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.FeatureSettingsModelI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.ScoreModelI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.DBRefSource;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.FileLoader;
  69 import jalview.io.FormatAdapter;
  70 import jalview.io.HtmlSvgOutput;
  71 import jalview.io.IdentifyFile;
  72 import jalview.io.JalviewFileChooser;
  73 import jalview.io.JalviewFileView;
  74 import jalview.io.JnetAnnotationMaker;
  75 import jalview.io.NewickFile;
  76 import jalview.io.TCoffeeScoreFile;
  77 import jalview.io.gff.SequenceOntologyI;
  78 import jalview.jbgui.GAlignFrame;
  79 import jalview.schemes.Blosum62ColourScheme;
  80 import jalview.schemes.BuriedColourScheme;
  81 import jalview.schemes.ClustalxColourScheme;
  82 import jalview.schemes.ColourSchemeI;
  83 import jalview.schemes.ColourSchemeProperty;
  84 import jalview.schemes.HelixColourScheme;
  85 import jalview.schemes.HydrophobicColourScheme;
  86 import jalview.schemes.NucleotideColourScheme;
  87 import jalview.schemes.PIDColourScheme;
  88 import jalview.schemes.PurinePyrimidineColourScheme;
  89 import jalview.schemes.RNAHelicesColourChooser;
  90 import jalview.schemes.ResidueProperties;
  91 import jalview.schemes.StrandColourScheme;
  92 import jalview.schemes.TCoffeeColourScheme;
  93 import jalview.schemes.TaylorColourScheme;
  94 import jalview.schemes.TurnColourScheme;
  95 import jalview.schemes.UserColourScheme;
  96 import jalview.schemes.ZappoColourScheme;
  97 import jalview.structure.StructureSelectionManager;
  98 import jalview.util.MessageManager;
  99 import jalview.viewmodel.AlignmentViewport;
 100 import jalview.ws.DBRefFetcher;
 101 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 102 import jalview.ws.SequenceFetcher;
 103 import jalview.ws.jws1.Discoverer;
 104 import jalview.ws.jws2.Jws2Discoverer;
 105 import jalview.ws.jws2.jabaws2.Jws2Instance;
 106 import jalview.ws.seqfetcher.DbSourceProxy;
 107
 108 import java.awt.BorderLayout;
 109 import java.awt.Component;
 110 import java.awt.Rectangle;
 111 import java.awt.Toolkit;
 112 import java.awt.datatransfer.Clipboard;
 113 import java.awt.datatransfer.DataFlavor;
 114 import java.awt.datatransfer.StringSelection;
 115 import java.awt.datatransfer.Transferable;
 116 import java.awt.dnd.DropTargetDragEvent;
 117 import java.awt.dnd.DropTargetDropEvent;
 118 import java.awt.dnd.DropTargetEvent;
 119 import java.awt.dnd.DropTargetListener;
 120 import java.awt.event.ActionEvent;
 121 import java.awt.event.ActionListener;
 122 import java.awt.event.FocusAdapter;
 123 import java.awt.event.FocusEvent;
 124 import java.awt.event.ItemEvent;
 125 import java.awt.event.ItemListener;
 126 import java.awt.event.KeyAdapter;
 127 import java.awt.event.KeyEvent;
 128 import java.awt.event.MouseAdapter;
 129 import java.awt.event.MouseEvent;
 130 import java.awt.print.PageFormat;
 131 import java.awt.print.PrinterJob;
 132 import java.beans.PropertyChangeEvent;
 133 import java.io.File;
 134 import java.net.URL;
 135 import java.util.ArrayList;
 136 import java.util.Arrays;
 137 import java.util.Deque;
 138 import java.util.Enumeration;
 139 import java.util.Hashtable;
 140 import java.util.List;
 141 import java.util.Vector;
 142
 143 import javax.swing.JCheckBoxMenuItem;
 144 import javax.swing.JEditorPane;
 145 import javax.swing.JInternalFrame;
 146 import javax.swing.JLayeredPane;
 147 import javax.swing.JMenu;
 148 import javax.swing.JMenuItem;
 149 import javax.swing.JOptionPane;
 150 import javax.swing.JRadioButtonMenuItem;
 151 import javax.swing.JScrollPane;
 152 import javax.swing.SwingUtilities;
 153
 154 /**
 155  * DOCUMENT ME!
 156  *
 157  * @author $author$
 158  * @version $Revision$
 159  */
 160 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 161         IProgressIndicator, AlignViewControllerGuiI
 162 {
 163
 164   public static final int DEFAULT_WIDTH = 700;
 165
 166   public static final int DEFAULT_HEIGHT = 500;
 167
 168   /*
 169    * The currently displayed panel (selected tabbed view if more than one)
 170    */
 171   public AlignmentPanel alignPanel;
 172
 173   AlignViewport viewport;
 174
 175   public AlignViewControllerI avc;
 176
 177   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 178
 179   /**
 180    * Last format used to load or save alignments in this window
 181    */
 182   String currentFileFormat = null;
 183
 184   /**
 185    * Current filename for this alignment
 186    */
 187   String fileName = null;
 188
 189   /**
 190    * Creates a new AlignFrame object with specific width and height.
 191    *
 192    * @param al
 193    * @param width
 194    * @param height
 195    */
 196   public AlignFrame(AlignmentI al, int width, int height)
 197   {
 198     this(al, null, width, height);
 199   }
 200
 201   /**
 202    * Creates a new AlignFrame object with specific width, height and
 203    * sequenceSetId
 204    *
 205    * @param al
 206    * @param width
 207    * @param height
 208    * @param sequenceSetId
 209    */
 210   public AlignFrame(AlignmentI al, int width, int height,
 211           String sequenceSetId)
 212   {
 213     this(al, null, width, height, sequenceSetId);
 214   }
 215
 216   /**
 217    * Creates a new AlignFrame object with specific width, height and
 218    * sequenceSetId
 219    *
 220    * @param al
 221    * @param width
 222    * @param height
 223    * @param sequenceSetId
 224    * @param viewId
 225    */
 226   public AlignFrame(AlignmentI al, int width, int height,
 227           String sequenceSetId, String viewId)
 228   {
 229     this(al, null, width, height, sequenceSetId, viewId);
 230   }
 231
 232   /**
 233    * new alignment window with hidden columns
 234    *
 235    * @param al
 236    *          AlignmentI
 237    * @param hiddenColumns
 238    *          ColumnSelection or null
 239    * @param width
 240    *          Width of alignment frame
 241    * @param height
 242    *          height of frame.
 243    */
 244   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 245           int width, int height)
 246   {
 247     this(al, hiddenColumns, width, height, null);
 248   }
 249
 250   /**
 251    * Create alignment frame for al with hiddenColumns, a specific width and
 252    * height, and specific sequenceId
 253    *
 254    * @param al
 255    * @param hiddenColumns
 256    * @param width
 257    * @param height
 258    * @param sequenceSetId
 259    *          (may be null)
 260    */
 261   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 262           int width, int height, String sequenceSetId)
 263   {
 264     this(al, hiddenColumns, width, height, sequenceSetId, null);
 265   }
 266
 267   /**
 268    * Create alignment frame for al with hiddenColumns, a specific width and
 269    * height, and specific sequenceId
 270    *
 271    * @param al
 272    * @param hiddenColumns
 273    * @param width
 274    * @param height
 275    * @param sequenceSetId
 276    *          (may be null)
 277    * @param viewId
 278    *          (may be null)
 279    */
 280   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 281           int width, int height, String sequenceSetId, String viewId)
 282   {
 283     setSize(width, height);
 284
 285     if (al.getDataset() == null)
 286     {
 287       al.setDataset(null);
 288     }
 289
 290     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 291
 292     alignPanel = new AlignmentPanel(this, viewport);
 293
 294     addAlignmentPanel(alignPanel, true);
 295     init();
 296   }
 297
 298   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 299           ColumnSelection hiddenColumns, int width, int height)
 300   {
 301     setSize(width, height);
 302
 303     if (al.getDataset() == null)
 304     {
 305       al.setDataset(null);
 306     }
 307
 308     viewport = new AlignViewport(al, hiddenColumns);
 309
 310     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 311     {
 312       viewport.hideSequence(hiddenSeqs);
 313     }
 314     alignPanel = new AlignmentPanel(this, viewport);
 315     addAlignmentPanel(alignPanel, true);
 316     init();
 317   }
 318
 319   /**
 320    * Make a new AlignFrame from existing alignmentPanels
 321    *
 322    * @param ap
 323    *          AlignmentPanel
 324    * @param av
 325    *          AlignViewport
 326    */
 327   public AlignFrame(AlignmentPanel ap)
 328   {
 329     viewport = ap.av;
 330     alignPanel = ap;
 331     addAlignmentPanel(ap, false);
 332     init();
 333   }
 334
 335   /**
 336    * initalise the alignframe from the underlying viewport data and the
 337    * configurations
 338    */
 339   void init()
 340   {
 341     if (!Jalview.isHeadlessMode())
 342     {
 343       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 344     }
 345
 346     avc = new jalview.controller.AlignViewController(this, viewport,
 347             alignPanel);
 348     if (viewport.getAlignmentConservationAnnotation() == null)
 349     {
 350       BLOSUM62Colour.setEnabled(false);
 351       conservationMenuItem.setEnabled(false);
 352       modifyConservation.setEnabled(false);
 353       // PIDColour.setEnabled(false);
 354       // abovePIDThreshold.setEnabled(false);
 355       // modifyPID.setEnabled(false);
 356     }
 357
 358     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 359             "No sort");
 360
 361     if (sortby.equals("Id"))
 362     {
 363       sortIDMenuItem_actionPerformed(null);
 364     }
 365     else if (sortby.equals("Pairwise Identity"))
 366     {
 367       sortPairwiseMenuItem_actionPerformed(null);
 368     }
 369
 370     if (Desktop.desktop != null)
 371     {
 372       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 373       addServiceListeners();
 374       setGUINucleotide(viewport.getAlignment().isNucleotide());
 375     }
 376
 377     this.alignPanel.av
 378             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 379
 380     setMenusFromViewport(viewport);
 381     buildSortByAnnotationScoresMenu();
 382     buildTreeMenu();
 383
 384     if (viewport.getWrapAlignment())
 385     {
 386       wrapMenuItem_actionPerformed(null);
 387     }
 388
 389     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 390     {
 391       this.overviewMenuItem_actionPerformed(null);
 392     }
 393
 394     addKeyListener();
 395
 396     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 397     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 398     final String menuLabel = MessageManager
 399             .getString("label.copy_format_from");
 400     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 401             new ViewSetProvider()
 402             {
 403
 404               @Override
 405               public AlignmentPanel[] getAllAlignmentPanels()
 406               {
 407                 origview.clear();
 408                 origview.add(alignPanel);
 409                 // make an array of all alignment panels except for this one
 410                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 411                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 412                 aps.remove(AlignFrame.this.alignPanel);
 413                 return aps.toArray(new AlignmentPanel[aps.size()]);
 414               }
 415             }, selviews, new ItemListener()
 416             {
 417
 418               @Override
 419               public void itemStateChanged(ItemEvent e)
 420               {
 421                 if (origview.size() > 0)
 422                 {
 423                   final AlignmentPanel ap = origview.get(0);
 424
 425                   /*
 426                    * Copy the ViewStyle of the selected panel to 'this one'.
 427                    * Don't change value of 'scaleProteinAsCdna' unless copying
 428                    * from a SplitFrame.
 429                    */
 430                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 431                           .getViewStyle();
 432                   boolean fromSplitFrame = selviews.get(0)
 433                           .getAlignViewport().getCodingComplement() != null;
 434                   if (!fromSplitFrame)
 435                   {
 436                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 437                             .getViewStyle().isScaleProteinAsCdna());
 438                   }
 439                   ap.getAlignViewport().setViewStyle(vs);
 440
 441                   /*
 442                    * Also rescale ViewStyle of SplitFrame complement if there is
 443                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 444                    * the whole ViewStyle (allow cDNA protein to have different
 445                    * fonts)
 446                    */
 447                   AlignViewportI complement = ap.getAlignViewport()
 448                           .getCodingComplement();
 449                   if (complement != null && vs.isScaleProteinAsCdna())
 450                   {
 451                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 452                     ((SplitFrame) af.getSplitViewContainer())
 453                             .adjustLayout();
 454                     af.setMenusForViewport();
 455                   }
 456
 457                   ap.updateLayout();
 458                   ap.setSelected(true);
 459                   ap.alignFrame.setMenusForViewport();
 460
 461                 }
 462               }
 463             });
 464     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 465             .indexOf("devel") > -1
 466             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 467                     .indexOf("test") > -1)
 468     {
 469       formatMenu.add(vsel);
 470     }
 471     addFocusListener(new FocusAdapter()
 472     {
 473       @Override
 474       public void focusGained(FocusEvent e)
 475       {
 476         Jalview.setCurrentAlignFrame(AlignFrame.this);
 477       }
 478     });
 479
 480   }
 481
 482   /**
 483    * Change the filename and format for the alignment, and enable the 'reload'
 484    * button functionality.
