sequences
2117       for (int i = 0; i < sequences.length; i++)
2118       {
2119         if (sequences[i].getAnnotation() != null)
2120         {
2121           AlignmentAnnotation newann;
2122           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2123           {
2124             annotationAdded = true;
2125             newann = sequences[i].getAnnotation()[a];
2126             newann.adjustForAlignment();
2127             newann.padAnnotation(alwidth);
2128             if (newann.graphGroup > -1)
2129             {
2130               if (newann.graphGroup > -1)
2131               {
2132                 if (newGraphGroups.size() <= newann.graphGroup
2133                         || newGraphGroups.get(newann.graphGroup) == null)
2134                 {
2135                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2136                   {
2137                     newGraphGroups.add(q, null);
2138                   }
2139                   newGraphGroups.set(newann.graphGroup, new Integer(
2140                           ++fgroup));
2141                 }
2142                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2143                         .intValue();
2144               }
2145             }
2146             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2147             // was
2148             // duplicated
2149             // earlier
2150             alignment
2151                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2152           }
2153         }
2154       }
2155       if (!newAlignment)
2156       {
2157
2158         // propagate alignment changed.
2159         viewport.setEndSeq(alignment.getHeight());
2160         if (annotationAdded)
2161         {
2162           // Duplicate sequence annotation in all views.
2163           AlignmentI[] alview = this.getViewAlignments();
2164           for (int i = 0; i < sequences.length; i++)
2165           {
2166             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2167             if (sann == null)
2168             {
2169               continue;
2170             }
2171             for (int avnum = 0; avnum < alview.length; avnum++)
2172             {
2173               if (alview[avnum] != alignment)
2174               {
2175                 // duplicate in a view other than the one with input focus
2176                 int avwidth = alview[avnum].getWidth() + 1;
2177                 // this relies on sann being preserved after we
2178                 // modify the sequence's annotation array for each duplication
2179                 for (int a = 0; a < sann.length; a++)
2180                 {
2181                   AlignmentAnnotation newann = new AlignmentAnnotation(
2182                           sann[a]);
2183                   sequences[i].addAlignmentAnnotation(newann);
2184                   newann.padAnnotation(avwidth);
2185                   alview[avnum].addAnnotation(newann); // annotation was
2186                   // duplicated earlier
2187                   // TODO JAL-1145 graphGroups are not updated for sequence
2188                   // annotation added to several views. This may cause
2189                   // strangeness
2190                   alview[avnum].setAnnotationIndex(newann, a);
2191                 }
2192               }
2193             }
2194           }
2195           buildSortByAnnotationScoresMenu();
2196         }
2197         viewport.firePropertyChange("alignment", null,
2198                 alignment.getSequences());
2199         if (alignPanels != null)
2200         {
2201           for (AlignmentPanel ap : alignPanels)
2202           {
2203             ap.validateAnnotationDimensions(false);
2204           }
2205         }
2206         else
2207         {
2208           alignPanel.validateAnnotationDimensions(false);
2209         }
2210
2211       }
2212       else
2213       {
2214         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2215                 DEFAULT_HEIGHT);
2216         String newtitle = new String("Copied sequences");
2217
2218         if (Desktop.jalviewClipboard != null
2219                 && Desktop.jalviewClipboard[2] != null)
2220         {
2221           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2222           for (int[] region : hc)
2223           {
2224             af.viewport.hideColumns(region[0], region[1]);
2225           }
2226         }
2227
2228         // >>>This is a fix for the moment, until a better solution is
2229         // found!!<<<
2230         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2231                 .transferSettings(
2232                         alignPanel.getSeqPanel().seqCanvas
2233                                 .getFeatureRenderer());
2234
2235         // TODO: maintain provenance of an alignment, rather than just make the
2236         // title a concatenation of operations.
2237         if (!externalPaste)
2238         {
2239           if (title.startsWith("Copied sequences"))
2240           {
2241             newtitle = title;
2242           }
2243           else
2244           {
2245             newtitle = newtitle.concat("- from " + title);
2246           }
2247         }
2248         else
2249         {
2250           newtitle = new String("Pasted sequences");
2251         }
2252
2253         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2254                 DEFAULT_HEIGHT);
2255
2256       }
2257
2258     } catch (Exception ex)
2259     {
2260       ex.printStackTrace();
2261       System.out.println("Exception whilst pasting: " + ex);
2262       // could be anything being pasted in here
2263     }
2264
2265   }
2266
2267   @Override
2268   protected void expand_newalign(ActionEvent e)
2269   {
2270     try
2271     {
2272       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2273               .getAlignment(), -1);
2274       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2275               DEFAULT_HEIGHT);
2276       String newtitle = new String("Flanking alignment");
2277
2278       if (Desktop.jalviewClipboard != null
2279               && Desktop.jalviewClipboard[2] != null)
2280       {
2281         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2282         for (int region[] : hc)
2283         {
2284           af.viewport.hideColumns(region[0], region[1]);
2285         }
2286       }
2287
2288       // >>>This is a fix for the moment, until a better solution is
2289       // found!!<<<
2290       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2291               .transferSettings(
2292                       alignPanel.getSeqPanel().seqCanvas
2293                               .getFeatureRenderer());
2294
2295       // TODO: maintain provenance of an alignment, rather than just make the
2296       // title a concatenation of operations.
2297       {
2298         if (title.startsWith("Copied sequences"))
2299         {
2300           newtitle = title;
2301         }
2302         else
2303         {
2304           newtitle = newtitle.concat("- from " + title);
2305         }
2306       }
2307
2308       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2309
2310     } catch (Exception ex)
2311     {
2312       ex.printStackTrace();
2313       System.out.println("Exception whilst pasting: " + ex);
2314       // could be anything being pasted in here
2315     } catch (OutOfMemoryError oom)
2316     {
2317       new OOMWarning("Viewing flanking region of alignment", oom);
2318     }
2319   }
2320
2321   /**
2322    * DOCUMENT ME!
2323    *
2324    * @param e
2325    *          DOCUMENT ME!
2326    */
2327   @Override
2328   protected void cut_actionPerformed(ActionEvent e)
2329   {
2330     copy_actionPerformed(null);
2331     delete_actionPerformed(null);
2332   }
2333
2334   /**
2335    * DOCUMENT ME!
2336    *
2337    * @param e
2338    *          DOCUMENT ME!
2339    */
2340   @Override
2341   protected void delete_actionPerformed(ActionEvent evt)
2342   {
2343
2344     SequenceGroup sg = viewport.getSelectionGroup();
2345     if (sg == null)
2346     {
2347       return;
2348     }
2349
2350     /*
2351      * If the cut affects all sequences, warn, remove highlighted columns
2352      */
2353     if (sg.getSize() == viewport.getAlignment().getHeight())
2354     {
2355       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2356               .getAlignment().getWidth()) ? true : false;
2357       if (isEntireAlignWidth)
2358       {
2359         int confirm = JOptionPane.showConfirmDialog(this,
2360                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2361                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2362                 JOptionPane.OK_CANCEL_OPTION);
2363
2364         if (confirm == JOptionPane.CANCEL_OPTION
2365                 || confirm == JOptionPane.CLOSED_OPTION)
2366         {
2367           return;
2368         }
2369       }
2370       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2371               sg.getEndRes() + 1);
2372     }
2373     SequenceI[] cut = sg.getSequences()
2374             .toArray(new SequenceI[sg.getSize()]);
2375
2376     addHistoryItem(new EditCommand(
2377             MessageManager.getString("label.cut_sequences"), Action.CUT,
2378             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2379             viewport.getAlignment()));
2380
2381     viewport.setSelectionGroup(null);
2382     viewport.sendSelection();
2383     viewport.getAlignment().deleteGroup(sg);
2384
2385     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2386             .getSequences());
2387     if (viewport.getAlignment().getHeight() < 1)
2388     {
2389       try
2390       {
2391         this.setClosed(true);
2392       } catch (Exception ex)
2393       {
2394       }
2395     }
2396   }
2397
2398   /**
2399    * DOCUMENT ME!
2400    *
2401    * @param e
2402    *          DOCUMENT ME!
2403    */
2404   @Override
2405   protected void deleteGroups_actionPerformed(ActionEvent e)
2406   {
2407     if (avc.deleteGroups())
2408     {
2409       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2410       alignPanel.updateAnnotation();
2411       alignPanel.paintAlignment(true);
2412     }
2413   }
2414
2415   /**
2416    * DOCUMENT ME!
2417    *
2418    * @param e
2419    *          DOCUMENT ME!
2420    */
2421   @Override
2422   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2423   {
2424     SequenceGroup sg = new SequenceGroup();
2425
2426     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2427     {
2428       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2429     }
2430
2431     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2432     viewport.setSelectionGroup(sg);
2433     viewport.sendSelection();
2434     // JAL-2034 - should delegate to
2435     // alignPanel to decide if overview needs
2436     // updating.
2437     alignPanel.paintAlignment(false);
2438     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2439   }
2440
2441   /**
2442    * DOCUMENT ME!
2443    *
2444    * @param e
2445    *          DOCUMENT ME!
2446    */
2447   @Override
2448   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2449   {
2450     if (viewport.cursorMode)
2451     {
2452       alignPanel.getSeqPanel().keyboardNo1 = null;
2453       alignPanel.getSeqPanel().keyboardNo2 = null;
2454     }
2455     viewport.setSelectionGroup(null);
2456     viewport.getColumnSelection().clear();
2457     viewport.setSelectionGroup(null);
2458     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2459     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2460     // JAL-2034 - should delegate to
2461     // alignPanel to decide if overview needs
2462     // updating.
2463     alignPanel.paintAlignment(false);
2464     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2465     viewport.sendSelection();
2466   }
2467
2468   /**
2469    * DOCUMENT ME!
2470    *
2471    * @param e
2472    *          DOCUMENT ME!
2473    */
2474   @Override
2475   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2476   {
2477     SequenceGroup sg = viewport.getSelectionGroup();
2478
2479     if (sg == null)
2480     {
2481       selectAllSequenceMenuItem_actionPerformed(null);
2482
2483       return;
2484     }
2485
2486     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2487     {
2488       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2489     }
2490     // JAL-2034 - should delegate to
2491     // alignPanel to decide if overview needs
2492     // updating.
2493
2494     alignPanel.paintAlignment(true);
2495     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2496     viewport.sendSelection();
2497   }
2498
2499   @Override
2500   public void invertColSel_actionPerformed(ActionEvent e)
2501   {
2502     viewport.invertColumnSelection();
2503     alignPanel.paintAlignment(true);
2504     viewport.sendSelection();
2505   }
2506
2507   /**
2508    * DOCUMENT ME!
2509    *
2510    * @param e
2511    *          DOCUMENT ME!
2512    */
2513   @Override
2514   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2515   {
2516     trimAlignment(true);
2517   }
2518
2519   /**
2520    * DOCUMENT ME!
2521    *
2522    * @param e
2523    *          DOCUMENT ME!
2524    */
2525   @Override
2526   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2527   {
2528     trimAlignment(false);
2529   }
2530
2531   void trimAlignment(boolean trimLeft)
2532   {
2533     ColumnSelection colSel = viewport.getColumnSelection();
2534     int column;
2535
2536     if (!colSel.isEmpty())
2537     {
2538       if (trimLeft)
2539       {
2540         column = colSel.getMin();
2541       }
2542       else
2543       {
2544         column = colSel.getMax();
2545       }
2546
2547       SequenceI[] seqs;
2548       if (viewport.getSelectionGroup() != null)
2549       {
2550         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2551                 viewport.getHiddenRepSequences());
2552       }
2553       else
2554       {
2555         seqs = viewport.getAlignment().getSequencesArray();
2556       }
2557
2558       TrimRegionCommand trimRegion;
2559       if (trimLeft)
2560       {
2561         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2562                 column, viewport.getAlignment());
2563         viewport.setStartRes(0);
2564       }
2565       else
2566       {
2567         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2568                 column, viewport.getAlignment());
2569       }
2570
2571       statusBar.setText(MessageManager.formatMessage(
2572               "label.removed_columns",
2573               new String[] { Integer.valueOf(trimRegion.getSize())
2574                       .toString() }));
2575
2576       addHistoryItem(trimRegion);
2577
2578       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2579       {
2580         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2581                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2582         {
2583           viewport.getAlignment().deleteGroup(sg);
2584         }
2585       }
2586
2587       viewport.firePropertyChange("alignment", null, viewport
2588               .getAlignment().getSequences());
2589     }
2590   }
2591
2592   /**
2593    * DOCUMENT ME!
2594    *
2595    * @param e
2596    *          DOCUMENT ME!
