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.StructureFile;
  75 import jalview.io.TCoffeeScoreFile;
  76 import jalview.jbgui.GAlignFrame;
  77 import jalview.schemes.Blosum62ColourScheme;
  78 import jalview.schemes.BuriedColourScheme;
  79 import jalview.schemes.ClustalxColourScheme;
  80 import jalview.schemes.ColourSchemeI;
  81 import jalview.schemes.ColourSchemeProperty;
  82 import jalview.schemes.HelixColourScheme;
  83 import jalview.schemes.HydrophobicColourScheme;
  84 import jalview.schemes.NucleotideColourScheme;
  85 import jalview.schemes.PIDColourScheme;
  86 import jalview.schemes.PurinePyrimidineColourScheme;
  87 import jalview.schemes.RNAHelicesColourChooser;
  88 import jalview.schemes.ResidueProperties;
  89 import jalview.schemes.StrandColourScheme;
  90 import jalview.schemes.TCoffeeColourScheme;
  91 import jalview.schemes.TaylorColourScheme;
  92 import jalview.schemes.TurnColourScheme;
  93 import jalview.schemes.UserColourScheme;
  94 import jalview.schemes.ZappoColourScheme;
  95 import jalview.util.MessageManager;
  96 import jalview.viewmodel.AlignmentViewport;
  97 import jalview.ws.DBRefFetcher;
  98 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  99 import jalview.ws.jws1.Discoverer;
 100 import jalview.ws.jws2.Jws2Discoverer;
 101 import jalview.ws.jws2.jabaws2.Jws2Instance;
 102 import jalview.ws.seqfetcher.DbSourceProxy;
 103
 104 import java.awt.BorderLayout;
 105 import java.awt.Component;
 106 import java.awt.Rectangle;
 107 import java.awt.Toolkit;
 108 import java.awt.datatransfer.Clipboard;
 109 import java.awt.datatransfer.DataFlavor;
 110 import java.awt.datatransfer.StringSelection;
 111 import java.awt.datatransfer.Transferable;
 112 import java.awt.dnd.DnDConstants;
 113 import java.awt.dnd.DropTargetDragEvent;
 114 import java.awt.dnd.DropTargetDropEvent;
 115 import java.awt.dnd.DropTargetEvent;
 116 import java.awt.dnd.DropTargetListener;
 117 import java.awt.event.ActionEvent;
 118 import java.awt.event.ActionListener;
 119 import java.awt.event.FocusAdapter;
 120 import java.awt.event.FocusEvent;
 121 import java.awt.event.ItemEvent;
 122 import java.awt.event.ItemListener;
 123 import java.awt.event.KeyAdapter;
 124 import java.awt.event.KeyEvent;
 125 import java.awt.event.MouseAdapter;
 126 import java.awt.event.MouseEvent;
 127 import java.awt.print.PageFormat;
 128 import java.awt.print.PrinterJob;
 129 import java.beans.PropertyChangeEvent;
 130 import java.io.File;
 131 import java.net.URL;
 132 import java.util.ArrayList;
 133 import java.util.Arrays;
 134 import java.util.Deque;
 135 import java.util.Enumeration;
 136 import java.util.Hashtable;
 137 import java.util.List;
 138 import java.util.Vector;
 139
 140 import javax.swing.JCheckBoxMenuItem;
 141 import javax.swing.JEditorPane;
 142 import javax.swing.JInternalFrame;
 143 import javax.swing.JLayeredPane;
 144 import javax.swing.JMenu;
 145 import javax.swing.JMenuItem;
 146 import javax.swing.JOptionPane;
 147 import javax.swing.JRadioButtonMenuItem;
 148 import javax.swing.JScrollPane;
 149 import javax.swing.SwingUtilities;
 150
 151 /**
 152  * DOCUMENT ME!
 153  *
 154  * @author $author$
 155  * @version $Revision$
 156  */
 157 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 158         IProgressIndicator, AlignViewControllerGuiI
 159 {
 160
 161   public static final int DEFAULT_WIDTH = 700;
 162
 163   public static final int DEFAULT_HEIGHT = 500;
 164
 165   /*
 166    * The currently displayed panel (selected tabbed view if more than one)
 167    */
 168   public AlignmentPanel alignPanel;
 169
 170   AlignViewport viewport;
 171
 172   public AlignViewControllerI avc;
 173
 174   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 175
 176   /**
 177    * Last format used to load or save alignments in this window
 178    */
 179   String currentFileFormat = null;
 180
 181   /**
 182    * Current filename for this alignment
 183    */
 184   String fileName = null;
 185
 186   /**
 187    * Creates a new AlignFrame object with specific width and height.
 188    *
 189    * @param al
 190    * @param width
 191    * @param height
 192    */
 193   public AlignFrame(AlignmentI al, int width, int height)
 194   {
 195     this(al, null, width, height);
 196   }
 197
 198   /**
 199    * Creates a new AlignFrame object with specific width, height and
 200    * sequenceSetId
 201    *
 202    * @param al
 203    * @param width
 204    * @param height
 205    * @param sequenceSetId
 206    */
 207   public AlignFrame(AlignmentI al, int width, int height,
 208           String sequenceSetId)
 209   {
 210     this(al, null, width, height, sequenceSetId);
 211   }
 212
 213   /**
 214    * Creates a new AlignFrame object with specific width, height and
 215    * sequenceSetId
 216    *
 217    * @param al
 218    * @param width
 219    * @param height
 220    * @param sequenceSetId
 221    * @param viewId
 222    */
 223   public AlignFrame(AlignmentI al, int width, int height,
 224           String sequenceSetId, String viewId)
 225   {
 226     this(al, null, width, height, sequenceSetId, viewId);
 227   }
 228
 229   /**
 230    * new alignment window with hidden columns
 231    *
 232    * @param al
 233    *          AlignmentI
 234    * @param hiddenColumns
 235    *          ColumnSelection or null
 236    * @param width
 237    *          Width of alignment frame
 238    * @param height
 239    *          height of frame.
 240    */
 241   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 242           int width, int height)
 243   {
 244     this(al, hiddenColumns, width, height, null);
 245   }
 246
 247   /**
 248    * Create alignment frame for al with hiddenColumns, a specific width and
 249    * height, and specific sequenceId
 250    *
 251    * @param al
 252    * @param hiddenColumns
 253    * @param width
 254    * @param height
 255    * @param sequenceSetId
 256    *          (may be null)
 257    */
 258   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 259           int width, int height, String sequenceSetId)
 260   {
 261     this(al, hiddenColumns, width, height, sequenceSetId, null);
 262   }
 263
 264   /**
 265    * Create alignment frame for al with hiddenColumns, a specific width and
 266    * height, and specific sequenceId
 267    *
 268    * @param al
 269    * @param hiddenColumns
 270    * @param width
 271    * @param height
 272    * @param sequenceSetId
 273    *          (may be null)
 274    * @param viewId
 275    *          (may be null)
 276    */
 277   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 278           int width, int height, String sequenceSetId, String viewId)
 279   {
 280     setSize(width, height);
 281
 282     if (al.getDataset() == null)
 283     {
 284       al.setDataset(null);
 285     }
 286
 287     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 288
 289     alignPanel = new AlignmentPanel(this, viewport);
 290
 291     addAlignmentPanel(alignPanel, true);
 292     init();
 293   }
 294
 295   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 296           ColumnSelection hiddenColumns, int width, int height)
 297   {
 298     setSize(width, height);
 299
 300     if (al.getDataset() == null)
 301     {
 302       al.setDataset(null);
 303     }
 304
 305     viewport = new AlignViewport(al, hiddenColumns);
 306
 307     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 308     {
 309       viewport.hideSequence(hiddenSeqs);
 310     }
 311     alignPanel = new AlignmentPanel(this, viewport);
 312     addAlignmentPanel(alignPanel, true);
 313     init();
 314   }
 315
 316   /**
 317    * Make a new AlignFrame from existing alignmentPanels
 318    *
 319    * @param ap
 320    *          AlignmentPanel
 321    * @param av
 322    *          AlignViewport
 323    */
 324   public AlignFrame(AlignmentPanel ap)
 325   {
 326     viewport = ap.av;
 327     alignPanel = ap;
 328     addAlignmentPanel(ap, false);
 329     init();
 330   }
 331
 332   /**
 333    * initalise the alignframe from the underlying viewport data and the
 334    * configurations
 335    */
 336   void init()
 337   {
 338     if (!Jalview.isHeadlessMode())
 339     {
 340       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 341     }
 342
 343     avc = new jalview.controller.AlignViewController(this, viewport,
 344             alignPanel);
 345     if (viewport.getAlignmentConservationAnnotation() == null)
 346     {
 347       BLOSUM62Colour.setEnabled(false);
 348       conservationMenuItem.setEnabled(false);
 349       modifyConservation.setEnabled(false);
 350       // PIDColour.setEnabled(false);
 351       // abovePIDThreshold.setEnabled(false);
 352       // modifyPID.setEnabled(false);
 353     }
 354
 355     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 356             "No sort");
 357
 358     if (sortby.equals("Id"))
 359     {
 360       sortIDMenuItem_actionPerformed(null);
 361     }
 362     else if (sortby.equals("Pairwise Identity"))
 363     {
 364       sortPairwiseMenuItem_actionPerformed(null);
 365     }
 366
 367     if (Desktop.desktop != null)
 368     {
 369       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 370       addServiceListeners();
 371       setGUINucleotide(viewport.getAlignment().isNucleotide());
 372     }
 373
 374     this.alignPanel.av
 375             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 376
 377     setMenusFromViewport(viewport);
 378     buildSortByAnnotationScoresMenu();
 379     buildTreeMenu();
 380
 381     if (viewport.getWrapAlignment())
 382     {
 383       wrapMenuItem_actionPerformed(null);
 384     }
 385
 386     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 387     {
 388       this.overviewMenuItem_actionPerformed(null);
 389     }
 390
 391     addKeyListener();
 392
 393     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 394     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 395     final String menuLabel = MessageManager
 396             .getString("label.copy_format_from");
 397     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 398             new ViewSetProvider()
 399             {
 400
 401               @Override
 402               public AlignmentPanel[] getAllAlignmentPanels()
 403               {
 404                 origview.clear();
 405                 origview.add(alignPanel);
 406                 // make an array of all alignment panels except for this one
 407                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 408                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 409                 aps.remove(AlignFrame.this.alignPanel);
 410                 return aps.toArray(new AlignmentPanel[aps.size()]);
 411               }
 412             }, selviews, new ItemListener()
 413             {
 414
 415               @Override
 416               public void itemStateChanged(ItemEvent e)
 417               {
 418                 if (origview.size() > 0)
 419                 {
 420                   final AlignmentPanel ap = origview.get(0);
 421
 422                   /*
 423                    * Copy the ViewStyle of the selected panel to 'this one'.
 424                    * Don't change value of 'scaleProteinAsCdna' unless copying
 425                    * from a SplitFrame.
 426                    */
 427                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 428                           .getViewStyle();
 429                   boolean fromSplitFrame = selviews.get(0)
 430                           .getAlignViewport().getCodingComplement() != null;
 431                   if (!fromSplitFrame)
 432                   {
 433                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 434                             .getViewStyle().isScaleProteinAsCdna());
 435                   }
 436                   ap.getAlignViewport().setViewStyle(vs);
 437
 438                   /*
 439                    * Also rescale ViewStyle of SplitFrame complement if there is
 440                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 441                    * the whole ViewStyle (allow cDNA protein to have different
 442                    * fonts)
 443                    */
 444                   AlignViewportI complement = ap.getAlignViewport()
 445                           .getCodingComplement();
 446                   if (complement != null && vs.isScaleProteinAsCdna())
 447                   {
 448                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 449                     ((SplitFrame) af.getSplitViewContainer())
 450                             .adjustLayout();
 451                     af.setMenusForViewport();
 452                   }
 453
 454                   ap.updateLayout();
 455                   ap.setSelected(true);
 456                   ap.alignFrame.setMenusForViewport();
 457
 458                 }
 459               }
 460             });
 461     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 462             .indexOf("devel") > -1
 463             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 464                     .indexOf("test") > -1)
 465     {
 466       formatMenu.add(vsel);
 467     }
 468     addFocusListener(new FocusAdapter()
 469     {
 470       @Override
 471       public void focusGained(FocusEvent e)
 472       {
 473         Jalview.setCurrentAlignFrame(AlignFrame.this);
 474       }
 475     });
 476
 477   }
 478
 479   /**
 480    * Change the filename and format for the alignment, and enable the 'reload'
 481    * button functionality.
 482    *
 483    * @param file
 484    *          valid filename
 485    * @param format
 486    *          format of file
 487    */
 488   public void setFileName(String file, String format)
 489   {
 490     fileName = file;
 491     setFileFormat(format);
 492     reload.setEnabled(true);
 493   }
 494
 495   /**
 496    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 497    * events
 498    */
 499   void addKeyListener()
 500   {
 501     addKeyListener(new KeyAdapter()
 502     {
 503       @Override
 504       public void keyPressed(KeyEvent evt)
 505       {
 506         if (viewport.cursorMode
 507                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 508                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 509                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 510                 && Character.isDigit(evt.getKeyChar()))
 511         {
 512           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 513         }
 514
 515         switch (evt.getKeyCode())
 516         {
 517
 518         case 27: // escape key
 519           deselectAllSequenceMenuItem_actionPerformed(null);
 520
 521           break;
 522
 523         case KeyEvent.VK_DOWN:
 524           if (evt.isAltDown() || !viewport.cursorMode)
 525           {
 526             moveSelectedSequences(false);
 527           }
 528           if (viewport.cursorMode)
 529           {
 530             alignPanel.getSeqPanel().moveCursor(0, 1);
 531           }
 532           break;
 533
 534         case KeyEvent.VK_UP:
 535           if (evt.isAltDown() || !viewport.cursorMode)
 536           {
 537             moveSelectedSequences(true);
 538           }
 539           if (viewport.cursorMode)
 540           {
 541             alignPanel.getSeqPanel().moveCursor(0, -1);
 542           }
 543
 544           break;
 545
 546         case KeyEvent.VK_LEFT:
 547           if (evt.isAltDown() || !viewport.cursorMode)
 548           {
 549             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 550           }
 551           else
 552           {
 553             alignPanel.getSeqPanel().moveCursor(-1, 0);
 554           }
 555
 556           break;
 557
 558         case KeyEvent.VK_RIGHT:
 559           if (evt.isAltDown() || !viewport.cursorMode)
 560           {
 561             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 562           }
 563           else
 564           {
 565             alignPanel.getSeqPanel().moveCursor(1, 0);
 566           }
 567           break;
 568
 569         case KeyEvent.VK_SPACE:
 570           if (viewport.cursorMode)
 571           {
 572             alignPanel.getSeqPanel().insertGapAtCursor(
 573                     evt.isControlDown() || evt.isShiftDown()
 574                             || evt.isAltDown());
 575           }
 576           break;
 577
 578         // case KeyEvent.VK_A:
 579         // if (viewport.cursorMode)
 580         // {
 581         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 582         // //System.out.println("A");
 583         // }
 584         // break;
 585         /*
 586          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 587          * System.out.println("closing bracket"); } break;
 588          */
 589         case KeyEvent.VK_DELETE:
 590         case KeyEvent.VK_BACK_SPACE:
 591           if (!viewport.cursorMode)
 592           {
 593             cut_actionPerformed(null);
 594           }
 595           else
 596           {
 597             alignPanel.getSeqPanel().deleteGapAtCursor(
 598                     evt.isControlDown() || evt.isShiftDown()
 599                             || evt.isAltDown());
 600           }
 601
 602           break;
 603
 604         case KeyEvent.VK_S:
 605           if (viewport.cursorMode)
 606           {
 607             alignPanel.getSeqPanel().setCursorRow();
 608           }
 609           break;
 610         case KeyEvent.VK_C:
 611           if (viewport.cursorMode && !evt.isControlDown())
 612           {
 613             alignPanel.getSeqPanel().setCursorColumn();
 614           }
 615           break;
 616         case KeyEvent.VK_P:
 617           if (viewport.cursorMode)
 618           {
 619             alignPanel.getSeqPanel().setCursorPosition();
 620           }
 621           break;
 622
 623         case KeyEvent.VK_ENTER:
 624         case KeyEvent.VK_COMMA:
 625           if (viewport.cursorMode)
 626           {
 627             alignPanel.getSeqPanel().setCursorRowAndColumn();
 628           }
 629           break;
 630
 631         case KeyEvent.VK_Q:
 632           if (viewport.cursorMode)
 633           {
 634             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 635           }
 636           break;
 637         case KeyEvent.VK_M:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 641           }
 642           break;
 643
 644         case KeyEvent.VK_F2:
 645           viewport.cursorMode = !viewport.cursorMode;
 646           statusBar.setText(MessageManager.formatMessage(
 647                   "label.keyboard_editing_mode",
 648                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 649           if (viewport.cursorMode)
 650           {
 651             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 652             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 653           }
 654           alignPanel.getSeqPanel().seqCanvas.repaint();
 655           break;
 656
 657         case KeyEvent.VK_F1:
 658           try
 659           {
 660             Help.showHelpWindow();
 661           } catch (Exception ex)
 662           {
 663             ex.printStackTrace();
 664           }
 665           break;
 666         case KeyEvent.VK_H:
 667         {
 668           boolean toggleSeqs = !evt.isControlDown();
 669           boolean toggleCols = !evt.isShiftDown();
 670           toggleHiddenRegions(toggleSeqs, toggleCols);
 671           break;
 672         }
 673         case KeyEvent.VK_PAGE_UP:
 674           if (viewport.getWrapAlignment())
 675           {
 676             alignPanel.scrollUp(true);
 677           }
 678           else
 679           {
 680             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 681                     - viewport.endSeq + viewport.startSeq);
 682           }
 683           break;
 684         case KeyEvent.VK_PAGE_DOWN:
 685           if (viewport.getWrapAlignment())
 686           {
 687             alignPanel.scrollUp(false);
 688           }
 689           else
 690           {
 691             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 692                     + viewport.endSeq - viewport.startSeq);
 693           }
 694           break;
 695         }
 696       }
 697
 698       @Override
 699       public void keyReleased(KeyEvent evt)
 700       {
 701         switch (evt.getKeyCode())
 702         {
 703         case KeyEvent.VK_LEFT:
 704           if (evt.isAltDown() || !viewport.cursorMode)
 705           {
 706             viewport.firePropertyChange("alignment", null, viewport
 707                     .getAlignment().getSequences());
 708           }
 709           break;
 710
 711         case KeyEvent.VK_RIGHT:
 712           if (evt.isAltDown() || !viewport.cursorMode)
 713           {
 714             viewport.firePropertyChange("alignment", null, viewport
 715                     .getAlignment().getSequences());
 716           }
 717           break;
 718         }
 719       }
 720     });
 721   }
 722
 723   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 724   {
 725     ap.alignFrame = this;
 726     avc = new jalview.controller.AlignViewController(this, viewport,
 727             alignPanel);
 728
 729     alignPanels.add(ap);
 730
 731     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 732
 733     int aSize = alignPanels.size();
 734
 735     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 736
 737     if (aSize == 1 && ap.av.viewName == null)
 738     {
 739       this.getContentPane().add(ap, BorderLayout.CENTER);
 740     }
 741     else
 742     {
 743       if (aSize == 2)
 744       {
 745         setInitialTabVisible();
 746       }
 747
 748       expandViews.setEnabled(true);
 749       gatherViews.setEnabled(true);
 750       tabbedPane.addTab(ap.av.viewName, ap);
 751
 752       ap.setVisible(false);
 753     }
 754
 755     if (newPanel)
 756     {
 757       if (ap.av.isPadGaps())
 758       {
 759         ap.av.getAlignment().padGaps();
 760       }
 761       ap.av.updateConservation(ap);
 762       ap.av.updateConsensus(ap);
 763       ap.av.updateStrucConsensus(ap);
 764     }
 765   }
 766
 767   public void setInitialTabVisible()
 768   {
 769     expandViews.setEnabled(true);
 770     gatherViews.setEnabled(true);
 771     tabbedPane.setVisible(true);
 772     AlignmentPanel first = alignPanels.get(0);
 773     tabbedPane.addTab(first.av.viewName, first);
 774     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 775   }
 776
 777   public AlignViewport getViewport()
 778   {
 779     return viewport;
 780   }
 781
 782   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 783   private void addServiceListeners()
 784   {
 785     final java.beans.PropertyChangeListener thisListener;
 786     Desktop.instance.addJalviewPropertyChangeListener("services",
 787             thisListener = new java.beans.PropertyChangeListener()
 788             {
 789               @Override
 790               public void propertyChange(PropertyChangeEvent evt)
 791               {
 792                 // // System.out.println("Discoverer property change.");
 793                 // if (evt.getPropertyName().equals("services"))
 794                 {
 795                   SwingUtilities.invokeLater(new Runnable()
 796                   {
 797
 798                     @Override
 799                     public void run()
 800                     {
 801                       System.err
 802                               .println("Rebuild WS Menu for service change");
 803                       BuildWebServiceMenu();
 804                     }
 805
 806                   });
 807                 }
 808               }
 809             });
 810     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 811     {
 812       @Override
 813       public void internalFrameClosed(
 814               javax.swing.event.InternalFrameEvent evt)
 815       {
 816         // System.out.println("deregistering discoverer listener");
 817         Desktop.instance.removeJalviewPropertyChangeListener("services",
 818                 thisListener);
 819         closeMenuItem_actionPerformed(true);
 820       };
 821     });
 822     // Finally, build the menu once to get current service state
 823     new Thread(new Runnable()
 824     {
 825       @Override
 826       public void run()
 827       {
 828         BuildWebServiceMenu();
 829       }
 830     }).start();
 831   }
 832
 833   /**
 834    * Configure menu items that vary according to whether the alignment is
 835    * nucleotide or protein
 836    *
 837    * @param nucleotide
 838    */
 839   public void setGUINucleotide(boolean nucleotide)
 840   {
 841     showTranslation.setVisible(nucleotide);
 842     showReverse.setVisible(nucleotide);
 843     showReverseComplement.setVisible(nucleotide);
 844     conservationMenuItem.setEnabled(!nucleotide);
 845     modifyConservation.setEnabled(!nucleotide);
 846     showGroupConservation.setEnabled(!nucleotide);
 847     rnahelicesColour.setEnabled(nucleotide);
 848     purinePyrimidineColour.setEnabled(nucleotide);
 849     showComplementMenuItem.setText(nucleotide ? MessageManager
 850             .getString("label.protein") : MessageManager
 851             .getString("label.nucleotide"));
 852     setColourSelected(jalview.bin.Cache.getDefault(
 853             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 854                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 855   }
 856
 857   /**
 858    * set up menus for the current viewport. This may be called after any
 859    * operation that affects the data in the current view (selection changed,
 860    * etc) to update the menus to reflect the new state.