 485    *
 486    * @param file
 487    *          valid filename
 488    * @param format
 489    *          format of file
 490    */
 491   public void setFileName(String file, String format)
 492   {
 493     fileName = file;
 494     setFileFormat(format);
 495     reload.setEnabled(true);
 496   }
 497
 498   /**
 499    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 500    * events
 501    */
 502   void addKeyListener()
 503   {
 504     addKeyListener(new KeyAdapter()
 505     {
 506       @Override
 507       public void keyPressed(KeyEvent evt)
 508       {
 509         if (viewport.cursorMode
 510                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 511                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 512                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 513                 && Character.isDigit(evt.getKeyChar()))
 514         {
 515           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 516         }
 517
 518         switch (evt.getKeyCode())
 519         {
 520
 521         case 27: // escape key
 522           deselectAllSequenceMenuItem_actionPerformed(null);
 523
 524           break;
 525
 526         case KeyEvent.VK_DOWN:
 527           if (evt.isAltDown() || !viewport.cursorMode)
 528           {
 529             moveSelectedSequences(false);
 530           }
 531           if (viewport.cursorMode)
 532           {
 533             alignPanel.getSeqPanel().moveCursor(0, 1);
 534           }
 535           break;
 536
 537         case KeyEvent.VK_UP:
 538           if (evt.isAltDown() || !viewport.cursorMode)
 539           {
 540             moveSelectedSequences(true);
 541           }
 542           if (viewport.cursorMode)
 543           {
 544             alignPanel.getSeqPanel().moveCursor(0, -1);
 545           }
 546
 547           break;
 548
 549         case KeyEvent.VK_LEFT:
 550           if (evt.isAltDown() || !viewport.cursorMode)
 551           {
 552             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 553           }
 554           else
 555           {
 556             alignPanel.getSeqPanel().moveCursor(-1, 0);
 557           }
 558
 559           break;
 560
 561         case KeyEvent.VK_RIGHT:
 562           if (evt.isAltDown() || !viewport.cursorMode)
 563           {
 564             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 565           }
 566           else
 567           {
 568             alignPanel.getSeqPanel().moveCursor(1, 0);
 569           }
 570           break;
 571
 572         case KeyEvent.VK_SPACE:
 573           if (viewport.cursorMode)
 574           {
 575             alignPanel.getSeqPanel().insertGapAtCursor(
 576                     evt.isControlDown() || evt.isShiftDown()
 577                             || evt.isAltDown());
 578           }
 579           break;
 580
 581         // case KeyEvent.VK_A:
 582         // if (viewport.cursorMode)
 583         // {
 584         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 585         // //System.out.println("A");
 586         // }
 587         // break;
 588         /*
 589          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 590          * System.out.println("closing bracket"); } break;
 591          */
 592         case KeyEvent.VK_DELETE:
 593         case KeyEvent.VK_BACK_SPACE:
 594           if (!viewport.cursorMode)
 595           {
 596             cut_actionPerformed(null);
 597           }
 598           else
 599           {
 600             alignPanel.getSeqPanel().deleteGapAtCursor(
 601                     evt.isControlDown() || evt.isShiftDown()
 602                             || evt.isAltDown());
 603           }
 604
 605           break;
 606
 607         case KeyEvent.VK_S:
 608           if (viewport.cursorMode)
 609           {
 610             alignPanel.getSeqPanel().setCursorRow();
 611           }
 612           break;
 613         case KeyEvent.VK_C:
 614           if (viewport.cursorMode && !evt.isControlDown())
 615           {
 616             alignPanel.getSeqPanel().setCursorColumn();
 617           }
 618           break;
 619         case KeyEvent.VK_P:
 620           if (viewport.cursorMode)
 621           {
 622             alignPanel.getSeqPanel().setCursorPosition();
 623           }
 624           break;
 625
 626         case KeyEvent.VK_ENTER:
 627         case KeyEvent.VK_COMMA:
 628           if (viewport.cursorMode)
 629           {
 630             alignPanel.getSeqPanel().setCursorRowAndColumn();
 631           }
 632           break;
 633
 634         case KeyEvent.VK_Q:
 635           if (viewport.cursorMode)
 636           {
 637             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 638           }
 639           break;
 640         case KeyEvent.VK_M:
 641           if (viewport.cursorMode)
 642           {
 643             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 644           }
 645           break;
 646
 647         case KeyEvent.VK_F2:
 648           viewport.cursorMode = !viewport.cursorMode;
 649           statusBar.setText(MessageManager.formatMessage(
 650                   "label.keyboard_editing_mode",
 651                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 652           if (viewport.cursorMode)
 653           {
 654             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 655             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 656           }
 657           alignPanel.getSeqPanel().seqCanvas.repaint();
 658           break;
 659
 660         case KeyEvent.VK_F1:
 661           try
 662           {
 663             Help.showHelpWindow();
 664           } catch (Exception ex)
 665           {
 666             ex.printStackTrace();
 667           }
 668           break;
 669         case KeyEvent.VK_H:
 670         {
 671           boolean toggleSeqs = !evt.isControlDown();
 672           boolean toggleCols = !evt.isShiftDown();
 673           toggleHiddenRegions(toggleSeqs, toggleCols);
 674           break;
 675         }
 676         case KeyEvent.VK_PAGE_UP:
 677           if (viewport.getWrapAlignment())
 678           {
 679             alignPanel.scrollUp(true);
 680           }
 681           else
 682           {
 683             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 684                     - viewport.endSeq + viewport.startSeq);
 685           }
 686           break;
 687         case KeyEvent.VK_PAGE_DOWN:
 688           if (viewport.getWrapAlignment())
 689           {
 690             alignPanel.scrollUp(false);
 691           }
 692           else
 693           {
 694             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 695                     + viewport.endSeq - viewport.startSeq);
 696           }
 697           break;
 698         }
 699       }
 700
 701       @Override
 702       public void keyReleased(KeyEvent evt)
 703       {
 704         switch (evt.getKeyCode())
 705         {
 706         case KeyEvent.VK_LEFT:
 707           if (evt.isAltDown() || !viewport.cursorMode)
 708           {
 709             viewport.firePropertyChange("alignment", null, viewport
 710                     .getAlignment().getSequences());
 711           }
 712           break;
 713
 714         case KeyEvent.VK_RIGHT:
 715           if (evt.isAltDown() || !viewport.cursorMode)
 716           {
 717             viewport.firePropertyChange("alignment", null, viewport
 718                     .getAlignment().getSequences());
 719           }
 720           break;
 721         }
 722       }
 723     });
 724   }
 725
 726   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 727   {
 728     ap.alignFrame = this;
 729     avc = new jalview.controller.AlignViewController(this, viewport,
 730             alignPanel);
 731
 732     alignPanels.add(ap);
 733
 734     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 735
 736     int aSize = alignPanels.size();
 737
 738     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 739
 740     if (aSize == 1 && ap.av.viewName == null)
 741     {
 742       this.getContentPane().add(ap, BorderLayout.CENTER);
 743     }
 744     else
 745     {
 746       if (aSize == 2)
 747       {
 748         setInitialTabVisible();
 749       }
 750
 751       expandViews.setEnabled(true);
 752       gatherViews.setEnabled(true);
 753       tabbedPane.addTab(ap.av.viewName, ap);
 754
 755       ap.setVisible(false);
 756     }
 757
 758     if (newPanel)
 759     {
 760       if (ap.av.isPadGaps())
 761       {
 762         ap.av.getAlignment().padGaps();
 763       }
 764       ap.av.updateConservation(ap);
 765       ap.av.updateConsensus(ap);
 766       ap.av.updateStrucConsensus(ap);
 767     }
 768   }
 769
 770   public void setInitialTabVisible()
 771   {
 772     expandViews.setEnabled(true);
 773     gatherViews.setEnabled(true);
 774     tabbedPane.setVisible(true);
 775     AlignmentPanel first = alignPanels.get(0);
 776     tabbedPane.addTab(first.av.viewName, first);
 777     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 778   }
 779
 780   public AlignViewport getViewport()
 781   {
 782     return viewport;
 783   }
 784
 785   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 786   private void addServiceListeners()
 787   {
 788     final java.beans.PropertyChangeListener thisListener;
 789     Desktop.instance.addJalviewPropertyChangeListener("services",
 790             thisListener = new java.beans.PropertyChangeListener()
 791             {
 792               @Override
 793               public void propertyChange(PropertyChangeEvent evt)
 794               {
 795                 // // System.out.println("Discoverer property change.");
 796                 // if (evt.getPropertyName().equals("services"))
 797                 {
 798                   SwingUtilities.invokeLater(new Runnable()
 799                   {
 800
 801                     @Override
 802                     public void run()
 803                     {
 804                       System.err
 805                               .println("Rebuild WS Menu for service change");
 806                       BuildWebServiceMenu();
 807                     }
 808
 809                   });
 810                 }
 811               }
 812             });
 813     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 814     {
 815       @Override
 816       public void internalFrameClosed(
 817               javax.swing.event.InternalFrameEvent evt)
 818       {
 819         // System.out.println("deregistering discoverer listener");
 820         Desktop.instance.removeJalviewPropertyChangeListener("services",
 821                 thisListener);
 822         closeMenuItem_actionPerformed(true);
 823       };
 824     });
 825     // Finally, build the menu once to get current service state
 826     new Thread(new Runnable()
 827     {
 828       @Override
 829       public void run()
 830       {
 831         BuildWebServiceMenu();
 832       }
 833     }).start();
 834   }
 835
 836   /**
 837    * Configure menu items that vary according to whether the alignment is
 838    * nucleotide or protein
 839    *
 840    * @param nucleotide
 841    */
 842   public void setGUINucleotide(boolean nucleotide)
 843   {
 844     showTranslation.setVisible(nucleotide);
 845     showReverse.setVisible(nucleotide);
 846     showReverseComplement.setVisible(nucleotide);
 847     conservationMenuItem.setEnabled(!nucleotide);
 848     modifyConservation.setEnabled(!nucleotide);
 849     showGroupConservation.setEnabled(!nucleotide);
 850     rnahelicesColour.setEnabled(nucleotide);
 851     purinePyrimidineColour.setEnabled(nucleotide);
 852     showComplementMenuItem.setText(nucleotide ? MessageManager
 853             .getString("label.protein") : MessageManager
 854             .getString("label.nucleotide"));
 855     setColourSelected(jalview.bin.Cache.getDefault(
 856             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 857                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 858   }
 859
 860   /**
 861    * set up menus for the current viewport. This may be called after any
 862    * operation that affects the data in the current view (selection changed,
 863    * etc) to update the menus to reflect the new state.
 864    */
 865   @Override
 866   public void setMenusForViewport()
 867   {
 868     setMenusFromViewport(viewport);
 869   }
 870
 871   /**
 872    * Need to call this method when tabs are selected for multiple views, or when
 873    * loading from Jalview2XML.java
 874    *
 875    * @param av
 876    *          AlignViewport
 877    */
 878   void setMenusFromViewport(AlignViewport av)
 879   {
 880     padGapsMenuitem.setSelected(av.isPadGaps());
 881     colourTextMenuItem.setSelected(av.isShowColourText());
 882     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 883     conservationMenuItem.setSelected(av.getConservationSelected());
 884     seqLimits.setSelected(av.getShowJVSuffix());
 885     idRightAlign.setSelected(av.isRightAlignIds());
 886     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 887     renderGapsMenuItem.setSelected(av.isRenderGaps());
 888     wrapMenuItem.setSelected(av.getWrapAlignment());
 889     scaleAbove.setVisible(av.getWrapAlignment());
 890     scaleLeft.setVisible(av.getWrapAlignment());
 891     scaleRight.setVisible(av.getWrapAlignment());
 892     annotationPanelMenuItem.setState(av.isShowAnnotation());
 893     /*
 894      * Show/hide annotations only enabled if annotation panel is shown
 895      */
 896     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 898     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 900     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 901     viewTextMenuItem.setSelected(av.getShowText());
 902     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 903     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 904     showGroupConservation.setSelected(av.isShowGroupConservation());
 905     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 906     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 907     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 908
 909     setColourSelected(ColourSchemeProperty.getColourName(av
 910             .getGlobalColourScheme()));
 911
 912     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 913     hiddenMarkers.setState(av.getShowHiddenMarkers());
 914     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 915     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 916     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 917     autoCalculate.setSelected(av.autoCalculateConsensus);
 918     sortByTree.setSelected(av.sortByTree);
 919     listenToViewSelections.setSelected(av.followSelection);
 920     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 921     rnahelicesColour
 922             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 923
 924     showProducts.setEnabled(canShowProducts());
 925     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 926
 927     updateEditMenuBar();
 928   }
 929
 930   /**
 931    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 932    *
 933    * @param b
 934    */
 935   public void setGroovyEnabled(boolean b)
 936   {
 937     runGroovy.setEnabled(b);
 938   }
 939
 940   private IProgressIndicator progressBar;
 941
 942   /*
 943    * (non-Javadoc)
 944    *
 945    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 946    */
 947   @Override
 948   public void setProgressBar(String message, long id)
 949   {
 950     progressBar.setProgressBar(message, id);
 951   }
 952
 953   @Override
 954   public void registerHandler(final long id,
 955           final IProgressIndicatorHandler handler)
 956   {
 957     progressBar.registerHandler(id, handler);
 958   }
 959
 960   /**
 961    *
 962    * @return true if any progress bars are still active
 963    */
 964   @Override
 965   public boolean operationInProgress()
 966   {
 967     return progressBar.operationInProgress();
 968   }
 969
 970   @Override
 971   public void setStatus(String text)
 972   {
 973     statusBar.setText(text);
 974   }
 975
 976   /*
 977    * Added so Castor Mapping file can obtain Jalview Version
 978    */
 979   public String getVersion()
 980   {
 981     return jalview.bin.Cache.getProperty("VERSION");
 982   }
 983
 984   public FeatureRenderer getFeatureRenderer()
 985   {
 986     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 987   }
 988
 989   @Override
 990   public void fetchSequence_actionPerformed(ActionEvent e)
 991   {
 992     new jalview.gui.SequenceFetcher(this);
 993   }
 994
 995   @Override
 996   public void addFromFile_actionPerformed(ActionEvent e)
 997   {
 998     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 999   }
1000
1001   @Override
1002   public void reload_actionPerformed(ActionEvent e)
1003   {
1004     if (fileName != null)
1005     {
1006       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1007       // originating file's format
1008       // TODO: work out how to recover feature settings for correct view(s) when
1009       // file is reloaded.
1010       if (currentFileFormat.equals("Jalview"))
1011       {
1012         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1013         for (int i = 0; i < frames.length; i++)
1014         {
1015           if (frames[i] instanceof AlignFrame && frames[i] != this
1016                   && ((AlignFrame) frames[i]).fileName != null
1017                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1018           {
1019             try
1020             {
1021               frames[i].setSelected(true);
1022               Desktop.instance.closeAssociatedWindows();
1023             } catch (java.beans.PropertyVetoException ex)
1024             {
1025             }
1026           }
1027
1028         }
1029         Desktop.instance.closeAssociatedWindows();
1030
1031         FileLoader loader = new FileLoader();
1032         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1033         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1034       }
1035       else
1036       {
1037         Rectangle bounds = this.getBounds();
1038
1039         FileLoader loader = new FileLoader();
1040         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1041         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1042                 protocol, currentFileFormat);
1043
1044         newframe.setBounds(bounds);
1045         if (featureSettings != null && featureSettings.isShowing())
1046         {
1047           final Rectangle fspos = featureSettings.frame.getBounds();
1048           // TODO: need a 'show feature settings' function that takes bounds -
1049           // need to refactor Desktop.addFrame
1050           newframe.featureSettings_actionPerformed(null);
1051           final FeatureSettings nfs = newframe.featureSettings;
1052           SwingUtilities.invokeLater(new Runnable()
1053           {
1054             @Override
1055             public void run()
1056             {
1057               nfs.frame.setBounds(fspos);
1058             }
1059           });
1060           this.featureSettings.close();
1061           this.featureSettings = null;
1062         }
1063         this.closeMenuItem_actionPerformed(true);
1064       }
1065     }
1066   }
1067
1068   @Override
1069   public void addFromText_actionPerformed(ActionEvent e)
1070   {
1071     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1072             .getAlignPanel());
1073   }
1074
1075   @Override
1076   public void addFromURL_actionPerformed(ActionEvent e)
1077   {
1078     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1079   }
1080
1081   @Override
1082   public void save_actionPerformed(ActionEvent e)
1083   {
1084     if (fileName == null
1085             || (currentFileFormat == null || !jalview.io.FormatAdapter
1086                     .isValidIOFormat(currentFileFormat, true))
1087             || fileName.startsWith("http"))
1088     {
1089       saveAs_actionPerformed(null);
1090     }
1091     else
1092     {
1093       saveAlignment(fileName, currentFileFormat);
1094     }
1095   }
1096
1097   /**
1098    * DOCUMENT ME!
1099    *
1100    * @param e
1101    *          DOCUMENT ME!