2597    */
2598   @Override
2599   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2600   {
2601     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2602
2603     SequenceI[] seqs;
2604     if (viewport.getSelectionGroup() != null)
2605     {
2606       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2607               viewport.getHiddenRepSequences());
2608       start = viewport.getSelectionGroup().getStartRes();
2609       end = viewport.getSelectionGroup().getEndRes();
2610     }
2611     else
2612     {
2613       seqs = viewport.getAlignment().getSequencesArray();
2614     }
2615
2616     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2617             "Remove Gapped Columns", seqs, start, end,
2618             viewport.getAlignment());
2619
2620     addHistoryItem(removeGapCols);
2621
2622     statusBar.setText(MessageManager.formatMessage(
2623             "label.removed_empty_columns",
2624             new Object[] { Integer.valueOf(removeGapCols.getSize())
2625                     .toString() }));
2626
2627     // This is to maintain viewport position on first residue
2628     // of first sequence
2629     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2630     int startRes = seq.findPosition(viewport.startRes);
2631     // ShiftList shifts;
2632     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2633     // edit.alColumnChanges=shifts.getInverse();
2634     // if (viewport.hasHiddenColumns)
2635     // viewport.getColumnSelection().compensateForEdits(shifts);
2636     viewport.setStartRes(seq.findIndex(startRes) - 1);
2637     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2638             .getSequences());
2639
2640   }
2641
2642   /**
2643    * DOCUMENT ME!
2644    *
2645    * @param e
2646    *          DOCUMENT ME!
2647    */
2648   @Override
2649   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2650   {
2651     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2652
2653     SequenceI[] seqs;
2654     if (viewport.getSelectionGroup() != null)
2655     {
2656       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2657               viewport.getHiddenRepSequences());
2658       start = viewport.getSelectionGroup().getStartRes();
2659       end = viewport.getSelectionGroup().getEndRes();
2660     }
2661     else
2662     {
2663       seqs = viewport.getAlignment().getSequencesArray();
2664     }
2665
2666     // This is to maintain viewport position on first residue
2667     // of first sequence
2668     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2669     int startRes = seq.findPosition(viewport.startRes);
2670
2671     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2672             viewport.getAlignment()));
2673
2674     viewport.setStartRes(seq.findIndex(startRes) - 1);
2675
2676     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2677             .getSequences());
2678
2679   }
2680
2681   /**
2682    * DOCUMENT ME!
2683    *
2684    * @param e
2685    *          DOCUMENT ME!
2686    */
2687   @Override
2688   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2689   {
2690     viewport.setPadGaps(padGapsMenuitem.isSelected());
2691     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2692             .getSequences());
2693   }
2694
2695   /**
2696    * DOCUMENT ME!
2697    *
2698    * @param e
2699    *          DOCUMENT ME!
2700    */
2701   @Override
2702   public void findMenuItem_actionPerformed(ActionEvent e)
2703   {
2704     new Finder();
2705   }
2706
2707   /**
2708    * Create a new view of the current alignment.
2709    */
2710   @Override
2711   public void newView_actionPerformed(ActionEvent e)
2712   {
2713     newView(null, true);
2714   }
2715
2716   /**
2717    * Creates and shows a new view of the current alignment.
2718    *
2719    * @param viewTitle
2720    *          title of newly created view; if null, one will be generated
2721    * @param copyAnnotation
2722    *          if true then duplicate all annnotation, groups and settings
2723    * @return new alignment panel, already displayed.
2724    */
2725   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2726   {
2727     /*
2728      * Create a new AlignmentPanel (with its own, new Viewport)
2729      */
2730     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2731             true);
2732     if (!copyAnnotation)
2733     {
2734       /*
2735        * remove all groups and annotation except for the automatic stuff
2736        */
2737       newap.av.getAlignment().deleteAllGroups();
2738       newap.av.getAlignment().deleteAllAnnotations(false);
2739     }
2740
2741     newap.av.setGatherViewsHere(false);
2742
2743     if (viewport.viewName == null)
2744     {
2745       viewport.viewName = MessageManager
2746               .getString("label.view_name_original");
2747     }
2748
2749     /*
2750      * Views share the same edits undo and redo stacks
2751      */
2752     newap.av.setHistoryList(viewport.getHistoryList());
2753     newap.av.setRedoList(viewport.getRedoList());
2754
2755     /*
2756      * Views share the same mappings; need to deregister any new mappings
2757      * created by copyAlignPanel, and register the new reference to the shared
2758      * mappings
2759      */
2760     newap.av.replaceMappings(viewport.getAlignment());
2761
2762     newap.av.viewName = getNewViewName(viewTitle);
2763
2764     addAlignmentPanel(newap, true);
2765     newap.alignmentChanged();
2766
2767     if (alignPanels.size() == 2)
2768     {
2769       viewport.setGatherViewsHere(true);
2770     }
2771     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2772     return newap;
2773   }
2774
2775   /**
2776    * Make a new name for the view, ensuring it is unique within the current
2777    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2778    * these now use viewId. Unique view names are still desirable for usability.)
2779    *
2780    * @param viewTitle
2781    * @return
2782    */
2783   protected String getNewViewName(String viewTitle)
2784   {
2785     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2786     boolean addFirstIndex = false;
2787     if (viewTitle == null || viewTitle.trim().length() == 0)
2788     {
2789       viewTitle = MessageManager.getString("action.view");
2790       addFirstIndex = true;
2791     }
2792     else
2793     {
2794       index = 1;// we count from 1 if given a specific name
2795     }
2796     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2797
2798     List<Component> comps = PaintRefresher.components.get(viewport
2799             .getSequenceSetId());
2800
2801     List<String> existingNames = getExistingViewNames(comps);
2802
2803     while (existingNames.contains(newViewName))
2804     {
2805       newViewName = viewTitle + " " + (++index);
2806     }
2807     return newViewName;
2808   }
2809
2810   /**
2811    * Returns a list of distinct view names found in the given list of
2812    * components. View names are held on the viewport of an AlignmentPanel.
2813    *
2814    * @param comps
2815    * @return
2816    */
2817   protected List<String> getExistingViewNames(List<Component> comps)
2818   {
2819     List<String> existingNames = new ArrayList<String>();
2820     for (Component comp : comps)
2821     {
2822       if (comp instanceof AlignmentPanel)
2823       {
2824         AlignmentPanel ap = (AlignmentPanel) comp;
2825         if (!existingNames.contains(ap.av.viewName))
2826         {
2827           existingNames.add(ap.av.viewName);
2828         }
2829       }
2830     }
2831     return existingNames;
2832   }
2833
2834   /**
2835    * Explode tabbed views into separate windows.
2836    */
2837   @Override
2838   public void expandViews_actionPerformed(ActionEvent e)
2839   {
2840     Desktop.explodeViews(this);
2841   }
2842
2843   /**
2844    * Gather views in separate windows back into a tabbed presentation.
2845    */
2846   @Override
2847   public void gatherViews_actionPerformed(ActionEvent e)
2848   {
2849     Desktop.instance.gatherViews(this);
2850   }
2851
2852   /**
2853    * DOCUMENT ME!
2854    *
2855    * @param e
2856    *          DOCUMENT ME!
2857    */
2858   @Override
2859   public void font_actionPerformed(ActionEvent e)
2860   {
2861     new FontChooser(alignPanel);
2862   }
2863
2864   /**
2865    * DOCUMENT ME!
2866    *
2867    * @param e
2868    *          DOCUMENT ME!
2869    */
2870   @Override
2871   protected void seqLimit_actionPerformed(ActionEvent e)
2872   {
2873     viewport.setShowJVSuffix(seqLimits.isSelected());
2874
2875     alignPanel.getIdPanel().getIdCanvas()
2876             .setPreferredSize(alignPanel.calculateIdWidth());
2877     alignPanel.paintAlignment(true);
2878   }
2879
2880   @Override
2881   public void idRightAlign_actionPerformed(ActionEvent e)
2882   {
2883     viewport.setRightAlignIds(idRightAlign.isSelected());
2884     alignPanel.paintAlignment(true);
2885   }
2886
2887   @Override
2888   public void centreColumnLabels_actionPerformed(ActionEvent e)
2889   {
2890     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2891     alignPanel.paintAlignment(true);
2892   }
2893
2894   /*
2895    * (non-Javadoc)
2896    *
2897    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2898    */
2899   @Override
2900   protected void followHighlight_actionPerformed()
2901   {
2902     /*
2903      * Set the 'follow' flag on the Viewport (and scroll to position if now
2904      * true).
2905      */
2906     final boolean state = this.followHighlightMenuItem.getState();
2907     viewport.setFollowHighlight(state);
2908     if (state)
2909     {
2910       alignPanel.scrollToPosition(
2911               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2912     }
2913   }
2914
2915   /**
2916    * DOCUMENT ME!
2917    *
2918    * @param e
2919    *          DOCUMENT ME!
2920    */
2921   @Override
2922   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2923   {
2924     viewport.setColourText(colourTextMenuItem.isSelected());
2925     alignPanel.paintAlignment(true);
2926   }
2927
2928   /**
2929    * DOCUMENT ME!
2930    *
2931    * @param e
2932    *          DOCUMENT ME!
2933    */
2934   @Override
2935   public void wrapMenuItem_actionPerformed(ActionEvent e)
2936   {
2937     scaleAbove.setVisible(wrapMenuItem.isSelected());
2938     scaleLeft.setVisible(wrapMenuItem.isSelected());
2939     scaleRight.setVisible(wrapMenuItem.isSelected());
2940     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2941     alignPanel.updateLayout();
2942   }
2943
2944   @Override
2945   public void showAllSeqs_actionPerformed(ActionEvent e)
2946   {
2947     viewport.showAllHiddenSeqs();
2948   }
2949
2950   @Override
2951   public void showAllColumns_actionPerformed(ActionEvent e)
2952   {
2953     viewport.showAllHiddenColumns();
2954     repaint();
2955     viewport.sendSelection();
2956   }
2957
2958   @Override
2959   public void hideSelSequences_actionPerformed(ActionEvent e)
2960   {
2961     viewport.hideAllSelectedSeqs();
2962     // alignPanel.paintAlignment(true);
2963   }
2964
2965   /**
2966    * called by key handler and the hide all/show all menu items
2967    *
2968    * @param toggleSeqs
2969    * @param toggleCols
2970    */
2971   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2972   {
2973
2974     boolean hide = false;
2975     SequenceGroup sg = viewport.getSelectionGroup();
2976     if (!toggleSeqs && !toggleCols)
2977     {
2978       // Hide everything by the current selection - this is a hack - we do the
2979       // invert and then hide
2980       // first check that there will be visible columns after the invert.
2981       if (viewport.hasSelectedColumns()
2982               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2983                       .getEndRes()))
2984       {
2985         // now invert the sequence set, if required - empty selection implies
2986         // that no hiding is required.
2987         if (sg != null)
2988         {
2989           invertSequenceMenuItem_actionPerformed(null);
2990           sg = viewport.getSelectionGroup();
2991           toggleSeqs = true;
2992
2993         }
2994         viewport.expandColSelection(sg, true);
2995         // finally invert the column selection and get the new sequence
2996         // selection.
2997         invertColSel_actionPerformed(null);
2998         toggleCols = true;
2999       }
3000     }
3001
3002     if (toggleSeqs)
3003     {
3004       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3005       {
3006         hideSelSequences_actionPerformed(null);
3007         hide = true;
3008       }
3009       else if (!(toggleCols && viewport.hasSelectedColumns()))
3010       {
3011         showAllSeqs_actionPerformed(null);
3012       }
3013     }
3014
3015     if (toggleCols)
3016     {
3017       if (viewport.hasSelectedColumns())
3018       {
3019         hideSelColumns_actionPerformed(null);
3020         if (!toggleSeqs)
3021         {
3022           viewport.setSelectionGroup(sg);
3023         }
3024       }
3025       else if (!hide)
3026       {
3027         showAllColumns_actionPerformed(null);
3028       }
3029     }
3030   }
3031
3032   /*
3033    * (non-Javadoc)
3034    *
3035    * @see
3036    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3037    * event.ActionEvent)
3038    */
3039   @Override
3040   public void hideAllButSelection_actionPerformed(ActionEvent e)
3041   {
3042     toggleHiddenRegions(false, false);
3043     viewport.sendSelection();
3044   }
3045
3046   /*
3047    * (non-Javadoc)
3048    *
3049    * @see
3050    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3051    * .ActionEvent)
3052    */
3053   @Override
3054   public void hideAllSelection_actionPerformed(ActionEvent e)
3055   {
3056     SequenceGroup sg = viewport.getSelectionGroup();
3057     viewport.expandColSelection(sg, false);
3058     viewport.hideAllSelectedSeqs();
3059     viewport.hideSelectedColumns();
3060     alignPanel.paintAlignment(true);
3061     viewport.sendSelection();
3062   }
3063
3064   /*
3065    * (non-Javadoc)
3066    *
3067    * @see
3068    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3069    * ActionEvent)
3070    */
3071   @Override
3072   public void showAllhidden_actionPerformed(ActionEvent e)
3073   {
3074     viewport.showAllHiddenColumns();
3075     viewport.showAllHiddenSeqs();
3076     alignPanel.paintAlignment(true);
3077     viewport.sendSelection();
3078   }
3079
3080   @Override
3081   public void hideSelColumns_actionPerformed(ActionEvent e)
3082   {
3083     viewport.hideSelectedColumns();
3084     alignPanel.paintAlignment(true);
3085     viewport.sendSelection();
3086   }
3087
3088   @Override
3089   public void hiddenMarkers_actionPerformed(ActionEvent e)
3090   {
3091     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3092     repaint();
3093   }
3094
3095   /**
3096    * DOCUMENT ME!