 861    */
 862   @Override
 863   public void setMenusForViewport()
 864   {
 865     setMenusFromViewport(viewport);
 866   }
 867
 868   /**
 869    * Need to call this method when tabs are selected for multiple views, or when
 870    * loading from Jalview2XML.java
 871    *
 872    * @param av
 873    *          AlignViewport
 874    */
 875   void setMenusFromViewport(AlignViewport av)
 876   {
 877     padGapsMenuitem.setSelected(av.isPadGaps());
 878     colourTextMenuItem.setSelected(av.isShowColourText());
 879     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 880     conservationMenuItem.setSelected(av.getConservationSelected());
 881     seqLimits.setSelected(av.getShowJVSuffix());
 882     idRightAlign.setSelected(av.isRightAlignIds());
 883     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 884     renderGapsMenuItem.setSelected(av.isRenderGaps());
 885     wrapMenuItem.setSelected(av.getWrapAlignment());
 886     scaleAbove.setVisible(av.getWrapAlignment());
 887     scaleLeft.setVisible(av.getWrapAlignment());
 888     scaleRight.setVisible(av.getWrapAlignment());
 889     annotationPanelMenuItem.setState(av.isShowAnnotation());
 890     /*
 891      * Show/hide annotations only enabled if annotation panel is shown
 892      */
 893     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 894     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 895     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 898     viewTextMenuItem.setSelected(av.getShowText());
 899     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 900     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 901     showGroupConservation.setSelected(av.isShowGroupConservation());
 902     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 903     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 904     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 905
 906     setColourSelected(ColourSchemeProperty.getColourName(av
 907             .getGlobalColourScheme()));
 908
 909     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 910     hiddenMarkers.setState(av.getShowHiddenMarkers());
 911     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 912     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 913     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 914     autoCalculate.setSelected(av.autoCalculateConsensus);
 915     sortByTree.setSelected(av.sortByTree);
 916     listenToViewSelections.setSelected(av.followSelection);
 917     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 918     rnahelicesColour
 919             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 920
 921     showProducts.setEnabled(canShowProducts());
 922     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 923
 924     updateEditMenuBar();
 925   }
 926
 927   /**
 928    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 929    *
 930    * @param b
 931    */
 932   public void setGroovyEnabled(boolean b)
 933   {
 934     runGroovy.setEnabled(b);
 935   }
 936
 937   private IProgressIndicator progressBar;
 938
 939   /*
 940    * (non-Javadoc)
 941    *
 942    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 943    */
 944   @Override
 945   public void setProgressBar(String message, long id)
 946   {
 947     progressBar.setProgressBar(message, id);
 948   }
 949
 950   @Override
 951   public void registerHandler(final long id,
 952           final IProgressIndicatorHandler handler)
 953   {
 954     progressBar.registerHandler(id, handler);
 955   }
 956
 957   /**
 958    *
 959    * @return true if any progress bars are still active
 960    */
 961   @Override
 962   public boolean operationInProgress()
 963   {
 964     return progressBar.operationInProgress();
 965   }
 966
 967   @Override
 968   public void setStatus(String text)
 969   {
 970     statusBar.setText(text);
 971   }
 972
 973   /*
 974    * Added so Castor Mapping file can obtain Jalview Version
 975    */
 976   public String getVersion()
 977   {
 978     return jalview.bin.Cache.getProperty("VERSION");
 979   }
 980
 981   public FeatureRenderer getFeatureRenderer()
 982   {
 983     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 984   }
 985
 986   @Override
 987   public void fetchSequence_actionPerformed(ActionEvent e)
 988   {
 989     new jalview.gui.SequenceFetcher(this);
 990   }
 991
 992   @Override
 993   public void addFromFile_actionPerformed(ActionEvent e)
 994   {
 995     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 996   }
 997
 998   @Override
 999   public void reload_actionPerformed(ActionEvent e)
1000   {
1001     if (fileName != null)
1002     {
1003       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1004       // originating file's format
1005       // TODO: work out how to recover feature settings for correct view(s) when
1006       // file is reloaded.
1007       if (currentFileFormat.equals("Jalview"))
1008       {
1009         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1010         for (int i = 0; i < frames.length; i++)
1011         {
1012           if (frames[i] instanceof AlignFrame && frames[i] != this
1013                   && ((AlignFrame) frames[i]).fileName != null
1014                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1015           {
1016             try
1017             {
1018               frames[i].setSelected(true);
1019               Desktop.instance.closeAssociatedWindows();
1020             } catch (java.beans.PropertyVetoException ex)
1021             {
1022             }
1023           }
1024
1025         }
1026         Desktop.instance.closeAssociatedWindows();
1027
1028         FileLoader loader = new FileLoader();
1029         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1030         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1031       }
1032       else
1033       {
1034         Rectangle bounds = this.getBounds();
1035
1036         FileLoader loader = new FileLoader();
1037         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1038         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1039                 protocol, currentFileFormat);
1040
1041         newframe.setBounds(bounds);
1042         if (featureSettings != null && featureSettings.isShowing())
1043         {
1044           final Rectangle fspos = featureSettings.frame.getBounds();
1045           // TODO: need a 'show feature settings' function that takes bounds -
1046           // need to refactor Desktop.addFrame
1047           newframe.featureSettings_actionPerformed(null);
1048           final FeatureSettings nfs = newframe.featureSettings;
1049           SwingUtilities.invokeLater(new Runnable()
1050           {
1051             @Override
1052             public void run()
1053             {
1054               nfs.frame.setBounds(fspos);
1055             }
1056           });
1057           this.featureSettings.close();
1058           this.featureSettings = null;
1059         }
1060         this.closeMenuItem_actionPerformed(true);
1061       }
1062     }
1063   }
1064
1065   @Override
1066   public void addFromText_actionPerformed(ActionEvent e)
1067   {
1068     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1069             .getAlignPanel());
1070   }
1071
1072   @Override
1073   public void addFromURL_actionPerformed(ActionEvent e)
1074   {
1075     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1076   }
1077
1078   @Override
1079   public void save_actionPerformed(ActionEvent e)
1080   {
1081     if (fileName == null
1082             || (currentFileFormat == null || !jalview.io.FormatAdapter
1083                     .isValidIOFormat(currentFileFormat, true))
1084             || fileName.startsWith("http"))
1085     {
1086       saveAs_actionPerformed(null);
1087     }
1088     else
1089     {
1090       saveAlignment(fileName, currentFileFormat);
1091     }
1092   }
1093
1094   /**
1095    * DOCUMENT ME!
1096    *
1097    * @param e
1098    *          DOCUMENT ME!
1099    */
1100   @Override
1101   public void saveAs_actionPerformed(ActionEvent e)
1102   {
1103     JalviewFileChooser chooser = new JalviewFileChooser(
1104             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1105             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1106             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1107             currentFileFormat, false);
1108
1109     chooser.setFileView(new JalviewFileView());
1110     chooser.setDialogTitle(MessageManager
1111             .getString("label.save_alignment_to_file"));
1112     chooser.setToolTipText(MessageManager.getString("action.save"));
1113
1114     int value = chooser.showSaveDialog(this);
1115
1116     if (value == JalviewFileChooser.APPROVE_OPTION)
1117     {
1118       currentFileFormat = chooser.getSelectedFormat();
1119       while (currentFileFormat == null)
1120       {
1121         JOptionPane
1122                 .showInternalMessageDialog(
1123                         Desktop.desktop,
1124                         MessageManager
1125                                 .getString("label.select_file_format_before_saving"),
1126                         MessageManager
1127                                 .getString("label.file_format_not_specified"),
1128                         JOptionPane.WARNING_MESSAGE);
1129         currentFileFormat = chooser.getSelectedFormat();
1130         value = chooser.showSaveDialog(this);
1131         if (value != JalviewFileChooser.APPROVE_OPTION)
1132         {
1133           return;
1134         }
1135       }
1136
1137       fileName = chooser.getSelectedFile().getPath();
1138
1139       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1140               currentFileFormat);
1141
1142       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1143       if (currentFileFormat.indexOf(" ") > -1)
1144       {
1145         currentFileFormat = currentFileFormat.substring(0,
1146                 currentFileFormat.indexOf(" "));
1147       }
1148       saveAlignment(fileName, currentFileFormat);
1149     }
1150   }
1151
1152   public boolean saveAlignment(String file, String format)
1153   {
1154     boolean success = true;
1155
1156     if (format.equalsIgnoreCase("Jalview"))
1157     {
1158       String shortName = title;
1159
1160       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1161       {
1162         shortName = shortName.substring(shortName
1163                 .lastIndexOf(java.io.File.separatorChar) + 1);
1164       }
1165
1166       success = new Jalview2XML().saveAlignment(this, file, shortName);
1167
1168       statusBar.setText(MessageManager.formatMessage(
1169               "label.successfully_saved_to_file_in_format", new Object[] {
1170                   fileName, format }));
1171
1172     }
1173     else
1174     {
1175       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1176       {
1177         warningMessage("Cannot save file " + fileName + " using format "
1178                 + format, "Alignment output format not supported");
1179         if (!Jalview.isHeadlessMode())
1180         {
1181           saveAs_actionPerformed(null);
1182         }
1183         return false;
1184       }
1185
1186       AlignmentExportData exportData = getAlignmentForExport(format,
1187               viewport, null);
1188       if (exportData.getSettings().isCancelled())
1189       {
1190         return false;
1191       }
1192       FormatAdapter f = new FormatAdapter(alignPanel,
1193               exportData.getSettings());
1194       String output = f.formatSequences(
1195               format,
1196               exportData.getAlignment(), // class cast exceptions will
1197               // occur in the distant future
1198               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1199               f.getCacheSuffixDefault(format),
1200               viewport.getColumnSelection());
1201
1202       if (output == null)
1203       {
1204         success = false;
1205       }
1206       else
1207       {
1208         try
1209         {
1210           java.io.PrintWriter out = new java.io.PrintWriter(
1211                   new java.io.FileWriter(file));
1212
1213           out.print(output);
1214           out.close();
1215           this.setTitle(file);
1216           statusBar.setText(MessageManager.formatMessage(
1217                   "label.successfully_saved_to_file_in_format",
1218                   new Object[] { fileName, format }));
1219         } catch (Exception ex)
1220         {
1221           success = false;
1222           ex.printStackTrace();
1223         }
1224       }
1225     }
1226
1227     if (!success)
1228     {
1229       JOptionPane.showInternalMessageDialog(this, MessageManager
1230               .formatMessage("label.couldnt_save_file",
1231                       new Object[] { fileName }), MessageManager
1232               .getString("label.error_saving_file"),
1233               JOptionPane.WARNING_MESSAGE);
1234     }
1235
1236     return success;
1237   }
1238
1239   private void warningMessage(String warning, String title)
1240   {
1241     if (new jalview.util.Platform().isHeadless())
1242     {
1243       System.err.println("Warning: " + title + "\nWarning: " + warning);
1244
1245     }
1246     else
1247     {
1248       JOptionPane.showInternalMessageDialog(this, warning, title,
1249               JOptionPane.WARNING_MESSAGE);
1250     }
1251     return;
1252   }
1253
1254   /**
1255    * DOCUMENT ME!
1256    *
1257    * @param e
1258    *          DOCUMENT ME!
1259    */
1260   @Override
1261   protected void outputText_actionPerformed(ActionEvent e)
1262   {
1263
1264     AlignmentExportData exportData = getAlignmentForExport(
1265             e.getActionCommand(), viewport, null);
1266     if (exportData.getSettings().isCancelled())
1267     {
1268       return;
1269     }
1270     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1271     cap.setForInput(null);
1272     try
1273     {
1274       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1275               .formatSequences(e.getActionCommand(),
1276                       exportData.getAlignment(),
1277                       exportData.getOmitHidden(),
1278                       exportData.getStartEndPostions(),
1279                       viewport.getColumnSelection()));
1280       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1281               "label.alignment_output_command",
1282               new Object[] { e.getActionCommand() }), 600, 500);
1283     } catch (OutOfMemoryError oom)
1284     {
1285       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1286       cap.dispose();
1287     }
1288
1289   }
1290
1291   public static AlignmentExportData getAlignmentForExport(
1292           String exportFormat, AlignViewportI viewport,
1293           AlignExportSettingI exportSettings)
1294   {
1295     AlignmentI alignmentToExport = null;
1296     AlignExportSettingI settings = exportSettings;
1297     String[] omitHidden = null;
1298
1299     HiddenSequences hiddenSeqs = viewport.getAlignment()
1300             .getHiddenSequences();
1301
1302     alignmentToExport = viewport.getAlignment();
1303
1304     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1305     if (settings == null)
1306     {
1307       settings = new AlignExportSettings(hasHiddenSeqs,
1308               viewport.hasHiddenColumns(), exportFormat);
1309     }
1310     // settings.isExportAnnotations();
1311
1312     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1313     {
1314       omitHidden = viewport.getViewAsString(false,
1315               settings.isExportHiddenSequences());
1316     }
1317
1318     int[] alignmentStartEnd = new int[2];
1319     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1320     {
1321       alignmentToExport = hiddenSeqs.getFullAlignment();
1322     }
1323     else
1324     {
1325       alignmentToExport = viewport.getAlignment();
1326     }
1327     alignmentStartEnd = alignmentToExport
1328             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1329                     .getHiddenColumns());
1330     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1331             omitHidden, alignmentStartEnd, settings);
1332     return ed;
1333   }
1334
1335   /**
1336    * DOCUMENT ME!
1337    *
1338    * @param e
1339    *          DOCUMENT ME!
1340    */
1341   @Override
1342   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1343   {
1344     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1345     htmlSVG.generateHtmlSvgOutput(null);
1346   }
1347
1348   @Override
1349   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1350   {
1351     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1352     bjs.exportJalviewAlignmentAsBioJsHtmlFile(null);
1353   }
1354
1355   public void createImageMap(File file, String image)
1356   {
1357     alignPanel.makePNGImageMap(file, image);
1358   }
1359
1360   /**
1361    * DOCUMENT ME!
1362    *
1363    * @param e
1364    *          DOCUMENT ME!
1365    */
1366   @Override
1367   public void createPNG(File f)
1368   {
1369     alignPanel.makePNG(f);
1370   }
1371
1372   /**
1373    * DOCUMENT ME!
1374    *
1375    * @param e
1376    *          DOCUMENT ME!
1377    */
1378   @Override
1379   public void createEPS(File f)
1380   {
1381     alignPanel.makeEPS(f);
1382   }
1383
1384   @Override
1385   public void createSVG(File f)
1386   {
1387     alignPanel.makeSVG(f);
1388   }
1389
1390   @Override
1391   public void pageSetup_actionPerformed(ActionEvent e)
1392   {
1393     PrinterJob printJob = PrinterJob.getPrinterJob();
1394     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1395   }
1396
1397   /**
1398    * DOCUMENT ME!
1399    *
1400    * @param e
1401    *          DOCUMENT ME!
1402    */
1403   @Override
1404   public void printMenuItem_actionPerformed(ActionEvent e)
1405   {
1406     // Putting in a thread avoids Swing painting problems
1407     PrintThread thread = new PrintThread(alignPanel);
1408     thread.start();
1409   }
1410
1411   @Override
1412   public void exportFeatures_actionPerformed(ActionEvent e)
1413   {
1414     new AnnotationExporter().exportFeatures(alignPanel);
1415   }
1416
1417   @Override
1418   public void exportAnnotations_actionPerformed(ActionEvent e)
1419   {
1420     new AnnotationExporter().exportAnnotations(alignPanel);
1421   }
1422
1423   @Override
1424   public void associatedData_actionPerformed(ActionEvent e)
1425   {
1426     // Pick the tree file
1427     JalviewFileChooser chooser = new JalviewFileChooser(
1428             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1429     chooser.setFileView(new JalviewFileView());
1430     chooser.setDialogTitle(MessageManager
1431             .getString("label.load_jalview_annotations"));
1432     chooser.setToolTipText(MessageManager
1433             .getString("label.load_jalview_annotations"));
1434
1435     int value = chooser.showOpenDialog(null);
1436
1437     if (value == JalviewFileChooser.APPROVE_OPTION)
1438     {
1439       String choice = chooser.getSelectedFile().getPath();
1440       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1441       loadJalviewDataFile(choice, null, null, null);
1442     }
1443
1444   }
1445
1446   /**
1447    * Close the current view or all views in the alignment frame. If the frame
1448    * only contains one view then the alignment will be removed from memory.
1449    *
1450    * @param closeAllTabs
1451    */
1452   @Override
1453   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1454   {
1455     if (alignPanels != null && alignPanels.size() < 2)
1456     {
1457       closeAllTabs = true;
1458     }
1459
1460     try
1461     {
1462       if (alignPanels != null)
1463       {
1464         if (closeAllTabs)
1465         {
1466           if (this.isClosed())
1467           {
1468             // really close all the windows - otherwise wait till
1469             // setClosed(true) is called
1470             for (int i = 0; i < alignPanels.size(); i++)
1471             {
1472               AlignmentPanel ap = alignPanels.get(i);
1473               ap.closePanel();
1474             }
1475           }
1476         }
1477         else
1478         {
1479           closeView(alignPanel);
1480         }
1481       }
1482
1483       if (closeAllTabs)
1484       {
1485         /*
1486          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1487          * be called recursively, with the frame now in 'closed' state
1488          */
1489         this.setClosed(true);
1490       }
1491     } catch (Exception ex)
1492     {
1493       ex.printStackTrace();
1494     }
1495   }
1496
1497   /**
1498    * Close the specified panel and close up tabs appropriately.