1102    */
1103   @Override
1104   public void saveAs_actionPerformed(ActionEvent e)
1105   {
1106     JalviewFileChooser chooser = new JalviewFileChooser(
1107             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1108             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1109             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1110             currentFileFormat, false);
1111
1112     chooser.setFileView(new JalviewFileView());
1113     chooser.setDialogTitle(MessageManager
1114             .getString("label.save_alignment_to_file"));
1115     chooser.setToolTipText(MessageManager.getString("action.save"));
1116
1117     int value = chooser.showSaveDialog(this);
1118
1119     if (value == JalviewFileChooser.APPROVE_OPTION)
1120     {
1121       currentFileFormat = chooser.getSelectedFormat();
1122       while (currentFileFormat == null)
1123       {
1124         JOptionPane
1125                 .showInternalMessageDialog(
1126                         Desktop.desktop,
1127                         MessageManager
1128                                 .getString("label.select_file_format_before_saving"),
1129                         MessageManager
1130                                 .getString("label.file_format_not_specified"),
1131                         JOptionPane.WARNING_MESSAGE);
1132         currentFileFormat = chooser.getSelectedFormat();
1133         value = chooser.showSaveDialog(this);
1134         if (value != JalviewFileChooser.APPROVE_OPTION)
1135         {
1136           return;
1137         }
1138       }
1139
1140       fileName = chooser.getSelectedFile().getPath();
1141
1142       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1143               currentFileFormat);
1144
1145       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1146       if (currentFileFormat.indexOf(" ") > -1)
1147       {
1148         currentFileFormat = currentFileFormat.substring(0,
1149                 currentFileFormat.indexOf(" "));
1150       }
1151       saveAlignment(fileName, currentFileFormat);
1152     }
1153   }
1154
1155   public boolean saveAlignment(String file, String format)
1156   {
1157     boolean success = true;
1158
1159     if (format.equalsIgnoreCase("Jalview"))
1160     {
1161       String shortName = title;
1162
1163       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1164       {
1165         shortName = shortName.substring(shortName
1166                 .lastIndexOf(java.io.File.separatorChar) + 1);
1167       }
1168
1169       success = new Jalview2XML().saveAlignment(this, file, shortName);
1170
1171       statusBar.setText(MessageManager.formatMessage(
1172               "label.successfully_saved_to_file_in_format", new Object[] {
1173                   fileName, format }));
1174
1175     }
1176     else
1177     {
1178       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1179       {
1180         warningMessage("Cannot save file " + fileName + " using format "
1181                 + format, "Alignment output format not supported");
1182         if (!Jalview.isHeadlessMode())
1183         {
1184           saveAs_actionPerformed(null);
1185         }
1186         return false;
1187       }
1188
1189       AlignmentExportData exportData = getAlignmentForExport(format,
1190               viewport, null);
1191       if (exportData.getSettings().isCancelled())
1192       {
1193         return false;
1194       }
1195       FormatAdapter f = new FormatAdapter(alignPanel,
1196               exportData.getSettings());
1197       String output = f.formatSequences(
1198               format,
1199               exportData.getAlignment(), // class cast exceptions will
1200               // occur in the distant future
1201               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1202               f.getCacheSuffixDefault(format),
1203               viewport.getColumnSelection());
1204
1205       if (output == null)
1206       {
1207         success = false;
1208       }
1209       else
1210       {
1211         try
1212         {
1213           java.io.PrintWriter out = new java.io.PrintWriter(
1214                   new java.io.FileWriter(file));
1215
1216           out.print(output);
1217           out.close();
1218           this.setTitle(file);
1219           statusBar.setText(MessageManager.formatMessage(
1220                   "label.successfully_saved_to_file_in_format",
1221                   new Object[] { fileName, format }));
1222         } catch (Exception ex)
1223         {
1224           success = false;
1225           ex.printStackTrace();
1226         }
1227       }
1228     }
1229
1230     if (!success)
1231     {
1232       JOptionPane.showInternalMessageDialog(this, MessageManager
1233               .formatMessage("label.couldnt_save_file",
1234                       new Object[] { fileName }), MessageManager
1235               .getString("label.error_saving_file"),
1236               JOptionPane.WARNING_MESSAGE);
1237     }
1238
1239     return success;
1240   }
1241
1242   private void warningMessage(String warning, String title)
1243   {
1244     if (new jalview.util.Platform().isHeadless())
1245     {
1246       System.err.println("Warning: " + title + "\nWarning: " + warning);
1247
1248     }
1249     else
1250     {
1251       JOptionPane.showInternalMessageDialog(this, warning, title,
1252               JOptionPane.WARNING_MESSAGE);
1253     }
1254     return;
1255   }
1256
1257   /**
1258    * DOCUMENT ME!
1259    *
1260    * @param e
1261    *          DOCUMENT ME!
1262    */
1263   @Override
1264   protected void outputText_actionPerformed(ActionEvent e)
1265   {
1266
1267     AlignmentExportData exportData = getAlignmentForExport(
1268             e.getActionCommand(), viewport, null);
1269     if (exportData.getSettings().isCancelled())
1270     {
1271       return;
1272     }
1273     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1274     cap.setForInput(null);
1275     try
1276     {
1277       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1278               .formatSequences(e.getActionCommand(),
1279                       exportData.getAlignment(),
1280                       exportData.getOmitHidden(),
1281                       exportData.getStartEndPostions(),
1282                       viewport.getColumnSelection()));
1283       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1284               "label.alignment_output_command",
1285               new Object[] { e.getActionCommand() }), 600, 500);
1286     } catch (OutOfMemoryError oom)
1287     {
1288       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1289       cap.dispose();
1290     }
1291
1292   }
1293
1294   public static AlignmentExportData getAlignmentForExport(
1295           String exportFormat, AlignViewportI viewport,
1296           AlignExportSettingI exportSettings)
1297   {
1298     AlignmentI alignmentToExport = null;
1299     AlignExportSettingI settings = exportSettings;
1300     String[] omitHidden = null;
1301
1302     HiddenSequences hiddenSeqs = viewport.getAlignment()
1303             .getHiddenSequences();
1304
1305     alignmentToExport = viewport.getAlignment();
1306
1307     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1308     if (settings == null)
1309     {
1310       settings = new AlignExportSettings(hasHiddenSeqs,
1311               viewport.hasHiddenColumns(), exportFormat);
1312     }
1313     // settings.isExportAnnotations();
1314
1315     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1316     {
1317       omitHidden = viewport.getViewAsString(false,
1318               settings.isExportHiddenSequences());
1319     }
1320
1321     int[] alignmentStartEnd = new int[2];
1322     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1323     {
1324       alignmentToExport = hiddenSeqs.getFullAlignment();
1325     }
1326     else
1327     {
1328       alignmentToExport = viewport.getAlignment();
1329     }
1330     alignmentStartEnd = alignmentToExport
1331             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1332                     .getHiddenColumns());
1333     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1334             omitHidden, alignmentStartEnd, settings);
1335     return ed;
1336   }
1337
1338   /**
1339    * DOCUMENT ME!
1340    *
1341    * @param e
1342    *          DOCUMENT ME!
1343    */
1344   @Override
1345   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1346   {
1347     new HtmlSvgOutput(null, alignPanel);
1348   }
1349
1350   @Override
1351   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1352   {
1353     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1354     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1355   }
1356
1357   public void createImageMap(File file, String image)
1358   {
1359     alignPanel.makePNGImageMap(file, image);
1360   }
1361
1362   /**
1363    * DOCUMENT ME!
1364    *
1365    * @param e
1366    *          DOCUMENT ME!
1367    */
1368   @Override
1369   public void createPNG(File f)
1370   {
1371     alignPanel.makePNG(f);
1372   }
1373
1374   /**
1375    * DOCUMENT ME!
1376    *
1377    * @param e
1378    *          DOCUMENT ME!
1379    */
1380   @Override
1381   public void createEPS(File f)
1382   {
1383     alignPanel.makeEPS(f);
1384   }
1385
1386   @Override
1387   public void createSVG(File f)
1388   {
1389     alignPanel.makeSVG(f);
1390   }
1391
1392   @Override
1393   public void pageSetup_actionPerformed(ActionEvent e)
1394   {
1395     PrinterJob printJob = PrinterJob.getPrinterJob();
1396     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1397   }
1398
1399   /**
1400    * DOCUMENT ME!
1401    *
1402    * @param e
1403    *          DOCUMENT ME!
1404    */
1405   @Override
1406   public void printMenuItem_actionPerformed(ActionEvent e)
1407   {
1408     // Putting in a thread avoids Swing painting problems
1409     PrintThread thread = new PrintThread(alignPanel);
1410     thread.start();
1411   }
1412
1413   @Override
1414   public void exportFeatures_actionPerformed(ActionEvent e)
1415   {
1416     new AnnotationExporter().exportFeatures(alignPanel);
1417   }
1418
1419   @Override
1420   public void exportAnnotations_actionPerformed(ActionEvent e)
1421   {
1422     new AnnotationExporter().exportAnnotations(alignPanel);
1423   }
1424
1425   @Override
1426   public void associatedData_actionPerformed(ActionEvent e)
1427   {
1428     // Pick the tree file
1429     JalviewFileChooser chooser = new JalviewFileChooser(
1430             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1431     chooser.setFileView(new JalviewFileView());
1432     chooser.setDialogTitle(MessageManager
1433             .getString("label.load_jalview_annotations"));
1434     chooser.setToolTipText(MessageManager
1435             .getString("label.load_jalview_annotations"));
1436
1437     int value = chooser.showOpenDialog(null);
1438
1439     if (value == JalviewFileChooser.APPROVE_OPTION)
1440     {
1441       String choice = chooser.getSelectedFile().getPath();
1442       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1443       loadJalviewDataFile(choice, null, null, null);
1444     }
1445
1446   }
1447
1448   /**
1449    * Close the current view or all views in the alignment frame. If the frame
1450    * only contains one view then the alignment will be removed from memory.
1451    *
1452    * @param closeAllTabs
1453    */
1454   @Override
1455   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1456   {
1457     if (alignPanels != null && alignPanels.size() < 2)
1458     {
1459       closeAllTabs = true;
1460     }
1461
1462     try
1463     {
1464       if (alignPanels != null)
1465       {
1466         if (closeAllTabs)
1467         {
1468           if (this.isClosed())
1469           {
1470             // really close all the windows - otherwise wait till
1471             // setClosed(true) is called
1472             for (int i = 0; i < alignPanels.size(); i++)
1473             {
1474               AlignmentPanel ap = alignPanels.get(i);
1475               ap.closePanel();
1476             }
1477           }
1478         }
1479         else
1480         {
1481           closeView(alignPanel);
1482         }
1483       }
1484
1485       if (closeAllTabs)
1486       {
1487         /*
1488          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1489          * be called recursively, with the frame now in 'closed' state
1490          */
1491         this.setClosed(true);
1492       }
1493     } catch (Exception ex)
1494     {
1495       ex.printStackTrace();
1496     }
1497   }
1498
1499   /**
1500    * Close the specified panel and close up tabs appropriately.
1501    *
1502    * @param panelToClose
1503    */
1504   public void closeView(AlignmentPanel panelToClose)
1505   {
1506     int index = tabbedPane.getSelectedIndex();
1507     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1508     alignPanels.remove(panelToClose);
1509     panelToClose.closePanel();
1510     panelToClose = null;
1511
1512     tabbedPane.removeTabAt(closedindex);
1513     tabbedPane.validate();
1514
1515     if (index > closedindex || index == tabbedPane.getTabCount())
1516     {
1517       // modify currently selected tab index if necessary.
1518       index--;
1519     }
1520
1521     this.tabSelectionChanged(index);
1522   }
1523
1524   /**
1525    * DOCUMENT ME!
1526    */
1527   void updateEditMenuBar()
1528   {
1529
1530     if (viewport.getHistoryList().size() > 0)
1531     {
1532       undoMenuItem.setEnabled(true);
1533       CommandI command = viewport.getHistoryList().peek();
1534       undoMenuItem.setText(MessageManager.formatMessage(
1535               "label.undo_command",
1536               new Object[] { command.getDescription() }));
1537     }
1538     else
1539     {
1540       undoMenuItem.setEnabled(false);
1541       undoMenuItem.setText(MessageManager.getString("action.undo"));
1542     }
1543
1544     if (viewport.getRedoList().size() > 0)
1545     {
1546       redoMenuItem.setEnabled(true);
1547
1548       CommandI command = viewport.getRedoList().peek();
1549       redoMenuItem.setText(MessageManager.formatMessage(
1550               "label.redo_command",
1551               new Object[] { command.getDescription() }));
1552     }
1553     else
1554     {
1555       redoMenuItem.setEnabled(false);
1556       redoMenuItem.setText(MessageManager.getString("action.redo"));
1557     }
1558   }
1559
1560   @Override
1561   public void addHistoryItem(CommandI command)
1562   {
1563     if (command.getSize() > 0)
1564     {
1565       viewport.addToHistoryList(command);
1566       viewport.clearRedoList();
1567       updateEditMenuBar();
1568       viewport.updateHiddenColumns();
1569       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1570       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1571       // viewport.getColumnSelection()
1572       // .getHiddenColumns().size() > 0);
1573     }
1574   }
1575
1576   /**
1577    *
1578    * @return alignment objects for all views
1579    */
1580   AlignmentI[] getViewAlignments()
1581   {
1582     if (alignPanels != null)
1583     {
1584       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1585       int i = 0;
1586       for (AlignmentPanel ap : alignPanels)
1587       {
1588         als[i++] = ap.av.getAlignment();
1589       }
1590       return als;
1591     }
1592     if (viewport != null)
1593     {
1594       return new AlignmentI[] { viewport.getAlignment() };
1595     }
1596     return null;
1597   }
1598
1599   /**
1600    * DOCUMENT ME!
1601    *
1602    * @param e
1603    *          DOCUMENT ME!
1604    */
1605   @Override
1606   protected void undoMenuItem_actionPerformed(ActionEvent e)
1607   {
1608     if (viewport.getHistoryList().isEmpty())
1609     {
1610       return;
1611     }
1612     CommandI command = viewport.getHistoryList().pop();
1613     viewport.addToRedoList(command);
1614     command.undoCommand(getViewAlignments());
1615
1616     AlignmentViewport originalSource = getOriginatingSource(command);
1617     updateEditMenuBar();
1618
1619     if (originalSource != null)
1620     {
1621       if (originalSource != viewport)
1622       {
1623         Cache.log
1624                 .warn("Implementation worry: mismatch of viewport origin for undo");
1625       }
1626       originalSource.updateHiddenColumns();
1627       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1628       // null
1629       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1630       // viewport.getColumnSelection()
1631       // .getHiddenColumns().size() > 0);
1632       originalSource.firePropertyChange("alignment", null, originalSource
1633               .getAlignment().getSequences());
1634     }
1635   }
1636
1637   /**
1638    * DOCUMENT ME!
1639    *
1640    * @param e
1641    *          DOCUMENT ME!
1642    */
1643   @Override
1644   protected void redoMenuItem_actionPerformed(ActionEvent e)
1645   {
1646     if (viewport.getRedoList().size() < 1)
1647     {
1648       return;
1649     }
1650
1651     CommandI command = viewport.getRedoList().pop();
1652     viewport.addToHistoryList(command);
1653     command.doCommand(getViewAlignments());
1654
1655     AlignmentViewport originalSource = getOriginatingSource(command);
1656     updateEditMenuBar();
1657
1658     if (originalSource != null)
1659     {
1660
1661       if (originalSource != viewport)
1662       {
1663         Cache.log
1664                 .warn("Implementation worry: mismatch of viewport origin for redo");
1665       }
1666       originalSource.updateHiddenColumns();
1667       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1668       // null
1669       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1670       // viewport.getColumnSelection()
1671       // .getHiddenColumns().size() > 0);
1672       originalSource.firePropertyChange("alignment", null, originalSource
1673               .getAlignment().getSequences());
1674     }
1675   }
1676
1677   AlignmentViewport getOriginatingSource(CommandI command)
1678   {
1679     AlignmentViewport originalSource = null;
1680     // For sequence removal and addition, we need to fire
1681     // the property change event FROM the viewport where the
1682     // original alignment was altered
1683     AlignmentI al = null;
1684     if (command instanceof EditCommand)
1685     {
1686       EditCommand editCommand = (EditCommand) command;
1687       al = editCommand.getAlignment();
1688       List<Component> comps = PaintRefresher.components.get(viewport
1689               .getSequenceSetId());
1690
1691       for (Component comp : comps)
1692       {
1693         if (comp instanceof AlignmentPanel)
1694         {
1695           if (al == ((AlignmentPanel) comp).av.getAlignment())
1696           {
1697             originalSource = ((AlignmentPanel) comp).av;
1698             break;
1699           }
1700         }
1701       }
1702     }
1703
1704     if (originalSource == null)
1705     {
1706       // The original view is closed, we must validate
1707       // the current view against the closed view first
1708       if (al != null)
1709       {
1710         PaintRefresher.validateSequences(al, viewport.getAlignment());
1711       }
1712
1713       originalSource = viewport;
1714     }
1715
1716     return originalSource;
1717   }
1718
1719   /**
1720    * DOCUMENT ME!