3097    *
3098    * @param e
3099    *          DOCUMENT ME!
3100    */
3101   @Override
3102   protected void scaleAbove_actionPerformed(ActionEvent e)
3103   {
3104     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3105     alignPanel.paintAlignment(true);
3106   }
3107
3108   /**
3109    * DOCUMENT ME!
3110    *
3111    * @param e
3112    *          DOCUMENT ME!
3113    */
3114   @Override
3115   protected void scaleLeft_actionPerformed(ActionEvent e)
3116   {
3117     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3118     alignPanel.paintAlignment(true);
3119   }
3120
3121   /**
3122    * DOCUMENT ME!
3123    *
3124    * @param e
3125    *          DOCUMENT ME!
3126    */
3127   @Override
3128   protected void scaleRight_actionPerformed(ActionEvent e)
3129   {
3130     viewport.setScaleRightWrapped(scaleRight.isSelected());
3131     alignPanel.paintAlignment(true);
3132   }
3133
3134   /**
3135    * DOCUMENT ME!
3136    *
3137    * @param e
3138    *          DOCUMENT ME!
3139    */
3140   @Override
3141   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3142   {
3143     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3144     alignPanel.paintAlignment(true);
3145   }
3146
3147   /**
3148    * DOCUMENT ME!
3149    *
3150    * @param e
3151    *          DOCUMENT ME!
3152    */
3153   @Override
3154   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3155   {
3156     viewport.setShowText(viewTextMenuItem.isSelected());
3157     alignPanel.paintAlignment(true);
3158   }
3159
3160   /**
3161    * DOCUMENT ME!
3162    *
3163    * @param e
3164    *          DOCUMENT ME!
3165    */
3166   @Override
3167   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3168   {
3169     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3170     alignPanel.paintAlignment(true);
3171   }
3172
3173   public FeatureSettings featureSettings;
3174
3175   @Override
3176   public FeatureSettingsControllerI getFeatureSettingsUI()
3177   {
3178     return featureSettings;
3179   }
3180
3181   @Override
3182   public void featureSettings_actionPerformed(ActionEvent e)
3183   {
3184     if (featureSettings != null)
3185     {
3186       featureSettings.close();
3187       featureSettings = null;
3188     }
3189     if (!showSeqFeatures.isSelected())
3190     {
3191       // make sure features are actually displayed
3192       showSeqFeatures.setSelected(true);
3193       showSeqFeatures_actionPerformed(null);
3194     }
3195     featureSettings = new FeatureSettings(this);
3196   }
3197
3198   /**
3199    * Set or clear 'Show Sequence Features'
3200    *
3201    * @param evt
3202    *          DOCUMENT ME!
3203    */
3204   @Override
3205   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3206   {
3207     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3208     alignPanel.paintAlignment(true);
3209     if (alignPanel.getOverviewPanel() != null)
3210     {
3211       alignPanel.getOverviewPanel().updateOverviewImage();
3212     }
3213   }
3214
3215   /**
3216    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3217    * the annotations panel as a whole.
3218    *
3219    * The options to show/hide all annotations should be enabled when the panel
3220    * is shown, and disabled when the panel is hidden.
3221    *
3222    * @param e
3223    */
3224   @Override
3225   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3226   {
3227     final boolean setVisible = annotationPanelMenuItem.isSelected();
3228     viewport.setShowAnnotation(setVisible);
3229     this.showAllSeqAnnotations.setEnabled(setVisible);
3230     this.hideAllSeqAnnotations.setEnabled(setVisible);
3231     this.showAllAlAnnotations.setEnabled(setVisible);
3232     this.hideAllAlAnnotations.setEnabled(setVisible);
3233     alignPanel.updateLayout();
3234   }
3235
3236   @Override
3237   public void alignmentProperties()
3238   {
3239     JEditorPane editPane = new JEditorPane("text/html", "");
3240     editPane.setEditable(false);
3241     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3242             .formatAsHtml();
3243     editPane.setText(MessageManager.formatMessage("label.html_content",
3244             new Object[] { contents.toString() }));
3245     JInternalFrame frame = new JInternalFrame();
3246     frame.getContentPane().add(new JScrollPane(editPane));
3247
3248     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3249             "label.alignment_properties", new Object[] { getTitle() }),
3250             500, 400);
3251   }
3252
3253   /**
3254    * DOCUMENT ME!
3255    *
3256    * @param e
3257    *          DOCUMENT ME!
3258    */
3259   @Override
3260   public void overviewMenuItem_actionPerformed(ActionEvent e)
3261   {
3262     if (alignPanel.overviewPanel != null)
3263     {
3264       return;
3265     }
3266
3267     JInternalFrame frame = new JInternalFrame();
3268     OverviewPanel overview = new OverviewPanel(alignPanel);
3269     frame.setContentPane(overview);
3270     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3271             "label.overview_params", new Object[] { this.getTitle() }),
3272             frame.getWidth(), frame.getHeight());
3273     frame.pack();
3274     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3275     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3276     {
3277       @Override
3278       public void internalFrameClosed(
3279               javax.swing.event.InternalFrameEvent evt)
3280       {
3281         alignPanel.setOverviewPanel(null);
3282       };
3283     });
3284
3285     alignPanel.setOverviewPanel(overview);
3286   }
3287
3288   @Override
3289   public void textColour_actionPerformed(ActionEvent e)
3290   {
3291     new TextColourChooser().chooseColour(alignPanel, null);
3292   }
3293
3294   /**
3295    * DOCUMENT ME!
3296    *
3297    * @param e
3298    *          DOCUMENT ME!
3299    */
3300   @Override
3301   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3302   {
3303     changeColour(null);
3304   }
3305
3306   /**
3307    * DOCUMENT ME!
3308    *
3309    * @param e
3310    *          DOCUMENT ME!
3311    */
3312   @Override
3313   public void clustalColour_actionPerformed(ActionEvent e)
3314   {
3315     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3316             viewport.getHiddenRepSequences()));
3317   }
3318
3319   /**
3320    * DOCUMENT ME!
3321    *
3322    * @param e
3323    *          DOCUMENT ME!
3324    */
3325   @Override
3326   public void zappoColour_actionPerformed(ActionEvent e)
3327   {
3328     changeColour(new ZappoColourScheme());
3329   }
3330
3331   /**
3332    * DOCUMENT ME!
3333    *
3334    * @param e
3335    *          DOCUMENT ME!
3336    */
3337   @Override
3338   public void taylorColour_actionPerformed(ActionEvent e)
3339   {
3340     changeColour(new TaylorColourScheme());
3341   }
3342
3343   /**
3344    * DOCUMENT ME!
3345    *
3346    * @param e
3347    *          DOCUMENT ME!
3348    */
3349   @Override
3350   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3351   {
3352     changeColour(new HydrophobicColourScheme());
3353   }
3354
3355   /**
3356    * DOCUMENT ME!
3357    *
3358    * @param e
3359    *          DOCUMENT ME!
3360    */
3361   @Override
3362   public void helixColour_actionPerformed(ActionEvent e)
3363   {
3364     changeColour(new HelixColourScheme());
3365   }
3366
3367   /**
3368    * DOCUMENT ME!
3369    *
3370    * @param e
3371    *          DOCUMENT ME!
3372    */
3373   @Override
3374   public void strandColour_actionPerformed(ActionEvent e)
3375   {
3376     changeColour(new StrandColourScheme());
3377   }
3378
3379   /**
3380    * DOCUMENT ME!
3381    *
3382    * @param e
3383    *          DOCUMENT ME!
3384    */
3385   @Override
3386   public void turnColour_actionPerformed(ActionEvent e)
3387   {
3388     changeColour(new TurnColourScheme());
3389   }
3390
3391   /**
3392    * DOCUMENT ME!
3393    *
3394    * @param e
3395    *          DOCUMENT ME!
3396    */
3397   @Override
3398   public void buriedColour_actionPerformed(ActionEvent e)
3399   {
3400     changeColour(new BuriedColourScheme());
3401   }
3402
3403   /**
3404    * DOCUMENT ME!
3405    *
3406    * @param e
3407    *          DOCUMENT ME!
3408    */
3409   @Override
3410   public void nucleotideColour_actionPerformed(ActionEvent e)
3411   {
3412     changeColour(new NucleotideColourScheme());
3413   }
3414
3415   @Override
3416   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3417   {
3418     changeColour(new PurinePyrimidineColourScheme());
3419   }
3420
3421   /*
3422    * public void covariationColour_actionPerformed(ActionEvent e) {
3423    * changeColour(new
3424    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3425    * ()[0])); }
3426    */
3427   @Override
3428   public void annotationColour_actionPerformed(ActionEvent e)
3429   {
3430     new AnnotationColourChooser(viewport, alignPanel);
3431   }
3432
3433   @Override
3434   public void annotationColumn_actionPerformed(ActionEvent e)
3435   {
3436     new AnnotationColumnChooser(viewport, alignPanel);
3437   }
3438
3439   @Override
3440   public void rnahelicesColour_actionPerformed(ActionEvent e)
3441   {
3442     new RNAHelicesColourChooser(viewport, alignPanel);
3443   }
3444
3445   /**
3446    * DOCUMENT ME!
3447    *
3448    * @param e
3449    *          DOCUMENT ME!
3450    */
3451   @Override
3452   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3453   {
3454     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3455   }
3456
3457   /**
3458    * DOCUMENT ME!
3459    *
3460    * @param cs
3461    *          DOCUMENT ME!
3462    */
3463   @Override
3464   public void changeColour(ColourSchemeI cs)
3465   {
3466     // TODO: pull up to controller method
3467
3468     if (cs != null)
3469     {
3470       // Make sure viewport is up to date w.r.t. any sliders
3471       if (viewport.getAbovePIDThreshold())
3472       {
3473         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3474                 "Background");
3475         viewport.setThreshold(threshold);
3476       }
3477
3478       if (viewport.getConservationSelected())
3479       {
3480         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3481                 cs, "Background"));
3482       }
3483       if (cs instanceof TCoffeeColourScheme)
3484       {
3485         tcoffeeColour.setEnabled(true);
3486         tcoffeeColour.setSelected(true);
3487       }
3488     }
3489
3490     viewport.setGlobalColourScheme(cs);
3491
3492     alignPanel.paintAlignment(true);
3493   }
3494
3495   /**
3496    * DOCUMENT ME!
3497    *
3498    * @param e
3499    *          DOCUMENT ME!
3500    */
3501   @Override
3502   protected void modifyPID_actionPerformed(ActionEvent e)
3503   {
3504     if (viewport.getAbovePIDThreshold()
3505             && viewport.getGlobalColourScheme() != null)
3506     {
3507       SliderPanel.setPIDSliderSource(alignPanel,
3508               viewport.getGlobalColourScheme(), "Background");
3509       SliderPanel.showPIDSlider();
3510     }
3511   }
3512
3513   /**
3514    * DOCUMENT ME!
3515    *
3516    * @param e
3517    *          DOCUMENT ME!
3518    */
3519   @Override
3520   protected void modifyConservation_actionPerformed(ActionEvent e)
3521   {
3522     if (viewport.getConservationSelected()
3523             && viewport.getGlobalColourScheme() != null)
3524     {
3525       SliderPanel.setConservationSlider(alignPanel,
3526               viewport.getGlobalColourScheme(), "Background");
3527       SliderPanel.showConservationSlider();
3528     }
3529   }
3530
3531   /**
3532    * DOCUMENT ME!
3533    *
3534    * @param e
3535    *          DOCUMENT ME!
3536    */
3537   @Override
3538   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3539   {
3540     viewport.setConservationSelected(conservationMenuItem.isSelected());
3541
3542     viewport.setAbovePIDThreshold(false);
3543     abovePIDThreshold.setSelected(false);
3544
3545     changeColour(viewport.getGlobalColourScheme());
3546
3547     modifyConservation_actionPerformed(null);
3548   }
3549
3550   /**
3551    * DOCUMENT ME!
3552    *
3553    * @param e
3554    *          DOCUMENT ME!
3555    */
3556   @Override
3557   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3558   {
3559     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3560
3561     conservationMenuItem.setSelected(false);
3562     viewport.setConservationSelected(false);
3563
3564     changeColour(viewport.getGlobalColourScheme());
3565
3566     modifyPID_actionPerformed(null);
3567   }
3568
3569   /**
3570    * DOCUMENT ME!
3571    *
3572    * @param e
3573    *          DOCUMENT ME!