1499    *
1500    * @param panelToClose
1501    */
1502   public void closeView(AlignmentPanel panelToClose)
1503   {
1504     int index = tabbedPane.getSelectedIndex();
1505     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1506     alignPanels.remove(panelToClose);
1507     panelToClose.closePanel();
1508     panelToClose = null;
1509
1510     tabbedPane.removeTabAt(closedindex);
1511     tabbedPane.validate();
1512
1513     if (index > closedindex || index == tabbedPane.getTabCount())
1514     {
1515       // modify currently selected tab index if necessary.
1516       index--;
1517     }
1518
1519     this.tabSelectionChanged(index);
1520   }
1521
1522   /**
1523    * DOCUMENT ME!
1524    */
1525   void updateEditMenuBar()
1526   {
1527
1528     if (viewport.getHistoryList().size() > 0)
1529     {
1530       undoMenuItem.setEnabled(true);
1531       CommandI command = viewport.getHistoryList().peek();
1532       undoMenuItem.setText(MessageManager.formatMessage(
1533               "label.undo_command",
1534               new Object[] { command.getDescription() }));
1535     }
1536     else
1537     {
1538       undoMenuItem.setEnabled(false);
1539       undoMenuItem.setText(MessageManager.getString("action.undo"));
1540     }
1541
1542     if (viewport.getRedoList().size() > 0)
1543     {
1544       redoMenuItem.setEnabled(true);
1545
1546       CommandI command = viewport.getRedoList().peek();
1547       redoMenuItem.setText(MessageManager.formatMessage(
1548               "label.redo_command",
1549               new Object[] { command.getDescription() }));
1550     }
1551     else
1552     {
1553       redoMenuItem.setEnabled(false);
1554       redoMenuItem.setText(MessageManager.getString("action.redo"));
1555     }
1556   }
1557
1558   @Override
1559   public void addHistoryItem(CommandI command)
1560   {
1561     if (command.getSize() > 0)
1562     {
1563       viewport.addToHistoryList(command);
1564       viewport.clearRedoList();
1565       updateEditMenuBar();
1566       viewport.updateHiddenColumns();
1567       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1568       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1569       // viewport.getColumnSelection()
1570       // .getHiddenColumns().size() > 0);
1571     }
1572   }
1573
1574   /**
1575    *
1576    * @return alignment objects for all views
1577    */
1578   AlignmentI[] getViewAlignments()
1579   {
1580     if (alignPanels != null)
1581     {
1582       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1583       int i = 0;
1584       for (AlignmentPanel ap : alignPanels)
1585       {
1586         als[i++] = ap.av.getAlignment();
1587       }
1588       return als;
1589     }
1590     if (viewport != null)
1591     {
1592       return new AlignmentI[] { viewport.getAlignment() };
1593     }
1594     return null;
1595   }
1596
1597   /**
1598    * DOCUMENT ME!
1599    *
1600    * @param e
1601    *          DOCUMENT ME!
1602    */
1603   @Override
1604   protected void undoMenuItem_actionPerformed(ActionEvent e)
1605   {
1606     if (viewport.getHistoryList().isEmpty())
1607     {
1608       return;
1609     }
1610     CommandI command = viewport.getHistoryList().pop();
1611     viewport.addToRedoList(command);
1612     command.undoCommand(getViewAlignments());
1613
1614     AlignmentViewport originalSource = getOriginatingSource(command);
1615     updateEditMenuBar();
1616
1617     if (originalSource != null)
1618     {
1619       if (originalSource != viewport)
1620       {
1621         Cache.log
1622                 .warn("Implementation worry: mismatch of viewport origin for undo");
1623       }
1624       originalSource.updateHiddenColumns();
1625       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1626       // null
1627       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1628       // viewport.getColumnSelection()
1629       // .getHiddenColumns().size() > 0);
1630       originalSource.firePropertyChange("alignment", null, originalSource
1631               .getAlignment().getSequences());
1632     }
1633   }
1634
1635   /**
1636    * DOCUMENT ME!
1637    *
1638    * @param e
1639    *          DOCUMENT ME!
1640    */
1641   @Override
1642   protected void redoMenuItem_actionPerformed(ActionEvent e)
1643   {
1644     if (viewport.getRedoList().size() < 1)
1645     {
1646       return;
1647     }
1648
1649     CommandI command = viewport.getRedoList().pop();
1650     viewport.addToHistoryList(command);
1651     command.doCommand(getViewAlignments());
1652
1653     AlignmentViewport originalSource = getOriginatingSource(command);
1654     updateEditMenuBar();
1655
1656     if (originalSource != null)
1657     {
1658
1659       if (originalSource != viewport)
1660       {
1661         Cache.log
1662                 .warn("Implementation worry: mismatch of viewport origin for redo");
1663       }
1664       originalSource.updateHiddenColumns();
1665       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1666       // null
1667       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1668       // viewport.getColumnSelection()
1669       // .getHiddenColumns().size() > 0);
1670       originalSource.firePropertyChange("alignment", null, originalSource
1671               .getAlignment().getSequences());
1672     }
1673   }
1674
1675   AlignmentViewport getOriginatingSource(CommandI command)
1676   {
1677     AlignmentViewport originalSource = null;
1678     // For sequence removal and addition, we need to fire
1679     // the property change event FROM the viewport where the
1680     // original alignment was altered
1681     AlignmentI al = null;
1682     if (command instanceof EditCommand)
1683     {
1684       EditCommand editCommand = (EditCommand) command;
1685       al = editCommand.getAlignment();
1686       List<Component> comps = PaintRefresher.components.get(viewport
1687               .getSequenceSetId());
1688
1689       for (Component comp : comps)
1690       {
1691         if (comp instanceof AlignmentPanel)
1692         {
1693           if (al == ((AlignmentPanel) comp).av.getAlignment())
1694           {
1695             originalSource = ((AlignmentPanel) comp).av;
1696             break;
1697           }
1698         }
1699       }
1700     }
1701
1702     if (originalSource == null)
1703     {
1704       // The original view is closed, we must validate
1705       // the current view against the closed view first
1706       if (al != null)
1707       {
1708         PaintRefresher.validateSequences(al, viewport.getAlignment());
1709       }
1710
1711       originalSource = viewport;
1712     }
1713
1714     return originalSource;
1715   }
1716
1717   /**
1718    * DOCUMENT ME!
1719    *
1720    * @param up
1721    *          DOCUMENT ME!
1722    */
1723   public void moveSelectedSequences(boolean up)
1724   {
1725     SequenceGroup sg = viewport.getSelectionGroup();
1726
1727     if (sg == null)
1728     {
1729       return;
1730     }
1731     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1732             viewport.getHiddenRepSequences(), up);
1733     alignPanel.paintAlignment(true);
1734   }
1735
1736   synchronized void slideSequences(boolean right, int size)
1737   {
1738     List<SequenceI> sg = new ArrayList<SequenceI>();
1739     if (viewport.cursorMode)
1740     {
1741       sg.add(viewport.getAlignment().getSequenceAt(
1742               alignPanel.getSeqPanel().seqCanvas.cursorY));
1743     }
1744     else if (viewport.getSelectionGroup() != null
1745             && viewport.getSelectionGroup().getSize() != viewport
1746                     .getAlignment().getHeight())
1747     {
1748       sg = viewport.getSelectionGroup().getSequences(
1749               viewport.getHiddenRepSequences());
1750     }
1751
1752     if (sg.size() < 1)
1753     {
1754       return;
1755     }
1756
1757     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1758
1759     for (SequenceI seq : viewport.getAlignment().getSequences())
1760     {
1761       if (!sg.contains(seq))
1762       {
1763         invertGroup.add(seq);
1764       }
1765     }
1766
1767     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1768
1769     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1770     for (int i = 0; i < invertGroup.size(); i++)
1771     {
1772       seqs2[i] = invertGroup.get(i);
1773     }
1774
1775     SlideSequencesCommand ssc;
1776     if (right)
1777     {
1778       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1779               size, viewport.getGapCharacter());
1780     }
1781     else
1782     {
1783       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1784               size, viewport.getGapCharacter());
1785     }
1786
1787     int groupAdjustment = 0;
1788     if (ssc.getGapsInsertedBegin() && right)
1789     {
1790       if (viewport.cursorMode)
1791       {
1792         alignPanel.getSeqPanel().moveCursor(size, 0);
1793       }
1794       else
1795       {
1796         groupAdjustment = size;
1797       }
1798     }
1799     else if (!ssc.getGapsInsertedBegin() && !right)
1800     {
1801       if (viewport.cursorMode)
1802       {
1803         alignPanel.getSeqPanel().moveCursor(-size, 0);
1804       }
1805       else
1806       {
1807         groupAdjustment = -size;
1808       }
1809     }
1810
1811     if (groupAdjustment != 0)
1812     {
1813       viewport.getSelectionGroup().setStartRes(
1814               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1815       viewport.getSelectionGroup().setEndRes(
1816               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1817     }
1818
1819     /*
1820      * just extend the last slide command if compatible; but not if in
1821      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1822      */
1823     boolean appendHistoryItem = false;
1824     Deque<CommandI> historyList = viewport.getHistoryList();
1825     boolean inSplitFrame = getSplitViewContainer() != null;
1826     if (!inSplitFrame && historyList != null && historyList.size() > 0
1827             && historyList.peek() instanceof SlideSequencesCommand)
1828     {
1829       appendHistoryItem = ssc
1830               .appendSlideCommand((SlideSequencesCommand) historyList
1831                       .peek());
1832     }
1833
1834     if (!appendHistoryItem)
1835     {
1836       addHistoryItem(ssc);
1837     }
1838
1839     repaint();
1840   }
1841
1842   /**
1843    * DOCUMENT ME!
1844    *
1845    * @param e
1846    *          DOCUMENT ME!
1847    */
1848   @Override
1849   protected void copy_actionPerformed(ActionEvent e)
1850   {
1851     System.gc();
1852     if (viewport.getSelectionGroup() == null)
1853     {
1854       return;
1855     }
1856     // TODO: preserve the ordering of displayed alignment annotation in any
1857     // internal paste (particularly sequence associated annotation)
1858     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1859     String[] omitHidden = null;
1860
1861     if (viewport.hasHiddenColumns())
1862     {
1863       omitHidden = viewport.getViewAsString(true);
1864     }
1865
1866     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1867             omitHidden, null);
1868
1869     StringSelection ss = new StringSelection(output);
1870
1871     try
1872     {
1873       jalview.gui.Desktop.internalCopy = true;
1874       // Its really worth setting the clipboard contents
1875       // to empty before setting the large StringSelection!!
1876       Toolkit.getDefaultToolkit().getSystemClipboard()
1877               .setContents(new StringSelection(""), null);
1878
1879       Toolkit.getDefaultToolkit().getSystemClipboard()
1880               .setContents(ss, Desktop.instance);
1881     } catch (OutOfMemoryError er)
1882     {
1883       new OOMWarning("copying region", er);
1884       return;
1885     }
1886
1887     ArrayList<int[]> hiddenColumns = null;
1888     if (viewport.hasHiddenColumns())
1889     {
1890       hiddenColumns = new ArrayList<int[]>();
1891       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1892               .getSelectionGroup().getEndRes();
1893       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1894       {
1895         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1896         {
1897           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1898               region[1] - hiddenOffset });
1899         }
1900       }
1901     }
1902
1903     Desktop.jalviewClipboard = new Object[] { seqs,
1904         viewport.getAlignment().getDataset(), hiddenColumns };
1905     statusBar.setText(MessageManager.formatMessage(
1906             "label.copied_sequences_to_clipboard", new Object[] { Integer
1907                     .valueOf(seqs.length).toString() }));
1908   }
1909
1910   /**
1911    * DOCUMENT ME!
1912    *
1913    * @param e
1914    *          DOCUMENT ME!
1915    */
1916   @Override
1917   protected void pasteNew_actionPerformed(ActionEvent e)
1918   {
1919     paste(true);
1920   }
1921
1922   /**
1923    * DOCUMENT ME!
1924    *
1925    * @param e
1926    *          DOCUMENT ME!
1927    */
1928   @Override
1929   protected void pasteThis_actionPerformed(ActionEvent e)
1930   {
1931     paste(false);
1932   }
1933
1934   /**
1935    * Paste contents of Jalview clipboard
1936    *
1937    * @param newAlignment
1938    *          true to paste to a new alignment, otherwise add to this.
1939    */
1940   void paste(boolean newAlignment)
1941   {
1942     boolean externalPaste = true;
1943     try
1944     {
1945       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1946       Transferable contents = c.getContents(this);
1947
1948       if (contents == null)
1949       {
1950         return;
1951       }
1952
1953       String str, format;
1954       try
1955       {
1956         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1957         if (str.length() < 1)
1958         {
1959           return;
1960         }
1961
1962         format = new IdentifyFile().identify(str, "Paste");
1963
1964       } catch (OutOfMemoryError er)
1965       {
1966         new OOMWarning("Out of memory pasting sequences!!", er);
1967         return;
1968       }
1969
1970       SequenceI[] sequences;
1971       boolean annotationAdded = false;
1972       AlignmentI alignment = null;
1973
1974       if (Desktop.jalviewClipboard != null)
1975       {
1976         // The clipboard was filled from within Jalview, we must use the
1977         // sequences
1978         // And dataset from the copied alignment
1979         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1980         // be doubly sure that we create *new* sequence objects.
1981         sequences = new SequenceI[newseq.length];
1982         for (int i = 0; i < newseq.length; i++)
1983         {
1984           sequences[i] = new Sequence(newseq[i]);
1985         }
1986         alignment = new Alignment(sequences);
1987         externalPaste = false;
1988       }
1989       else
1990       {
1991         // parse the clipboard as an alignment.
1992         alignment = new FormatAdapter().readFile(str, "Paste", format);
1993         sequences = alignment.getSequencesArray();
1994       }
1995
1996       int alwidth = 0;
1997       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1998       int fgroup = -1;
1999
2000       if (newAlignment)
2001       {
2002
2003         if (Desktop.jalviewClipboard != null)
2004         {
2005           // dataset is inherited
2006           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2007         }
2008         else
2009         {
2010           // new dataset is constructed
2011           alignment.setDataset(null);
2012         }
2013         alwidth = alignment.getWidth() + 1;
2014       }
2015       else
2016       {
2017         AlignmentI pastedal = alignment; // preserve pasted alignment object
2018         // Add pasted sequences and dataset into existing alignment.
2019         alignment = viewport.getAlignment();
2020         alwidth = alignment.getWidth() + 1;
2021         // decide if we need to import sequences from an existing dataset
2022         boolean importDs = Desktop.jalviewClipboard != null
2023                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2024         // importDs==true instructs us to copy over new dataset sequences from
2025         // an existing alignment
2026         Vector newDs = (importDs) ? new Vector() : null; // used to create
2027         // minimum dataset set
2028
2029         for (int i = 0; i < sequences.length; i++)
2030         {
2031           if (importDs)
2032           {
2033             newDs.addElement(null);
2034           }
2035           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2036           // paste
2037           if (importDs && ds != null)
2038           {
2039             if (!newDs.contains(ds))
2040             {
2041               newDs.setElementAt(ds, i);
2042               ds = new Sequence(ds);
2043               // update with new dataset sequence
2044               sequences[i].setDatasetSequence(ds);
2045             }
2046             else
2047             {
2048               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2049             }
2050           }
2051           else
2052           {
2053             // copy and derive new dataset sequence
2054             sequences[i] = sequences[i].deriveSequence();
2055             alignment.getDataset().addSequence(
2056                     sequences[i].getDatasetSequence());
2057             // TODO: avoid creation of duplicate dataset sequences with a
2058             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2059           }
2060           alignment.addSequence(sequences[i]); // merges dataset
2061         }
2062         if (newDs != null)
2063         {
2064           newDs.clear(); // tidy up
2065         }
2066         if (alignment.getAlignmentAnnotation() != null)
2067         {
2068           for (AlignmentAnnotation alan : alignment
2069                   .getAlignmentAnnotation())
2070           {
2071             if (alan.graphGroup > fgroup)
2072             {
2073               fgroup = alan.graphGroup;
2074             }
2075           }
2076         }
2077         if (pastedal.getAlignmentAnnotation() != null)
2078         {
2079           // Add any annotation attached to alignment.
2080           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2081           for (int i = 0; i < alann.length; i++)
2082           {
2083             annotationAdded = true;
2084             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2085             {
2086               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2087               if (newann.graphGroup > -1)
2088               {
2089                 if (newGraphGroups.size() <= newann.graphGroup
2090                         || newGraphGroups.get(newann.graphGroup) == null)
2091                 {
2092                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2093                   {
2094                     newGraphGroups.add(q, null);
2095                   }
2096                   newGraphGroups.set(newann.graphGroup, new Integer(
2097                           ++fgroup));
2098                 }
2099                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2100                         .intValue();
2101               }
2102
2103               newann.padAnnotation(alwidth);
2104               alignment.addAnnotation(newann);
2105             }
2106           }
2107         }
2108       }
2109       if (!newAlignment)
2110       {
2111         // /////
2112         // ADD HISTORY ITEM
2113         //
2114         addHistoryItem(new EditCommand(
2115                 MessageManager.getString("label.add_sequences"),
2116                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2117       }
2118       // Add any annotations attached to sequences
2119       for (int i = 0; i < sequences.length; i++)
2120       {
2121         if (sequences[i].getAnnotation() != null)
2122         {
2123           AlignmentAnnotation newann;
2124           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2125           {
2126             annotationAdded = true;
2127             newann = sequences[i].getAnnotation()[a];
2128             newann.adjustForAlignment();
2129             newann.padAnnotation(alwidth);
2130             if (newann.graphGroup > -1)
2131             {
2132               if (newann.graphGroup > -1)
2133               {
2134                 if (newGraphGroups.size() <= newann.graphGroup
2135                         || newGraphGroups.get(newann.graphGroup) == null)
2136                 {
2137                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2138                   {
2139                     newGraphGroups.add(q, null);
2140                   }
2141                   newGraphGroups.set(newann.graphGroup, new Integer(
2142                           ++fgroup));
2143                 }
2144                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2145                         .intValue();
2146               }
2147             }
2148             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2149             // was
2150             // duplicated
2151             // earlier
2152             alignment
2153                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2154           }
2155         }
2156       }
2157       if (!newAlignment)
2158       {
2159
2160         // propagate alignment changed.
2161         viewport.setEndSeq(alignment.getHeight());
2162         if (annotationAdded)
2163         {
2164           // Duplicate sequence annotation in all views.
2165           AlignmentI[] alview = this.getViewAlignments();
2166           for (int i = 0; i < sequences.length; i++)
2167           {
2168             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2169             if (sann == null)
2170             {
2171               continue;
2172             }
2173             for (int avnum = 0; avnum < alview.length; avnum++)
2174             {
2175               if (alview[avnum] != alignment)
2176               {
2177                 // duplicate in a view other than the one with input focus
2178                 int avwidth = alview[avnum].getWidth() + 1;
2179                 // this relies on sann being preserved after we
2180                 // modify the sequence's annotation array for each duplication
2181                 for (int a = 0; a < sann.length; a++)
2182                 {
2183                   AlignmentAnnotation newann = new AlignmentAnnotation(
2184                           sann[a]);
2185                   sequences[i].addAlignmentAnnotation(newann);
2186                   newann.padAnnotation(avwidth);
2187                   alview[avnum].addAnnotation(newann); // annotation was
2188                   // duplicated earlier
2189                   // TODO JAL-1145 graphGroups are not updated for sequence
2190                   // annotation added to several views. This may cause
2191                   // strangeness
2192                   alview[avnum].setAnnotationIndex(newann, a);
2193                 }
2194               }
2195             }
2196           }
2197           buildSortByAnnotationScoresMenu();
2198         }
2199         viewport.firePropertyChange("alignment", null,
2200                 alignment.getSequences());
2201         if (alignPanels != null)
2202         {
2203           for (AlignmentPanel ap : alignPanels)
2204           {
2205             ap.validateAnnotationDimensions(false);
2206           }
2207         }
2208         else
2209         {
2210           alignPanel.validateAnnotationDimensions(false);
2211         }
2212
2213       }
2214       else
2215       {
2216         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2217                 DEFAULT_HEIGHT);
2218         String newtitle = new String("Copied sequences");
2219
2220         if (Desktop.jalviewClipboard != null
2221                 && Desktop.jalviewClipboard[2] != null)
2222         {
2223           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2224           for (int[] region : hc)
2225           {
2226             af.viewport.hideColumns(region[0], region[1]);
2227           }
2228         }
2229
2230         // >>>This is a fix for the moment, until a better solution is
2231         // found!!<<<
2232         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2233                 .transferSettings(
2234                         alignPanel.getSeqPanel().seqCanvas
2235                                 .getFeatureRenderer());
2236
2237         // TODO: maintain provenance of an alignment, rather than just make the
2238         // title a concatenation of operations.