1721    *
1722    * @param up
1723    *          DOCUMENT ME!
1724    */
1725   public void moveSelectedSequences(boolean up)
1726   {
1727     SequenceGroup sg = viewport.getSelectionGroup();
1728
1729     if (sg == null)
1730     {
1731       return;
1732     }
1733     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1734             viewport.getHiddenRepSequences(), up);
1735     alignPanel.paintAlignment(true);
1736   }
1737
1738   synchronized void slideSequences(boolean right, int size)
1739   {
1740     List<SequenceI> sg = new ArrayList<SequenceI>();
1741     if (viewport.cursorMode)
1742     {
1743       sg.add(viewport.getAlignment().getSequenceAt(
1744               alignPanel.getSeqPanel().seqCanvas.cursorY));
1745     }
1746     else if (viewport.getSelectionGroup() != null
1747             && viewport.getSelectionGroup().getSize() != viewport
1748                     .getAlignment().getHeight())
1749     {
1750       sg = viewport.getSelectionGroup().getSequences(
1751               viewport.getHiddenRepSequences());
1752     }
1753
1754     if (sg.size() < 1)
1755     {
1756       return;
1757     }
1758
1759     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1760
1761     for (SequenceI seq : viewport.getAlignment().getSequences())
1762     {
1763       if (!sg.contains(seq))
1764       {
1765         invertGroup.add(seq);
1766       }
1767     }
1768
1769     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1770
1771     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1772     for (int i = 0; i < invertGroup.size(); i++)
1773     {
1774       seqs2[i] = invertGroup.get(i);
1775     }
1776
1777     SlideSequencesCommand ssc;
1778     if (right)
1779     {
1780       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1781               size, viewport.getGapCharacter());
1782     }
1783     else
1784     {
1785       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1786               size, viewport.getGapCharacter());
1787     }
1788
1789     int groupAdjustment = 0;
1790     if (ssc.getGapsInsertedBegin() && right)
1791     {
1792       if (viewport.cursorMode)
1793       {
1794         alignPanel.getSeqPanel().moveCursor(size, 0);
1795       }
1796       else
1797       {
1798         groupAdjustment = size;
1799       }
1800     }
1801     else if (!ssc.getGapsInsertedBegin() && !right)
1802     {
1803       if (viewport.cursorMode)
1804       {
1805         alignPanel.getSeqPanel().moveCursor(-size, 0);
1806       }
1807       else
1808       {
1809         groupAdjustment = -size;
1810       }
1811     }
1812
1813     if (groupAdjustment != 0)
1814     {
1815       viewport.getSelectionGroup().setStartRes(
1816               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1817       viewport.getSelectionGroup().setEndRes(
1818               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1819     }
1820
1821     /*
1822      * just extend the last slide command if compatible; but not if in
1823      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1824      */
1825     boolean appendHistoryItem = false;
1826     Deque<CommandI> historyList = viewport.getHistoryList();
1827     boolean inSplitFrame = getSplitViewContainer() != null;
1828     if (!inSplitFrame && historyList != null && historyList.size() > 0
1829             && historyList.peek() instanceof SlideSequencesCommand)
1830     {
1831       appendHistoryItem = ssc
1832               .appendSlideCommand((SlideSequencesCommand) historyList
1833                       .peek());
1834     }
1835
1836     if (!appendHistoryItem)
1837     {
1838       addHistoryItem(ssc);
1839     }
1840
1841     repaint();
1842   }
1843
1844   /**
1845    * DOCUMENT ME!
1846    *
1847    * @param e
1848    *          DOCUMENT ME!
1849    */
1850   @Override
1851   protected void copy_actionPerformed(ActionEvent e)
1852   {
1853     System.gc();
1854     if (viewport.getSelectionGroup() == null)
1855     {
1856       return;
1857     }
1858     // TODO: preserve the ordering of displayed alignment annotation in any
1859     // internal paste (particularly sequence associated annotation)
1860     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1861     String[] omitHidden = null;
1862
1863     if (viewport.hasHiddenColumns())
1864     {
1865       omitHidden = viewport.getViewAsString(true);
1866     }
1867
1868     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1869             omitHidden, null);
1870
1871     StringSelection ss = new StringSelection(output);
1872
1873     try
1874     {
1875       jalview.gui.Desktop.internalCopy = true;
1876       // Its really worth setting the clipboard contents
1877       // to empty before setting the large StringSelection!!
1878       Toolkit.getDefaultToolkit().getSystemClipboard()
1879               .setContents(new StringSelection(""), null);
1880
1881       Toolkit.getDefaultToolkit().getSystemClipboard()
1882               .setContents(ss, Desktop.instance);
1883     } catch (OutOfMemoryError er)
1884     {
1885       new OOMWarning("copying region", er);
1886       return;
1887     }
1888
1889     ArrayList<int[]> hiddenColumns = null;
1890     if (viewport.hasHiddenColumns())
1891     {
1892       hiddenColumns = new ArrayList<int[]>();
1893       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1894               .getSelectionGroup().getEndRes();
1895       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1896       {
1897         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1898         {
1899           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1900               region[1] - hiddenOffset });
1901         }
1902       }
1903     }
1904
1905     Desktop.jalviewClipboard = new Object[] { seqs,
1906         viewport.getAlignment().getDataset(), hiddenColumns };
1907     statusBar.setText(MessageManager.formatMessage(
1908             "label.copied_sequences_to_clipboard", new Object[] { Integer
1909                     .valueOf(seqs.length).toString() }));
1910   }
1911
1912   /**
1913    * DOCUMENT ME!
1914    *
1915    * @param e
1916    *          DOCUMENT ME!
1917    */
1918   @Override
1919   protected void pasteNew_actionPerformed(ActionEvent e)
1920   {
1921     paste(true);
1922   }
1923
1924   /**
1925    * DOCUMENT ME!
1926    *
1927    * @param e
1928    *          DOCUMENT ME!
1929    */
1930   @Override
1931   protected void pasteThis_actionPerformed(ActionEvent e)
1932   {
1933     paste(false);
1934   }
1935
1936   /**
1937    * Paste contents of Jalview clipboard
1938    *
1939    * @param newAlignment
1940    *          true to paste to a new alignment, otherwise add to this.
1941    */
1942   void paste(boolean newAlignment)
1943   {
1944     boolean externalPaste = true;
1945     try
1946     {
1947       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1948       Transferable contents = c.getContents(this);
1949
1950       if (contents == null)
1951       {
1952         return;
1953       }
1954
1955       String str, format;
1956       try
1957       {
1958         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1959         if (str.length() < 1)
1960         {
1961           return;
1962         }
1963
1964         format = new IdentifyFile().identify(str, "Paste");
1965
1966       } catch (OutOfMemoryError er)
1967       {
1968         new OOMWarning("Out of memory pasting sequences!!", er);
1969         return;
1970       }
1971
1972       SequenceI[] sequences;
1973       boolean annotationAdded = false;
1974       AlignmentI alignment = null;
1975
1976       if (Desktop.jalviewClipboard != null)
1977       {
1978         // The clipboard was filled from within Jalview, we must use the
1979         // sequences
1980         // And dataset from the copied alignment
1981         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1982         // be doubly sure that we create *new* sequence objects.
1983         sequences = new SequenceI[newseq.length];
1984         for (int i = 0; i < newseq.length; i++)
1985         {
1986           sequences[i] = new Sequence(newseq[i]);
1987         }
1988         alignment = new Alignment(sequences);
1989         externalPaste = false;
1990       }
1991       else
1992       {
1993         // parse the clipboard as an alignment.
1994         alignment = new FormatAdapter().readFile(str, "Paste", format);
1995         sequences = alignment.getSequencesArray();
1996       }
1997
1998       int alwidth = 0;
1999       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2000       int fgroup = -1;
2001
2002       if (newAlignment)
2003       {
2004
2005         if (Desktop.jalviewClipboard != null)
2006         {
2007           // dataset is inherited
2008           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2009         }
2010         else
2011         {
2012           // new dataset is constructed
2013           alignment.setDataset(null);
2014         }
2015         alwidth = alignment.getWidth() + 1;
2016       }
2017       else
2018       {
2019         AlignmentI pastedal = alignment; // preserve pasted alignment object
2020         // Add pasted sequences and dataset into existing alignment.
2021         alignment = viewport.getAlignment();
2022         alwidth = alignment.getWidth() + 1;
2023         // decide if we need to import sequences from an existing dataset
2024         boolean importDs = Desktop.jalviewClipboard != null
2025                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2026         // importDs==true instructs us to copy over new dataset sequences from
2027         // an existing alignment
2028         Vector newDs = (importDs) ? new Vector() : null; // used to create
2029         // minimum dataset set
2030
2031         for (int i = 0; i < sequences.length; i++)
2032         {
2033           if (importDs)
2034           {
2035             newDs.addElement(null);
2036           }
2037           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2038           // paste
2039           if (importDs && ds != null)
2040           {
2041             if (!newDs.contains(ds))
2042             {
2043               newDs.setElementAt(ds, i);
2044               ds = new Sequence(ds);
2045               // update with new dataset sequence
2046               sequences[i].setDatasetSequence(ds);
2047             }
2048             else
2049             {
2050               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2051             }
2052           }
2053           else
2054           {
2055             // copy and derive new dataset sequence
2056             sequences[i] = sequences[i].deriveSequence();
2057             alignment.getDataset().addSequence(
2058                     sequences[i].getDatasetSequence());
2059             // TODO: avoid creation of duplicate dataset sequences with a
2060             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2061           }
2062           alignment.addSequence(sequences[i]); // merges dataset
2063         }
2064         if (newDs != null)
2065         {
2066           newDs.clear(); // tidy up
2067         }
2068         if (alignment.getAlignmentAnnotation() != null)
2069         {
2070           for (AlignmentAnnotation alan : alignment
2071                   .getAlignmentAnnotation())
2072           {
2073             if (alan.graphGroup > fgroup)
2074             {
2075               fgroup = alan.graphGroup;
2076             }
2077           }
2078         }
2079         if (pastedal.getAlignmentAnnotation() != null)
2080         {
2081           // Add any annotation attached to alignment.
2082           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2083           for (int i = 0; i < alann.length; i++)
2084           {
2085             annotationAdded = true;
2086             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2087             {
2088               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2089               if (newann.graphGroup > -1)
2090               {
2091                 if (newGraphGroups.size() <= newann.graphGroup
2092                         || newGraphGroups.get(newann.graphGroup) == null)
2093                 {
2094                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2095                   {
2096                     newGraphGroups.add(q, null);
2097                   }
2098                   newGraphGroups.set(newann.graphGroup, new Integer(
2099                           ++fgroup));
2100                 }
2101                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2102                         .intValue();
2103               }
2104
2105               newann.padAnnotation(alwidth);
2106               alignment.addAnnotation(newann);
2107             }
2108           }
2109         }
2110       }
2111       if (!newAlignment)
2112       {
2113         // /////
2114         // ADD HISTORY ITEM
2115         //
2116         addHistoryItem(new EditCommand(
2117                 MessageManager.getString("label.add_sequences"),
2118                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2119       }
2120       // Add any annotations attached to sequences
2121       for (int i = 0; i < sequences.length; i++)
2122       {
2123         if (sequences[i].getAnnotation() != null)
2124         {
2125           AlignmentAnnotation newann;
2126           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2127           {
2128             annotationAdded = true;
2129             newann = sequences[i].getAnnotation()[a];
2130             newann.adjustForAlignment();
2131             newann.padAnnotation(alwidth);
2132             if (newann.graphGroup > -1)
2133             {
2134               if (newann.graphGroup > -1)
2135               {
2136                 if (newGraphGroups.size() <= newann.graphGroup
2137                         || newGraphGroups.get(newann.graphGroup) == null)
2138                 {
2139                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2140                   {
2141                     newGraphGroups.add(q, null);
2142                   }
2143                   newGraphGroups.set(newann.graphGroup, new Integer(
2144                           ++fgroup));
2145                 }
2146                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2147                         .intValue();
2148               }
2149             }
2150             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2151             // was
2152             // duplicated
2153             // earlier
2154             alignment
2155                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2156           }
2157         }
2158       }
2159       if (!newAlignment)
2160       {
2161
2162         // propagate alignment changed.
2163         viewport.setEndSeq(alignment.getHeight());
2164         if (annotationAdded)
2165         {
2166           // Duplicate sequence annotation in all views.
2167           AlignmentI[] alview = this.getViewAlignments();
2168           for (int i = 0; i < sequences.length; i++)
2169           {
2170             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2171             if (sann == null)
2172             {
2173               continue;
2174             }
2175             for (int avnum = 0; avnum < alview.length; avnum++)
2176             {
2177               if (alview[avnum] != alignment)
2178               {
2179                 // duplicate in a view other than the one with input focus
2180                 int avwidth = alview[avnum].getWidth() + 1;
2181                 // this relies on sann being preserved after we
2182                 // modify the sequence's annotation array for each duplication
2183                 for (int a = 0; a < sann.length; a++)
2184                 {
2185                   AlignmentAnnotation newann = new AlignmentAnnotation(
2186                           sann[a]);
2187                   sequences[i].addAlignmentAnnotation(newann);
2188                   newann.padAnnotation(avwidth);
2189                   alview[avnum].addAnnotation(newann); // annotation was
2190                   // duplicated earlier
2191                   // TODO JAL-1145 graphGroups are not updated for sequence
2192                   // annotation added to several views. This may cause
2193                   // strangeness
2194                   alview[avnum].setAnnotationIndex(newann, a);
2195                 }
2196               }
2197             }
2198           }
2199           buildSortByAnnotationScoresMenu();
2200         }
2201         viewport.firePropertyChange("alignment", null,
2202                 alignment.getSequences());
2203         if (alignPanels != null)
2204         {
2205           for (AlignmentPanel ap : alignPanels)
2206           {
2207             ap.validateAnnotationDimensions(false);
2208           }
2209         }
2210         else
2211         {
2212           alignPanel.validateAnnotationDimensions(false);
2213         }
2214
2215       }
2216       else
2217       {
2218         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2219                 DEFAULT_HEIGHT);
2220         String newtitle = new String("Copied sequences");
2221
2222         if (Desktop.jalviewClipboard != null
2223                 && Desktop.jalviewClipboard[2] != null)
2224         {
2225           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2226           for (int[] region : hc)
2227           {
2228             af.viewport.hideColumns(region[0], region[1]);
2229           }
2230         }
2231
2232         // >>>This is a fix for the moment, until a better solution is
2233         // found!!<<<
2234         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2235                 .transferSettings(
2236                         alignPanel.getSeqPanel().seqCanvas
2237                                 .getFeatureRenderer());
2238
2239         // TODO: maintain provenance of an alignment, rather than just make the
2240         // title a concatenation of operations.