3574    */
3575   @Override
3576   public void userDefinedColour_actionPerformed(ActionEvent e)
3577   {
3578     if (e.getActionCommand().equals(
3579             MessageManager.getString("action.user_defined")))
3580     {
3581       new UserDefinedColours(alignPanel, null);
3582     }
3583     else
3584     {
3585       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3586               .getUserColourSchemes().get(e.getActionCommand());
3587
3588       changeColour(udc);
3589     }
3590   }
3591
3592   public void updateUserColourMenu()
3593   {
3594
3595     Component[] menuItems = colourMenu.getMenuComponents();
3596     int iSize = menuItems.length;
3597     for (int i = 0; i < iSize; i++)
3598     {
3599       if (menuItems[i].getName() != null
3600               && menuItems[i].getName().equals("USER_DEFINED"))
3601       {
3602         colourMenu.remove(menuItems[i]);
3603         iSize--;
3604       }
3605     }
3606     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3607     {
3608       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3609               .getUserColourSchemes().keys();
3610
3611       while (userColours.hasMoreElements())
3612       {
3613         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3614                 userColours.nextElement().toString());
3615         radioItem.setName("USER_DEFINED");
3616         radioItem.addMouseListener(new MouseAdapter()
3617         {
3618           @Override
3619           public void mousePressed(MouseEvent evt)
3620           {
3621             if (evt.isPopupTrigger()) // Mac
3622             {
3623               offerRemoval(radioItem);
3624             }
3625           }
3626
3627           @Override
3628           public void mouseReleased(MouseEvent evt)
3629           {
3630             if (evt.isPopupTrigger()) // Windows
3631             {
3632               offerRemoval(radioItem);
3633             }
3634           }
3635
3636           /**
3637            * @param radioItem
3638            */
3639           void offerRemoval(final JRadioButtonMenuItem radioItem)
3640           {
3641             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3642
3643             int option = JOptionPane.showInternalConfirmDialog(
3644                     jalview.gui.Desktop.desktop, MessageManager
3645                             .getString("label.remove_from_default_list"),
3646                     MessageManager
3647                             .getString("label.remove_user_defined_colour"),
3648                     JOptionPane.YES_NO_OPTION);
3649             if (option == JOptionPane.YES_OPTION)
3650             {
3651               jalview.gui.UserDefinedColours
3652                       .removeColourFromDefaults(radioItem.getText());
3653               colourMenu.remove(radioItem);
3654             }
3655             else
3656             {
3657               radioItem.addActionListener(new ActionListener()
3658               {
3659                 @Override
3660                 public void actionPerformed(ActionEvent evt)
3661                 {
3662                   userDefinedColour_actionPerformed(evt);
3663                 }
3664               });
3665             }
3666           }
3667         });
3668         radioItem.addActionListener(new ActionListener()
3669         {
3670           @Override
3671           public void actionPerformed(ActionEvent evt)
3672           {
3673             userDefinedColour_actionPerformed(evt);
3674           }
3675         });
3676
3677         colourMenu.insert(radioItem, 15);
3678         colours.add(radioItem);
3679       }
3680     }
3681   }
3682
3683   /**
3684    * DOCUMENT ME!
3685    *
3686    * @param e
3687    *          DOCUMENT ME!
3688    */
3689   @Override
3690   public void PIDColour_actionPerformed(ActionEvent e)
3691   {
3692     changeColour(new PIDColourScheme());
3693   }
3694
3695   /**
3696    * DOCUMENT ME!
3697    *
3698    * @param e
3699    *          DOCUMENT ME!
3700    */
3701   @Override
3702   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3703   {
3704     changeColour(new Blosum62ColourScheme());
3705   }
3706
3707   /**
3708    * DOCUMENT ME!
3709    *
3710    * @param e
3711    *          DOCUMENT ME!
3712    */
3713   @Override
3714   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3715   {
3716     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3717     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3718             .getAlignment().getSequenceAt(0), null);
3719     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3720             viewport.getAlignment()));
3721     alignPanel.paintAlignment(true);
3722   }
3723
3724   /**
3725    * DOCUMENT ME!
3726    *
3727    * @param e
3728    *          DOCUMENT ME!
3729    */
3730   @Override
3731   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3732   {
3733     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3734     AlignmentSorter.sortByID(viewport.getAlignment());
3735     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3736             viewport.getAlignment()));
3737     alignPanel.paintAlignment(true);
3738   }
3739
3740   /**
3741    * DOCUMENT ME!
3742    *
3743    * @param e
3744    *          DOCUMENT ME!
3745    */
3746   @Override
3747   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3748   {
3749     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3750     AlignmentSorter.sortByLength(viewport.getAlignment());
3751     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3752             viewport.getAlignment()));
3753     alignPanel.paintAlignment(true);
3754   }
3755
3756   /**
3757    * DOCUMENT ME!
3758    *
3759    * @param e
3760    *          DOCUMENT ME!
3761    */
3762   @Override
3763   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3764   {
3765     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3766     AlignmentSorter.sortByGroup(viewport.getAlignment());
3767     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3768             viewport.getAlignment()));
3769
3770     alignPanel.paintAlignment(true);
3771   }
3772
3773   /**
3774    * DOCUMENT ME!
3775    *
3776    * @param e
3777    *          DOCUMENT ME!
3778    */
3779   @Override
3780   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3781   {
3782     new RedundancyPanel(alignPanel, this);
3783   }
3784
3785   /**
3786    * DOCUMENT ME!
3787    *
3788    * @param e
3789    *          DOCUMENT ME!
3790    */
3791   @Override
3792   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3793   {
3794     if ((viewport.getSelectionGroup() == null)
3795             || (viewport.getSelectionGroup().getSize() < 2))
3796     {
3797       JOptionPane.showInternalMessageDialog(this, MessageManager
3798               .getString("label.you_must_select_least_two_sequences"),
3799               MessageManager.getString("label.invalid_selection"),
3800               JOptionPane.WARNING_MESSAGE);
3801     }
3802     else
3803     {
3804       JInternalFrame frame = new JInternalFrame();
3805       frame.setContentPane(new PairwiseAlignPanel(viewport));
3806       Desktop.addInternalFrame(frame,
3807               MessageManager.getString("action.pairwise_alignment"), 600,
3808               500);
3809     }
3810   }
3811
3812   /**
3813    * DOCUMENT ME!
3814    *
3815    * @param e
3816    *          DOCUMENT ME!
3817    */
3818   @Override
3819   public void PCAMenuItem_actionPerformed(ActionEvent e)
3820   {
3821     if (((viewport.getSelectionGroup() != null)
3822             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3823             .getSelectionGroup().getSize() > 0))
3824             || (viewport.getAlignment().getHeight() < 4))
3825     {
3826       JOptionPane
3827               .showInternalMessageDialog(
3828                       this,
3829                       MessageManager
3830                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3831                       MessageManager
3832                               .getString("label.sequence_selection_insufficient"),
3833                       JOptionPane.WARNING_MESSAGE);
3834
3835       return;
3836     }
3837
3838     new PCAPanel(alignPanel);
3839   }
3840
3841   @Override
3842   public void autoCalculate_actionPerformed(ActionEvent e)
3843   {
3844     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3845     if (viewport.autoCalculateConsensus)
3846     {
3847       viewport.firePropertyChange("alignment", null, viewport
3848               .getAlignment().getSequences());
3849     }
3850   }
3851
3852   @Override
3853   public void sortByTreeOption_actionPerformed(ActionEvent e)
3854   {
3855     viewport.sortByTree = sortByTree.isSelected();
3856   }
3857
3858   @Override
3859   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3860   {
3861     viewport.followSelection = listenToViewSelections.isSelected();
3862   }
3863
3864   /**
3865    * DOCUMENT ME!
3866    *
3867    * @param e
3868    *          DOCUMENT ME!
3869    */
3870   @Override
3871   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3872   {
3873     newTreePanel("AV", "PID", "Average distance tree using PID");
3874   }
3875
3876   /**
3877    * DOCUMENT ME!
3878    *
3879    * @param e
3880    *          DOCUMENT ME!
3881    */
3882   @Override
3883   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3884   {
3885     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3886   }
3887
3888   /**
3889    * DOCUMENT ME!
3890    *
3891    * @param e
3892    *          DOCUMENT ME!
3893    */
3894   @Override
3895   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3896   {
3897     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3898   }
3899
3900   /**
3901    * DOCUMENT ME!
3902    *
3903    * @param e
3904    *          DOCUMENT ME!
3905    */
3906   @Override
3907   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3908   {
3909     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3910   }
3911
3912   /**
3913    * DOCUMENT ME!
3914    *
3915    * @param type
3916    *          DOCUMENT ME!
3917    * @param pwType
3918    *          DOCUMENT ME!
3919    * @param title
3920    *          DOCUMENT ME!
3921    */
3922   void newTreePanel(String type, String pwType, String title)
3923   {
3924     TreePanel tp;
3925
3926     if (viewport.getSelectionGroup() != null
3927             && viewport.getSelectionGroup().getSize() > 0)
3928     {
3929       if (viewport.getSelectionGroup().getSize() < 3)
3930       {
3931         JOptionPane
3932                 .showMessageDialog(
3933                         Desktop.desktop,
3934                         MessageManager
3935                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3936                         MessageManager
3937                                 .getString("label.not_enough_sequences"),
3938                         JOptionPane.WARNING_MESSAGE);
3939         return;
3940       }
3941
3942       SequenceGroup sg = viewport.getSelectionGroup();
3943
3944       /* Decide if the selection is a column region */
3945       for (SequenceI _s : sg.getSequences())
3946       {
3947         if (_s.getLength() < sg.getEndRes())
3948         {
3949           JOptionPane
3950                   .showMessageDialog(
3951                           Desktop.desktop,
3952                           MessageManager
3953                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3954                           MessageManager
3955                                   .getString("label.sequences_selection_not_aligned"),
3956                           JOptionPane.WARNING_MESSAGE);
3957
3958           return;
3959         }
3960       }
3961
3962       title = title + " on region";
3963       tp = new TreePanel(alignPanel, type, pwType);
3964     }
3965     else
3966     {
3967       // are the visible sequences aligned?
3968       if (!viewport.getAlignment().isAligned(false))
3969       {
3970         JOptionPane
3971                 .showMessageDialog(
3972                         Desktop.desktop,
3973                         MessageManager
3974                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3975                         MessageManager
3976                                 .getString("label.sequences_not_aligned"),
3977                         JOptionPane.WARNING_MESSAGE);
3978
3979         return;
3980       }
3981
3982       if (viewport.getAlignment().getHeight() < 2)
3983       {
3984         return;
3985       }
3986
3987       tp = new TreePanel(alignPanel, type, pwType);
3988     }
3989
3990     title += " from ";
3991
3992     if (viewport.viewName != null)
3993     {
3994       title += viewport.viewName + " of ";
3995     }
3996
3997     title += this.title;
3998
3999     Desktop.addInternalFrame(tp, title, 600, 500);
4000   }
4001
4002   /**
4003    * DOCUMENT ME!
4004    *
4005    * @param title
4006    *          DOCUMENT ME!
4007    * @param order
4008    *          DOCUMENT ME!
4009    */
4010   public void addSortByOrderMenuItem(String title,
4011           final AlignmentOrder order)
4012   {
4013     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4014             "action.by_title_param", new Object[] { title }));
4015     sort.add(item);
4016     item.addActionListener(new java.awt.event.ActionListener()
4017     {
4018       @Override
4019       public void actionPerformed(ActionEvent e)
4020       {
4021         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4022
4023         // TODO: JBPNote - have to map order entries to curent SequenceI
4024         // pointers
4025         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4026
4027         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4028                 .getAlignment()));
4029
4030         alignPanel.paintAlignment(true);
4031       }
4032     });
4033   }
4034
4035   /**
4036    * Add a new sort by annotation score menu item
4037    *
4038    * @param sort
4039    *          the menu to add the option to
4040    * @param scoreLabel
4041    *          the label used to retrieve scores for each sequence on the
4042    *          alignment
4043    */
4044   public void addSortByAnnotScoreMenuItem(JMenu sort,
4045           final String scoreLabel)
4046   {
4047     final JMenuItem item = new JMenuItem(scoreLabel);
4048     sort.add(item);
4049     item.addActionListener(new java.awt.event.ActionListener()
4050     {
4051       @Override
4052       public void actionPerformed(ActionEvent e)
4053       {
4054         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4055         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4056                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4057         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4058                 viewport.getAlignment()));
4059         alignPanel.paintAlignment(true);
4060       }
4061     });
4062   }
4063
4064   /**
4065    * last hash for alignment's annotation array - used to minimise cost of
4066    * rebuild.
4067    */
4068   protected int _annotationScoreVectorHash;
4069
4070   /**
4071    * search the alignment and rebuild the sort by annotation score submenu the
4072    * last alignment annotation vector hash is stored to minimize cost of
4073    * rebuilding in subsequence calls.
4074    *
4075    */
4076   @Override
4077   public void buildSortByAnnotationScoresMenu()
4078   {
4079     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4080     {
4081       return;
4082     }
4083
4084     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4085     {
4086       sortByAnnotScore.removeAll();
4087       // almost certainly a quicker way to do this - but we keep it simple
4088       Hashtable scoreSorts = new Hashtable();
4089       AlignmentAnnotation aann[];
4090       for (SequenceI sqa : viewport.getAlignment().getSequences())
4091       {
4092         aann = sqa.getAnnotation();
4093         for (int i = 0; aann != null && i < aann.length; i++)
4094         {
4095           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4096           {
4097             scoreSorts.put(aann[i].label, aann[i].label);
4098           }
4099         }
4100       }
4101       Enumeration labels = scoreSorts.keys();
4102       while (labels.hasMoreElements())
4103       {
4104         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4105                 (String) labels.nextElement());
4106       }
4107       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4108       scoreSorts.clear();
4109
4110       _annotationScoreVectorHash = viewport.getAlignment()
4111               .getAlignmentAnnotation().hashCode();
4112     }
4113   }
4114
4115   /**
4116    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4117    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4118    * call. Listeners are added to remove the menu item when the treePanel is
4119    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4120    * modified.