2239         if (!externalPaste)
2240         {
2241           if (title.startsWith("Copied sequences"))
2242           {
2243             newtitle = title;
2244           }
2245           else
2246           {
2247             newtitle = newtitle.concat("- from " + title);
2248           }
2249         }
2250         else
2251         {
2252           newtitle = new String("Pasted sequences");
2253         }
2254
2255         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2256                 DEFAULT_HEIGHT);
2257
2258       }
2259
2260     } catch (Exception ex)
2261     {
2262       ex.printStackTrace();
2263       System.out.println("Exception whilst pasting: " + ex);
2264       // could be anything being pasted in here
2265     }
2266
2267   }
2268
2269   @Override
2270   protected void expand_newalign(ActionEvent e)
2271   {
2272     try
2273     {
2274       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2275               .getAlignment(), -1);
2276       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2277               DEFAULT_HEIGHT);
2278       String newtitle = new String("Flanking alignment");
2279
2280       if (Desktop.jalviewClipboard != null
2281               && Desktop.jalviewClipboard[2] != null)
2282       {
2283         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2284         for (int region[] : hc)
2285         {
2286           af.viewport.hideColumns(region[0], region[1]);
2287         }
2288       }
2289
2290       // >>>This is a fix for the moment, until a better solution is
2291       // found!!<<<
2292       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2293               .transferSettings(
2294                       alignPanel.getSeqPanel().seqCanvas
2295                               .getFeatureRenderer());
2296
2297       // TODO: maintain provenance of an alignment, rather than just make the
2298       // title a concatenation of operations.
2299       {
2300         if (title.startsWith("Copied sequences"))
2301         {
2302           newtitle = title;
2303         }
2304         else
2305         {
2306           newtitle = newtitle.concat("- from " + title);
2307         }
2308       }
2309
2310       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2311
2312     } catch (Exception ex)
2313     {
2314       ex.printStackTrace();
2315       System.out.println("Exception whilst pasting: " + ex);
2316       // could be anything being pasted in here
2317     } catch (OutOfMemoryError oom)
2318     {
2319       new OOMWarning("Viewing flanking region of alignment", oom);
2320     }
2321   }
2322
2323   /**
2324    * DOCUMENT ME!
2325    *
2326    * @param e
2327    *          DOCUMENT ME!
2328    */
2329   @Override
2330   protected void cut_actionPerformed(ActionEvent e)
2331   {
2332     copy_actionPerformed(null);
2333     delete_actionPerformed(null);
2334   }
2335
2336   /**
2337    * DOCUMENT ME!
2338    *
2339    * @param e
2340    *          DOCUMENT ME!
2341    */
2342   @Override
2343   protected void delete_actionPerformed(ActionEvent evt)
2344   {
2345
2346     SequenceGroup sg = viewport.getSelectionGroup();
2347     if (sg == null)
2348     {
2349       return;
2350     }
2351
2352     /*
2353      * If the cut affects all sequences, warn, remove highlighted columns
2354      */
2355     if (sg.getSize() == viewport.getAlignment().getHeight())
2356     {
2357       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2358               .getAlignment().getWidth()) ? true : false;
2359       if (isEntireAlignWidth)
2360       {
2361         int confirm = JOptionPane.showConfirmDialog(this,
2362                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2363                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2364                 JOptionPane.OK_CANCEL_OPTION);
2365
2366         if (confirm == JOptionPane.CANCEL_OPTION
2367                 || confirm == JOptionPane.CLOSED_OPTION)
2368         {
2369           return;
2370         }
2371       }
2372       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2373               sg.getEndRes() + 1);
2374     }
2375     SequenceI[] cut = sg.getSequences()
2376             .toArray(new SequenceI[sg.getSize()]);
2377
2378     addHistoryItem(new EditCommand(
2379             MessageManager.getString("label.cut_sequences"), Action.CUT,
2380             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2381             viewport.getAlignment()));
2382
2383     viewport.setSelectionGroup(null);
2384     viewport.sendSelection();
2385     viewport.getAlignment().deleteGroup(sg);
2386
2387     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2388             .getSequences());
2389     if (viewport.getAlignment().getHeight() < 1)
2390     {
2391       try
2392       {
2393         this.setClosed(true);
2394       } catch (Exception ex)
2395       {
2396       }
2397     }
2398   }
2399
2400   /**
2401    * DOCUMENT ME!
2402    *
2403    * @param e
2404    *          DOCUMENT ME!
2405    */
2406   @Override
2407   protected void deleteGroups_actionPerformed(ActionEvent e)
2408   {
2409     if (avc.deleteGroups())
2410     {
2411       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2412       alignPanel.updateAnnotation();
2413       alignPanel.paintAlignment(true);
2414     }
2415   }
2416
2417   /**
2418    * DOCUMENT ME!
2419    *
2420    * @param e
2421    *          DOCUMENT ME!
2422    */
2423   @Override
2424   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2425   {
2426     SequenceGroup sg = new SequenceGroup();
2427
2428     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2429     {
2430       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2431     }
2432
2433     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2434     viewport.setSelectionGroup(sg);
2435     viewport.sendSelection();
2436     // JAL-2034 - should delegate to
2437     // alignPanel to decide if overview needs
2438     // updating.
2439     alignPanel.paintAlignment(false);
2440     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2441   }
2442
2443   /**
2444    * DOCUMENT ME!
2445    *
2446    * @param e
2447    *          DOCUMENT ME!
2448    */
2449   @Override
2450   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2451   {
2452     if (viewport.cursorMode)
2453     {
2454       alignPanel.getSeqPanel().keyboardNo1 = null;
2455       alignPanel.getSeqPanel().keyboardNo2 = null;
2456     }
2457     viewport.setSelectionGroup(null);
2458     viewport.getColumnSelection().clear();
2459     viewport.setSelectionGroup(null);
2460     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2461     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2462     // JAL-2034 - should delegate to
2463     // alignPanel to decide if overview needs
2464     // updating.
2465     alignPanel.paintAlignment(false);
2466     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2467     viewport.sendSelection();
2468   }
2469
2470   /**
2471    * DOCUMENT ME!
2472    *
2473    * @param e
2474    *          DOCUMENT ME!
2475    */
2476   @Override
2477   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2478   {
2479     SequenceGroup sg = viewport.getSelectionGroup();
2480
2481     if (sg == null)
2482     {
2483       selectAllSequenceMenuItem_actionPerformed(null);
2484
2485       return;
2486     }
2487
2488     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2489     {
2490       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2491     }
2492     // JAL-2034 - should delegate to
2493     // alignPanel to decide if overview needs
2494     // updating.
2495
2496     alignPanel.paintAlignment(true);
2497     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2498     viewport.sendSelection();
2499   }
2500
2501   @Override
2502   public void invertColSel_actionPerformed(ActionEvent e)
2503   {
2504     viewport.invertColumnSelection();
2505     alignPanel.paintAlignment(true);
2506     viewport.sendSelection();
2507   }
2508
2509   /**
2510    * DOCUMENT ME!
2511    *
2512    * @param e
2513    *          DOCUMENT ME!
2514    */
2515   @Override
2516   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2517   {
2518     trimAlignment(true);
2519   }
2520
2521   /**
2522    * DOCUMENT ME!
2523    *
2524    * @param e
2525    *          DOCUMENT ME!
2526    */
2527   @Override
2528   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2529   {
2530     trimAlignment(false);
2531   }
2532
2533   void trimAlignment(boolean trimLeft)
2534   {
2535     ColumnSelection colSel = viewport.getColumnSelection();
2536     int column;
2537
2538     if (!colSel.isEmpty())
2539     {
2540       if (trimLeft)
2541       {
2542         column = colSel.getMin();
2543       }
2544       else
2545       {
2546         column = colSel.getMax();
2547       }
2548
2549       SequenceI[] seqs;
2550       if (viewport.getSelectionGroup() != null)
2551       {
2552         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2553                 viewport.getHiddenRepSequences());
2554       }
2555       else
2556       {
2557         seqs = viewport.getAlignment().getSequencesArray();
2558       }
2559
2560       TrimRegionCommand trimRegion;
2561       if (trimLeft)
2562       {
2563         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2564                 column, viewport.getAlignment());
2565         viewport.setStartRes(0);
2566       }
2567       else
2568       {
2569         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2570                 column, viewport.getAlignment());
2571       }
2572
2573       statusBar.setText(MessageManager.formatMessage(
2574               "label.removed_columns",
2575               new String[] { Integer.valueOf(trimRegion.getSize())
2576                       .toString() }));
2577
2578       addHistoryItem(trimRegion);
2579
2580       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2581       {
2582         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2583                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2584         {
2585           viewport.getAlignment().deleteGroup(sg);
2586         }
2587       }
2588
2589       viewport.firePropertyChange("alignment", null, viewport
2590               .getAlignment().getSequences());
2591     }
2592   }
2593
2594   /**
2595    * DOCUMENT ME!
2596    *
2597    * @param e
2598    *          DOCUMENT ME!
2599    */
2600   @Override
2601   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2602   {
2603     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2604
2605     SequenceI[] seqs;
2606     if (viewport.getSelectionGroup() != null)
2607     {
2608       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2609               viewport.getHiddenRepSequences());
2610       start = viewport.getSelectionGroup().getStartRes();
2611       end = viewport.getSelectionGroup().getEndRes();
2612     }
2613     else
2614     {
2615       seqs = viewport.getAlignment().getSequencesArray();
2616     }
2617
2618     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2619             "Remove Gapped Columns", seqs, start, end,
2620             viewport.getAlignment());
2621
2622     addHistoryItem(removeGapCols);
2623
2624     statusBar.setText(MessageManager.formatMessage(
2625             "label.removed_empty_columns",
2626             new Object[] { Integer.valueOf(removeGapCols.getSize())
2627                     .toString() }));
2628
2629     // This is to maintain viewport position on first residue
2630     // of first sequence
2631     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2632     int startRes = seq.findPosition(viewport.startRes);
2633     // ShiftList shifts;
2634     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2635     // edit.alColumnChanges=shifts.getInverse();
2636     // if (viewport.hasHiddenColumns)
2637     // viewport.getColumnSelection().compensateForEdits(shifts);
2638     viewport.setStartRes(seq.findIndex(startRes) - 1);
2639     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2640             .getSequences());
2641
2642   }
2643
2644   /**
2645    * DOCUMENT ME!
2646    *
2647    * @param e
2648    *          DOCUMENT ME!
2649    */
2650   @Override
2651   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2652   {
2653     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2654
2655     SequenceI[] seqs;
2656     if (viewport.getSelectionGroup() != null)
2657     {
2658       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2659               viewport.getHiddenRepSequences());
2660       start = viewport.getSelectionGroup().getStartRes();
2661       end = viewport.getSelectionGroup().getEndRes();
2662     }
2663     else
2664     {
2665       seqs = viewport.getAlignment().getSequencesArray();
2666     }
2667
2668     // This is to maintain viewport position on first residue
2669     // of first sequence
2670     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2671     int startRes = seq.findPosition(viewport.startRes);
2672
2673     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2674             viewport.getAlignment()));
2675
2676     viewport.setStartRes(seq.findIndex(startRes) - 1);
2677
2678     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2679             .getSequences());
2680
2681   }
2682
2683   /**
2684    * DOCUMENT ME!
2685    *
2686    * @param e
2687    *          DOCUMENT ME!
2688    */
2689   @Override
2690   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2691   {
2692     viewport.setPadGaps(padGapsMenuitem.isSelected());
2693     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2694             .getSequences());
2695   }
2696
2697   /**
2698    * DOCUMENT ME!
2699    *
2700    * @param e
2701    *          DOCUMENT ME!
2702    */
2703   @Override
2704   public void findMenuItem_actionPerformed(ActionEvent e)
2705   {
2706     new Finder();
2707   }
2708
2709   /**
2710    * Create a new view of the current alignment.
2711    */
2712   @Override
2713   public void newView_actionPerformed(ActionEvent e)
2714   {
2715     newView(null, true);
2716   }
2717
2718   /**
2719    * Creates and shows a new view of the current alignment.
2720    *
2721    * @param viewTitle
2722    *          title of newly created view; if null, one will be generated
2723    * @param copyAnnotation
2724    *          if true then duplicate all annnotation, groups and settings
2725    * @return new alignment panel, already displayed.
2726    */
2727   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2728   {
2729     /*
2730      * Create a new AlignmentPanel (with its own, new Viewport)
2731      */
2732     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2733             true);
2734     if (!copyAnnotation)
2735     {
2736       /*
2737        * remove all groups and annotation except for the automatic stuff
2738        */
2739       newap.av.getAlignment().deleteAllGroups();
2740       newap.av.getAlignment().deleteAllAnnotations(false);
2741     }
2742
2743     newap.av.setGatherViewsHere(false);
2744
2745     if (viewport.viewName == null)
2746     {
2747       viewport.viewName = MessageManager
2748               .getString("label.view_name_original");
2749     }
2750
2751     /*
2752      * Views share the same edits undo and redo stacks
2753      */
2754     newap.av.setHistoryList(viewport.getHistoryList());
2755     newap.av.setRedoList(viewport.getRedoList());
2756
2757     /*
2758      * Views share the same mappings; need to deregister any new mappings
2759      * created by copyAlignPanel, and register the new reference to the shared
2760      * mappings
2761      */
2762     newap.av.replaceMappings(viewport.getAlignment());
2763
2764     newap.av.viewName = getNewViewName(viewTitle);
2765
2766     addAlignmentPanel(newap, true);
2767     newap.alignmentChanged();
2768
2769     if (alignPanels.size() == 2)
2770     {
2771       viewport.setGatherViewsHere(true);
2772     }
2773     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2774     return newap;
2775   }
2776
2777   /**
2778    * Make a new name for the view, ensuring it is unique within the current
2779    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2780    * these now use viewId. Unique view names are still desirable for usability.)
2781    *
2782    * @param viewTitle
2783    * @return
2784    */
2785   protected String getNewViewName(String viewTitle)
2786   {
2787     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2788     boolean addFirstIndex = false;
2789     if (viewTitle == null || viewTitle.trim().length() == 0)
2790     {
2791       viewTitle = MessageManager.getString("action.view");
2792       addFirstIndex = true;
2793     }
2794     else
2795     {
2796       index = 1;// we count from 1 if given a specific name
2797     }
2798     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2799
2800     List<Component> comps = PaintRefresher.components.get(viewport
2801             .getSequenceSetId());
2802
2803     List<String> existingNames = getExistingViewNames(comps);
2804
2805     while (existingNames.contains(newViewName))
2806     {
2807       newViewName = viewTitle + " " + (++index);
2808     }
2809     return newViewName;
2810   }
2811
2812   /**
2813    * Returns a list of distinct view names found in the given list of
2814    * components. View names are held on the viewport of an AlignmentPanel.
2815    *
2816    * @param comps
2817    * @return
2818    */
2819   protected List<String> getExistingViewNames(List<Component> comps)
2820   {
2821     List<String> existingNames = new ArrayList<String>();
2822     for (Component comp : comps)
2823     {
2824       if (comp instanceof AlignmentPanel)
2825       {
2826         AlignmentPanel ap = (AlignmentPanel) comp;
2827         if (!existingNames.contains(ap.av.viewName))
2828         {
2829           existingNames.add(ap.av.viewName);
2830         }
2831       }
2832     }
2833     return existingNames;
2834   }
2835
2836   /**
2837    * Explode tabbed views into separate windows.
2838    */
2839   @Override
2840   public void expandViews_actionPerformed(ActionEvent e)
2841   {
2842     Desktop.explodeViews(this);
2843   }
2844
2845   /**
2846    * Gather views in separate windows back into a tabbed presentation.
2847    */
2848   @Override
2849   public void gatherViews_actionPerformed(ActionEvent e)
2850   {
2851     Desktop.instance.gatherViews(this);
2852   }
2853
2854   /**
2855    * DOCUMENT ME!
2856    *
2857    * @param e
2858    *          DOCUMENT ME!
2859    */
2860   @Override
2861   public void font_actionPerformed(ActionEvent e)
2862   {
2863     new FontChooser(alignPanel);
2864   }
2865
2866   /**
2867    * DOCUMENT ME!
2868    *
2869    * @param e
2870    *          DOCUMENT ME!
2871    */
2872   @Override
2873   protected void seqLimit_actionPerformed(ActionEvent e)
2874   {
2875     viewport.setShowJVSuffix(seqLimits.isSelected());
2876
2877     alignPanel.getIdPanel().getIdCanvas()
2878             .setPreferredSize(alignPanel.calculateIdWidth());
2879     alignPanel.paintAlignment(true);
2880   }
2881
2882   @Override
2883   public void idRightAlign_actionPerformed(ActionEvent e)
2884   {
2885     viewport.setRightAlignIds(idRightAlign.isSelected());
2886     alignPanel.paintAlignment(true);
2887   }
2888
2889   @Override
2890   public void centreColumnLabels_actionPerformed(ActionEvent e)
2891   {
2892     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2893     alignPanel.paintAlignment(true);
2894   }
2895
2896   /*
2897    * (non-Javadoc)
2898    *
2899    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2900    */
2901   @Override
2902   protected void followHighlight_actionPerformed()
2903   {
2904     /*
2905      * Set the 'follow' flag on the Viewport (and scroll to position if now
2906      * true).
2907      */
2908     final boolean state = this.followHighlightMenuItem.getState();
2909     viewport.setFollowHighlight(state);
2910     if (state)
2911     {
2912       alignPanel.scrollToPosition(
2913               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2914     }
2915   }
2916
2917   /**
2918    * DOCUMENT ME!
2919    *
2920    * @param e
2921    *          DOCUMENT ME!
2922    */
2923   @Override
2924   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2925   {
2926     viewport.setColourText(colourTextMenuItem.isSelected());
2927     alignPanel.paintAlignment(true);
2928   }
2929
2930   /**
2931    * DOCUMENT ME!
2932    *
2933    * @param e
2934    *          DOCUMENT ME!
2935    */
2936   @Override
2937   public void wrapMenuItem_actionPerformed(ActionEvent e)
2938   {
2939     scaleAbove.setVisible(wrapMenuItem.isSelected());
2940     scaleLeft.setVisible(wrapMenuItem.isSelected());
2941     scaleRight.setVisible(wrapMenuItem.isSelected());
2942     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2943     alignPanel.updateLayout();
2944   }
2945
2946   @Override
2947   public void showAllSeqs_actionPerformed(ActionEvent e)
2948   {
2949     viewport.showAllHiddenSeqs();
2950   }
2951
2952   @Override
2953   public void showAllColumns_actionPerformed(ActionEvent e)
2954   {
2955     viewport.showAllHiddenColumns();
2956     repaint();
2957     viewport.sendSelection();
2958   }
2959
2960   @Override
2961   public void hideSelSequences_actionPerformed(ActionEvent e)
2962   {
2963     viewport.hideAllSelectedSeqs();
2964     // alignPanel.paintAlignment(true);
2965   }
2966
2967   /**
2968    * called by key handler and the hide all/show all menu items
2969    *
2970    * @param toggleSeqs
2971    * @param toggleCols
2972    */
2973   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2974   {
2975
2976     boolean hide = false;
2977     SequenceGroup sg = viewport.getSelectionGroup();
2978     if (!toggleSeqs && !toggleCols)
2979     {
2980       // Hide everything by the current selection - this is a hack - we do the
2981       // invert and then hide
2982       // first check that there will be visible columns after the invert.
2983       if (viewport.hasSelectedColumns()
2984               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2985                       .getEndRes()))
2986       {
2987         // now invert the sequence set, if required - empty selection implies
2988         // that no hiding is required.