2241         if (!externalPaste)
2242         {
2243           if (title.startsWith("Copied sequences"))
2244           {
2245             newtitle = title;
2246           }
2247           else
2248           {
2249             newtitle = newtitle.concat("- from " + title);
2250           }
2251         }
2252         else
2253         {
2254           newtitle = new String("Pasted sequences");
2255         }
2256
2257         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2258                 DEFAULT_HEIGHT);
2259
2260       }
2261
2262     } catch (Exception ex)
2263     {
2264       ex.printStackTrace();
2265       System.out.println("Exception whilst pasting: " + ex);
2266       // could be anything being pasted in here
2267     }
2268
2269   }
2270
2271   @Override
2272   protected void expand_newalign(ActionEvent e)
2273   {
2274     try
2275     {
2276       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2277               .getAlignment(), -1);
2278       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2279               DEFAULT_HEIGHT);
2280       String newtitle = new String("Flanking alignment");
2281
2282       if (Desktop.jalviewClipboard != null
2283               && Desktop.jalviewClipboard[2] != null)
2284       {
2285         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2286         for (int region[] : hc)
2287         {
2288           af.viewport.hideColumns(region[0], region[1]);
2289         }
2290       }
2291
2292       // >>>This is a fix for the moment, until a better solution is
2293       // found!!<<<
2294       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2295               .transferSettings(
2296                       alignPanel.getSeqPanel().seqCanvas
2297                               .getFeatureRenderer());
2298
2299       // TODO: maintain provenance of an alignment, rather than just make the
2300       // title a concatenation of operations.
2301       {
2302         if (title.startsWith("Copied sequences"))
2303         {
2304           newtitle = title;
2305         }
2306         else
2307         {
2308           newtitle = newtitle.concat("- from " + title);
2309         }
2310       }
2311
2312       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2313
2314     } catch (Exception ex)
2315     {
2316       ex.printStackTrace();
2317       System.out.println("Exception whilst pasting: " + ex);
2318       // could be anything being pasted in here
2319     } catch (OutOfMemoryError oom)
2320     {
2321       new OOMWarning("Viewing flanking region of alignment", oom);
2322     }
2323   }
2324
2325   /**
2326    * DOCUMENT ME!
2327    *
2328    * @param e
2329    *          DOCUMENT ME!
2330    */
2331   @Override
2332   protected void cut_actionPerformed(ActionEvent e)
2333   {
2334     copy_actionPerformed(null);
2335     delete_actionPerformed(null);
2336   }
2337
2338   /**
2339    * DOCUMENT ME!
2340    *
2341    * @param e
2342    *          DOCUMENT ME!
2343    */
2344   @Override
2345   protected void delete_actionPerformed(ActionEvent evt)
2346   {
2347
2348     SequenceGroup sg = viewport.getSelectionGroup();
2349     if (sg == null)
2350     {
2351       return;
2352     }
2353
2354     /*
2355      * If the cut affects all sequences, warn, remove highlighted columns
2356      */
2357     if (sg.getSize() == viewport.getAlignment().getHeight())
2358     {
2359       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2360               .getAlignment().getWidth()) ? true : false;
2361       if (isEntireAlignWidth)
2362       {
2363         int confirm = JOptionPane.showConfirmDialog(this,
2364                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2365                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2366                 JOptionPane.OK_CANCEL_OPTION);
2367
2368         if (confirm == JOptionPane.CANCEL_OPTION
2369                 || confirm == JOptionPane.CLOSED_OPTION)
2370         {
2371           return;
2372         }
2373       }
2374       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2375               sg.getEndRes() + 1);
2376     }
2377     SequenceI[] cut = sg.getSequences()
2378             .toArray(new SequenceI[sg.getSize()]);
2379
2380     addHistoryItem(new EditCommand(
2381             MessageManager.getString("label.cut_sequences"), Action.CUT,
2382             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2383             viewport.getAlignment()));
2384
2385     viewport.setSelectionGroup(null);
2386     viewport.sendSelection();
2387     viewport.getAlignment().deleteGroup(sg);
2388
2389     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2390             .getSequences());
2391     if (viewport.getAlignment().getHeight() < 1)
2392     {
2393       try
2394       {
2395         this.setClosed(true);
2396       } catch (Exception ex)
2397       {
2398       }
2399     }
2400   }
2401
2402   /**
2403    * DOCUMENT ME!
2404    *
2405    * @param e
2406    *          DOCUMENT ME!
2407    */
2408   @Override
2409   protected void deleteGroups_actionPerformed(ActionEvent e)
2410   {
2411     if (avc.deleteGroups())
2412     {
2413       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2414       alignPanel.updateAnnotation();
2415       alignPanel.paintAlignment(true);
2416     }
2417   }
2418
2419   /**
2420    * DOCUMENT ME!
2421    *
2422    * @param e
2423    *          DOCUMENT ME!
2424    */
2425   @Override
2426   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2427   {
2428     SequenceGroup sg = new SequenceGroup();
2429
2430     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2431     {
2432       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2433     }
2434
2435     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2436     viewport.setSelectionGroup(sg);
2437     viewport.sendSelection();
2438     // JAL-2034 - should delegate to
2439     // alignPanel to decide if overview needs
2440     // updating.
2441     alignPanel.paintAlignment(false);
2442     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2443   }
2444
2445   /**
2446    * DOCUMENT ME!
2447    *
2448    * @param e
2449    *          DOCUMENT ME!
2450    */
2451   @Override
2452   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2453   {
2454     if (viewport.cursorMode)
2455     {
2456       alignPanel.getSeqPanel().keyboardNo1 = null;
2457       alignPanel.getSeqPanel().keyboardNo2 = null;
2458     }
2459     viewport.setSelectionGroup(null);
2460     viewport.getColumnSelection().clear();
2461     viewport.setSelectionGroup(null);
2462     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2463     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2464     // JAL-2034 - should delegate to
2465     // alignPanel to decide if overview needs
2466     // updating.
2467     alignPanel.paintAlignment(false);
2468     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2469     viewport.sendSelection();
2470   }
2471
2472   /**
2473    * DOCUMENT ME!
2474    *
2475    * @param e
2476    *          DOCUMENT ME!
2477    */
2478   @Override
2479   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2480   {
2481     SequenceGroup sg = viewport.getSelectionGroup();
2482
2483     if (sg == null)
2484     {
2485       selectAllSequenceMenuItem_actionPerformed(null);
2486
2487       return;
2488     }
2489
2490     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2491     {
2492       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2493     }
2494     // JAL-2034 - should delegate to
2495     // alignPanel to decide if overview needs
2496     // updating.
2497
2498     alignPanel.paintAlignment(true);
2499     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2500     viewport.sendSelection();
2501   }
2502
2503   @Override
2504   public void invertColSel_actionPerformed(ActionEvent e)
2505   {
2506     viewport.invertColumnSelection();
2507     alignPanel.paintAlignment(true);
2508     viewport.sendSelection();
2509   }
2510
2511   /**
2512    * DOCUMENT ME!
2513    *
2514    * @param e
2515    *          DOCUMENT ME!
2516    */
2517   @Override
2518   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2519   {
2520     trimAlignment(true);
2521   }
2522
2523   /**
2524    * DOCUMENT ME!
2525    *
2526    * @param e
2527    *          DOCUMENT ME!
2528    */
2529   @Override
2530   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2531   {
2532     trimAlignment(false);
2533   }
2534
2535   void trimAlignment(boolean trimLeft)
2536   {
2537     ColumnSelection colSel = viewport.getColumnSelection();
2538     int column;
2539
2540     if (!colSel.isEmpty())
2541     {
2542       if (trimLeft)
2543       {
2544         column = colSel.getMin();
2545       }
2546       else
2547       {
2548         column = colSel.getMax();
2549       }
2550
2551       SequenceI[] seqs;
2552       if (viewport.getSelectionGroup() != null)
2553       {
2554         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2555                 viewport.getHiddenRepSequences());
2556       }
2557       else
2558       {
2559         seqs = viewport.getAlignment().getSequencesArray();
2560       }
2561
2562       TrimRegionCommand trimRegion;
2563       if (trimLeft)
2564       {
2565         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2566                 column, viewport.getAlignment());
2567         viewport.setStartRes(0);
2568       }
2569       else
2570       {
2571         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2572                 column, viewport.getAlignment());
2573       }
2574
2575       statusBar.setText(MessageManager.formatMessage(
2576               "label.removed_columns",
2577               new String[] { Integer.valueOf(trimRegion.getSize())
2578                       .toString() }));
2579
2580       addHistoryItem(trimRegion);
2581
2582       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2583       {
2584         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2585                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2586         {
2587           viewport.getAlignment().deleteGroup(sg);
2588         }
2589       }
2590
2591       viewport.firePropertyChange("alignment", null, viewport
2592               .getAlignment().getSequences());
2593     }
2594   }
2595
2596   /**
2597    * DOCUMENT ME!
2598    *
2599    * @param e
2600    *          DOCUMENT ME!
2601    */
2602   @Override
2603   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2604   {
2605     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2606
2607     SequenceI[] seqs;
2608     if (viewport.getSelectionGroup() != null)
2609     {
2610       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2611               viewport.getHiddenRepSequences());
2612       start = viewport.getSelectionGroup().getStartRes();
2613       end = viewport.getSelectionGroup().getEndRes();
2614     }
2615     else
2616     {
2617       seqs = viewport.getAlignment().getSequencesArray();
2618     }
2619
2620     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2621             "Remove Gapped Columns", seqs, start, end,
2622             viewport.getAlignment());
2623
2624     addHistoryItem(removeGapCols);
2625
2626     statusBar.setText(MessageManager.formatMessage(
2627             "label.removed_empty_columns",
2628             new Object[] { Integer.valueOf(removeGapCols.getSize())
2629                     .toString() }));
2630
2631     // This is to maintain viewport position on first residue
2632     // of first sequence
2633     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2634     int startRes = seq.findPosition(viewport.startRes);
2635     // ShiftList shifts;
2636     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2637     // edit.alColumnChanges=shifts.getInverse();
2638     // if (viewport.hasHiddenColumns)
2639     // viewport.getColumnSelection().compensateForEdits(shifts);
2640     viewport.setStartRes(seq.findIndex(startRes) - 1);
2641     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2642             .getSequences());
2643
2644   }
2645
2646   /**
2647    * DOCUMENT ME!
2648    *
2649    * @param e
2650    *          DOCUMENT ME!
2651    */
2652   @Override
2653   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2654   {
2655     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2656
2657     SequenceI[] seqs;
2658     if (viewport.getSelectionGroup() != null)
2659     {
2660       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2661               viewport.getHiddenRepSequences());
2662       start = viewport.getSelectionGroup().getStartRes();
2663       end = viewport.getSelectionGroup().getEndRes();
2664     }
2665     else
2666     {
2667       seqs = viewport.getAlignment().getSequencesArray();
2668     }
2669
2670     // This is to maintain viewport position on first residue
2671     // of first sequence
2672     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2673     int startRes = seq.findPosition(viewport.startRes);
2674
2675     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2676             viewport.getAlignment()));
2677
2678     viewport.setStartRes(seq.findIndex(startRes) - 1);
2679
2680     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2681             .getSequences());
2682
2683   }
2684
2685   /**
2686    * DOCUMENT ME!
2687    *
2688    * @param e
2689    *          DOCUMENT ME!
2690    */
2691   @Override
2692   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2693   {
2694     viewport.setPadGaps(padGapsMenuitem.isSelected());
2695     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2696             .getSequences());
2697   }
2698
2699   /**
2700    * DOCUMENT ME!
2701    *
2702    * @param e
2703    *          DOCUMENT ME!
2704    */
2705   @Override
2706   public void findMenuItem_actionPerformed(ActionEvent e)
2707   {
2708     new Finder();
2709   }
2710
2711   /**
2712    * Create a new view of the current alignment.
2713    */
2714   @Override
2715   public void newView_actionPerformed(ActionEvent e)
2716   {
2717     newView(null, true);
2718   }
2719
2720   /**
2721    * Creates and shows a new view of the current alignment.
2722    *
2723    * @param viewTitle
2724    *          title of newly created view; if null, one will be generated
2725    * @param copyAnnotation
2726    *          if true then duplicate all annnotation, groups and settings
2727    * @return new alignment panel, already displayed.
2728    */
2729   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2730   {
2731     /*
2732      * Create a new AlignmentPanel (with its own, new Viewport)
2733      */
2734     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2735             true);
2736     if (!copyAnnotation)
2737     {
2738       /*
2739        * remove all groups and annotation except for the automatic stuff
2740        */
2741       newap.av.getAlignment().deleteAllGroups();
2742       newap.av.getAlignment().deleteAllAnnotations(false);
2743     }
2744
2745     newap.av.setGatherViewsHere(false);
2746
2747     if (viewport.viewName == null)
2748     {
2749       viewport.viewName = MessageManager
2750               .getString("label.view_name_original");
2751     }
2752
2753     /*
2754      * Views share the same edits undo and redo stacks
2755      */
2756     newap.av.setHistoryList(viewport.getHistoryList());
2757     newap.av.setRedoList(viewport.getRedoList());
2758
2759     /*
2760      * Views share the same mappings; need to deregister any new mappings
2761      * created by copyAlignPanel, and register the new reference to the shared
2762      * mappings
2763      */
2764     newap.av.replaceMappings(viewport.getAlignment());
2765
2766     newap.av.viewName = getNewViewName(viewTitle);
2767
2768     addAlignmentPanel(newap, true);
2769     newap.alignmentChanged();
2770
2771     if (alignPanels.size() == 2)
2772     {
2773       viewport.setGatherViewsHere(true);
2774     }
2775     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2776     return newap;
2777   }
2778
2779   /**
2780    * Make a new name for the view, ensuring it is unique within the current
2781    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2782    * these now use viewId. Unique view names are still desirable for usability.)
2783    *
2784    * @param viewTitle
2785    * @return
2786    */
2787   protected String getNewViewName(String viewTitle)
2788   {
2789     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2790     boolean addFirstIndex = false;
2791     if (viewTitle == null || viewTitle.trim().length() == 0)
2792     {
2793       viewTitle = MessageManager.getString("action.view");
2794       addFirstIndex = true;
2795     }
2796     else
2797     {
2798       index = 1;// we count from 1 if given a specific name
2799     }
2800     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2801
2802     List<Component> comps = PaintRefresher.components.get(viewport
2803             .getSequenceSetId());
2804
2805     List<String> existingNames = getExistingViewNames(comps);
2806
2807     while (existingNames.contains(newViewName))
2808     {
2809       newViewName = viewTitle + " " + (++index);
2810     }
2811     return newViewName;
2812   }
2813
2814   /**
2815    * Returns a list of distinct view names found in the given list of
2816    * components. View names are held on the viewport of an AlignmentPanel.
2817    *
2818    * @param comps
2819    * @return
2820    */
2821   protected List<String> getExistingViewNames(List<Component> comps)
2822   {
2823     List<String> existingNames = new ArrayList<String>();
2824     for (Component comp : comps)
2825     {
2826       if (comp instanceof AlignmentPanel)
2827       {
2828         AlignmentPanel ap = (AlignmentPanel) comp;
2829         if (!existingNames.contains(ap.av.viewName))
2830         {
2831           existingNames.add(ap.av.viewName);
2832         }
2833       }
2834     }
2835     return existingNames;
2836   }
2837
2838   /**
2839    * Explode tabbed views into separate windows.