4121    *
4122    * @param treePanel
4123    *          Displayed tree window.
4124    * @param title
4125    *          SortBy menu item title.
4126    */
4127   @Override
4128   public void buildTreeMenu()
4129   {
4130     calculateTree.removeAll();
4131     // build the calculate menu
4132
4133     for (final String type : new String[] { "NJ", "AV" })
4134     {
4135       String treecalcnm = MessageManager.getString("label.tree_calc_"
4136               + type.toLowerCase());
4137       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4138       {
4139         JMenuItem tm = new JMenuItem();
4140         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4141         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4142                 || sm.isProtein() == !viewport.getAlignment()
4143                         .isNucleotide())
4144         {
4145           String smn = MessageManager.getStringOrReturn(
4146                   "label.score_model_", sm.getName());
4147           final String title = MessageManager.formatMessage(
4148                   "label.treecalc_title", treecalcnm, smn);
4149           tm.setText(title);//
4150           tm.addActionListener(new java.awt.event.ActionListener()
4151           {
4152             @Override
4153             public void actionPerformed(ActionEvent e)
4154             {
4155               newTreePanel(type, pwtype, title);
4156             }
4157           });
4158           calculateTree.add(tm);
4159         }
4160
4161       }
4162     }
4163     sortByTreeMenu.removeAll();
4164
4165     List<Component> comps = PaintRefresher.components.get(viewport
4166             .getSequenceSetId());
4167     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4168     for (Component comp : comps)
4169     {
4170       if (comp instanceof TreePanel)
4171       {
4172         treePanels.add((TreePanel) comp);
4173       }
4174     }
4175
4176     if (treePanels.size() < 1)
4177     {
4178       sortByTreeMenu.setVisible(false);
4179       return;
4180     }
4181
4182     sortByTreeMenu.setVisible(true);
4183
4184     for (final TreePanel tp : treePanels)
4185     {
4186       final JMenuItem item = new JMenuItem(tp.getTitle());
4187       item.addActionListener(new java.awt.event.ActionListener()
4188       {
4189         @Override
4190         public void actionPerformed(ActionEvent e)
4191         {
4192           tp.sortByTree_actionPerformed();
4193           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4194
4195         }
4196       });
4197
4198       sortByTreeMenu.add(item);
4199     }
4200   }
4201
4202   public boolean sortBy(AlignmentOrder alorder, String undoname)
4203   {
4204     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4205     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4206     if (undoname != null)
4207     {
4208       addHistoryItem(new OrderCommand(undoname, oldOrder,
4209               viewport.getAlignment()));
4210     }
4211     alignPanel.paintAlignment(true);
4212     return true;
4213   }
4214
4215   /**
4216    * Work out whether the whole set of sequences or just the selected set will
4217    * be submitted for multiple alignment.
4218    *
4219    */
4220   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4221   {
4222     // Now, check we have enough sequences
4223     AlignmentView msa = null;
4224
4225     if ((viewport.getSelectionGroup() != null)
4226             && (viewport.getSelectionGroup().getSize() > 1))
4227     {
4228       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4229       // some common interface!
4230       /*
4231        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4232        * SequenceI[sz = seqs.getSize(false)];
4233        *
4234        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4235        * seqs.getSequenceAt(i); }
4236        */
4237       msa = viewport.getAlignmentView(true);
4238     }
4239     else if (viewport.getSelectionGroup() != null
4240             && viewport.getSelectionGroup().getSize() == 1)
4241     {
4242       int option = JOptionPane.showConfirmDialog(this,
4243               MessageManager.getString("warn.oneseq_msainput_selection"),
4244               MessageManager.getString("label.invalid_selection"),
4245               JOptionPane.OK_CANCEL_OPTION);
4246       if (option == JOptionPane.OK_OPTION)
4247       {
4248         msa = viewport.getAlignmentView(false);
4249       }
4250     }
4251     else
4252     {
4253       msa = viewport.getAlignmentView(false);
4254     }
4255     return msa;
4256   }
4257
4258   /**
4259    * Decides what is submitted to a secondary structure prediction service: the
4260    * first sequence in the alignment, or in the current selection, or, if the
4261    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4262    * region or the whole alignment. (where the first sequence in the set is the
4263    * one that the prediction will be for).
4264    */
4265   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4266   {
4267     AlignmentView seqs = null;
4268
4269     if ((viewport.getSelectionGroup() != null)
4270             && (viewport.getSelectionGroup().getSize() > 0))
4271     {
4272       seqs = viewport.getAlignmentView(true);
4273     }
4274     else
4275     {
4276       seqs = viewport.getAlignmentView(false);
4277     }
4278     // limit sequences - JBPNote in future - could spawn multiple prediction
4279     // jobs
4280     // TODO: viewport.getAlignment().isAligned is a global state - the local
4281     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4282     if (!viewport.getAlignment().isAligned(false))
4283     {
4284       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4285       // TODO: if seqs.getSequences().length>1 then should really have warned
4286       // user!
4287
4288     }
4289     return seqs;
4290   }
4291
4292   /**
4293    * DOCUMENT ME!
4294    *
4295    * @param e
4296    *          DOCUMENT ME!
4297    */
4298   @Override
4299   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4300   {
4301     // Pick the tree file
4302     JalviewFileChooser chooser = new JalviewFileChooser(
4303             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4304     chooser.setFileView(new JalviewFileView());
4305     chooser.setDialogTitle(MessageManager
4306             .getString("label.select_newick_like_tree_file"));
4307     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4308
4309     int value = chooser.showOpenDialog(null);
4310
4311     if (value == JalviewFileChooser.APPROVE_OPTION)
4312     {
4313       String choice = chooser.getSelectedFile().getPath();
4314       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4315       jalview.io.NewickFile fin = null;
4316       try
4317       {
4318         fin = new jalview.io.NewickFile(choice, "File");
4319         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4320       } catch (Exception ex)
4321       {
4322         JOptionPane
4323                 .showMessageDialog(
4324                         Desktop.desktop,
4325                         ex.getMessage(),
4326                         MessageManager
4327                                 .getString("label.problem_reading_tree_file"),
4328                         JOptionPane.WARNING_MESSAGE);
4329         ex.printStackTrace();
4330       }
4331       if (fin != null && fin.hasWarningMessage())
4332       {
4333         JOptionPane.showMessageDialog(Desktop.desktop, fin
4334                 .getWarningMessage(), MessageManager
4335                 .getString("label.possible_problem_with_tree_file"),
4336                 JOptionPane.WARNING_MESSAGE);
4337       }
4338     }
4339   }
4340
4341   @Override
4342   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4343   {
4344     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4345   }
4346
4347   public TreePanel ShowNewickTree(NewickFile nf, String title)
4348   {
4349     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4350   }
4351
4352   public TreePanel ShowNewickTree(NewickFile nf, String title,
4353           AlignmentView input)
4354   {
4355     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4356   }
4357
4358   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4359           int h, int x, int y)
4360   {
4361     return ShowNewickTree(nf, title, null, w, h, x, y);
4362   }
4363
4364   /**
4365    * Add a treeviewer for the tree extracted from a newick file object to the
4366    * current alignment view
4367    *
4368    * @param nf
4369    *          the tree
4370    * @param title
4371    *          tree viewer title
4372    * @param input
4373    *          Associated alignment input data (or null)
4374    * @param w
4375    *          width
4376    * @param h
4377    *          height
4378    * @param x
4379    *          position
4380    * @param y
4381    *          position
4382    * @return TreePanel handle
4383    */
4384   public TreePanel ShowNewickTree(NewickFile nf, String title,
4385           AlignmentView input, int w, int h, int x, int y)
4386   {
4387     TreePanel tp = null;
4388
4389     try
4390     {
4391       nf.parse();
4392
4393       if (nf.getTree() != null)
4394       {
4395         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4396
4397         tp.setSize(w, h);
4398
4399         if (x > 0 && y > 0)
4400         {
4401           tp.setLocation(x, y);
4402         }
4403
4404         Desktop.addInternalFrame(tp, title, w, h);
4405       }
4406     } catch (Exception ex)
4407     {
4408       ex.printStackTrace();
4409     }
4410
4411     return tp;
4412   }
4413
4414   private boolean buildingMenu = false;
4415
4416   /**
4417    * Generates menu items and listener event actions for web service clients
4418    *
4419    */
4420   public void BuildWebServiceMenu()
4421   {
4422     while (buildingMenu)
4423     {
4424       try
4425       {
4426         System.err.println("Waiting for building menu to finish.");
4427         Thread.sleep(10);
4428       } catch (Exception e)
4429       {
4430       }
4431     }
4432     final AlignFrame me = this;
4433     buildingMenu = true;
4434     new Thread(new Runnable()
4435     {
4436       @Override
4437       public void run()
4438       {
4439         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4440         try
4441         {
4442           // System.err.println("Building ws menu again "
4443           // + Thread.currentThread());
4444           // TODO: add support for context dependent disabling of services based
4445           // on
4446           // alignment and current selection
4447           // TODO: add additional serviceHandle parameter to specify abstract
4448           // handler
4449           // class independently of AbstractName
4450           // TODO: add in rediscovery GUI function to restart discoverer
4451           // TODO: group services by location as well as function and/or
4452           // introduce
4453           // object broker mechanism.
4454           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4455           final IProgressIndicator af = me;
4456
4457           /*
4458            * do not i18n these strings - they are hard-coded in class
4459            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4460            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4461            */
4462           final JMenu msawsmenu = new JMenu("Alignment");
4463           final JMenu secstrmenu = new JMenu(
4464                   "Secondary Structure Prediction");
4465           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4466           final JMenu analymenu = new JMenu("Analysis");
4467           final JMenu dismenu = new JMenu("Protein Disorder");
4468           // JAL-940 - only show secondary structure prediction services from
4469           // the legacy server
4470           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4471               // &&
4472           Discoverer.services != null && (Discoverer.services.size() > 0))
4473           {
4474             // TODO: refactor to allow list of AbstractName/Handler bindings to
4475             // be
4476             // stored or retrieved from elsewhere
4477             // No MSAWS used any more:
4478             // Vector msaws = null; // (Vector)
4479             // Discoverer.services.get("MsaWS");
4480             Vector secstrpr = (Vector) Discoverer.services
4481                     .get("SecStrPred");
4482             if (secstrpr != null)
4483             {
4484               // Add any secondary structure prediction services
4485               for (int i = 0, j = secstrpr.size(); i < j; i++)
4486               {
4487                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4488                         .get(i);
4489                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4490                         .getServiceClient(sh);
4491                 int p = secstrmenu.getItemCount();
4492                 impl.attachWSMenuEntry(secstrmenu, me);
4493                 int q = secstrmenu.getItemCount();
4494                 for (int litm = p; litm < q; litm++)
4495                 {
4496                   legacyItems.add(secstrmenu.getItem(litm));
4497                 }
4498               }
4499             }
4500           }
4501
4502           // Add all submenus in the order they should appear on the web
4503           // services menu
4504           wsmenu.add(msawsmenu);
4505           wsmenu.add(secstrmenu);
4506           wsmenu.add(dismenu);
4507           wsmenu.add(analymenu);
4508           // No search services yet
4509           // wsmenu.add(seqsrchmenu);
4510
4511           javax.swing.SwingUtilities.invokeLater(new Runnable()
4512           {
4513             @Override
4514             public void run()
4515             {
4516               try
4517               {
4518                 webService.removeAll();
4519                 // first, add discovered services onto the webservices menu
4520                 if (wsmenu.size() > 0)
4521                 {
4522                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4523                   {
4524                     webService.add(wsmenu.get(i));
4525                   }
4526                 }
4527                 else
4528                 {
4529                   webService.add(me.webServiceNoServices);
4530                 }
4531                 // TODO: move into separate menu builder class.
4532                 boolean new_sspred = false;
4533                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4534                 {
4535                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4536                   if (jws2servs != null)
4537                   {
4538                     if (jws2servs.hasServices())
4539                     {
4540                       jws2servs.attachWSMenuEntry(webService, me);
4541                       for (Jws2Instance sv : jws2servs.getServices())
4542                       {
4543                         if (sv.description.toLowerCase().contains("jpred"))
4544                         {
4545                           for (JMenuItem jmi : legacyItems)
4546                           {
4547                             jmi.setVisible(false);
4548                           }
4549                         }
4550                       }
4551
4552                     }
4553                     if (jws2servs.isRunning())
4554                     {
4555                       JMenuItem tm = new JMenuItem(
4556                               "Still discovering JABA Services");
4557                       tm.setEnabled(false);
4558                       webService.add(tm);
4559                     }
4560                   }
4561                 }
4562                 build_urlServiceMenu(me.webService);
4563                 build_fetchdbmenu(webService);
4564                 for (JMenu item : wsmenu)
4565                 {
4566                   if (item.getItemCount() == 0)
4567                   {
4568                     item.setEnabled(false);
4569                   }
4570                   else
4571                   {
4572                     item.setEnabled(true);
4573                   }
4574                 }
4575               } catch (Exception e)
4576               {
4577                 Cache.log
4578                         .debug("Exception during web service menu building process.",
4579                                 e);
4580               }
4581             }
4582           });
4583         } catch (Exception e)
4584         {
4585         }
4586         buildingMenu = false;
4587       }
4588     }).start();
4589
4590   }
4591
4592   /**
4593    * construct any groupURL type service menu entries.