2989         if (sg != null)
2990         {
2991           invertSequenceMenuItem_actionPerformed(null);
2992           sg = viewport.getSelectionGroup();
2993           toggleSeqs = true;
2994
2995         }
2996         viewport.expandColSelection(sg, true);
2997         // finally invert the column selection and get the new sequence
2998         // selection.
2999         invertColSel_actionPerformed(null);
3000         toggleCols = true;
3001       }
3002     }
3003
3004     if (toggleSeqs)
3005     {
3006       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3007       {
3008         hideSelSequences_actionPerformed(null);
3009         hide = true;
3010       }
3011       else if (!(toggleCols && viewport.hasSelectedColumns()))
3012       {
3013         showAllSeqs_actionPerformed(null);
3014       }
3015     }
3016
3017     if (toggleCols)
3018     {
3019       if (viewport.hasSelectedColumns())
3020       {
3021         hideSelColumns_actionPerformed(null);
3022         if (!toggleSeqs)
3023         {
3024           viewport.setSelectionGroup(sg);
3025         }
3026       }
3027       else if (!hide)
3028       {
3029         showAllColumns_actionPerformed(null);
3030       }
3031     }
3032   }
3033
3034   /*
3035    * (non-Javadoc)
3036    *
3037    * @see
3038    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3039    * event.ActionEvent)
3040    */
3041   @Override
3042   public void hideAllButSelection_actionPerformed(ActionEvent e)
3043   {
3044     toggleHiddenRegions(false, false);
3045     viewport.sendSelection();
3046   }
3047
3048   /*
3049    * (non-Javadoc)
3050    *
3051    * @see
3052    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3053    * .ActionEvent)
3054    */
3055   @Override
3056   public void hideAllSelection_actionPerformed(ActionEvent e)
3057   {
3058     SequenceGroup sg = viewport.getSelectionGroup();
3059     viewport.expandColSelection(sg, false);
3060     viewport.hideAllSelectedSeqs();
3061     viewport.hideSelectedColumns();
3062     alignPanel.paintAlignment(true);
3063     viewport.sendSelection();
3064   }
3065
3066   /*
3067    * (non-Javadoc)
3068    *
3069    * @see
3070    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3071    * ActionEvent)
3072    */
3073   @Override
3074   public void showAllhidden_actionPerformed(ActionEvent e)
3075   {
3076     viewport.showAllHiddenColumns();
3077     viewport.showAllHiddenSeqs();
3078     alignPanel.paintAlignment(true);
3079     viewport.sendSelection();
3080   }
3081
3082   @Override
3083   public void hideSelColumns_actionPerformed(ActionEvent e)
3084   {
3085     viewport.hideSelectedColumns();
3086     alignPanel.paintAlignment(true);
3087     viewport.sendSelection();
3088   }
3089
3090   @Override
3091   public void hiddenMarkers_actionPerformed(ActionEvent e)
3092   {
3093     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3094     repaint();
3095   }
3096
3097   /**
3098    * DOCUMENT ME!
3099    *
3100    * @param e
3101    *          DOCUMENT ME!
3102    */
3103   @Override
3104   protected void scaleAbove_actionPerformed(ActionEvent e)
3105   {
3106     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3107     alignPanel.paintAlignment(true);
3108   }
3109
3110   /**
3111    * DOCUMENT ME!
3112    *
3113    * @param e
3114    *          DOCUMENT ME!
3115    */
3116   @Override
3117   protected void scaleLeft_actionPerformed(ActionEvent e)
3118   {
3119     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3120     alignPanel.paintAlignment(true);
3121   }
3122
3123   /**
3124    * DOCUMENT ME!
3125    *
3126    * @param e
3127    *          DOCUMENT ME!
3128    */
3129   @Override
3130   protected void scaleRight_actionPerformed(ActionEvent e)
3131   {
3132     viewport.setScaleRightWrapped(scaleRight.isSelected());
3133     alignPanel.paintAlignment(true);
3134   }
3135
3136   /**
3137    * DOCUMENT ME!
3138    *
3139    * @param e
3140    *          DOCUMENT ME!
3141    */
3142   @Override
3143   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3144   {
3145     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3146     alignPanel.paintAlignment(true);
3147   }
3148
3149   /**
3150    * DOCUMENT ME!
3151    *
3152    * @param e
3153    *          DOCUMENT ME!
3154    */
3155   @Override
3156   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3157   {
3158     viewport.setShowText(viewTextMenuItem.isSelected());
3159     alignPanel.paintAlignment(true);
3160   }
3161
3162   /**
3163    * DOCUMENT ME!
3164    *
3165    * @param e
3166    *          DOCUMENT ME!
3167    */
3168   @Override
3169   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3170   {
3171     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3172     alignPanel.paintAlignment(true);
3173   }
3174
3175   public FeatureSettings featureSettings;
3176
3177   @Override
3178   public FeatureSettingsControllerI getFeatureSettingsUI()
3179   {
3180     return featureSettings;
3181   }
3182
3183   @Override
3184   public void featureSettings_actionPerformed(ActionEvent e)
3185   {
3186     if (featureSettings != null)
3187     {
3188       featureSettings.close();
3189       featureSettings = null;
3190     }
3191     if (!showSeqFeatures.isSelected())
3192     {
3193       // make sure features are actually displayed
3194       showSeqFeatures.setSelected(true);
3195       showSeqFeatures_actionPerformed(null);
3196     }
3197     featureSettings = new FeatureSettings(this);
3198   }
3199
3200   /**
3201    * Set or clear 'Show Sequence Features'
3202    *
3203    * @param evt
3204    *          DOCUMENT ME!
3205    */
3206   @Override
3207   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3208   {
3209     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3210     alignPanel.paintAlignment(true);
3211     if (alignPanel.getOverviewPanel() != null)
3212     {
3213       alignPanel.getOverviewPanel().updateOverviewImage();
3214     }
3215   }
3216
3217   /**
3218    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3219    * the annotations panel as a whole.
3220    *
3221    * The options to show/hide all annotations should be enabled when the panel
3222    * is shown, and disabled when the panel is hidden.
3223    *
3224    * @param e
3225    */
3226   @Override
3227   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3228   {
3229     final boolean setVisible = annotationPanelMenuItem.isSelected();
3230     viewport.setShowAnnotation(setVisible);
3231     this.showAllSeqAnnotations.setEnabled(setVisible);
3232     this.hideAllSeqAnnotations.setEnabled(setVisible);
3233     this.showAllAlAnnotations.setEnabled(setVisible);
3234     this.hideAllAlAnnotations.setEnabled(setVisible);
3235     alignPanel.updateLayout();
3236   }
3237
3238   @Override
3239   public void alignmentProperties()
3240   {
3241     JEditorPane editPane = new JEditorPane("text/html", "");
3242     editPane.setEditable(false);
3243     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3244             .formatAsHtml();
3245     editPane.setText(MessageManager.formatMessage("label.html_content",
3246             new Object[] { contents.toString() }));
3247     JInternalFrame frame = new JInternalFrame();
3248     frame.getContentPane().add(new JScrollPane(editPane));
3249
3250     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3251             "label.alignment_properties", new Object[] { getTitle() }),
3252             500, 400);
3253   }
3254
3255   /**
3256    * DOCUMENT ME!
3257    *
3258    * @param e
3259    *          DOCUMENT ME!
3260    */
3261   @Override
3262   public void overviewMenuItem_actionPerformed(ActionEvent e)
3263   {
3264     if (alignPanel.overviewPanel != null)
3265     {
3266       return;
3267     }
3268
3269     JInternalFrame frame = new JInternalFrame();
3270     OverviewPanel overview = new OverviewPanel(alignPanel);
3271     frame.setContentPane(overview);
3272     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3273             "label.overview_params", new Object[] { this.getTitle() }),
3274             frame.getWidth(), frame.getHeight());
3275     frame.pack();
3276     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3277     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3278     {
3279       @Override
3280       public void internalFrameClosed(
3281               javax.swing.event.InternalFrameEvent evt)
3282       {
3283         alignPanel.setOverviewPanel(null);
3284       };
3285     });
3286
3287     alignPanel.setOverviewPanel(overview);
3288   }
3289
3290   @Override
3291   public void textColour_actionPerformed(ActionEvent e)
3292   {
3293     new TextColourChooser().chooseColour(alignPanel, null);
3294   }
3295
3296   /**
3297    * DOCUMENT ME!
3298    *
3299    * @param e
3300    *          DOCUMENT ME!
3301    */
3302   @Override
3303   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3304   {
3305     changeColour(null);
3306   }
3307
3308   /**
3309    * DOCUMENT ME!
3310    *
3311    * @param e
3312    *          DOCUMENT ME!
3313    */
3314   @Override
3315   public void clustalColour_actionPerformed(ActionEvent e)
3316   {
3317     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3318             viewport.getHiddenRepSequences()));
3319   }
3320
3321   /**
3322    * DOCUMENT ME!
3323    *
3324    * @param e
3325    *          DOCUMENT ME!
3326    */
3327   @Override
3328   public void zappoColour_actionPerformed(ActionEvent e)
3329   {
3330     changeColour(new ZappoColourScheme());
3331   }
3332
3333   /**
3334    * DOCUMENT ME!
3335    *
3336    * @param e
3337    *          DOCUMENT ME!
3338    */
3339   @Override
3340   public void taylorColour_actionPerformed(ActionEvent e)
3341   {
3342     changeColour(new TaylorColourScheme());
3343   }
3344
3345   /**
3346    * DOCUMENT ME!
3347    *
3348    * @param e
3349    *          DOCUMENT ME!
3350    */
3351   @Override
3352   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3353   {
3354     changeColour(new HydrophobicColourScheme());
3355   }
3356
3357   /**
3358    * DOCUMENT ME!
3359    *
3360    * @param e
3361    *          DOCUMENT ME!
3362    */
3363   @Override
3364   public void helixColour_actionPerformed(ActionEvent e)
3365   {
3366     changeColour(new HelixColourScheme());
3367   }
3368
3369   /**
3370    * DOCUMENT ME!
3371    *
3372    * @param e
3373    *          DOCUMENT ME!
3374    */
3375   @Override
3376   public void strandColour_actionPerformed(ActionEvent e)
3377   {
3378     changeColour(new StrandColourScheme());
3379   }
3380
3381   /**
3382    * DOCUMENT ME!
3383    *
3384    * @param e
3385    *          DOCUMENT ME!
3386    */
3387   @Override
3388   public void turnColour_actionPerformed(ActionEvent e)
3389   {
3390     changeColour(new TurnColourScheme());
3391   }
3392
3393   /**
3394    * DOCUMENT ME!
3395    *
3396    * @param e
3397    *          DOCUMENT ME!
3398    */
3399   @Override
3400   public void buriedColour_actionPerformed(ActionEvent e)
3401   {
3402     changeColour(new BuriedColourScheme());
3403   }
3404
3405   /**
3406    * DOCUMENT ME!
3407    *
3408    * @param e
3409    *          DOCUMENT ME!
3410    */
3411   @Override
3412   public void nucleotideColour_actionPerformed(ActionEvent e)
3413   {
3414     changeColour(new NucleotideColourScheme());
3415   }
3416
3417   @Override
3418   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3419   {
3420     changeColour(new PurinePyrimidineColourScheme());
3421   }
3422
3423   /*
3424    * public void covariationColour_actionPerformed(ActionEvent e) {
3425    * changeColour(new
3426    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3427    * ()[0])); }
3428    */
3429   @Override
3430   public void annotationColour_actionPerformed(ActionEvent e)
3431   {
3432     new AnnotationColourChooser(viewport, alignPanel);
3433   }
3434
3435   @Override
3436   public void annotationColumn_actionPerformed(ActionEvent e)
3437   {
3438     new AnnotationColumnChooser(viewport, alignPanel);
3439   }
3440
3441   @Override
3442   public void rnahelicesColour_actionPerformed(ActionEvent e)
3443   {
3444     new RNAHelicesColourChooser(viewport, alignPanel);
3445   }
3446
3447   /**
3448    * DOCUMENT ME!
3449    *
3450    * @param e
3451    *          DOCUMENT ME!
3452    */
3453   @Override
3454   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3455   {
3456     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3457   }
3458
3459   /**
3460    * DOCUMENT ME!
3461    *
3462    * @param cs
3463    *          DOCUMENT ME!
3464    */
3465   @Override
3466   public void changeColour(ColourSchemeI cs)
3467   {
3468     // TODO: pull up to controller method
3469
3470     if (cs != null)
3471     {
3472       // Make sure viewport is up to date w.r.t. any sliders
3473       if (viewport.getAbovePIDThreshold())
3474       {
3475         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3476                 "Background");
3477         viewport.setThreshold(threshold);
3478       }
3479
3480       if (viewport.getConservationSelected())
3481       {
3482         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3483                 cs, "Background"));
3484       }
3485       if (cs instanceof TCoffeeColourScheme)
3486       {
3487         tcoffeeColour.setEnabled(true);
3488         tcoffeeColour.setSelected(true);
3489       }
3490     }
3491
3492     viewport.setGlobalColourScheme(cs);
3493
3494     alignPanel.paintAlignment(true);
3495   }
3496
3497   /**
3498    * DOCUMENT ME!
3499    *
3500    * @param e
3501    *          DOCUMENT ME!
3502    */
3503   @Override
3504   protected void modifyPID_actionPerformed(ActionEvent e)
3505   {
3506     if (viewport.getAbovePIDThreshold()
3507             && viewport.getGlobalColourScheme() != null)
3508     {
3509       SliderPanel.setPIDSliderSource(alignPanel,
3510               viewport.getGlobalColourScheme(), "Background");
3511       SliderPanel.showPIDSlider();
3512     }
3513   }
3514
3515   /**
3516    * DOCUMENT ME!
3517    *
3518    * @param e
3519    *          DOCUMENT ME!
3520    */
3521   @Override
3522   protected void modifyConservation_actionPerformed(ActionEvent e)
3523   {
3524     if (viewport.getConservationSelected()
3525             && viewport.getGlobalColourScheme() != null)
3526     {
3527       SliderPanel.setConservationSlider(alignPanel,
3528               viewport.getGlobalColourScheme(), "Background");
3529       SliderPanel.showConservationSlider();
3530     }
3531   }
3532
3533   /**
3534    * DOCUMENT ME!
3535    *
3536    * @param e
3537    *          DOCUMENT ME!
3538    */
3539   @Override
3540   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3541   {
3542     viewport.setConservationSelected(conservationMenuItem.isSelected());
3543
3544     viewport.setAbovePIDThreshold(false);
3545     abovePIDThreshold.setSelected(false);
3546
3547     changeColour(viewport.getGlobalColourScheme());
3548
3549     modifyConservation_actionPerformed(null);
3550   }
3551
3552   /**
3553    * DOCUMENT ME!
3554    *
3555    * @param e
3556    *          DOCUMENT ME!
3557    */
3558   @Override
3559   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3560   {
3561     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3562
3563     conservationMenuItem.setSelected(false);
3564     viewport.setConservationSelected(false);
3565
3566     changeColour(viewport.getGlobalColourScheme());
3567
3568     modifyPID_actionPerformed(null);
3569   }
3570
3571   /**
3572    * DOCUMENT ME!
3573    *
3574    * @param e
3575    *          DOCUMENT ME!
3576    */
3577   @Override
3578   public void userDefinedColour_actionPerformed(ActionEvent e)
3579   {
3580     if (e.getActionCommand().equals(
3581             MessageManager.getString("action.user_defined")))
3582     {
3583       new UserDefinedColours(alignPanel, null);
3584     }
3585     else
3586     {
3587       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3588               .getUserColourSchemes().get(e.getActionCommand());
3589
3590       changeColour(udc);
3591     }
3592   }
3593
3594   public void updateUserColourMenu()
3595   {
3596
3597     Component[] menuItems = colourMenu.getMenuComponents();
3598     int iSize = menuItems.length;
3599     for (int i = 0; i < iSize; i++)
3600     {
3601       if (menuItems[i].getName() != null
3602               && menuItems[i].getName().equals("USER_DEFINED"))
3603       {
3604         colourMenu.remove(menuItems[i]);
3605         iSize--;
3606       }
3607     }
3608     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3609     {
3610       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3611               .getUserColourSchemes().keys();
3612
3613       while (userColours.hasMoreElements())
3614       {
3615         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3616                 userColours.nextElement().toString());
3617         radioItem.setName("USER_DEFINED");
3618         radioItem.addMouseListener(new MouseAdapter()
3619         {
3620           @Override
3621           public void mousePressed(MouseEvent evt)
3622           {
3623             if (evt.isPopupTrigger()) // Mac
3624             {
3625               offerRemoval(radioItem);
3626             }
3627           }
3628
3629           @Override
3630           public void mouseReleased(MouseEvent evt)
3631           {
3632             if (evt.isPopupTrigger()) // Windows
3633             {
3634               offerRemoval(radioItem);
3635             }
3636           }
3637
3638           /**
3639            * @param radioItem
3640            */
3641           void offerRemoval(final JRadioButtonMenuItem radioItem)
3642           {
3643             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3644
3645             int option = JOptionPane.showInternalConfirmDialog(
3646                     jalview.gui.Desktop.desktop, MessageManager
3647                             .getString("label.remove_from_default_list"),
3648                     MessageManager
3649                             .getString("label.remove_user_defined_colour"),
3650                     JOptionPane.YES_NO_OPTION);
3651             if (option == JOptionPane.YES_OPTION)
3652             {
3653               jalview.gui.UserDefinedColours
3654                       .removeColourFromDefaults(radioItem.getText());
3655               colourMenu.remove(radioItem);
3656             }
3657             else
3658             {
3659               radioItem.addActionListener(new ActionListener()
3660               {
3661                 @Override
3662                 public void actionPerformed(ActionEvent evt)
3663                 {
3664                   userDefinedColour_actionPerformed(evt);
3665                 }
3666               });
3667             }
3668           }
3669         });
3670         radioItem.addActionListener(new ActionListener()
3671         {
3672           @Override
3673           public void actionPerformed(ActionEvent evt)
3674           {
3675             userDefinedColour_actionPerformed(evt);
3676           }
3677         });
3678
3679         colourMenu.insert(radioItem, 15);
3680         colours.add(radioItem);
3681       }
3682     }
3683   }
3684
3685   /**
3686    * DOCUMENT ME!
3687    *
3688    * @param e
3689    *          DOCUMENT ME!
3690    */
3691   @Override
3692   public void PIDColour_actionPerformed(ActionEvent e)
3693   {
3694     changeColour(new PIDColourScheme());
3695   }
3696
3697   /**
3698    * DOCUMENT ME!
3699    *
3700    * @param e
3701    *          DOCUMENT ME!
3702    */
3703   @Override
3704   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3705   {
3706     changeColour(new Blosum62ColourScheme());
3707   }
3708
3709   /**
3710    * DOCUMENT ME!
3711    *
3712    * @param e
3713    *          DOCUMENT ME!
3714    */
3715   @Override
3716   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3717   {
3718     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3719     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3720             .getAlignment().getSequenceAt(0), null);
3721     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3722             viewport.getAlignment()));
3723     alignPanel.paintAlignment(true);
3724   }
3725
3726   /**
3727    * DOCUMENT ME!
3728    *
3729    * @param e
3730    *          DOCUMENT ME!
3731    */
3732   @Override
3733   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3734   {
3735     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3736     AlignmentSorter.sortByID(viewport.getAlignment());
3737     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3738             viewport.getAlignment()));
3739     alignPanel.paintAlignment(true);
3740   }
3741
3742   /**
3743    * DOCUMENT ME!
3744    *
3745    * @param e
3746    *          DOCUMENT ME!
3747    */
3748   @Override
3749   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3750   {
3751     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3752     AlignmentSorter.sortByLength(viewport.getAlignment());
3753     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3754             viewport.getAlignment()));
3755     alignPanel.paintAlignment(true);
3756   }
3757
3758   /**
3759    * DOCUMENT ME!
3760    *
3761    * @param e
3762    *          DOCUMENT ME!
3763    */
3764   @Override
3765   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3766   {
3767     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3768     AlignmentSorter.sortByGroup(viewport.getAlignment());
3769     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3770             viewport.getAlignment()));
3771
3772     alignPanel.paintAlignment(true);
3773   }
3774
3775   /**
3776    * DOCUMENT ME!
3777    *
3778    * @param e
3779    *          DOCUMENT ME!