2840    */
2841   @Override
2842   public void expandViews_actionPerformed(ActionEvent e)
2843   {
2844     Desktop.explodeViews(this);
2845   }
2846
2847   /**
2848    * Gather views in separate windows back into a tabbed presentation.
2849    */
2850   @Override
2851   public void gatherViews_actionPerformed(ActionEvent e)
2852   {
2853     Desktop.instance.gatherViews(this);
2854   }
2855
2856   /**
2857    * DOCUMENT ME!
2858    *
2859    * @param e
2860    *          DOCUMENT ME!
2861    */
2862   @Override
2863   public void font_actionPerformed(ActionEvent e)
2864   {
2865     new FontChooser(alignPanel);
2866   }
2867
2868   /**
2869    * DOCUMENT ME!
2870    *
2871    * @param e
2872    *          DOCUMENT ME!
2873    */
2874   @Override
2875   protected void seqLimit_actionPerformed(ActionEvent e)
2876   {
2877     viewport.setShowJVSuffix(seqLimits.isSelected());
2878
2879     alignPanel.getIdPanel().getIdCanvas()
2880             .setPreferredSize(alignPanel.calculateIdWidth());
2881     alignPanel.paintAlignment(true);
2882   }
2883
2884   @Override
2885   public void idRightAlign_actionPerformed(ActionEvent e)
2886   {
2887     viewport.setRightAlignIds(idRightAlign.isSelected());
2888     alignPanel.paintAlignment(true);
2889   }
2890
2891   @Override
2892   public void centreColumnLabels_actionPerformed(ActionEvent e)
2893   {
2894     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2895     alignPanel.paintAlignment(true);
2896   }
2897
2898   /*
2899    * (non-Javadoc)
2900    *
2901    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2902    */
2903   @Override
2904   protected void followHighlight_actionPerformed()
2905   {
2906     /*
2907      * Set the 'follow' flag on the Viewport (and scroll to position if now
2908      * true).
2909      */
2910     final boolean state = this.followHighlightMenuItem.getState();
2911     viewport.setFollowHighlight(state);
2912     if (state)
2913     {
2914       alignPanel.scrollToPosition(
2915               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2916     }
2917   }
2918
2919   /**
2920    * DOCUMENT ME!
2921    *
2922    * @param e
2923    *          DOCUMENT ME!
2924    */
2925   @Override
2926   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2927   {
2928     viewport.setColourText(colourTextMenuItem.isSelected());
2929     alignPanel.paintAlignment(true);
2930   }
2931
2932   /**
2933    * DOCUMENT ME!
2934    *
2935    * @param e
2936    *          DOCUMENT ME!
2937    */
2938   @Override
2939   public void wrapMenuItem_actionPerformed(ActionEvent e)
2940   {
2941     scaleAbove.setVisible(wrapMenuItem.isSelected());
2942     scaleLeft.setVisible(wrapMenuItem.isSelected());
2943     scaleRight.setVisible(wrapMenuItem.isSelected());
2944     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2945     alignPanel.updateLayout();
2946   }
2947
2948   @Override
2949   public void showAllSeqs_actionPerformed(ActionEvent e)
2950   {
2951     viewport.showAllHiddenSeqs();
2952   }
2953
2954   @Override
2955   public void showAllColumns_actionPerformed(ActionEvent e)
2956   {
2957     viewport.showAllHiddenColumns();
2958     repaint();
2959     viewport.sendSelection();
2960   }
2961
2962   @Override
2963   public void hideSelSequences_actionPerformed(ActionEvent e)
2964   {
2965     viewport.hideAllSelectedSeqs();
2966     // alignPanel.paintAlignment(true);
2967   }
2968
2969   /**
2970    * called by key handler and the hide all/show all menu items
2971    *
2972    * @param toggleSeqs
2973    * @param toggleCols
2974    */
2975   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2976   {
2977
2978     boolean hide = false;
2979     SequenceGroup sg = viewport.getSelectionGroup();
2980     if (!toggleSeqs && !toggleCols)
2981     {
2982       // Hide everything by the current selection - this is a hack - we do the
2983       // invert and then hide
2984       // first check that there will be visible columns after the invert.
2985       if ((viewport.getColumnSelection() != null
2986               && viewport.getColumnSelection().getSelected() != null && viewport
2987               .getColumnSelection().getSelected().size() > 0)
2988               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2989                       .getEndRes()))
2990       {
2991         // now invert the sequence set, if required - empty selection implies
2992         // that no hiding is required.
2993         if (sg != null)
2994         {
2995           invertSequenceMenuItem_actionPerformed(null);
2996           sg = viewport.getSelectionGroup();
2997           toggleSeqs = true;
2998
2999         }
3000         viewport.expandColSelection(sg, true);
3001         // finally invert the column selection and get the new sequence
3002         // selection.
3003         invertColSel_actionPerformed(null);
3004         toggleCols = true;
3005       }
3006     }
3007
3008     if (toggleSeqs)
3009     {
3010       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3011       {
3012         hideSelSequences_actionPerformed(null);
3013         hide = true;
3014       }
3015       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3016               .size() > 0))
3017       {
3018         showAllSeqs_actionPerformed(null);
3019       }
3020     }
3021
3022     if (toggleCols)
3023     {
3024       if (viewport.getColumnSelection().getSelected().size() > 0)
3025       {
3026         hideSelColumns_actionPerformed(null);
3027         if (!toggleSeqs)
3028         {
3029           viewport.setSelectionGroup(sg);
3030         }
3031       }
3032       else if (!hide)
3033       {
3034         showAllColumns_actionPerformed(null);
3035       }
3036     }
3037   }
3038
3039   /*
3040    * (non-Javadoc)
3041    *
3042    * @see
3043    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3044    * event.ActionEvent)
3045    */
3046   @Override
3047   public void hideAllButSelection_actionPerformed(ActionEvent e)
3048   {
3049     toggleHiddenRegions(false, false);
3050     viewport.sendSelection();
3051   }
3052
3053   /*
3054    * (non-Javadoc)
3055    *
3056    * @see
3057    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3058    * .ActionEvent)
3059    */
3060   @Override
3061   public void hideAllSelection_actionPerformed(ActionEvent e)
3062   {
3063     SequenceGroup sg = viewport.getSelectionGroup();
3064     viewport.expandColSelection(sg, false);
3065     viewport.hideAllSelectedSeqs();
3066     viewport.hideSelectedColumns();
3067     alignPanel.paintAlignment(true);
3068     viewport.sendSelection();
3069   }
3070
3071   /*
3072    * (non-Javadoc)
3073    *
3074    * @see
3075    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3076    * ActionEvent)
3077    */
3078   @Override
3079   public void showAllhidden_actionPerformed(ActionEvent e)
3080   {
3081     viewport.showAllHiddenColumns();
3082     viewport.showAllHiddenSeqs();
3083     alignPanel.paintAlignment(true);
3084     viewport.sendSelection();
3085   }
3086
3087   @Override
3088   public void hideSelColumns_actionPerformed(ActionEvent e)
3089   {
3090     viewport.hideSelectedColumns();
3091     alignPanel.paintAlignment(true);
3092     viewport.sendSelection();
3093   }
3094
3095   @Override
3096   public void hiddenMarkers_actionPerformed(ActionEvent e)
3097   {
3098     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3099     repaint();
3100   }
3101
3102   /**
3103    * DOCUMENT ME!
3104    *
3105    * @param e
3106    *          DOCUMENT ME!
3107    */
3108   @Override
3109   protected void scaleAbove_actionPerformed(ActionEvent e)
3110   {
3111     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3112     alignPanel.paintAlignment(true);
3113   }
3114
3115   /**
3116    * DOCUMENT ME!
3117    *
3118    * @param e
3119    *          DOCUMENT ME!
3120    */
3121   @Override
3122   protected void scaleLeft_actionPerformed(ActionEvent e)
3123   {
3124     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3125     alignPanel.paintAlignment(true);
3126   }
3127
3128   /**
3129    * DOCUMENT ME!
3130    *
3131    * @param e
3132    *          DOCUMENT ME!
3133    */
3134   @Override
3135   protected void scaleRight_actionPerformed(ActionEvent e)
3136   {
3137     viewport.setScaleRightWrapped(scaleRight.isSelected());
3138     alignPanel.paintAlignment(true);
3139   }
3140
3141   /**
3142    * DOCUMENT ME!
3143    *
3144    * @param e
3145    *          DOCUMENT ME!
3146    */
3147   @Override
3148   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3149   {
3150     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3151     alignPanel.paintAlignment(true);
3152   }
3153
3154   /**
3155    * DOCUMENT ME!
3156    *
3157    * @param e
3158    *          DOCUMENT ME!
3159    */
3160   @Override
3161   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3162   {
3163     viewport.setShowText(viewTextMenuItem.isSelected());
3164     alignPanel.paintAlignment(true);
3165   }
3166
3167   /**
3168    * DOCUMENT ME!
3169    *
3170    * @param e
3171    *          DOCUMENT ME!
3172    */
3173   @Override
3174   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3175   {
3176     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3177     alignPanel.paintAlignment(true);
3178   }
3179
3180   public FeatureSettings featureSettings;
3181
3182   @Override
3183   public FeatureSettingsControllerI getFeatureSettingsUI()
3184   {
3185     return featureSettings;
3186   }
3187
3188   @Override
3189   public void featureSettings_actionPerformed(ActionEvent e)
3190   {
3191     if (featureSettings != null)
3192     {
3193       featureSettings.close();
3194       featureSettings = null;
3195     }
3196     if (!showSeqFeatures.isSelected())
3197     {
3198       // make sure features are actually displayed
3199       showSeqFeatures.setSelected(true);
3200       showSeqFeatures_actionPerformed(null);
3201     }
3202     featureSettings = new FeatureSettings(this);
3203   }
3204
3205   /**
3206    * Set or clear 'Show Sequence Features'
3207    *
3208    * @param evt
3209    *          DOCUMENT ME!
3210    */
3211   @Override
3212   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3213   {
3214     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3215     alignPanel.paintAlignment(true);
3216     if (alignPanel.getOverviewPanel() != null)
3217     {
3218       alignPanel.getOverviewPanel().updateOverviewImage();
3219     }
3220   }
3221
3222   /**
3223    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3224    * the annotations panel as a whole.
3225    *
3226    * The options to show/hide all annotations should be enabled when the panel
3227    * is shown, and disabled when the panel is hidden.
3228    *
3229    * @param e
3230    */
3231   @Override
3232   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3233   {
3234     final boolean setVisible = annotationPanelMenuItem.isSelected();
3235     viewport.setShowAnnotation(setVisible);
3236     this.showAllSeqAnnotations.setEnabled(setVisible);
3237     this.hideAllSeqAnnotations.setEnabled(setVisible);
3238     this.showAllAlAnnotations.setEnabled(setVisible);
3239     this.hideAllAlAnnotations.setEnabled(setVisible);
3240     alignPanel.updateLayout();
3241   }
3242
3243   @Override
3244   public void alignmentProperties()
3245   {
3246     JEditorPane editPane = new JEditorPane("text/html", "");
3247     editPane.setEditable(false);
3248     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3249             .formatAsHtml();
3250     editPane.setText(MessageManager.formatMessage("label.html_content",
3251             new Object[] { contents.toString() }));
3252     JInternalFrame frame = new JInternalFrame();
3253     frame.getContentPane().add(new JScrollPane(editPane));
3254
3255     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3256             "label.alignment_properties", new Object[] { getTitle() }),
3257             500, 400);
3258   }
3259
3260   /**
3261    * DOCUMENT ME!
3262    *
3263    * @param e
3264    *          DOCUMENT ME!
3265    */
3266   @Override
3267   public void overviewMenuItem_actionPerformed(ActionEvent e)
3268   {
3269     if (alignPanel.overviewPanel != null)
3270     {
3271       return;
3272     }
3273
3274     JInternalFrame frame = new JInternalFrame();
3275     OverviewPanel overview = new OverviewPanel(alignPanel);
3276     frame.setContentPane(overview);
3277     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3278             "label.overview_params", new Object[] { this.getTitle() }),
3279             frame.getWidth(), frame.getHeight());
3280     frame.pack();
3281     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3282     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3283     {
3284       @Override
3285       public void internalFrameClosed(
3286               javax.swing.event.InternalFrameEvent evt)
3287       {
3288         alignPanel.setOverviewPanel(null);
3289       };
3290     });
3291
3292     alignPanel.setOverviewPanel(overview);
3293   }
3294
3295   @Override
3296   public void textColour_actionPerformed(ActionEvent e)
3297   {
3298     new TextColourChooser().chooseColour(alignPanel, null);
3299   }
3300
3301   /**
3302    * DOCUMENT ME!
3303    *
3304    * @param e
3305    *          DOCUMENT ME!
3306    */
3307   @Override
3308   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3309   {
3310     changeColour(null);
3311   }
3312
3313   /**
3314    * DOCUMENT ME!
3315    *
3316    * @param e
3317    *          DOCUMENT ME!
3318    */
3319   @Override
3320   public void clustalColour_actionPerformed(ActionEvent e)
3321   {
3322     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3323             viewport.getHiddenRepSequences()));
3324   }
3325
3326   /**
3327    * DOCUMENT ME!
3328    *
3329    * @param e
3330    *          DOCUMENT ME!
3331    */
3332   @Override
3333   public void zappoColour_actionPerformed(ActionEvent e)
3334   {
3335     changeColour(new ZappoColourScheme());
3336   }
3337
3338   /**
3339    * DOCUMENT ME!
3340    *
3341    * @param e
3342    *          DOCUMENT ME!
3343    */
3344   @Override
3345   public void taylorColour_actionPerformed(ActionEvent e)
3346   {
3347     changeColour(new TaylorColourScheme());
3348   }
3349
3350   /**
3351    * DOCUMENT ME!
3352    *
3353    * @param e
3354    *          DOCUMENT ME!
3355    */
3356   @Override
3357   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3358   {
3359     changeColour(new HydrophobicColourScheme());
3360   }
3361
3362   /**
3363    * DOCUMENT ME!
3364    *
3365    * @param e
3366    *          DOCUMENT ME!
3367    */
3368   @Override
3369   public void helixColour_actionPerformed(ActionEvent e)
3370   {
3371     changeColour(new HelixColourScheme());
3372   }
3373
3374   /**
3375    * DOCUMENT ME!
3376    *
3377    * @param e
3378    *          DOCUMENT ME!
3379    */
3380   @Override
3381   public void strandColour_actionPerformed(ActionEvent e)
3382   {
3383     changeColour(new StrandColourScheme());
3384   }
3385
3386   /**
3387    * DOCUMENT ME!
3388    *
3389    * @param e
3390    *          DOCUMENT ME!
3391    */
3392   @Override
3393   public void turnColour_actionPerformed(ActionEvent e)
3394   {
3395     changeColour(new TurnColourScheme());
3396   }
3397
3398   /**
3399    * DOCUMENT ME!
3400    *
3401    * @param e
3402    *          DOCUMENT ME!
3403    */
3404   @Override
3405   public void buriedColour_actionPerformed(ActionEvent e)
3406   {
3407     changeColour(new BuriedColourScheme());
3408   }
3409
3410   /**
3411    * DOCUMENT ME!
3412    *
3413    * @param e
3414    *          DOCUMENT ME!