4594    *
4595    * @param webService
4596    */
4597   private void build_urlServiceMenu(JMenu webService)
4598   {
4599     // TODO: remove this code when 2.7 is released
4600     // DEBUG - alignmentView
4601     /*
4602      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4603      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4604      *
4605      * @Override public void actionPerformed(ActionEvent e) {
4606      * jalview.datamodel.AlignmentView
4607      * .testSelectionViews(af.viewport.getAlignment(),
4608      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4609      *
4610      * }); webService.add(testAlView);
4611      */
4612     // TODO: refactor to RestClient discoverer and merge menu entries for
4613     // rest-style services with other types of analysis/calculation service
4614     // SHmmr test client - still being implemented.
4615     // DEBUG - alignmentView
4616
4617     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4618             .getRestClients())
4619     {
4620       client.attachWSMenuEntry(
4621               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4622               this);
4623     }
4624   }
4625
4626   /**
4627    * Searches the alignment sequences for xRefs and builds the Show
4628    * Cross-References menu (formerly called Show Products), with database
4629    * sources for which cross-references are found (protein sources for a
4630    * nucleotide alignment and vice versa)
4631    *
4632    * @return true if Show Cross-references menu should be enabled
4633    */
4634   public boolean canShowProducts()
4635   {
4636     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4637     AlignmentI dataset = viewport.getAlignment().getDataset();
4638
4639     showProducts.removeAll();
4640     final boolean dna = viewport.getAlignment().isNucleotide();
4641
4642     if (seqs == null || seqs.length == 0)
4643     {
4644       // nothing to see here.
4645       return false;
4646     }
4647
4648     boolean showp = false;
4649     try
4650     {
4651       List<String> ptypes = new CrossRef(seqs, dataset)
4652               .findXrefSourcesForSequences(dna);
4653
4654       for (final String source : ptypes)
4655       {
4656         showp = true;
4657         final AlignFrame af = this;
4658         JMenuItem xtype = new JMenuItem(source);
4659         xtype.addActionListener(new ActionListener()
4660         {
4661           @Override
4662           public void actionPerformed(ActionEvent e)
4663           {
4664             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4665           }
4666         });
4667         showProducts.add(xtype);
4668       }
4669       showProducts.setVisible(showp);
4670       showProducts.setEnabled(showp);
4671     } catch (Exception e)
4672     {
4673       Cache.log
4674               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4675                       e);
4676       return false;
4677     }
4678     return showp;
4679   }
4680
4681   /**
4682    * Finds and displays cross-references for the selected sequences (protein
4683    * products for nucleotide sequences, dna coding sequences for peptides).
4684    *
4685    * @param sel
4686    *          the sequences to show cross-references for
4687    * @param dna
4688    *          true if from a nucleotide alignment (so showing proteins)
4689    * @param source
4690    *          the database to show cross-references for
4691    */
4692   protected void showProductsFor(final SequenceI[] sel,
4693           final boolean _odna, final String source)
4694   {
4695     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4696             .start();
4697   }
4698
4699   /**
4700    * Construct and display a new frame containing the translation of this
4701    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4702    */
4703   @Override
4704   public void showTranslation_actionPerformed(ActionEvent e)
4705   {
4706     AlignmentI al = null;
4707     try
4708     {
4709       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4710
4711       al = dna.translateCdna();
4712     } catch (Exception ex)
4713     {
4714       jalview.bin.Cache.log.error(
4715               "Exception during translation. Please report this !", ex);
4716       final String msg = MessageManager
4717               .getString("label.error_when_translating_sequences_submit_bug_report");
4718       final String errorTitle = MessageManager
4719               .getString("label.implementation_error")
4720               + MessageManager.getString("label.translation_failed");
4721       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4722               JOptionPane.ERROR_MESSAGE);
4723       return;
4724     }
4725     if (al == null || al.getHeight() == 0)
4726     {
4727       final String msg = MessageManager
4728               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4729       final String errorTitle = MessageManager
4730               .getString("label.translation_failed");
4731       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4732               JOptionPane.WARNING_MESSAGE);
4733     }
4734     else
4735     {
4736       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4737       af.setFileFormat(this.currentFileFormat);
4738       final String newTitle = MessageManager.formatMessage(
4739               "label.translation_of_params",
4740               new Object[] { this.getTitle() });
4741       af.setTitle(newTitle);
4742       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4743       {
4744         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4745         viewport.openSplitFrame(af, new Alignment(seqs));
4746       }
4747       else
4748       {
4749         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4750                 DEFAULT_HEIGHT);
4751       }
4752     }
4753   }
4754
4755   /**
4756    * Set the file format
4757    *
4758    * @param fileFormat
4759    */
4760   public void setFileFormat(String fileFormat)
4761   {
4762     this.currentFileFormat = fileFormat;
4763   }
4764
4765   /**
4766    * Try to load a features file onto the alignment.
4767    *
4768    * @param file
4769    *          contents or path to retrieve file
4770    * @param type
4771    *          access mode of file (see jalview.io.AlignFile)
4772    * @return true if features file was parsed correctly.
4773    */
4774   public boolean parseFeaturesFile(String file, String type)
4775   {
4776     return avc.parseFeaturesFile(file, type,
4777             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4778
4779   }
4780
4781   @Override
4782   public void refreshFeatureUI(boolean enableIfNecessary)
4783   {
4784     // note - currently this is only still here rather than in the controller
4785     // because of the featureSettings hard reference that is yet to be
4786     // abstracted
4787     if (enableIfNecessary)
4788     {
4789       viewport.setShowSequenceFeatures(true);
4790       showSeqFeatures.setSelected(true);
4791     }
4792
4793   }
4794
4795   @Override
4796   public void dragEnter(DropTargetDragEvent evt)
4797   {
4798   }
4799
4800   @Override
4801   public void dragExit(DropTargetEvent evt)
4802   {
4803   }
4804
4805   @Override
4806   public void dragOver(DropTargetDragEvent evt)
4807   {
4808   }
4809
4810   @Override
4811   public void dropActionChanged(DropTargetDragEvent evt)
4812   {
4813   }
4814
4815   @Override
4816   public void drop(DropTargetDropEvent evt)
4817   {
4818     // JAL-1552 - acceptDrop required before getTransferable call for
4819     // Java's Transferable for native dnd
4820     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4821     Transferable t = evt.getTransferable();
4822     java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
4823
4824     try
4825     {
4826       Desktop.transferFromDropTarget(files, protocols, evt, t);
4827     } catch (Exception e)
4828     {
4829       e.printStackTrace();
4830     }
4831     if (files != null)
4832     {
4833       try
4834       {
4835         // check to see if any of these files have names matching sequences in
4836         // the alignment
4837         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4838                 .getAlignment().getSequencesArray());
4839         /**
4840          * Object[] { String,SequenceI}
4841          */
4842         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4843         ArrayList<String> filesnotmatched = new ArrayList<String>();
4844         for (int i = 0; i < files.size(); i++)
4845         {
4846           String file = files.get(i).toString();
4847           String pdbfn = "";
4848           String protocol = FormatAdapter.checkProtocol(file);
4849           if (protocol == jalview.io.FormatAdapter.FILE)
4850           {
4851             File fl = new File(file);
4852             pdbfn = fl.getName();
4853           }
4854           else if (protocol == jalview.io.FormatAdapter.URL)
4855           {
4856             URL url = new URL(file);
4857             pdbfn = url.getFile();
4858           }
4859           if (pdbfn.length() > 0)
4860           {
4861             // attempt to find a match in the alignment
4862             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4863             int l = 0, c = pdbfn.indexOf(".");
4864             while (mtch == null && c != -1)
4865             {
4866               do
4867               {
4868                 l = c;
4869               } while ((c = pdbfn.indexOf(".", l)) > l);
4870               if (l > -1)
4871               {
4872                 pdbfn = pdbfn.substring(0, l);
4873               }
4874               mtch = idm.findAllIdMatches(pdbfn);
4875             }
4876             if (mtch != null)
4877             {
4878               String type = null;
4879               try
4880               {
4881                 type = new IdentifyFile().identify(file, protocol);
4882               } catch (Exception ex)
4883               {
4884                 type = null;
4885               }
4886               if (type != null)
4887               {
4888                 if (type.equalsIgnoreCase("PDB"))
4889                 {
4890                   filesmatched.add(new Object[] { file, protocol, mtch });
4891                   continue;
4892                 }
4893               }
4894             }
4895             // File wasn't named like one of the sequences or wasn't a PDB file.
4896             filesnotmatched.add(file);
4897           }
4898         }
4899         int assocfiles = 0;
4900         if (filesmatched.size() > 0)
4901         {
4902           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4903                   || JOptionPane
4904                           .showConfirmDialog(
4905                                   this,
4906                                   MessageManager
4907                                           .formatMessage(
4908                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
4909                                                   new Object[] { Integer
4910                                                           .valueOf(
4911                                                                   filesmatched
4912                                                                           .size())
4913                                                           .toString() }),
4914                                   MessageManager
4915                                           .getString("label.automatically_associate_pdb_files_by_name"),
4916                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4917
4918           {
4919             for (Object[] fm : filesmatched)
4920             {
4921               // try and associate
4922               // TODO: may want to set a standard ID naming formalism for
4923               // associating PDB files which have no IDs.
4924               for (SequenceI toassoc : (SequenceI[]) fm[2])
4925               {
4926                 PDBEntry pe = new AssociatePdbFileWithSeq()
4927                         .associatePdbWithSeq((String) fm[0],
4928                                 (String) fm[1], toassoc, false,
4929                                 Desktop.instance);
4930                 if (pe != null)
4931                 {
4932                   System.err.println("Associated file : "
4933                           + ((String) fm[0]) + " with "
4934                           + toassoc.getDisplayId(true));
4935                   assocfiles++;
4936                 }
4937               }
4938               alignPanel.paintAlignment(true);
4939             }
4940           }
4941         }
4942         if (filesnotmatched.size() > 0)
4943         {
4944           if (assocfiles > 0
4945                   && (Cache.getDefault(
4946                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4947                           .showConfirmDialog(
4948                                   this,
4949                                   "<html>"
4950                                           + MessageManager
4951                                                   .formatMessage(
4952                                                           "label.ignore_unmatched_dropped_files_info",
4953                                                           new Object[] { Integer
4954                                                                   .valueOf(
4955                                                                           filesnotmatched
4956                                                                                   .size())
4957                                                                   .toString() })
4958                                           + "</html>",
4959                                   MessageManager
4960                                           .getString("label.ignore_unmatched_dropped_files"),
4961                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4962           {
4963             return;
4964           }
4965           for (String fn : filesnotmatched)
4966           {
4967             loadJalviewDataFile(fn, null, null, null);
4968           }
4969
4970         }
4971       } catch (Exception ex)
4972       {
4973         ex.printStackTrace();
4974       }
4975     }
4976   }
4977
4978   /**
4979    * Attempt to load a "dropped" file or URL string: First by testing whether
4980    * it's an Annotation file, then a JNet file, and finally a features file. If
4981    * all are false then the user may have dropped an alignment file onto this
4982    * AlignFrame.
4983    *
4984    * @param file
4985    *          either a filename or a URL string.
4986    */
4987   public void loadJalviewDataFile(String file, String protocol,
4988           String format, SequenceI assocSeq)
4989   {
4990     try
4991     {
4992       if (protocol == null)
4993       {
4994         protocol = FormatAdapter.checkProtocol(file);
4995       }
4996       // if the file isn't identified, or not positively identified as some
4997       // other filetype (PFAM is default unidentified alignment file type) then
4998       // try to parse as annotation.