3780    */
3781   @Override
3782   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3783   {
3784     new RedundancyPanel(alignPanel, this);
3785   }
3786
3787   /**
3788    * DOCUMENT ME!
3789    *
3790    * @param e
3791    *          DOCUMENT ME!
3792    */
3793   @Override
3794   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3795   {
3796     if ((viewport.getSelectionGroup() == null)
3797             || (viewport.getSelectionGroup().getSize() < 2))
3798     {
3799       JOptionPane.showInternalMessageDialog(this, MessageManager
3800               .getString("label.you_must_select_least_two_sequences"),
3801               MessageManager.getString("label.invalid_selection"),
3802               JOptionPane.WARNING_MESSAGE);
3803     }
3804     else
3805     {
3806       JInternalFrame frame = new JInternalFrame();
3807       frame.setContentPane(new PairwiseAlignPanel(viewport));
3808       Desktop.addInternalFrame(frame,
3809               MessageManager.getString("action.pairwise_alignment"), 600,
3810               500);
3811     }
3812   }
3813
3814   /**
3815    * DOCUMENT ME!
3816    *
3817    * @param e
3818    *          DOCUMENT ME!
3819    */
3820   @Override
3821   public void PCAMenuItem_actionPerformed(ActionEvent e)
3822   {
3823     if (((viewport.getSelectionGroup() != null)
3824             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3825             .getSelectionGroup().getSize() > 0))
3826             || (viewport.getAlignment().getHeight() < 4))
3827     {
3828       JOptionPane
3829               .showInternalMessageDialog(
3830                       this,
3831                       MessageManager
3832                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3833                       MessageManager
3834                               .getString("label.sequence_selection_insufficient"),
3835                       JOptionPane.WARNING_MESSAGE);
3836
3837       return;
3838     }
3839
3840     new PCAPanel(alignPanel);
3841   }
3842
3843   @Override
3844   public void autoCalculate_actionPerformed(ActionEvent e)
3845   {
3846     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3847     if (viewport.autoCalculateConsensus)
3848     {
3849       viewport.firePropertyChange("alignment", null, viewport
3850               .getAlignment().getSequences());
3851     }
3852   }
3853
3854   @Override
3855   public void sortByTreeOption_actionPerformed(ActionEvent e)
3856   {
3857     viewport.sortByTree = sortByTree.isSelected();
3858   }
3859
3860   @Override
3861   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3862   {
3863     viewport.followSelection = listenToViewSelections.isSelected();
3864   }
3865
3866   /**
3867    * DOCUMENT ME!
3868    *
3869    * @param e
3870    *          DOCUMENT ME!
3871    */
3872   @Override
3873   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3874   {
3875     newTreePanel("AV", "PID", "Average distance tree using PID");
3876   }
3877
3878   /**
3879    * DOCUMENT ME!
3880    *
3881    * @param e
3882    *          DOCUMENT ME!
3883    */
3884   @Override
3885   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3886   {
3887     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3888   }
3889
3890   /**
3891    * DOCUMENT ME!
3892    *
3893    * @param e
3894    *          DOCUMENT ME!
3895    */
3896   @Override
3897   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3898   {
3899     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3900   }
3901
3902   /**
3903    * DOCUMENT ME!
3904    *
3905    * @param e
3906    *          DOCUMENT ME!
3907    */
3908   @Override
3909   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3910   {
3911     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3912   }
3913
3914   /**
3915    * DOCUMENT ME!
3916    *
3917    * @param type
3918    *          DOCUMENT ME!
3919    * @param pwType
3920    *          DOCUMENT ME!
3921    * @param title
3922    *          DOCUMENT ME!
3923    */
3924   void newTreePanel(String type, String pwType, String title)
3925   {
3926     TreePanel tp;
3927
3928     if (viewport.getSelectionGroup() != null
3929             && viewport.getSelectionGroup().getSize() > 0)
3930     {
3931       if (viewport.getSelectionGroup().getSize() < 3)
3932       {
3933         JOptionPane
3934                 .showMessageDialog(
3935                         Desktop.desktop,
3936                         MessageManager
3937                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3938                         MessageManager
3939                                 .getString("label.not_enough_sequences"),
3940                         JOptionPane.WARNING_MESSAGE);
3941         return;
3942       }
3943
3944       SequenceGroup sg = viewport.getSelectionGroup();
3945
3946       /* Decide if the selection is a column region */
3947       for (SequenceI _s : sg.getSequences())
3948       {
3949         if (_s.getLength() < sg.getEndRes())
3950         {
3951           JOptionPane
3952                   .showMessageDialog(
3953                           Desktop.desktop,
3954                           MessageManager
3955                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3956                           MessageManager
3957                                   .getString("label.sequences_selection_not_aligned"),
3958                           JOptionPane.WARNING_MESSAGE);
3959
3960           return;
3961         }
3962       }
3963
3964       title = title + " on region";
3965       tp = new TreePanel(alignPanel, type, pwType);
3966     }
3967     else
3968     {
3969       // are the visible sequences aligned?
3970       if (!viewport.getAlignment().isAligned(false))
3971       {
3972         JOptionPane
3973                 .showMessageDialog(
3974                         Desktop.desktop,
3975                         MessageManager
3976                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3977                         MessageManager
3978                                 .getString("label.sequences_not_aligned"),
3979                         JOptionPane.WARNING_MESSAGE);
3980
3981         return;
3982       }
3983
3984       if (viewport.getAlignment().getHeight() < 2)
3985       {
3986         return;
3987       }
3988
3989       tp = new TreePanel(alignPanel, type, pwType);
3990     }
3991
3992     title += " from ";
3993
3994     if (viewport.viewName != null)
3995     {
3996       title += viewport.viewName + " of ";
3997     }
3998
3999     title += this.title;
4000
4001     Desktop.addInternalFrame(tp, title, 600, 500);
4002   }
4003
4004   /**
4005    * DOCUMENT ME!
4006    *
4007    * @param title
4008    *          DOCUMENT ME!
4009    * @param order
4010    *          DOCUMENT ME!
4011    */
4012   public void addSortByOrderMenuItem(String title,
4013           final AlignmentOrder order)
4014   {
4015     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4016             "action.by_title_param", new Object[] { title }));
4017     sort.add(item);
4018     item.addActionListener(new java.awt.event.ActionListener()
4019     {
4020       @Override
4021       public void actionPerformed(ActionEvent e)
4022       {
4023         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4024
4025         // TODO: JBPNote - have to map order entries to curent SequenceI
4026         // pointers
4027         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4028
4029         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4030                 .getAlignment()));
4031
4032         alignPanel.paintAlignment(true);
4033       }
4034     });
4035   }
4036
4037   /**
4038    * Add a new sort by annotation score menu item
4039    *
4040    * @param sort
4041    *          the menu to add the option to
4042    * @param scoreLabel
4043    *          the label used to retrieve scores for each sequence on the
4044    *          alignment
4045    */
4046   public void addSortByAnnotScoreMenuItem(JMenu sort,
4047           final String scoreLabel)
4048   {
4049     final JMenuItem item = new JMenuItem(scoreLabel);
4050     sort.add(item);
4051     item.addActionListener(new java.awt.event.ActionListener()
4052     {
4053       @Override
4054       public void actionPerformed(ActionEvent e)
4055       {
4056         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4057         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4058                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4059         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4060                 viewport.getAlignment()));
4061         alignPanel.paintAlignment(true);
4062       }
4063     });
4064   }
4065
4066   /**
4067    * last hash for alignment's annotation array - used to minimise cost of
4068    * rebuild.
4069    */
4070   protected int _annotationScoreVectorHash;
4071
4072   /**
4073    * search the alignment and rebuild the sort by annotation score submenu the
4074    * last alignment annotation vector hash is stored to minimize cost of
4075    * rebuilding in subsequence calls.
4076    *
4077    */
4078   @Override
4079   public void buildSortByAnnotationScoresMenu()
4080   {
4081     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4082     {
4083       return;
4084     }
4085
4086     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4087     {
4088       sortByAnnotScore.removeAll();
4089       // almost certainly a quicker way to do this - but we keep it simple
4090       Hashtable scoreSorts = new Hashtable();
4091       AlignmentAnnotation aann[];
4092       for (SequenceI sqa : viewport.getAlignment().getSequences())
4093       {
4094         aann = sqa.getAnnotation();
4095         for (int i = 0; aann != null && i < aann.length; i++)
4096         {
4097           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4098           {
4099             scoreSorts.put(aann[i].label, aann[i].label);
4100           }
4101         }
4102       }
4103       Enumeration labels = scoreSorts.keys();
4104       while (labels.hasMoreElements())
4105       {
4106         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4107                 (String) labels.nextElement());
4108       }
4109       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4110       scoreSorts.clear();
4111
4112       _annotationScoreVectorHash = viewport.getAlignment()
4113               .getAlignmentAnnotation().hashCode();
4114     }
4115   }
4116
4117   /**
4118    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4119    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4120    * call. Listeners are added to remove the menu item when the treePanel is
4121    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4122    * modified.
4123    *
4124    * @param treePanel
4125    *          Displayed tree window.
4126    * @param title
4127    *          SortBy menu item title.
4128    */
4129   @Override
4130   public void buildTreeMenu()
4131   {
4132     calculateTree.removeAll();
4133     // build the calculate menu
4134
4135     for (final String type : new String[] { "NJ", "AV" })
4136     {
4137       String treecalcnm = MessageManager.getString("label.tree_calc_"
4138               + type.toLowerCase());
4139       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4140       {
4141         JMenuItem tm = new JMenuItem();
4142         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4143         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4144                 || sm.isProtein() == !viewport.getAlignment()
4145                         .isNucleotide())
4146         {
4147           String smn = MessageManager.getStringOrReturn(
4148                   "label.score_model_", sm.getName());
4149           final String title = MessageManager.formatMessage(
4150                   "label.treecalc_title", treecalcnm, smn);
4151           tm.setText(title);//
4152           tm.addActionListener(new java.awt.event.ActionListener()
4153           {
4154             @Override
4155             public void actionPerformed(ActionEvent e)
4156             {
4157               newTreePanel(type, pwtype, title);
4158             }
4159           });
4160           calculateTree.add(tm);
4161         }
4162
4163       }
4164     }
4165     sortByTreeMenu.removeAll();
4166
4167     List<Component> comps = PaintRefresher.components.get(viewport
4168             .getSequenceSetId());
4169     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4170     for (Component comp : comps)
4171     {
4172       if (comp instanceof TreePanel)
4173       {
4174         treePanels.add((TreePanel) comp);
4175       }
4176     }
4177
4178     if (treePanels.size() < 1)
4179     {
4180       sortByTreeMenu.setVisible(false);
4181       return;
4182     }
4183
4184     sortByTreeMenu.setVisible(true);
4185
4186     for (final TreePanel tp : treePanels)
4187     {
4188       final JMenuItem item = new JMenuItem(tp.getTitle());
4189       item.addActionListener(new java.awt.event.ActionListener()
4190       {
4191         @Override
4192         public void actionPerformed(ActionEvent e)
4193         {
4194           tp.sortByTree_actionPerformed();
4195           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4196
4197         }
4198       });
4199
4200       sortByTreeMenu.add(item);
4201     }
4202   }
4203
4204   public boolean sortBy(AlignmentOrder alorder, String undoname)
4205   {
4206     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4207     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4208     if (undoname != null)
4209     {
4210       addHistoryItem(new OrderCommand(undoname, oldOrder,
4211               viewport.getAlignment()));
4212     }
4213     alignPanel.paintAlignment(true);
4214     return true;
4215   }
4216
4217   /**
4218    * Work out whether the whole set of sequences or just the selected set will
4219    * be submitted for multiple alignment.
4220    *
4221    */
4222   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4223   {
4224     // Now, check we have enough sequences
4225     AlignmentView msa = null;
4226
4227     if ((viewport.getSelectionGroup() != null)
4228             && (viewport.getSelectionGroup().getSize() > 1))
4229     {
4230       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4231       // some common interface!
4232       /*
4233        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4234        * SequenceI[sz = seqs.getSize(false)];
4235        *
4236        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4237        * seqs.getSequenceAt(i); }
4238        */
4239       msa = viewport.getAlignmentView(true);
4240     }
4241     else if (viewport.getSelectionGroup() != null
4242             && viewport.getSelectionGroup().getSize() == 1)
4243     {
4244       int option = JOptionPane.showConfirmDialog(this,
4245               MessageManager.getString("warn.oneseq_msainput_selection"),
4246               MessageManager.getString("label.invalid_selection"),
4247               JOptionPane.OK_CANCEL_OPTION);
4248       if (option == JOptionPane.OK_OPTION)
4249       {
4250         msa = viewport.getAlignmentView(false);
4251       }
4252     }
4253     else
4254     {
4255       msa = viewport.getAlignmentView(false);
4256     }
4257     return msa;
4258   }
4259
4260   /**
4261    * Decides what is submitted to a secondary structure prediction service: the
4262    * first sequence in the alignment, or in the current selection, or, if the
4263    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4264    * region or the whole alignment. (where the first sequence in the set is the
4265    * one that the prediction will be for).
4266    */
4267   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4268   {
4269     AlignmentView seqs = null;
4270
4271     if ((viewport.getSelectionGroup() != null)
4272             && (viewport.getSelectionGroup().getSize() > 0))
4273     {
4274       seqs = viewport.getAlignmentView(true);
4275     }
4276     else
4277     {
4278       seqs = viewport.getAlignmentView(false);
4279     }
4280     // limit sequences - JBPNote in future - could spawn multiple prediction
4281     // jobs
4282     // TODO: viewport.getAlignment().isAligned is a global state - the local
4283     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4284     if (!viewport.getAlignment().isAligned(false))
4285     {
4286       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4287       // TODO: if seqs.getSequences().length>1 then should really have warned
4288       // user!
4289
4290     }
4291     return seqs;
4292   }
4293
4294   /**
4295    * DOCUMENT ME!
4296    *
4297    * @param e
4298    *          DOCUMENT ME!
4299    */
4300   @Override
4301   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4302   {
4303     // Pick the tree file
4304     JalviewFileChooser chooser = new JalviewFileChooser(
4305             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4306     chooser.setFileView(new JalviewFileView());
4307     chooser.setDialogTitle(MessageManager
4308             .getString("label.select_newick_like_tree_file"));
4309     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4310
4311     int value = chooser.showOpenDialog(null);
4312
4313     if (value == JalviewFileChooser.APPROVE_OPTION)
4314     {
4315       String choice = chooser.getSelectedFile().getPath();
4316       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4317       jalview.io.NewickFile fin = null;
4318       try
4319       {
4320         fin = new jalview.io.NewickFile(choice, "File");
4321         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4322       } catch (Exception ex)
4323       {
4324         JOptionPane
4325                 .showMessageDialog(
4326                         Desktop.desktop,
4327                         ex.getMessage(),
4328                         MessageManager
4329                                 .getString("label.problem_reading_tree_file"),
4330                         JOptionPane.WARNING_MESSAGE);
4331         ex.printStackTrace();
4332       }
4333       if (fin != null && fin.hasWarningMessage())
4334       {
4335         JOptionPane.showMessageDialog(Desktop.desktop, fin
4336                 .getWarningMessage(), MessageManager
4337                 .getString("label.possible_problem_with_tree_file"),
4338                 JOptionPane.WARNING_MESSAGE);
4339       }
4340     }
4341   }
4342
4343   @Override
4344   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4345   {
4346     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4347   }
4348
4349   public TreePanel ShowNewickTree(NewickFile nf, String title)
4350   {
4351     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4352   }
4353
4354   public TreePanel ShowNewickTree(NewickFile nf, String title,
4355           AlignmentView input)
4356   {
4357     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4358   }
4359
4360   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4361           int h, int x, int y)
4362   {
4363     return ShowNewickTree(nf, title, null, w, h, x, y);
4364   }
4365
4366   /**
4367    * Add a treeviewer for the tree extracted from a newick file object to the
4368    * current alignment view
4369    *
4370    * @param nf
4371    *          the tree
4372    * @param title
4373    *          tree viewer title
4374    * @param input
4375    *          Associated alignment input data (or null)
4376    * @param w
4377    *          width
4378    * @param h
4379    *          height
4380    * @param x
4381    *          position
4382    * @param y
4383    *          position
4384    * @return TreePanel handle
4385    */
4386   public TreePanel ShowNewickTree(NewickFile nf, String title,
4387           AlignmentView input, int w, int h, int x, int y)
4388   {
4389     TreePanel tp = null;
4390
4391     try
4392     {
4393       nf.parse();
4394
4395       if (nf.getTree() != null)
4396       {
4397         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4398
4399         tp.setSize(w, h);
4400
4401         if (x > 0 && y > 0)
4402         {
4403           tp.setLocation(x, y);
4404         }
4405
4406         Desktop.addInternalFrame(tp, title, w, h);
4407       }
4408     } catch (Exception ex)
4409     {
4410       ex.printStackTrace();
4411     }
4412
4413     return tp;
4414   }
4415
4416   private boolean buildingMenu = false;
4417
4418   /**
4419    * Generates menu items and listener event actions for web service clients
4420    *
4421    */
4422   public void BuildWebServiceMenu()
4423   {
4424     while (buildingMenu)
4425     {
4426       try
4427       {
4428         System.err.println("Waiting for building menu to finish.");
4429         Thread.sleep(10);
4430       } catch (Exception e)
4431       {
4432       }
4433     }
4434     final AlignFrame me = this;
4435     buildingMenu = true;
4436     new Thread(new Runnable()
4437     {
4438       @Override
4439       public void run()
4440       {
4441         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4442         try
4443         {
4444           // System.err.println("Building ws menu again "
4445           // + Thread.currentThread());
4446           // TODO: add support for context dependent disabling of services based
4447           // on
4448           // alignment and current selection
4449           // TODO: add additional serviceHandle parameter to specify abstract
4450           // handler
4451           // class independently of AbstractName
4452           // TODO: add in rediscovery GUI function to restart discoverer
4453           // TODO: group services by location as well as function and/or
4454           // introduce
4455           // object broker mechanism.
4456           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4457           final IProgressIndicator af = me;
4458
4459           /*
4460            * do not i18n these strings - they are hard-coded in class
4461            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4462            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4463            */
4464           final JMenu msawsmenu = new JMenu("Alignment");
4465           final JMenu secstrmenu = new JMenu(
4466                   "Secondary Structure Prediction");
4467           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4468           final JMenu analymenu = new JMenu("Analysis");
4469           final JMenu dismenu = new JMenu("Protein Disorder");
4470           // JAL-940 - only show secondary structure prediction services from
4471           // the legacy server
4472           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4473               // &&
4474           Discoverer.services != null && (Discoverer.services.size() > 0))
4475           {
4476             // TODO: refactor to allow list of AbstractName/Handler bindings to
4477             // be
4478             // stored or retrieved from elsewhere
4479             // No MSAWS used any more:
4480             // Vector msaws = null; // (Vector)
4481             // Discoverer.services.get("MsaWS");
4482             Vector secstrpr = (Vector) Discoverer.services
4483                     .get("SecStrPred");
4484             if (secstrpr != null)
4485             {
4486               // Add any secondary structure prediction services
4487               for (int i = 0, j = secstrpr.size(); i < j; i++)
4488               {
4489                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4490                         .get(i);
4491                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4492                         .getServiceClient(sh);
4493                 int p = secstrmenu.getItemCount();
4494                 impl.attachWSMenuEntry(secstrmenu, me);
4495                 int q = secstrmenu.getItemCount();
4496                 for (int litm = p; litm < q; litm++)
4497                 {
4498                   legacyItems.add(secstrmenu.getItem(litm));
4499                 }
4500               }
4501             }
4502           }
4503
4504           // Add all submenus in the order they should appear on the web
4505           // services menu
4506           wsmenu.add(msawsmenu);
4507           wsmenu.add(secstrmenu);
4508           wsmenu.add(dismenu);
4509           wsmenu.add(analymenu);
4510           // No search services yet
4511           // wsmenu.add(seqsrchmenu);
4512
4513           javax.swing.SwingUtilities.invokeLater(new Runnable()
4514           {
4515             @Override
4516             public void run()
4517             {
4518               try
4519               {
4520                 webService.removeAll();
4521                 // first, add discovered services onto the webservices menu
4522                 if (wsmenu.size() > 0)
4523                 {
4524                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4525                   {
4526                     webService.add(wsmenu.get(i));
4527                   }
4528                 }
4529                 else
4530                 {
4531                   webService.add(me.webServiceNoServices);
4532                 }
4533                 // TODO: move into separate menu builder class.