3415    */
3416   @Override
3417   public void nucleotideColour_actionPerformed(ActionEvent e)
3418   {
3419     changeColour(new NucleotideColourScheme());
3420   }
3421
3422   @Override
3423   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3424   {
3425     changeColour(new PurinePyrimidineColourScheme());
3426   }
3427
3428   /*
3429    * public void covariationColour_actionPerformed(ActionEvent e) {
3430    * changeColour(new
3431    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3432    * ()[0])); }
3433    */
3434   @Override
3435   public void annotationColour_actionPerformed(ActionEvent e)
3436   {
3437     new AnnotationColourChooser(viewport, alignPanel);
3438   }
3439
3440   @Override
3441   public void annotationColumn_actionPerformed(ActionEvent e)
3442   {
3443     new AnnotationColumnChooser(viewport, alignPanel);
3444   }
3445
3446   @Override
3447   public void rnahelicesColour_actionPerformed(ActionEvent e)
3448   {
3449     new RNAHelicesColourChooser(viewport, alignPanel);
3450   }
3451
3452   /**
3453    * DOCUMENT ME!
3454    *
3455    * @param e
3456    *          DOCUMENT ME!
3457    */
3458   @Override
3459   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3460   {
3461     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3462   }
3463
3464   /**
3465    * DOCUMENT ME!
3466    *
3467    * @param cs
3468    *          DOCUMENT ME!
3469    */
3470   @Override
3471   public void changeColour(ColourSchemeI cs)
3472   {
3473     // TODO: pull up to controller method
3474
3475     if (cs != null)
3476     {
3477       // Make sure viewport is up to date w.r.t. any sliders
3478       if (viewport.getAbovePIDThreshold())
3479       {
3480         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3481                 "Background");
3482         viewport.setThreshold(threshold);
3483       }
3484
3485       if (viewport.getConservationSelected())
3486       {
3487         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3488                 cs, "Background"));
3489       }
3490       if (cs instanceof TCoffeeColourScheme)
3491       {
3492         tcoffeeColour.setEnabled(true);
3493         tcoffeeColour.setSelected(true);
3494       }
3495     }
3496
3497     viewport.setGlobalColourScheme(cs);
3498
3499     alignPanel.paintAlignment(true);
3500   }
3501
3502   /**
3503    * DOCUMENT ME!
3504    *
3505    * @param e
3506    *          DOCUMENT ME!
3507    */
3508   @Override
3509   protected void modifyPID_actionPerformed(ActionEvent e)
3510   {
3511     if (viewport.getAbovePIDThreshold()
3512             && viewport.getGlobalColourScheme() != null)
3513     {
3514       SliderPanel.setPIDSliderSource(alignPanel,
3515               viewport.getGlobalColourScheme(), "Background");
3516       SliderPanel.showPIDSlider();
3517     }
3518   }
3519
3520   /**
3521    * DOCUMENT ME!
3522    *
3523    * @param e
3524    *          DOCUMENT ME!
3525    */
3526   @Override
3527   protected void modifyConservation_actionPerformed(ActionEvent e)
3528   {
3529     if (viewport.getConservationSelected()
3530             && viewport.getGlobalColourScheme() != null)
3531     {
3532       SliderPanel.setConservationSlider(alignPanel,
3533               viewport.getGlobalColourScheme(), "Background");
3534       SliderPanel.showConservationSlider();
3535     }
3536   }
3537
3538   /**
3539    * DOCUMENT ME!
3540    *
3541    * @param e
3542    *          DOCUMENT ME!
3543    */
3544   @Override
3545   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3546   {
3547     viewport.setConservationSelected(conservationMenuItem.isSelected());
3548
3549     viewport.setAbovePIDThreshold(false);
3550     abovePIDThreshold.setSelected(false);
3551
3552     changeColour(viewport.getGlobalColourScheme());
3553
3554     modifyConservation_actionPerformed(null);
3555   }
3556
3557   /**
3558    * DOCUMENT ME!
3559    *
3560    * @param e
3561    *          DOCUMENT ME!
3562    */
3563   @Override
3564   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3565   {
3566     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3567
3568     conservationMenuItem.setSelected(false);
3569     viewport.setConservationSelected(false);
3570
3571     changeColour(viewport.getGlobalColourScheme());
3572
3573     modifyPID_actionPerformed(null);
3574   }
3575
3576   /**
3577    * DOCUMENT ME!
3578    *
3579    * @param e
3580    *          DOCUMENT ME!
3581    */
3582   @Override
3583   public void userDefinedColour_actionPerformed(ActionEvent e)
3584   {
3585     if (e.getActionCommand().equals(
3586             MessageManager.getString("action.user_defined")))
3587     {
3588       new UserDefinedColours(alignPanel, null);
3589     }
3590     else
3591     {
3592       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3593               .getUserColourSchemes().get(e.getActionCommand());
3594
3595       changeColour(udc);
3596     }
3597   }
3598
3599   public void updateUserColourMenu()
3600   {
3601
3602     Component[] menuItems = colourMenu.getMenuComponents();
3603     int iSize = menuItems.length;
3604     for (int i = 0; i < iSize; i++)
3605     {
3606       if (menuItems[i].getName() != null
3607               && menuItems[i].getName().equals("USER_DEFINED"))
3608       {
3609         colourMenu.remove(menuItems[i]);
3610         iSize--;
3611       }
3612     }
3613     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3614     {
3615       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3616               .getUserColourSchemes().keys();
3617
3618       while (userColours.hasMoreElements())
3619       {
3620         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3621                 userColours.nextElement().toString());
3622         radioItem.setName("USER_DEFINED");
3623         radioItem.addMouseListener(new MouseAdapter()
3624         {
3625           @Override
3626           public void mousePressed(MouseEvent evt)
3627           {
3628             if (evt.isPopupTrigger())
3629             {
3630               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3631
3632               int option = JOptionPane.showInternalConfirmDialog(
3633                       jalview.gui.Desktop.desktop,
3634                       MessageManager
3635                               .getString("label.remove_from_default_list"),
3636                       MessageManager
3637                               .getString("label.remove_user_defined_colour"),
3638                       JOptionPane.YES_NO_OPTION);
3639               if (option == JOptionPane.YES_OPTION)
3640               {
3641                 jalview.gui.UserDefinedColours
3642                         .removeColourFromDefaults(radioItem.getText());
3643                 colourMenu.remove(radioItem);
3644               }
3645               else
3646               {
3647                 radioItem.addActionListener(new ActionListener()
3648                 {
3649                   @Override
3650                   public void actionPerformed(ActionEvent evt)
3651                   {
3652                     userDefinedColour_actionPerformed(evt);
3653                   }
3654                 });
3655               }
3656             }
3657           }
3658         });
3659         radioItem.addActionListener(new ActionListener()
3660         {
3661           @Override
3662           public void actionPerformed(ActionEvent evt)
3663           {
3664             userDefinedColour_actionPerformed(evt);
3665           }
3666         });
3667
3668         colourMenu.insert(radioItem, 15);
3669         colours.add(radioItem);
3670       }
3671     }
3672   }
3673
3674   /**
3675    * DOCUMENT ME!
3676    *
3677    * @param e
3678    *          DOCUMENT ME!
3679    */
3680   @Override
3681   public void PIDColour_actionPerformed(ActionEvent e)
3682   {
3683     changeColour(new PIDColourScheme());
3684   }
3685
3686   /**
3687    * DOCUMENT ME!
3688    *
3689    * @param e
3690    *          DOCUMENT ME!
3691    */
3692   @Override
3693   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3694   {
3695     changeColour(new Blosum62ColourScheme());
3696   }
3697
3698   /**
3699    * DOCUMENT ME!
3700    *
3701    * @param e
3702    *          DOCUMENT ME!
3703    */
3704   @Override
3705   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3706   {
3707     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3708     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3709             .getAlignment().getSequenceAt(0), null);
3710     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3711             viewport.getAlignment()));
3712     alignPanel.paintAlignment(true);
3713   }
3714
3715   /**
3716    * DOCUMENT ME!
3717    *
3718    * @param e
3719    *          DOCUMENT ME!
3720    */
3721   @Override
3722   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3723   {
3724     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3725     AlignmentSorter.sortByID(viewport.getAlignment());
3726     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3727             viewport.getAlignment()));
3728     alignPanel.paintAlignment(true);
3729   }
3730
3731   /**
3732    * DOCUMENT ME!
3733    *
3734    * @param e
3735    *          DOCUMENT ME!
3736    */
3737   @Override
3738   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3739   {
3740     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3741     AlignmentSorter.sortByLength(viewport.getAlignment());
3742     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3743             viewport.getAlignment()));
3744     alignPanel.paintAlignment(true);
3745   }
3746
3747   /**
3748    * DOCUMENT ME!
3749    *
3750    * @param e
3751    *          DOCUMENT ME!
3752    */
3753   @Override
3754   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3755   {
3756     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3757     AlignmentSorter.sortByGroup(viewport.getAlignment());
3758     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3759             viewport.getAlignment()));
3760
3761     alignPanel.paintAlignment(true);
3762   }
3763
3764   /**
3765    * DOCUMENT ME!
3766    *
3767    * @param e
3768    *          DOCUMENT ME!
3769    */
3770   @Override
3771   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3772   {
3773     new RedundancyPanel(alignPanel, this);
3774   }
3775
3776   /**
3777    * DOCUMENT ME!
3778    *
3779    * @param e
3780    *          DOCUMENT ME!
3781    */
3782   @Override
3783   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3784   {
3785     if ((viewport.getSelectionGroup() == null)
3786             || (viewport.getSelectionGroup().getSize() < 2))
3787     {
3788       JOptionPane.showInternalMessageDialog(this, MessageManager
3789               .getString("label.you_must_select_least_two_sequences"),
3790               MessageManager.getString("label.invalid_selection"),
3791               JOptionPane.WARNING_MESSAGE);
3792     }
3793     else
3794     {
3795       JInternalFrame frame = new JInternalFrame();
3796       frame.setContentPane(new PairwiseAlignPanel(viewport));
3797       Desktop.addInternalFrame(frame,
3798               MessageManager.getString("action.pairwise_alignment"), 600,
3799               500);
3800     }
3801   }
3802
3803   /**
3804    * DOCUMENT ME!
3805    *
3806    * @param e
3807    *          DOCUMENT ME!
3808    */
3809   @Override
3810   public void PCAMenuItem_actionPerformed(ActionEvent e)
3811   {
3812     if (((viewport.getSelectionGroup() != null)
3813             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3814             .getSelectionGroup().getSize() > 0))
3815             || (viewport.getAlignment().getHeight() < 4))
3816     {
3817       JOptionPane
3818               .showInternalMessageDialog(
3819                       this,
3820                       MessageManager
3821                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3822                       MessageManager
3823                               .getString("label.sequence_selection_insufficient"),
3824                       JOptionPane.WARNING_MESSAGE);
3825
3826       return;
3827     }
3828
3829     new PCAPanel(alignPanel);
3830   }
3831
3832   @Override
3833   public void autoCalculate_actionPerformed(ActionEvent e)
3834   {
3835     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3836     if (viewport.autoCalculateConsensus)
3837     {
3838       viewport.firePropertyChange("alignment", null, viewport
3839               .getAlignment().getSequences());
3840     }
3841   }
3842
3843   @Override
3844   public void sortByTreeOption_actionPerformed(ActionEvent e)
3845   {
3846     viewport.sortByTree = sortByTree.isSelected();
3847   }
3848
3849   @Override
3850   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3851   {
3852     viewport.followSelection = listenToViewSelections.isSelected();
3853   }
3854
3855   /**
3856    * DOCUMENT ME!
3857    *
3858    * @param e
3859    *          DOCUMENT ME!
3860    */
3861   @Override
3862   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3863   {
3864     newTreePanel("AV", "PID", "Average distance tree using PID");
3865   }
3866
3867   /**
3868    * DOCUMENT ME!
3869    *
3870    * @param e
3871    *          DOCUMENT ME!
3872    */
3873   @Override
3874   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3875   {
3876     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3877   }
3878
3879   /**
3880    * DOCUMENT ME!
3881    *
3882    * @param e
3883    *          DOCUMENT ME!
3884    */
3885   @Override
3886   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3887   {
3888     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3889   }
3890
3891   /**
3892    * DOCUMENT ME!
3893    *
3894    * @param e
3895    *          DOCUMENT ME!
3896    */
3897   @Override
3898   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3899   {
3900     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3901   }
3902
3903   /**
3904    * DOCUMENT ME!
3905    *
3906    * @param type
3907    *          DOCUMENT ME!
3908    * @param pwType
3909    *          DOCUMENT ME!
3910    * @param title
3911    *          DOCUMENT ME!
3912    */
3913   void newTreePanel(String type, String pwType, String title)
3914   {
3915     TreePanel tp;
3916
3917     if (viewport.getSelectionGroup() != null
3918             && viewport.getSelectionGroup().getSize() > 0)
3919     {
3920       if (viewport.getSelectionGroup().getSize() < 3)
3921       {
3922         JOptionPane
3923                 .showMessageDialog(
3924                         Desktop.desktop,
3925                         MessageManager
3926                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3927                         MessageManager
3928                                 .getString("label.not_enough_sequences"),
3929                         JOptionPane.WARNING_MESSAGE);
3930         return;
3931       }
3932
3933       SequenceGroup sg = viewport.getSelectionGroup();
3934
3935       /* Decide if the selection is a column region */
3936       for (SequenceI _s : sg.getSequences())
3937       {
3938         if (_s.getLength() < sg.getEndRes())
3939         {
3940           JOptionPane
3941                   .showMessageDialog(
3942                           Desktop.desktop,
3943                           MessageManager
3944                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3945                           MessageManager
3946                                   .getString("label.sequences_selection_not_aligned"),
3947                           JOptionPane.WARNING_MESSAGE);
3948
3949           return;
3950         }
3951       }
3952
3953       title = title + " on region";
3954       tp = new TreePanel(alignPanel, type, pwType);
3955     }
3956     else
3957     {
3958       // are the visible sequences aligned?
3959       if (!viewport.getAlignment().isAligned(false))
3960       {
3961         JOptionPane
3962                 .showMessageDialog(
3963                         Desktop.desktop,
3964                         MessageManager
3965                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3966                         MessageManager
3967                                 .getString("label.sequences_not_aligned"),
3968                         JOptionPane.WARNING_MESSAGE);
3969
3970         return;
3971       }
3972
3973       if (viewport.getAlignment().getHeight() < 2)
3974       {
3975         return;
3976       }
3977
3978       tp = new TreePanel(alignPanel, type, pwType);
3979     }
3980
3981     title += " from ";
3982
3983     if (viewport.viewName != null)
3984     {
3985       title += viewport.viewName + " of ";
3986     }
3987
3988     title += this.title;
3989
3990     Desktop.addInternalFrame(tp, title, 600, 500);
3991   }
3992
3993   /**
3994    * DOCUMENT ME!
3995    *
3996    * @param title
3997    *          DOCUMENT ME!
3998    * @param order
3999    *          DOCUMENT ME!