4999       boolean isAnnotation = (format == null || format
5000               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5001               .annotateAlignmentView(viewport, file, protocol) : false;
5002
5003       if (!isAnnotation)
5004       {
5005         // first see if its a T-COFFEE score file
5006         TCoffeeScoreFile tcf = null;
5007         try
5008         {
5009           tcf = new TCoffeeScoreFile(file, protocol);
5010           if (tcf.isValid())
5011           {
5012             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5013             {
5014               tcoffeeColour.setEnabled(true);
5015               tcoffeeColour.setSelected(true);
5016               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5017               isAnnotation = true;
5018               statusBar
5019                       .setText(MessageManager
5020                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5021             }
5022             else
5023             {
5024               // some problem - if no warning its probable that the ID matching
5025               // process didn't work
5026               JOptionPane
5027                       .showMessageDialog(
5028                               Desktop.desktop,
5029                               tcf.getWarningMessage() == null ? MessageManager
5030                                       .getString("label.check_file_matches_sequence_ids_alignment")
5031                                       : tcf.getWarningMessage(),
5032                               MessageManager
5033                                       .getString("label.problem_reading_tcoffee_score_file"),
5034                               JOptionPane.WARNING_MESSAGE);
5035             }
5036           }
5037           else
5038           {
5039             tcf = null;
5040           }
5041         } catch (Exception x)
5042         {
5043           Cache.log
5044                   .debug("Exception when processing data source as T-COFFEE score file",
5045                           x);
5046           tcf = null;
5047         }
5048         if (tcf == null)
5049         {
5050           // try to see if its a JNet 'concise' style annotation file *before*
5051           // we
5052           // try to parse it as a features file
5053           if (format == null)
5054           {
5055             format = new IdentifyFile().identify(file, protocol);
5056           }
5057           if (format.equalsIgnoreCase("JnetFile"))
5058           {
5059             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5060                     file, protocol);
5061             new JnetAnnotationMaker();
5062             JnetAnnotationMaker.add_annotation(predictions,
5063                     viewport.getAlignment(), 0, false);
5064             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5065             viewport.getAlignment().setSeqrep(repseq);
5066             ColumnSelection cs = new ColumnSelection();
5067             cs.hideInsertionsFor(repseq);
5068             viewport.setColumnSelection(cs);
5069             isAnnotation = true;
5070           }
5071           else if (IdentifyFile.FeaturesFile.equals(format))
5072           {
5073             if (parseFeaturesFile(file, protocol))
5074             {
5075               alignPanel.paintAlignment(true);
5076             }
5077           }
5078           else
5079           {
5080             new FileLoader().LoadFile(viewport, file, protocol, format);
5081           }
5082         }
5083       }
5084       if (isAnnotation)
5085       {
5086
5087         alignPanel.adjustAnnotationHeight();
5088         viewport.updateSequenceIdColours();
5089         buildSortByAnnotationScoresMenu();
5090         alignPanel.paintAlignment(true);
5091       }
5092     } catch (Exception ex)
5093     {
5094       ex.printStackTrace();
5095     } catch (OutOfMemoryError oom)
5096     {
5097       try
5098       {
5099         System.gc();
5100       } catch (Exception x)
5101       {
5102       }
5103       new OOMWarning(
5104               "loading data "
5105                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5106                               : "using " + protocol + " from " + file)
5107                               : ".")
5108                       + (format != null ? "(parsing as '" + format
5109                               + "' file)" : ""), oom, Desktop.desktop);
5110     }
5111   }
5112
5113   /**
5114    * Method invoked by the ChangeListener on the tabbed pane, in other words
5115    * when a different tabbed pane is selected by the user or programmatically.
5116    */
5117   @Override
5118   public void tabSelectionChanged(int index)
5119   {
5120     if (index > -1)
5121     {
5122       alignPanel = alignPanels.get(index);
5123       viewport = alignPanel.av;
5124       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5125       setMenusFromViewport(viewport);
5126     }
5127
5128     /*
5129      * If there is a frame linked to this one in a SplitPane, switch it to the
5130      * same view tab index. No infinite recursion of calls should happen, since
5131      * tabSelectionChanged() should not get invoked on setting the selected
5132      * index to an unchanged value. Guard against setting an invalid index
5133      * before the new view peer tab has been created.
5134      */
5135     final AlignViewportI peer = viewport.getCodingComplement();
5136     if (peer != null)
5137     {
5138       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5139       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5140       {
5141         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5142       }
5143     }
5144   }
5145
5146   /**
5147    * On right mouse click on view tab, prompt for and set new view name.
5148    */
5149   @Override
5150   public void tabbedPane_mousePressed(MouseEvent e)
5151   {
5152     if (e.isPopupTrigger())
5153     {
5154       String msg = MessageManager.getString("label.enter_view_name");
5155       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5156               JOptionPane.QUESTION_MESSAGE);
5157
5158       if (reply != null)
5159       {
5160         viewport.viewName = reply;
5161         // TODO warn if reply is in getExistingViewNames()?
5162         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5163       }
5164     }
5165   }
5166
5167   public AlignViewport getCurrentView()
5168   {
5169     return viewport;
5170   }
5171
5172   /**
5173    * Open the dialog for regex description parsing.
5174    */
5175   @Override
5176   protected void extractScores_actionPerformed(ActionEvent e)
5177   {
5178     ParseProperties pp = new jalview.analysis.ParseProperties(
5179             viewport.getAlignment());
5180     // TODO: verify regex and introduce GUI dialog for version 2.5
5181     // if (pp.getScoresFromDescription("col", "score column ",
5182     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5183     // true)>0)
5184     if (pp.getScoresFromDescription("description column",
5185             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5186     {
5187       buildSortByAnnotationScoresMenu();
5188     }
5189   }
5190
5191   /*
5192    * (non-Javadoc)
5193    *
5194    * @see
5195    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5196    * )
5197    */
5198   @Override
5199   protected void showDbRefs_actionPerformed(ActionEvent e)
5200   {
5201     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5202   }
5203
5204   /*
5205    * (non-Javadoc)
5206    *
5207    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5208    * ActionEvent)
5209    */
5210   @Override
5211   protected void showNpFeats_actionPerformed(ActionEvent e)
5212   {
5213     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5214   }
5215
5216   /**
5217    * find the viewport amongst the tabs in this alignment frame and close that
5218    * tab
5219    *
5220    * @param av
5221    */
5222   public boolean closeView(AlignViewportI av)
5223   {
5224     if (viewport == av)
5225     {
5226       this.closeMenuItem_actionPerformed(false);
5227       return true;
5228     }
5229     Component[] comp = tabbedPane.getComponents();
5230     for (int i = 0; comp != null && i < comp.length; i++)
5231     {
5232       if (comp[i] instanceof AlignmentPanel)
5233       {
5234         if (((AlignmentPanel) comp[i]).av == av)
5235         {
5236           // close the view.
5237           closeView((AlignmentPanel) comp[i]);
5238           return true;
5239         }
5240       }
5241     }
5242     return false;
5243   }
5244
5245   protected void build_fetchdbmenu(JMenu webService)
5246   {
5247     // Temporary hack - DBRef Fetcher always top level ws entry.
5248     // TODO We probably want to store a sequence database checklist in
5249     // preferences and have checkboxes.. rather than individual sources selected
5250     // here
5251     final JMenu rfetch = new JMenu(
5252             MessageManager.getString("action.fetch_db_references"));
5253     rfetch.setToolTipText(MessageManager
5254             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5255     webService.add(rfetch);
5256
5257     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5258             MessageManager.getString("option.trim_retrieved_seqs"));
5259     trimrs.setToolTipText(MessageManager
5260             .getString("label.trim_retrieved_sequences"));
5261     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5262     trimrs.addActionListener(new ActionListener()
5263     {
5264       @Override
5265       public void actionPerformed(ActionEvent e)
5266       {
5267         trimrs.setSelected(trimrs.isSelected());
5268         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5269                 Boolean.valueOf(trimrs.isSelected()).toString());
5270       };
5271     });
5272     rfetch.add(trimrs);
5273     JMenuItem fetchr = new JMenuItem(
5274             MessageManager.getString("label.standard_databases"));
5275     fetchr.setToolTipText(MessageManager
5276             .getString("label.fetch_embl_uniprot"));
5277     fetchr.addActionListener(new ActionListener()
5278     {
5279
5280       @Override
5281       public void actionPerformed(ActionEvent e)
5282       {
5283         new Thread(new Runnable()
5284         {
5285           @Override
5286           public void run()
5287           {
5288             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5289                     .getAlignment().isNucleotide();
5290             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5291                     .getSequenceSelection(), alignPanel.alignFrame, null,
5292                     alignPanel.alignFrame.featureSettings, isNucleotide);
5293             dbRefFetcher.addListener(new FetchFinishedListenerI()
5294             {
5295               @Override
5296               public void finished()
5297               {
5298                 AlignFrame.this.setMenusForViewport();
5299               }
5300             });
5301             dbRefFetcher.fetchDBRefs(false);
5302           }
5303         }).start();
5304
5305       }
5306
5307     });
5308     rfetch.add(fetchr);
5309     final AlignFrame me = this;
5310     new Thread(new Runnable()
5311     {
5312       @Override
5313       public void run()
5314       {
5315         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5316                 .getSequenceFetcherSingleton(me);
5317         javax.swing.SwingUtilities.invokeLater(new Runnable()
5318         {
5319           @Override
5320           public void run()
5321           {
5322             String[] dbclasses = sf.getOrderedSupportedSources();
5323             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5324             // jalview.util.QuickSort.sort(otherdb, otherdb);
5325             List<DbSourceProxy> otherdb;
5326             JMenu dfetch = new JMenu();
5327             JMenu ifetch = new JMenu();
5328             JMenuItem fetchr = null;
5329             int comp = 0, icomp = 0, mcomp = 15;
5330             String mname = null;
5331             int dbi = 0;
5332             for (String dbclass : dbclasses)
5333             {
5334               otherdb = sf.getSourceProxy(dbclass);
5335               // add a single entry for this class, or submenu allowing 'fetch
5336               // all' or pick one
5337               if (otherdb == null || otherdb.size() < 1)
5338               {
5339                 continue;
5340               }
5341               // List<DbSourceProxy> dbs=otherdb;
5342               // otherdb=new ArrayList<DbSourceProxy>();
5343               // for (DbSourceProxy db:dbs)
5344               // {
5345               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5346               // }
5347               if (mname == null)
5348               {
5349                 mname = "From " + dbclass;
5350               }
5351               if (otherdb.size() == 1)
5352               {
5353                 final DbSourceProxy[] dassource = otherdb
5354                         .toArray(new DbSourceProxy[0]);
5355                 DbSourceProxy src = otherdb.get(0);
5356                 fetchr = new JMenuItem(src.getDbSource());
5357                 fetchr.addActionListener(new ActionListener()
5358                 {
5359
5360                   @Override
5361                   public void actionPerformed(ActionEvent e)
5362                   {
5363                     new Thread(new Runnable()
5364                     {
5365
5366                       @Override
5367                       public void run()
5368                       {
5369                         boolean isNucleotide = alignPanel.alignFrame
5370                                 .getViewport().getAlignment()
5371                                 .isNucleotide();
5372                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5373                                 alignPanel.av.getSequenceSelection(),
5374                                 alignPanel.alignFrame, dassource,
5375                                 alignPanel.alignFrame.featureSettings,
5376                                 isNucleotide);
5377                         dbRefFetcher
5378                                 .addListener(new FetchFinishedListenerI()
5379                                 {
5380                                   @Override
5381                                   public void finished()
5382                                   {
5383                                     AlignFrame.this.setMenusForViewport();
5384                                   }
5385                                 });
5386                         dbRefFetcher.fetchDBRefs(false);
5387                       }
5388                     }).start();
5389                   }
5390
5391                 });
5392                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5393                         MessageManager.formatMessage(
5394                                 "label.fetch_retrieve_from",
5395                                 new Object[] { src.getDbName() })));
5396                 dfetch.add(fetchr);
5397                 comp++;
5398               }
5399               else
5400               {
5401                 final DbSourceProxy[] dassource = otherdb
5402                         .toArray(new DbSourceProxy[0]);
5403                 // fetch all entry
5404                 DbSourceProxy src = otherdb.get(0);
5405                 fetchr = new JMenuItem(MessageManager.formatMessage(
5406                         "label.fetch_all_param",
5407                         new Object[] { src.getDbSource() }));
5408                 fetchr.addActionListener(new ActionListener()
5409                 {
5410                   @Override
5411                   public void actionPerformed(ActionEvent e)
5412                   {
5413                     new Thread(new Runnable()
5414                     {
5415
5416                       @Override
5417                       public void run()
5418                       {
5419                         boolean isNucleotide = alignPanel.alignFrame
5420                                 .getViewport().getAlignment()
5421                                 .isNucleotide();
5422                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5423                                 alignPanel.av.getSequenceSelection(),
5424                                 alignPanel.alignFrame, dassource,
5425                                 alignPanel.alignFrame.featureSettings,
5426                                 isNucleotide);
5427                         dbRefFetcher
5428                                 .addListener(new FetchFinishedListenerI()
5429                                 {
5430                                   @Override
5431                                   public void finished()
5432                                   {
5433                                     AlignFrame.this.setMenusForViewport();
5434                                   }
5435                                 });
5436                         dbRefFetcher.fetchDBRefs(false);
5437                       }
5438                     }).start();
5439                   }
5440                 });
5441
5442                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5443                         MessageManager.formatMessage(
5444                                 "label.fetch_retrieve_from_all_sources",
5445                                 new Object[] {
5446                                     Integer.valueOf(otherdb.size())
5447                                             .toString(), src.getDbSource(),
5448                                     src.getDbName() })));
5449                 dfetch.add(fetchr);
5450                 comp++;
5451                 // and then build the rest of the individual menus
5452                 ifetch = new JMenu(MessageManager.formatMessage(
5453                         "label.source_from_db_source",
5454                         new Object[] { src.getDbSource() }));
5455                 icomp = 0;
5456                 String imname = null;
5457                 int i = 0;
5458                 for (DbSourceProxy sproxy : otherdb)
5459                 {
5460                   String dbname = sproxy.getDbName();
5461                   String sname = dbname.length() > 5 ? dbname.substring(0,
5462                           5) + "..." : dbname;
5463                   String msname = dbname.length() > 10 ? dbname.substring(
5464                           0, 10) + "..." : dbname;
5465                   if (imname == null)
5466                   {
5467                     imname = MessageManager.formatMessage(
5468                             "label.from_msname", new Object[] { sname });
5469                   }
5470                   fetchr = new JMenuItem(msname);
5471                   final DbSourceProxy[] dassrc = { sproxy };
5472                   fetchr.addActionListener(new ActionListener()
5473                   {
5474
5475                     @Override
5476                     public void actionPerformed(ActionEvent e)
5477                     {
5478                       new Thread(new Runnable()
5479                       {
5480
5481                         @Override
5482                         public void run()
5483                         {
5484                           boolean isNucleotide = alignPanel.alignFrame
5485                                   .getViewport().getAlignment()
5486                                   .isNucleotide();
5487                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5488                                   alignPanel.av.getSequenceSelection(),
5489                                   alignPanel.alignFrame, dassrc,
5490                                   alignPanel.alignFrame.featureSettings,
5491                                   isNucleotide);
5492                           dbRefFetcher
5493                                   .addListener(new FetchFinishedListenerI()
5494                                   {
5495                                     @Override
5496                                     public void finished()
5497                                     {
5498                                       AlignFrame.this.setMenusForViewport();
5499                                     }
5500                                   });
5501                           dbRefFetcher.fetchDBRefs(false);
5502                         }
5503                       }).start();
5504                     }
5505
5506                   });
5507                   fetchr.setToolTipText("<html>"
5508                           + MessageManager.formatMessage(
5509                                   "label.fetch_retrieve_from", new Object[]
5510                                   { dbname }));
5511                   ifetch.add(fetchr);
5512                   ++i;
5513                   if (++icomp >= mcomp || i == (otherdb.size()))
5514                   {
5515                     ifetch.setText(MessageManager.formatMessage(
5516                             "label.source_to_target", imname, sname));
5517                     dfetch.add(ifetch);
5518                     ifetch = new JMenu();
5519                     imname = null;
5520                     icomp = 0;
5521                     comp++;
5522                   }
5523                 }
5524               }
5525               ++dbi;
5526               if (comp >= mcomp || dbi >= (dbclasses.length))
5527               {
5528                 dfetch.setText(MessageManager.formatMessage(
5529                         "label.source_to_target", mname, dbclass));
5530                 rfetch.add(dfetch);
5531                 dfetch = new JMenu();
5532                 mname = null;
5533                 comp = 0;
5534               }
5535             }
5536           }
5537         });
5538       }
5539     }).start();
5540
5541   }
5542
5543   /**
5544    * Left justify the whole alignment.