4534                 boolean new_sspred = false;
4535                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4536                 {
4537                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4538                   if (jws2servs != null)
4539                   {
4540                     if (jws2servs.hasServices())
4541                     {
4542                       jws2servs.attachWSMenuEntry(webService, me);
4543                       for (Jws2Instance sv : jws2servs.getServices())
4544                       {
4545                         if (sv.description.toLowerCase().contains("jpred"))
4546                         {
4547                           for (JMenuItem jmi : legacyItems)
4548                           {
4549                             jmi.setVisible(false);
4550                           }
4551                         }
4552                       }
4553
4554                     }
4555                     if (jws2servs.isRunning())
4556                     {
4557                       JMenuItem tm = new JMenuItem(
4558                               "Still discovering JABA Services");
4559                       tm.setEnabled(false);
4560                       webService.add(tm);
4561                     }
4562                   }
4563                 }
4564                 build_urlServiceMenu(me.webService);
4565                 build_fetchdbmenu(webService);
4566                 for (JMenu item : wsmenu)
4567                 {
4568                   if (item.getItemCount() == 0)
4569                   {
4570                     item.setEnabled(false);
4571                   }
4572                   else
4573                   {
4574                     item.setEnabled(true);
4575                   }
4576                 }
4577               } catch (Exception e)
4578               {
4579                 Cache.log
4580                         .debug("Exception during web service menu building process.",
4581                                 e);
4582               }
4583             }
4584           });
4585         } catch (Exception e)
4586         {
4587         }
4588         buildingMenu = false;
4589       }
4590     }).start();
4591
4592   }
4593
4594   /**
4595    * construct any groupURL type service menu entries.
4596    *
4597    * @param webService
4598    */
4599   private void build_urlServiceMenu(JMenu webService)
4600   {
4601     // TODO: remove this code when 2.7 is released
4602     // DEBUG - alignmentView
4603     /*
4604      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4605      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4606      *
4607      * @Override public void actionPerformed(ActionEvent e) {
4608      * jalview.datamodel.AlignmentView
4609      * .testSelectionViews(af.viewport.getAlignment(),
4610      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4611      *
4612      * }); webService.add(testAlView);
4613      */
4614     // TODO: refactor to RestClient discoverer and merge menu entries for
4615     // rest-style services with other types of analysis/calculation service
4616     // SHmmr test client - still being implemented.
4617     // DEBUG - alignmentView
4618
4619     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4620             .getRestClients())
4621     {
4622       client.attachWSMenuEntry(
4623               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4624               this);
4625     }
4626   }
4627
4628   /**
4629    * Searches the alignment sequences for xRefs and builds the Show
4630    * Cross-References menu (formerly called Show Products), with database
4631    * sources for which cross-references are found (protein sources for a
4632    * nucleotide alignment and vice versa)
4633    *
4634    * @return true if Show Cross-references menu should be enabled
4635    */
4636   public boolean canShowProducts()
4637   {
4638     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4639     AlignmentI dataset = viewport.getAlignment().getDataset();
4640
4641     showProducts.removeAll();
4642     final boolean dna = viewport.getAlignment().isNucleotide();
4643
4644     if (seqs == null || seqs.length == 0)
4645     {
4646       // nothing to see here.
4647       return false;
4648     }
4649
4650     boolean showp = false;
4651     try
4652     {
4653       List<String> ptypes = new CrossRef(seqs, dataset)
4654               .findXrefSourcesForSequences(dna);
4655
4656       for (final String source : ptypes)
4657       {
4658         showp = true;
4659         final AlignFrame af = this;
4660         JMenuItem xtype = new JMenuItem(source);
4661         xtype.addActionListener(new ActionListener()
4662         {
4663           @Override
4664           public void actionPerformed(ActionEvent e)
4665           {
4666             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4667           }
4668         });
4669         showProducts.add(xtype);
4670       }
4671       showProducts.setVisible(showp);
4672       showProducts.setEnabled(showp);
4673     } catch (Exception e)
4674     {
4675       Cache.log
4676               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4677                       e);
4678       return false;
4679     }
4680     return showp;
4681   }
4682
4683   /**
4684    * Finds and displays cross-references for the selected sequences (protein
4685    * products for nucleotide sequences, dna coding sequences for peptides).
4686    *
4687    * @param sel
4688    *          the sequences to show cross-references for
4689    * @param dna
4690    *          true if from a nucleotide alignment (so showing proteins)
4691    * @param source
4692    *          the database to show cross-references for
4693    */
4694   protected void showProductsFor(final SequenceI[] sel,
4695           final boolean _odna, final String source)
4696   {
4697     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4698             .start();
4699   }
4700
4701   /**
4702    * Construct and display a new frame containing the translation of this
4703    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4704    */
4705   @Override
4706   public void showTranslation_actionPerformed(ActionEvent e)
4707   {
4708     AlignmentI al = null;
4709     try
4710     {
4711       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4712
4713       al = dna.translateCdna();
4714     } catch (Exception ex)
4715     {
4716       jalview.bin.Cache.log.error(
4717               "Exception during translation. Please report this !", ex);
4718       final String msg = MessageManager
4719               .getString("label.error_when_translating_sequences_submit_bug_report");
4720       final String errorTitle = MessageManager
4721               .getString("label.implementation_error")
4722               + MessageManager.getString("label.translation_failed");
4723       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4724               JOptionPane.ERROR_MESSAGE);
4725       return;
4726     }
4727     if (al == null || al.getHeight() == 0)
4728     {
4729       final String msg = MessageManager
4730               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4731       final String errorTitle = MessageManager
4732               .getString("label.translation_failed");
4733       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4734               JOptionPane.WARNING_MESSAGE);
4735     }
4736     else
4737     {
4738       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4739       af.setFileFormat(this.currentFileFormat);
4740       final String newTitle = MessageManager.formatMessage(
4741               "label.translation_of_params",
4742               new Object[] { this.getTitle() });
4743       af.setTitle(newTitle);
4744       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4745       {
4746         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4747         viewport.openSplitFrame(af, new Alignment(seqs));
4748       }
4749       else
4750       {
4751         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4752                 DEFAULT_HEIGHT);
4753       }
4754     }
4755   }
4756
4757   /**
4758    * Set the file format
4759    *
4760    * @param fileFormat
4761    */
4762   public void setFileFormat(String fileFormat)
4763   {
4764     this.currentFileFormat = fileFormat;
4765   }
4766
4767   /**
4768    * Try to load a features file onto the alignment.
4769    *
4770    * @param file
4771    *          contents or path to retrieve file
4772    * @param type
4773    *          access mode of file (see jalview.io.AlignFile)
4774    * @return true if features file was parsed correctly.
4775    */
4776   public boolean parseFeaturesFile(String file, String type)
4777   {
4778     return avc.parseFeaturesFile(file, type,
4779             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4780
4781   }
4782
4783   @Override
4784   public void refreshFeatureUI(boolean enableIfNecessary)
4785   {
4786     // note - currently this is only still here rather than in the controller
4787     // because of the featureSettings hard reference that is yet to be
4788     // abstracted
4789     if (enableIfNecessary)
4790     {
4791       viewport.setShowSequenceFeatures(true);
4792       showSeqFeatures.setSelected(true);
4793     }
4794
4795   }
4796
4797   @Override
4798   public void dragEnter(DropTargetDragEvent evt)
4799   {
4800   }
4801
4802   @Override
4803   public void dragExit(DropTargetEvent evt)
4804   {
4805   }
4806
4807   @Override
4808   public void dragOver(DropTargetDragEvent evt)
4809   {
4810   }
4811
4812   @Override
4813   public void dropActionChanged(DropTargetDragEvent evt)
4814   {
4815   }
4816
4817   @Override
4818   public void drop(DropTargetDropEvent evt)
4819   {
4820     // JAL-1552 - acceptDrop required before getTransferable call for
4821     // Java's Transferable for native dnd
4822     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4823     Transferable t = evt.getTransferable();
4824     java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
4825
4826     try
4827     {
4828       Desktop.transferFromDropTarget(files, protocols, evt, t);
4829     } catch (Exception e)
4830     {
4831       e.printStackTrace();
4832     }
4833     if (files != null)
4834     {
4835       try
4836       {
4837         // check to see if any of these files have names matching sequences in
4838         // the alignment
4839         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4840                 .getAlignment().getSequencesArray());
4841         /**
4842          * Object[] { String,SequenceI}
4843          */
4844         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4845         ArrayList<String> filesnotmatched = new ArrayList<String>();
4846         for (int i = 0; i < files.size(); i++)
4847         {
4848           String file = files.get(i).toString();
4849           String pdbfn = "";
4850           String protocol = FormatAdapter.checkProtocol(file);
4851           if (protocol == jalview.io.FormatAdapter.FILE)
4852           {
4853             File fl = new File(file);
4854             pdbfn = fl.getName();
4855           }
4856           else if (protocol == jalview.io.FormatAdapter.URL)
4857           {
4858             URL url = new URL(file);
4859             pdbfn = url.getFile();
4860           }
4861           if (pdbfn.length() > 0)
4862           {
4863             // attempt to find a match in the alignment
4864             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4865             int l = 0, c = pdbfn.indexOf(".");
4866             while (mtch == null && c != -1)
4867             {
4868               do
4869               {
4870                 l = c;
4871               } while ((c = pdbfn.indexOf(".", l)) > l);
4872               if (l > -1)
4873               {
4874                 pdbfn = pdbfn.substring(0, l);
4875               }
4876               mtch = idm.findAllIdMatches(pdbfn);
4877             }
4878             if (mtch != null)
4879             {
4880               String type = null;
4881               try
4882               {
4883                 type = new IdentifyFile().identify(file, protocol);
4884               } catch (Exception ex)
4885               {
4886                 type = null;
4887               }
4888               if (type != null)
4889               {
4890                 if (StructureFile.isStructureFile(type))
4891                 {
4892                   filesmatched.add(new Object[] { file, protocol, mtch });
4893                   continue;
4894                 }
4895               }
4896             }
4897             // File wasn't named like one of the sequences or wasn't a PDB file.
4898             filesnotmatched.add(file);
4899           }
4900         }
4901         int assocfiles = 0;
4902         if (filesmatched.size() > 0)
4903         {
4904           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4905                   || JOptionPane
4906                           .showConfirmDialog(
4907                                   this,
4908                                   MessageManager
4909                                           .formatMessage(
4910                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4911                                                   new Object[] { Integer
4912                                                           .valueOf(
4913                                                                   filesmatched
4914                                                                           .size())
4915                                                           .toString() }),
4916                                   MessageManager
4917                                           .getString("label.automatically_associate_structure_files_by_name"),
4918                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4919
4920           {
4921             for (Object[] fm : filesmatched)
4922             {
4923               // try and associate
4924               // TODO: may want to set a standard ID naming formalism for
4925               // associating PDB files which have no IDs.
4926               for (SequenceI toassoc : (SequenceI[]) fm[2])
4927               {
4928                 PDBEntry pe = new AssociatePdbFileWithSeq()
4929                         .associatePdbWithSeq((String) fm[0],
4930                                 (String) fm[1], toassoc, false,
4931                                 Desktop.instance);
4932                 if (pe != null)
4933                 {
4934                   System.err.println("Associated file : "
4935                           + ((String) fm[0]) + " with "
4936                           + toassoc.getDisplayId(true));
4937                   assocfiles++;
4938                 }
4939               }
4940               alignPanel.paintAlignment(true);
4941             }
4942           }
4943         }
4944         if (filesnotmatched.size() > 0)
4945         {
4946           if (assocfiles > 0
4947                   && (Cache.getDefault(
4948                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4949                           .showConfirmDialog(
4950                                   this,
4951                                   "<html>"
4952                                           + MessageManager
4953                                                   .formatMessage(
4954                                                           "label.ignore_unmatched_dropped_files_info",
4955                                                           new Object[] { Integer
4956                                                                   .valueOf(
4957                                                                           filesnotmatched
4958                                                                                   .size())
4959                                                                   .toString() })
4960                                           + "</html>",
4961                                   MessageManager
4962                                           .getString("label.ignore_unmatched_dropped_files"),
4963                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4964           {
4965             return;
4966           }
4967           for (String fn : filesnotmatched)
4968           {
4969             loadJalviewDataFile(fn, null, null, null);
4970           }
4971
4972         }
4973       } catch (Exception ex)
4974       {
4975         ex.printStackTrace();
4976       }
4977     }
4978   }
4979
4980   /**
4981    * Attempt to load a "dropped" file or URL string: First by testing whether
4982    * it's an Annotation file, then a JNet file, and finally a features file. If
4983    * all are false then the user may have dropped an alignment file onto this
4984    * AlignFrame.
4985    *
4986    * @param file
4987    *          either a filename or a URL string.
4988    */
4989   public void loadJalviewDataFile(String file, String protocol,
4990           String format, SequenceI assocSeq)
4991   {
4992     try
4993     {
4994       if (protocol == null)
4995       {
4996         protocol = FormatAdapter.checkProtocol(file);
4997       }
4998       // if the file isn't identified, or not positively identified as some
4999       // other filetype (PFAM is default unidentified alignment file type) then
5000       // try to parse as annotation.
5001       boolean isAnnotation = (format == null || format
5002               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5003               .annotateAlignmentView(viewport, file, protocol) : false;
5004
5005       if (!isAnnotation)
5006       {
5007         // first see if its a T-COFFEE score file
5008         TCoffeeScoreFile tcf = null;
5009         try
5010         {
5011           tcf = new TCoffeeScoreFile(file, protocol);
5012           if (tcf.isValid())
5013           {
5014             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5015             {
5016               tcoffeeColour.setEnabled(true);
5017               tcoffeeColour.setSelected(true);
5018               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5019               isAnnotation = true;
5020               statusBar
5021                       .setText(MessageManager
5022                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5023             }
5024             else
5025             {
5026               // some problem - if no warning its probable that the ID matching
5027               // process didn't work
5028               JOptionPane
5029                       .showMessageDialog(
5030                               Desktop.desktop,
5031                               tcf.getWarningMessage() == null ? MessageManager
5032                                       .getString("label.check_file_matches_sequence_ids_alignment")
5033                                       : tcf.getWarningMessage(),
5034                               MessageManager
5035                                       .getString("label.problem_reading_tcoffee_score_file"),
5036                               JOptionPane.WARNING_MESSAGE);
5037             }
5038           }
5039           else
5040           {
5041             tcf = null;
5042           }
5043         } catch (Exception x)
5044         {
5045           Cache.log
5046                   .debug("Exception when processing data source as T-COFFEE score file",
5047                           x);
5048           tcf = null;
5049         }
5050         if (tcf == null)
5051         {
5052           // try to see if its a JNet 'concise' style annotation file *before*
5053           // we
5054           // try to parse it as a features file
5055           if (format == null)
5056           {
5057             format = new IdentifyFile().identify(file, protocol);
5058           }
5059           if (format.equalsIgnoreCase("JnetFile"))
5060           {
5061             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5062                     file, protocol);
5063             new JnetAnnotationMaker();
5064             JnetAnnotationMaker.add_annotation(predictions,
5065                     viewport.getAlignment(), 0, false);
5066             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5067             viewport.getAlignment().setSeqrep(repseq);
5068             ColumnSelection cs = new ColumnSelection();
5069             cs.hideInsertionsFor(repseq);
5070             viewport.setColumnSelection(cs);
5071             isAnnotation = true;
5072           }
5073           else if (IdentifyFile.FeaturesFile.equals(format))
5074           {
5075             if (parseFeaturesFile(file, protocol))
5076             {
5077               alignPanel.paintAlignment(true);
5078             }
5079           }
5080           else
5081           {
5082             new FileLoader().LoadFile(viewport, file, protocol, format);
5083           }
5084         }
5085       }
5086       if (isAnnotation)
5087       {
5088
5089         alignPanel.adjustAnnotationHeight();
5090         viewport.updateSequenceIdColours();
5091         buildSortByAnnotationScoresMenu();
5092         alignPanel.paintAlignment(true);
5093       }
5094     } catch (Exception ex)
5095     {
5096       ex.printStackTrace();
5097     } catch (OutOfMemoryError oom)
5098     {
5099       try
5100       {
5101         System.gc();
5102       } catch (Exception x)
5103       {
5104       }
5105       new OOMWarning(
5106               "loading data "
5107                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5108                               : "using " + protocol + " from " + file)
5109                               : ".")
5110                       + (format != null ? "(parsing as '" + format
5111                               + "' file)" : ""), oom, Desktop.desktop);
5112     }
5113   }
5114
5115   /**
5116    * Method invoked by the ChangeListener on the tabbed pane, in other words
5117    * when a different tabbed pane is selected by the user or programmatically.
5118    */
5119   @Override
5120   public void tabSelectionChanged(int index)
5121   {
5122     if (index > -1)
5123     {
5124       alignPanel = alignPanels.get(index);
5125       viewport = alignPanel.av;
5126       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5127       setMenusFromViewport(viewport);
5128     }
5129
5130     /*
5131      * If there is a frame linked to this one in a SplitPane, switch it to the
5132      * same view tab index. No infinite recursion of calls should happen, since
5133      * tabSelectionChanged() should not get invoked on setting the selected
5134      * index to an unchanged value. Guard against setting an invalid index
5135      * before the new view peer tab has been created.
5136      */
5137     final AlignViewportI peer = viewport.getCodingComplement();
5138     if (peer != null)
5139     {
5140       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5141       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5142       {
5143         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5144       }
5145     }
5146   }
5147
5148   /**
5149    * On right mouse click on view tab, prompt for and set new view name.
5150    */
5151   @Override
5152   public void tabbedPane_mousePressed(MouseEvent e)
5153   {
5154     if (e.isPopupTrigger())
5155     {
5156       String msg = MessageManager.getString("label.enter_view_name");
5157       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5158               JOptionPane.QUESTION_MESSAGE);
5159
5160       if (reply != null)
5161       {
5162         viewport.viewName = reply;
5163         // TODO warn if reply is in getExistingViewNames()?
5164         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5165       }
5166     }
5167   }
5168
5169   public AlignViewport getCurrentView()
5170   {
5171     return viewport;
5172   }
5173
5174   /**
5175    * Open the dialog for regex description parsing.
5176    */
5177   @Override
5178   protected void extractScores_actionPerformed(ActionEvent e)
5179   {
5180     ParseProperties pp = new jalview.analysis.ParseProperties(
5181             viewport.getAlignment());
5182     // TODO: verify regex and introduce GUI dialog for version 2.5
5183     // if (pp.getScoresFromDescription("col", "score column ",
5184     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5185     // true)>0)
5186     if (pp.getScoresFromDescription("description column",
5187             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5188     {
5189       buildSortByAnnotationScoresMenu();
5190     }
5191   }
5192
5193   /*
5194    * (non-Javadoc)
5195    *
5196    * @see
5197    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5198    * )
5199    */
5200   @Override
5201   protected void showDbRefs_actionPerformed(ActionEvent e)
5202   {
5203     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5204   }
5205
5206   /*
5207    * (non-Javadoc)
5208    *
5209    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5210    * ActionEvent)
5211    */
5212   @Override
5213   protected void showNpFeats_actionPerformed(ActionEvent e)
5214   {
5215     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5216   }
5217
5218   /**
5219    * find the viewport amongst the tabs in this alignment frame and close that
5220    * tab
5221    *
5222    * @param av
5223    */
5224   public boolean closeView(AlignViewportI av)
5225   {
5226     if (viewport == av)
5227     {
5228       this.closeMenuItem_actionPerformed(false);
5229       return true;
5230     }
5231     Component[] comp = tabbedPane.getComponents();
5232     for (int i = 0; comp != null && i < comp.length; i++)
5233     {
5234       if (comp[i] instanceof AlignmentPanel)
5235       {
5236         if (((AlignmentPanel) comp[i]).av == av)
5237         {
5238           // close the view.
5239           closeView((AlignmentPanel) comp[i]);
5240           return true;
5241         }
5242       }
5243     }
5244     return false;
5245   }
5246
5247   protected void build_fetchdbmenu(JMenu webService)
5248   {
5249     // Temporary hack - DBRef Fetcher always top level ws entry.