5545    */
5546   @Override
5547   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5548   {
5549     AlignmentI al = viewport.getAlignment();
5550     al.justify(false);
5551     viewport.firePropertyChange("alignment", null, al);
5552   }
5553
5554   /**
5555    * Right justify the whole alignment.
5556    */
5557   @Override
5558   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5559   {
5560     AlignmentI al = viewport.getAlignment();
5561     al.justify(true);
5562     viewport.firePropertyChange("alignment", null, al);
5563   }
5564
5565   @Override
5566   public void setShowSeqFeatures(boolean b)
5567   {
5568     showSeqFeatures.setSelected(b);
5569     viewport.setShowSequenceFeatures(b);
5570   }
5571
5572   /*
5573    * (non-Javadoc)
5574    *
5575    * @see
5576    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5577    * awt.event.ActionEvent)
5578    */
5579   @Override
5580   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5581   {
5582     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5583     alignPanel.paintAlignment(true);
5584   }
5585
5586   /*
5587    * (non-Javadoc)
5588    *
5589    * @see
5590    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5591    * .ActionEvent)
5592    */
5593   @Override
5594   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5595   {
5596     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5597     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5598
5599   }
5600
5601   /*
5602    * (non-Javadoc)
5603    *
5604    * @see
5605    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5606    * .event.ActionEvent)
5607    */
5608   @Override
5609   protected void showGroupConservation_actionPerformed(ActionEvent e)
5610   {
5611     viewport.setShowGroupConservation(showGroupConservation.getState());
5612     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5613   }
5614
5615   /*
5616    * (non-Javadoc)
5617    *
5618    * @see
5619    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5620    * .event.ActionEvent)
5621    */
5622   @Override
5623   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5624   {
5625     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5626     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5627   }
5628
5629   /*
5630    * (non-Javadoc)
5631    *
5632    * @see
5633    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5634    * .event.ActionEvent)
5635    */
5636   @Override
5637   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5638   {
5639     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5640     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5641   }
5642
5643   @Override
5644   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5645   {
5646     showSequenceLogo.setState(true);
5647     viewport.setShowSequenceLogo(true);
5648     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5649     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5650   }
5651
5652   @Override
5653   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5654   {
5655     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5656   }
5657
5658   /*
5659    * (non-Javadoc)
5660    *
5661    * @see
5662    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5663    * .event.ActionEvent)
5664    */
5665   @Override
5666   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5667   {
5668     if (avc.makeGroupsFromSelection())
5669     {
5670       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5671       alignPanel.updateAnnotation();
5672       alignPanel.paintAlignment(true);
5673     }
5674   }
5675
5676   public void clearAlignmentSeqRep()
5677   {
5678     // TODO refactor alignmentseqrep to controller
5679     if (viewport.getAlignment().hasSeqrep())
5680     {
5681       viewport.getAlignment().setSeqrep(null);
5682       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5683       alignPanel.updateAnnotation();
5684       alignPanel.paintAlignment(true);
5685     }
5686   }
5687
5688   @Override
5689   protected void createGroup_actionPerformed(ActionEvent e)
5690   {
5691     if (avc.createGroup())
5692     {
5693       alignPanel.alignmentChanged();
5694     }
5695   }
5696
5697   @Override
5698   protected void unGroup_actionPerformed(ActionEvent e)
5699   {
5700     if (avc.unGroup())
5701     {
5702       alignPanel.alignmentChanged();
5703     }
5704   }
5705
5706   /**
5707    * make the given alignmentPanel the currently selected tab
5708    *
5709    * @param alignmentPanel
5710    */
5711   public void setDisplayedView(AlignmentPanel alignmentPanel)
5712   {
5713     if (!viewport.getSequenceSetId().equals(
5714             alignmentPanel.av.getSequenceSetId()))
5715     {
5716       throw new Error(
5717               MessageManager
5718                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5719     }
5720     if (tabbedPane != null
5721             && tabbedPane.getTabCount() > 0
5722             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5723                     .getSelectedIndex())
5724     {
5725       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5726     }
5727   }
5728
5729   /**
5730    * Action on selection of menu options to Show or Hide annotations.
5731    *
5732    * @param visible
5733    * @param forSequences
5734    *          update sequence-related annotations
5735    * @param forAlignment
5736    *          update non-sequence-related annotations
5737    */
5738   @Override
5739   protected void setAnnotationsVisibility(boolean visible,
5740           boolean forSequences, boolean forAlignment)
5741   {
5742     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5743             .getAlignmentAnnotation();
5744     if (anns == null)
5745     {
5746       return;
5747     }
5748     for (AlignmentAnnotation aa : anns)
5749     {
5750       /*
5751        * don't display non-positional annotations on an alignment
5752        */
5753       if (aa.annotations == null)
5754       {
5755         continue;
5756       }
5757       boolean apply = (aa.sequenceRef == null && forAlignment)
5758               || (aa.sequenceRef != null && forSequences);
5759       if (apply)
5760       {
5761         aa.visible = visible;
5762       }
5763     }
5764     alignPanel.validateAnnotationDimensions(true);
5765     alignPanel.alignmentChanged();
5766   }
5767
5768   /**
5769    * Store selected annotation sort order for the view and repaint.
5770    */
5771   @Override
5772   protected void sortAnnotations_actionPerformed()
5773   {
5774     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5775     this.alignPanel.av
5776             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5777     alignPanel.paintAlignment(true);
5778   }
5779
5780   /**
5781    *
5782    * @return alignment panels in this alignment frame
5783    */
5784   public List<? extends AlignmentViewPanel> getAlignPanels()
5785   {
5786     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5787   }
5788
5789   /**
5790    * Open a new alignment window, with the cDNA associated with this (protein)
5791    * alignment, aligned as is the protein.
5792    */
5793   protected void viewAsCdna_actionPerformed()
5794   {
5795     // TODO no longer a menu action - refactor as required
5796     final AlignmentI alignment = getViewport().getAlignment();
5797     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5798     if (mappings == null)
5799     {
5800       return;
5801     }
5802     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5803     for (SequenceI aaSeq : alignment.getSequences())
5804     {
5805       for (AlignedCodonFrame acf : mappings)
5806       {
5807         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5808         if (dnaSeq != null)
5809         {
5810           /*
5811            * There is a cDNA mapping for this protein sequence - add to new
5812            * alignment. It will share the same dataset sequence as other mapped
5813            * cDNA (no new mappings need to be created).
5814            */
5815           final Sequence newSeq = new Sequence(dnaSeq);
5816           newSeq.setDatasetSequence(dnaSeq);
5817           cdnaSeqs.add(newSeq);
5818         }
5819       }
5820     }
5821     if (cdnaSeqs.size() == 0)
5822     {
5823       // show a warning dialog no mapped cDNA
5824       return;
5825     }
5826     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5827             .size()]));
5828     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5829             AlignFrame.DEFAULT_HEIGHT);
5830     cdna.alignAs(alignment);
5831     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5832             + this.title;
5833     Desktop.addInternalFrame(alignFrame, newtitle,
5834             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5835   }
5836
5837   /**
5838    * Set visibility of dna/protein complement view (available when shown in a
5839    * split frame).
5840    *
5841    * @param show
5842    */
5843   @Override
5844   protected void showComplement_actionPerformed(boolean show)
5845   {
5846     SplitContainerI sf = getSplitViewContainer();
5847     if (sf != null)
5848     {
5849       sf.setComplementVisible(this, show);
5850     }
5851   }
5852
5853   /**
5854    * Generate the reverse (optionally complemented) of the selected sequences,
5855    * and add them to the alignment
5856    */
5857   @Override
5858   protected void showReverse_actionPerformed(boolean complement)
5859   {
5860     AlignmentI al = null;
5861     try
5862     {
5863       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5864       al = dna.reverseCdna(complement);
5865       viewport.addAlignment(al, "");
5866       addHistoryItem(new EditCommand(
5867               MessageManager.getString("label.add_sequences"),
5868               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5869               viewport.getAlignment()));
5870     } catch (Exception ex)
5871     {
5872       System.err.println(ex.getMessage());
5873       return;
5874     }
5875   }
5876
5877   /**
5878    * Try to run a script in the Groovy console, having first ensured that this
5879    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5880    * be targeted at this alignment.
5881    */
5882   @Override
5883   protected void runGroovy_actionPerformed()
5884   {
5885     Jalview.setCurrentAlignFrame(this);
5886     groovy.ui.Console console = Desktop.getGroovyConsole();
5887     if (console != null)
5888     {
5889       try
5890       {
5891         console.runScript();
5892       } catch (Exception ex)
5893       {
5894         System.err.println((ex.toString()));
5895         JOptionPane
5896                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5897                         .getString("label.couldnt_run_groovy_script"),
5898                         MessageManager
5899                                 .getString("label.groovy_support_failed"),
5900                         JOptionPane.ERROR_MESSAGE);
5901       }
5902     }
5903     else
5904     {
5905       System.err.println("Can't run Groovy script as console not found");
5906     }
5907   }
5908
5909   /**
5910    * Hides columns containing (or not containing) a specified feature, provided
5911    * that would not leave all columns hidden
5912    *
5913    * @param featureType
5914    * @param columnsContaining
5915    * @return
5916    */
5917   public boolean hideFeatureColumns(String featureType,
5918           boolean columnsContaining)
5919   {
5920     boolean notForHiding = avc.markColumnsContainingFeatures(
5921             columnsContaining, false, false, featureType);
5922     if (notForHiding)
5923     {
5924       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5925               false, featureType))
5926       {
5927         getViewport().hideSelectedColumns();
5928         return true;
5929       }
5930     }
5931     return false;
5932   }
5933 }
5934
5935 class PrintThread extends Thread
5936 {
5937   AlignmentPanel ap;
5938
5939   public PrintThread(AlignmentPanel ap)
5940   {
5941     this.ap = ap;
5942   }
5943
5944   static PageFormat pf;
5945
5946   @Override
5947   public void run()
5948   {
5949     PrinterJob printJob = PrinterJob.getPrinterJob();
5950
5951     if (pf != null)
5952     {
5953       printJob.setPrintable(ap, pf);
5954     }
5955     else
5956     {
5957       printJob.setPrintable(ap);
5958     }
5959
5960     if (printJob.printDialog())
5961     {
5962       try
5963       {
5964         printJob.print();
5965       } catch (Exception PrintException)
5966       {
5967         PrintException.printStackTrace();
5968       }
5969     }
5970   }
5971 }