5250     // TODO We probably want to store a sequence database checklist in
5251     // preferences and have checkboxes.. rather than individual sources selected
5252     // here
5253     final JMenu rfetch = new JMenu(
5254             MessageManager.getString("action.fetch_db_references"));
5255     rfetch.setToolTipText(MessageManager
5256             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5257     webService.add(rfetch);
5258
5259     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5260             MessageManager.getString("option.trim_retrieved_seqs"));
5261     trimrs.setToolTipText(MessageManager
5262             .getString("label.trim_retrieved_sequences"));
5263     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5264     trimrs.addActionListener(new ActionListener()
5265     {
5266       @Override
5267       public void actionPerformed(ActionEvent e)
5268       {
5269         trimrs.setSelected(trimrs.isSelected());
5270         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5271                 Boolean.valueOf(trimrs.isSelected()).toString());
5272       };
5273     });
5274     rfetch.add(trimrs);
5275     JMenuItem fetchr = new JMenuItem(
5276             MessageManager.getString("label.standard_databases"));
5277     fetchr.setToolTipText(MessageManager
5278             .getString("label.fetch_embl_uniprot"));
5279     fetchr.addActionListener(new ActionListener()
5280     {
5281
5282       @Override
5283       public void actionPerformed(ActionEvent e)
5284       {
5285         new Thread(new Runnable()
5286         {
5287           @Override
5288           public void run()
5289           {
5290             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5291                     .getAlignment().isNucleotide();
5292             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5293                     .getSequenceSelection(), alignPanel.alignFrame, null,
5294                     alignPanel.alignFrame.featureSettings, isNucleotide);
5295             dbRefFetcher.addListener(new FetchFinishedListenerI()
5296             {
5297               @Override
5298               public void finished()
5299               {
5300                 AlignFrame.this.setMenusForViewport();
5301               }
5302             });
5303             dbRefFetcher.fetchDBRefs(false);
5304           }
5305         }).start();
5306
5307       }
5308
5309     });
5310     rfetch.add(fetchr);
5311     final AlignFrame me = this;
5312     new Thread(new Runnable()
5313     {
5314       @Override
5315       public void run()
5316       {
5317         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5318                 .getSequenceFetcherSingleton(me);
5319         javax.swing.SwingUtilities.invokeLater(new Runnable()
5320         {
5321           @Override
5322           public void run()
5323           {
5324             String[] dbclasses = sf.getOrderedSupportedSources();
5325             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5326             // jalview.util.QuickSort.sort(otherdb, otherdb);
5327             List<DbSourceProxy> otherdb;
5328             JMenu dfetch = new JMenu();
5329             JMenu ifetch = new JMenu();
5330             JMenuItem fetchr = null;
5331             int comp = 0, icomp = 0, mcomp = 15;
5332             String mname = null;
5333             int dbi = 0;
5334             for (String dbclass : dbclasses)
5335             {
5336               otherdb = sf.getSourceProxy(dbclass);
5337               // add a single entry for this class, or submenu allowing 'fetch
5338               // all' or pick one
5339               if (otherdb == null || otherdb.size() < 1)
5340               {
5341                 continue;
5342               }
5343               // List<DbSourceProxy> dbs=otherdb;
5344               // otherdb=new ArrayList<DbSourceProxy>();
5345               // for (DbSourceProxy db:dbs)
5346               // {
5347               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5348               // }
5349               if (mname == null)
5350               {
5351                 mname = "From " + dbclass;
5352               }
5353               if (otherdb.size() == 1)
5354               {
5355                 final DbSourceProxy[] dassource = otherdb
5356                         .toArray(new DbSourceProxy[0]);
5357                 DbSourceProxy src = otherdb.get(0);
5358                 fetchr = new JMenuItem(src.getDbSource());
5359                 fetchr.addActionListener(new ActionListener()
5360                 {
5361
5362                   @Override
5363                   public void actionPerformed(ActionEvent e)
5364                   {
5365                     new Thread(new Runnable()
5366                     {
5367
5368                       @Override
5369                       public void run()
5370                       {
5371                         boolean isNucleotide = alignPanel.alignFrame
5372                                 .getViewport().getAlignment()
5373                                 .isNucleotide();
5374                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5375                                 alignPanel.av.getSequenceSelection(),
5376                                 alignPanel.alignFrame, dassource,
5377                                 alignPanel.alignFrame.featureSettings,
5378                                 isNucleotide);
5379                         dbRefFetcher
5380                                 .addListener(new FetchFinishedListenerI()
5381                                 {
5382                                   @Override
5383                                   public void finished()
5384                                   {
5385                                     AlignFrame.this.setMenusForViewport();
5386                                   }
5387                                 });
5388                         dbRefFetcher.fetchDBRefs(false);
5389                       }
5390                     }).start();
5391                   }
5392
5393                 });
5394                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5395                         MessageManager.formatMessage(
5396                                 "label.fetch_retrieve_from",
5397                                 new Object[] { src.getDbName() })));
5398                 dfetch.add(fetchr);
5399                 comp++;
5400               }
5401               else
5402               {
5403                 final DbSourceProxy[] dassource = otherdb
5404                         .toArray(new DbSourceProxy[0]);
5405                 // fetch all entry
5406                 DbSourceProxy src = otherdb.get(0);
5407                 fetchr = new JMenuItem(MessageManager.formatMessage(
5408                         "label.fetch_all_param",
5409                         new Object[] { src.getDbSource() }));
5410                 fetchr.addActionListener(new ActionListener()
5411                 {
5412                   @Override
5413                   public void actionPerformed(ActionEvent e)
5414                   {
5415                     new Thread(new Runnable()
5416                     {
5417
5418                       @Override
5419                       public void run()
5420                       {
5421                         boolean isNucleotide = alignPanel.alignFrame
5422                                 .getViewport().getAlignment()
5423                                 .isNucleotide();
5424                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5425                                 alignPanel.av.getSequenceSelection(),
5426                                 alignPanel.alignFrame, dassource,
5427                                 alignPanel.alignFrame.featureSettings,
5428                                 isNucleotide);
5429                         dbRefFetcher
5430                                 .addListener(new FetchFinishedListenerI()
5431                                 {
5432                                   @Override
5433                                   public void finished()
5434                                   {
5435                                     AlignFrame.this.setMenusForViewport();
5436                                   }
5437                                 });
5438                         dbRefFetcher.fetchDBRefs(false);
5439                       }
5440                     }).start();
5441                   }
5442                 });
5443
5444                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5445                         MessageManager.formatMessage(
5446                                 "label.fetch_retrieve_from_all_sources",
5447                                 new Object[] {
5448                                     Integer.valueOf(otherdb.size())
5449                                             .toString(), src.getDbSource(),
5450                                     src.getDbName() })));
5451                 dfetch.add(fetchr);
5452                 comp++;
5453                 // and then build the rest of the individual menus
5454                 ifetch = new JMenu(MessageManager.formatMessage(
5455                         "label.source_from_db_source",
5456                         new Object[] { src.getDbSource() }));
5457                 icomp = 0;
5458                 String imname = null;
5459                 int i = 0;
5460                 for (DbSourceProxy sproxy : otherdb)
5461                 {
5462                   String dbname = sproxy.getDbName();
5463                   String sname = dbname.length() > 5 ? dbname.substring(0,
5464                           5) + "..." : dbname;
5465                   String msname = dbname.length() > 10 ? dbname.substring(
5466                           0, 10) + "..." : dbname;
5467                   if (imname == null)
5468                   {
5469                     imname = MessageManager.formatMessage(
5470                             "label.from_msname", new Object[] { sname });
5471                   }
5472                   fetchr = new JMenuItem(msname);
5473                   final DbSourceProxy[] dassrc = { sproxy };
5474                   fetchr.addActionListener(new ActionListener()
5475                   {
5476
5477                     @Override
5478                     public void actionPerformed(ActionEvent e)
5479                     {
5480                       new Thread(new Runnable()
5481                       {
5482
5483                         @Override
5484                         public void run()
5485                         {
5486                           boolean isNucleotide = alignPanel.alignFrame
5487                                   .getViewport().getAlignment()
5488                                   .isNucleotide();
5489                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5490                                   alignPanel.av.getSequenceSelection(),
5491                                   alignPanel.alignFrame, dassrc,
5492                                   alignPanel.alignFrame.featureSettings,
5493                                   isNucleotide);
5494                           dbRefFetcher
5495                                   .addListener(new FetchFinishedListenerI()
5496                                   {
5497                                     @Override
5498                                     public void finished()
5499                                     {
5500                                       AlignFrame.this.setMenusForViewport();
5501                                     }
5502                                   });
5503                           dbRefFetcher.fetchDBRefs(false);
5504                         }
5505                       }).start();
5506                     }
5507
5508                   });
5509                   fetchr.setToolTipText("<html>"
5510                           + MessageManager.formatMessage(
5511                                   "label.fetch_retrieve_from", new Object[]
5512                                   { dbname }));
5513                   ifetch.add(fetchr);
5514                   ++i;
5515                   if (++icomp >= mcomp || i == (otherdb.size()))
5516                   {
5517                     ifetch.setText(MessageManager.formatMessage(
5518                             "label.source_to_target", imname, sname));
5519                     dfetch.add(ifetch);
5520                     ifetch = new JMenu();
5521                     imname = null;
5522                     icomp = 0;
5523                     comp++;
5524                   }
5525                 }
5526               }
5527               ++dbi;
5528               if (comp >= mcomp || dbi >= (dbclasses.length))
5529               {
5530                 dfetch.setText(MessageManager.formatMessage(
5531                         "label.source_to_target", mname, dbclass));
5532                 rfetch.add(dfetch);
5533                 dfetch = new JMenu();
5534                 mname = null;
5535                 comp = 0;
5536               }
5537             }
5538           }
5539         });
5540       }
5541     }).start();
5542
5543   }
5544
5545   /**
5546    * Left justify the whole alignment.
5547    */
5548   @Override
5549   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5550   {
5551     AlignmentI al = viewport.getAlignment();
5552     al.justify(false);
5553     viewport.firePropertyChange("alignment", null, al);
5554   }
5555
5556   /**
5557    * Right justify the whole alignment.
5558    */
5559   @Override
5560   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5561   {
5562     AlignmentI al = viewport.getAlignment();
5563     al.justify(true);
5564     viewport.firePropertyChange("alignment", null, al);
5565   }
5566
5567   @Override
5568   public void setShowSeqFeatures(boolean b)
5569   {
5570     showSeqFeatures.setSelected(b);
5571     viewport.setShowSequenceFeatures(b);
5572   }
5573
5574   /*
5575    * (non-Javadoc)
5576    *
5577    * @see
5578    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5579    * awt.event.ActionEvent)
5580    */
5581   @Override
5582   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5583   {
5584     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5585     alignPanel.paintAlignment(true);
5586   }
5587
5588   /*
5589    * (non-Javadoc)
5590    *
5591    * @see
5592    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5593    * .ActionEvent)
5594    */
5595   @Override
5596   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5597   {
5598     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5599     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5600
5601   }
5602
5603   /*
5604    * (non-Javadoc)
5605    *
5606    * @see
5607    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5608    * .event.ActionEvent)
5609    */
5610   @Override
5611   protected void showGroupConservation_actionPerformed(ActionEvent e)
5612   {
5613     viewport.setShowGroupConservation(showGroupConservation.getState());
5614     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5615   }
5616
5617   /*
5618    * (non-Javadoc)
5619    *
5620    * @see
5621    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5622    * .event.ActionEvent)
5623    */
5624   @Override
5625   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5626   {
5627     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5628     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5629   }
5630
5631   /*
5632    * (non-Javadoc)
5633    *
5634    * @see
5635    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5636    * .event.ActionEvent)
5637    */
5638   @Override
5639   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5640   {
5641     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5642     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5643   }
5644
5645   @Override
5646   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5647   {
5648     showSequenceLogo.setState(true);
5649     viewport.setShowSequenceLogo(true);
5650     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5651     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5652   }
5653
5654   @Override
5655   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5656   {
5657     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5658   }
5659
5660   /*
5661    * (non-Javadoc)
5662    *
5663    * @see
5664    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5665    * .event.ActionEvent)
5666    */
5667   @Override
5668   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5669   {
5670     if (avc.makeGroupsFromSelection())
5671     {
5672       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5673       alignPanel.updateAnnotation();
5674       alignPanel.paintAlignment(true);
5675     }
5676   }
5677
5678   public void clearAlignmentSeqRep()
5679   {
5680     // TODO refactor alignmentseqrep to controller
5681     if (viewport.getAlignment().hasSeqrep())
5682     {
5683       viewport.getAlignment().setSeqrep(null);
5684       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5685       alignPanel.updateAnnotation();
5686       alignPanel.paintAlignment(true);
5687     }
5688   }
5689
5690   @Override
5691   protected void createGroup_actionPerformed(ActionEvent e)
5692   {
5693     if (avc.createGroup())
5694     {
5695       alignPanel.alignmentChanged();
5696     }
5697   }
5698
5699   @Override
5700   protected void unGroup_actionPerformed(ActionEvent e)
5701   {
5702     if (avc.unGroup())
5703     {
5704       alignPanel.alignmentChanged();
5705     }
5706   }
5707
5708   /**
5709    * make the given alignmentPanel the currently selected tab
5710    *
5711    * @param alignmentPanel
5712    */
5713   public void setDisplayedView(AlignmentPanel alignmentPanel)
5714   {
5715     if (!viewport.getSequenceSetId().equals(
5716             alignmentPanel.av.getSequenceSetId()))
5717     {
5718       throw new Error(
5719               MessageManager
5720                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5721     }
5722     if (tabbedPane != null
5723             && tabbedPane.getTabCount() > 0
5724             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5725                     .getSelectedIndex())
5726     {
5727       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5728     }
5729   }
5730
5731   /**
5732    * Action on selection of menu options to Show or Hide annotations.
5733    *
5734    * @param visible
5735    * @param forSequences
5736    *          update sequence-related annotations
5737    * @param forAlignment
5738    *          update non-sequence-related annotations
5739    */
5740   @Override
5741   protected void setAnnotationsVisibility(boolean visible,
5742           boolean forSequences, boolean forAlignment)
5743   {
5744     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5745             .getAlignmentAnnotation();
5746     if (anns == null)
5747     {
5748       return;
5749     }
5750     for (AlignmentAnnotation aa : anns)
5751     {
5752       /*
5753        * don't display non-positional annotations on an alignment
5754        */
5755       if (aa.annotations == null)
5756       {
5757         continue;
5758       }
5759       boolean apply = (aa.sequenceRef == null && forAlignment)
5760               || (aa.sequenceRef != null && forSequences);
5761       if (apply)
5762       {
5763         aa.visible = visible;
5764       }
5765     }
5766     alignPanel.validateAnnotationDimensions(true);
5767     alignPanel.alignmentChanged();
5768   }
5769
5770   /**
5771    * Store selected annotation sort order for the view and repaint.
5772    */
5773   @Override
5774   protected void sortAnnotations_actionPerformed()
5775   {
5776     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5777     this.alignPanel.av
5778             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5779     alignPanel.paintAlignment(true);
5780   }
5781
5782   /**
5783    *
5784    * @return alignment panels in this alignment frame
5785    */
5786   public List<? extends AlignmentViewPanel> getAlignPanels()
5787   {
5788     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5789   }
5790
5791   /**
5792    * Open a new alignment window, with the cDNA associated with this (protein)
5793    * alignment, aligned as is the protein.
5794    */
5795   protected void viewAsCdna_actionPerformed()
5796   {
5797     // TODO no longer a menu action - refactor as required
5798     final AlignmentI alignment = getViewport().getAlignment();
5799     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5800     if (mappings == null)
5801     {
5802       return;
5803     }
5804     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5805     for (SequenceI aaSeq : alignment.getSequences())
5806     {
5807       for (AlignedCodonFrame acf : mappings)
5808       {
5809         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5810         if (dnaSeq != null)
5811         {
5812           /*
5813            * There is a cDNA mapping for this protein sequence - add to new
5814            * alignment. It will share the same dataset sequence as other mapped
5815            * cDNA (no new mappings need to be created).
5816            */
5817           final Sequence newSeq = new Sequence(dnaSeq);
5818           newSeq.setDatasetSequence(dnaSeq);
5819           cdnaSeqs.add(newSeq);
5820         }
5821       }
5822     }
5823     if (cdnaSeqs.size() == 0)
5824     {
5825       // show a warning dialog no mapped cDNA
5826       return;
5827     }
5828     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5829             .size()]));
5830     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5831             AlignFrame.DEFAULT_HEIGHT);
5832     cdna.alignAs(alignment);
5833     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5834             + this.title;
5835     Desktop.addInternalFrame(alignFrame, newtitle,
5836             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5837   }
5838
5839   /**
5840    * Set visibility of dna/protein complement view (available when shown in a
5841    * split frame).
5842    *
5843    * @param show
5844    */
5845   @Override
5846   protected void showComplement_actionPerformed(boolean show)
5847   {
5848     SplitContainerI sf = getSplitViewContainer();
5849     if (sf != null)
5850     {
5851       sf.setComplementVisible(this, show);
5852     }
5853   }
5854
5855   /**
5856    * Generate the reverse (optionally complemented) of the selected sequences,
5857    * and add them to the alignment
5858    */
5859   @Override
5860   protected void showReverse_actionPerformed(boolean complement)
5861   {
5862     AlignmentI al = null;
5863     try
5864     {
5865       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5866       al = dna.reverseCdna(complement);
5867       viewport.addAlignment(al, "");
5868       addHistoryItem(new EditCommand(
5869               MessageManager.getString("label.add_sequences"),
5870               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5871               viewport.getAlignment()));
5872     } catch (Exception ex)
5873     {
5874       System.err.println(ex.getMessage());
5875       return;
5876     }
5877   }
5878
5879   /**
5880    * Try to run a script in the Groovy console, having first ensured that this
5881    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5882    * be targeted at this alignment.
5883    */
5884   @Override
5885   protected void runGroovy_actionPerformed()
5886   {
5887     Jalview.setCurrentAlignFrame(this);
5888     groovy.ui.Console console = Desktop.getGroovyConsole();
5889     if (console != null)
5890     {
5891       try
5892       {
5893         console.runScript();
5894       } catch (Exception ex)
5895       {
5896         System.err.println((ex.toString()));
5897         JOptionPane
5898                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5899                         .getString("label.couldnt_run_groovy_script"),
5900                         MessageManager
5901                                 .getString("label.groovy_support_failed"),
5902                         JOptionPane.ERROR_MESSAGE);
5903       }
5904     }
5905     else
5906     {
5907       System.err.println("Can't run Groovy script as console not found");
5908     }
5909   }
5910
5911   /**
5912    * Hides columns containing (or not containing) a specified feature, provided
5913    * that would not leave all columns hidden
5914    *
5915    * @param featureType
5916    * @param columnsContaining
5917    * @return
5918    */
5919   public boolean hideFeatureColumns(String featureType,
5920           boolean columnsContaining)
5921   {
5922     boolean notForHiding = avc.markColumnsContainingFeatures(
5923             columnsContaining, false, false, featureType);
5924     if (notForHiding)
5925     {
5926       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5927               false, featureType))
5928       {
5929         getViewport().hideSelectedColumns();
5930         return true;
5931       }
5932     }
5933     return false;
5934   }
5935 }
5936
5937 class PrintThread extends Thread
5938 {
5939   AlignmentPanel ap;
5940
5941   public PrintThread(AlignmentPanel ap)
5942   {
5943     this.ap = ap;
5944   }
5945
5946   static PageFormat pf;
5947
5948   @Override
5949   public void run()
5950   {
5951     PrinterJob printJob = PrinterJob.getPrinterJob();
5952
5953     if (pf != null)
5954     {
5955       printJob.setPrintable(ap, pf);
5956     }
5957     else
5958     {
5959       printJob.setPrintable(ap);
5960     }
5961
5962     if (printJob.printDialog())
5963     {
5964       try
5965       {
5966         printJob.print();
5967       } catch (Exception PrintException)
5968       {
5969         PrintException.printStackTrace();
5970       }
5971     }
5972   }
5973 }