4000    */
4001   public void addSortByOrderMenuItem(String title,
4002           final AlignmentOrder order)
4003   {
4004     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4005             "action.by_title_param", new Object[] { title }));
4006     sort.add(item);
4007     item.addActionListener(new java.awt.event.ActionListener()
4008     {
4009       @Override
4010       public void actionPerformed(ActionEvent e)
4011       {
4012         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4013
4014         // TODO: JBPNote - have to map order entries to curent SequenceI
4015         // pointers
4016         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4017
4018         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4019                 .getAlignment()));
4020
4021         alignPanel.paintAlignment(true);
4022       }
4023     });
4024   }
4025
4026   /**
4027    * Add a new sort by annotation score menu item
4028    *
4029    * @param sort
4030    *          the menu to add the option to
4031    * @param scoreLabel
4032    *          the label used to retrieve scores for each sequence on the
4033    *          alignment
4034    */
4035   public void addSortByAnnotScoreMenuItem(JMenu sort,
4036           final String scoreLabel)
4037   {
4038     final JMenuItem item = new JMenuItem(scoreLabel);
4039     sort.add(item);
4040     item.addActionListener(new java.awt.event.ActionListener()
4041     {
4042       @Override
4043       public void actionPerformed(ActionEvent e)
4044       {
4045         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4046         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4047                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4048         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4049                 viewport.getAlignment()));
4050         alignPanel.paintAlignment(true);
4051       }
4052     });
4053   }
4054
4055   /**
4056    * last hash for alignment's annotation array - used to minimise cost of
4057    * rebuild.
4058    */
4059   protected int _annotationScoreVectorHash;
4060
4061   /**
4062    * search the alignment and rebuild the sort by annotation score submenu the
4063    * last alignment annotation vector hash is stored to minimize cost of
4064    * rebuilding in subsequence calls.
4065    *
4066    */
4067   @Override
4068   public void buildSortByAnnotationScoresMenu()
4069   {
4070     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4071     {
4072       return;
4073     }
4074
4075     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4076     {
4077       sortByAnnotScore.removeAll();
4078       // almost certainly a quicker way to do this - but we keep it simple
4079       Hashtable scoreSorts = new Hashtable();
4080       AlignmentAnnotation aann[];
4081       for (SequenceI sqa : viewport.getAlignment().getSequences())
4082       {
4083         aann = sqa.getAnnotation();
4084         for (int i = 0; aann != null && i < aann.length; i++)
4085         {
4086           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4087           {
4088             scoreSorts.put(aann[i].label, aann[i].label);
4089           }
4090         }
4091       }
4092       Enumeration labels = scoreSorts.keys();
4093       while (labels.hasMoreElements())
4094       {
4095         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4096                 (String) labels.nextElement());
4097       }
4098       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4099       scoreSorts.clear();
4100
4101       _annotationScoreVectorHash = viewport.getAlignment()
4102               .getAlignmentAnnotation().hashCode();
4103     }
4104   }
4105
4106   /**
4107    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4108    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4109    * call. Listeners are added to remove the menu item when the treePanel is
4110    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4111    * modified.
4112    *
4113    * @param treePanel
4114    *          Displayed tree window.
4115    * @param title
4116    *          SortBy menu item title.
4117    */
4118   @Override
4119   public void buildTreeMenu()
4120   {
4121     calculateTree.removeAll();
4122     // build the calculate menu
4123
4124     for (final String type : new String[] { "NJ", "AV" })
4125     {
4126       String treecalcnm = MessageManager.getString("label.tree_calc_"
4127               + type.toLowerCase());
4128       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4129       {
4130         JMenuItem tm = new JMenuItem();
4131         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4132         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4133                 || sm.isProtein() == !viewport.getAlignment()
4134                         .isNucleotide())
4135         {
4136           String smn = MessageManager.getStringOrReturn(
4137                   "label.score_model_", sm.getName());
4138           final String title = MessageManager.formatMessage(
4139                   "label.treecalc_title", treecalcnm, smn);
4140           tm.setText(title);//
4141           tm.addActionListener(new java.awt.event.ActionListener()
4142           {
4143             @Override
4144             public void actionPerformed(ActionEvent e)
4145             {
4146               newTreePanel(type, pwtype, title);
4147             }
4148           });
4149           calculateTree.add(tm);
4150         }
4151
4152       }
4153     }
4154     sortByTreeMenu.removeAll();
4155
4156     List<Component> comps = PaintRefresher.components.get(viewport
4157             .getSequenceSetId());
4158     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4159     for (Component comp : comps)
4160     {
4161       if (comp instanceof TreePanel)
4162       {
4163         treePanels.add((TreePanel) comp);
4164       }
4165     }
4166
4167     if (treePanels.size() < 1)
4168     {
4169       sortByTreeMenu.setVisible(false);
4170       return;
4171     }
4172
4173     sortByTreeMenu.setVisible(true);
4174
4175     for (final TreePanel tp : treePanels)
4176     {
4177       final JMenuItem item = new JMenuItem(tp.getTitle());
4178       item.addActionListener(new java.awt.event.ActionListener()
4179       {
4180         @Override
4181         public void actionPerformed(ActionEvent e)
4182         {
4183           tp.sortByTree_actionPerformed();
4184           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4185
4186         }
4187       });
4188
4189       sortByTreeMenu.add(item);
4190     }
4191   }
4192
4193   public boolean sortBy(AlignmentOrder alorder, String undoname)
4194   {
4195     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4196     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4197     if (undoname != null)
4198     {
4199       addHistoryItem(new OrderCommand(undoname, oldOrder,
4200               viewport.getAlignment()));
4201     }
4202     alignPanel.paintAlignment(true);
4203     return true;
4204   }
4205
4206   /**
4207    * Work out whether the whole set of sequences or just the selected set will
4208    * be submitted for multiple alignment.
4209    *
4210    */
4211   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4212   {
4213     // Now, check we have enough sequences
4214     AlignmentView msa = null;
4215
4216     if ((viewport.getSelectionGroup() != null)
4217             && (viewport.getSelectionGroup().getSize() > 1))
4218     {
4219       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4220       // some common interface!
4221       /*
4222        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4223        * SequenceI[sz = seqs.getSize(false)];
4224        *
4225        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4226        * seqs.getSequenceAt(i); }
4227        */
4228       msa = viewport.getAlignmentView(true);
4229     }
4230     else if (viewport.getSelectionGroup() != null
4231             && viewport.getSelectionGroup().getSize() == 1)
4232     {
4233       int option = JOptionPane.showConfirmDialog(this,
4234               MessageManager.getString("warn.oneseq_msainput_selection"),
4235               MessageManager.getString("label.invalid_selection"),
4236               JOptionPane.OK_CANCEL_OPTION);
4237       if (option == JOptionPane.OK_OPTION)
4238       {
4239         msa = viewport.getAlignmentView(false);
4240       }
4241     }
4242     else
4243     {
4244       msa = viewport.getAlignmentView(false);
4245     }
4246     return msa;
4247   }
4248
4249   /**
4250    * Decides what is submitted to a secondary structure prediction service: the
4251    * first sequence in the alignment, or in the current selection, or, if the
4252    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4253    * region or the whole alignment. (where the first sequence in the set is the
4254    * one that the prediction will be for).
4255    */
4256   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4257   {
4258     AlignmentView seqs = null;
4259
4260     if ((viewport.getSelectionGroup() != null)
4261             && (viewport.getSelectionGroup().getSize() > 0))
4262     {
4263       seqs = viewport.getAlignmentView(true);
4264     }
4265     else
4266     {
4267       seqs = viewport.getAlignmentView(false);
4268     }
4269     // limit sequences - JBPNote in future - could spawn multiple prediction
4270     // jobs
4271     // TODO: viewport.getAlignment().isAligned is a global state - the local
4272     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4273     if (!viewport.getAlignment().isAligned(false))
4274     {
4275       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4276       // TODO: if seqs.getSequences().length>1 then should really have warned
4277       // user!
4278
4279     }
4280     return seqs;
4281   }
4282
4283   /**
4284    * DOCUMENT ME!
4285    *
4286    * @param e
4287    *          DOCUMENT ME!
4288    */
4289   @Override
4290   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4291   {
4292     // Pick the tree file
4293     JalviewFileChooser chooser = new JalviewFileChooser(
4294             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4295     chooser.setFileView(new JalviewFileView());
4296     chooser.setDialogTitle(MessageManager
4297             .getString("label.select_newick_like_tree_file"));
4298     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4299
4300     int value = chooser.showOpenDialog(null);
4301
4302     if (value == JalviewFileChooser.APPROVE_OPTION)
4303     {
4304       String choice = chooser.getSelectedFile().getPath();
4305       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4306       jalview.io.NewickFile fin = null;
4307       try
4308       {
4309         fin = new jalview.io.NewickFile(choice, "File");
4310         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4311       } catch (Exception ex)
4312       {
4313         JOptionPane
4314                 .showMessageDialog(
4315                         Desktop.desktop,
4316                         ex.getMessage(),
4317                         MessageManager
4318                                 .getString("label.problem_reading_tree_file"),
4319                         JOptionPane.WARNING_MESSAGE);
4320         ex.printStackTrace();
4321       }
4322       if (fin != null && fin.hasWarningMessage())
4323       {
4324         JOptionPane.showMessageDialog(Desktop.desktop, fin
4325                 .getWarningMessage(), MessageManager
4326                 .getString("label.possible_problem_with_tree_file"),
4327                 JOptionPane.WARNING_MESSAGE);
4328       }
4329     }
4330   }
4331
4332   @Override
4333   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4334   {
4335     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4336   }
4337
4338   public TreePanel ShowNewickTree(NewickFile nf, String title)
4339   {
4340     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4341   }
4342
4343   public TreePanel ShowNewickTree(NewickFile nf, String title,
4344           AlignmentView input)
4345   {
4346     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4347   }
4348
4349   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4350           int h, int x, int y)
4351   {
4352     return ShowNewickTree(nf, title, null, w, h, x, y);
4353   }
4354
4355   /**
4356    * Add a treeviewer for the tree extracted from a newick file object to the
4357    * current alignment view
4358    *
4359    * @param nf
4360    *          the tree
4361    * @param title
4362    *          tree viewer title
4363    * @param input
4364    *          Associated alignment input data (or null)
4365    * @param w
4366    *          width
4367    * @param h
4368    *          height
4369    * @param x
4370    *          position
4371    * @param y
4372    *          position
4373    * @return TreePanel handle
4374    */
4375   public TreePanel ShowNewickTree(NewickFile nf, String title,
4376           AlignmentView input, int w, int h, int x, int y)
4377   {
4378     TreePanel tp = null;
4379
4380     try
4381     {
4382       nf.parse();
4383
4384       if (nf.getTree() != null)
4385       {
4386         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4387
4388         tp.setSize(w, h);
4389
4390         if (x > 0 && y > 0)
4391         {
4392           tp.setLocation(x, y);
4393         }
4394
4395         Desktop.addInternalFrame(tp, title, w, h);
4396       }
4397     } catch (Exception ex)
4398     {
4399       ex.printStackTrace();
4400     }
4401
4402     return tp;
4403   }
4404
4405   private boolean buildingMenu = false;
4406
4407   /**
4408    * Generates menu items and listener event actions for web service clients
4409    *
4410    */
4411   public void BuildWebServiceMenu()
4412   {
4413     while (buildingMenu)
4414     {
4415       try
4416       {
4417         System.err.println("Waiting for building menu to finish.");
4418         Thread.sleep(10);
4419       } catch (Exception e)
4420       {
4421       }
4422     }
4423     final AlignFrame me = this;
4424     buildingMenu = true;
4425     new Thread(new Runnable()
4426     {
4427       @Override
4428       public void run()
4429       {
4430         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4431         try
4432         {
4433           // System.err.println("Building ws menu again "
4434           // + Thread.currentThread());
4435           // TODO: add support for context dependent disabling of services based
4436           // on
4437           // alignment and current selection
4438           // TODO: add additional serviceHandle parameter to specify abstract
4439           // handler
4440           // class independently of AbstractName
4441           // TODO: add in rediscovery GUI function to restart discoverer
4442           // TODO: group services by location as well as function and/or
4443           // introduce
4444           // object broker mechanism.
4445           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4446           final IProgressIndicator af = me;
4447
4448           /*
4449            * do not i18n these strings - they are hard-coded in class
4450            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4451            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4452            */
4453           final JMenu msawsmenu = new JMenu("Alignment");
4454           final JMenu secstrmenu = new JMenu(
4455                   "Secondary Structure Prediction");
4456           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4457           final JMenu analymenu = new JMenu("Analysis");
4458           final JMenu dismenu = new JMenu("Protein Disorder");
4459           // JAL-940 - only show secondary structure prediction services from
4460           // the legacy server
4461           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4462               // &&
4463           Discoverer.services != null && (Discoverer.services.size() > 0))
4464           {
4465             // TODO: refactor to allow list of AbstractName/Handler bindings to
4466             // be
4467             // stored or retrieved from elsewhere
4468             // No MSAWS used any more:
4469             // Vector msaws = null; // (Vector)
4470             // Discoverer.services.get("MsaWS");
4471             Vector secstrpr = (Vector) Discoverer.services
4472                     .get("SecStrPred");
4473             if (secstrpr != null)
4474             {
4475               // Add any secondary structure prediction services
4476               for (int i = 0, j = secstrpr.size(); i < j; i++)
4477               {
4478                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4479                         .get(i);
4480                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4481                         .getServiceClient(sh);
4482                 int p = secstrmenu.getItemCount();
4483                 impl.attachWSMenuEntry(secstrmenu, me);
4484                 int q = secstrmenu.getItemCount();
4485                 for (int litm = p; litm < q; litm++)
4486                 {
4487                   legacyItems.add(secstrmenu.getItem(litm));
4488                 }
4489               }
4490             }
4491           }
4492
4493           // Add all submenus in the order they should appear on the web
4494           // services menu
4495           wsmenu.add(msawsmenu);
4496           wsmenu.add(secstrmenu);
4497           wsmenu.add(dismenu);
4498           wsmenu.add(analymenu);
4499           // No search services yet
4500           // wsmenu.add(seqsrchmenu);
4501
4502           javax.swing.SwingUtilities.invokeLater(new Runnable()
4503           {
4504             @Override
4505             public void run()
4506             {
4507               try
4508               {
4509                 webService.removeAll();
4510                 // first, add discovered services onto the webservices menu
4511                 if (wsmenu.size() > 0)
4512                 {
4513                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4514                   {
4515                     webService.add(wsmenu.get(i));
4516                   }
4517                 }
4518                 else
4519                 {
4520                   webService.add(me.webServiceNoServices);
4521                 }
4522                 // TODO: move into separate menu builder class.
4523                 boolean new_sspred = false;
4524                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4525                 {
4526                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4527                   if (jws2servs != null)
4528                   {
4529                     if (jws2servs.hasServices())
4530                     {
4531                       jws2servs.attachWSMenuEntry(webService, me);
4532                       for (Jws2Instance sv : jws2servs.getServices())
4533                       {
4534                         if (sv.description.toLowerCase().contains("jpred"))
4535                         {
4536                           for (JMenuItem jmi : legacyItems)
4537                           {
4538                             jmi.setVisible(false);
4539                           }
4540                         }
4541                       }
4542
4543                     }
4544                     if (jws2servs.isRunning())
4545                     {
4546                       JMenuItem tm = new JMenuItem(
4547                               "Still discovering JABA Services");
4548                       tm.setEnabled(false);
4549                       webService.add(tm);
4550                     }
4551                   }
4552                 }
4553                 build_urlServiceMenu(me.webService);
4554                 build_fetchdbmenu(webService);
4555                 for (JMenu item : wsmenu)
4556                 {
4557                   if (item.getItemCount() == 0)
4558                   {
4559                     item.setEnabled(false);
4560                   }
4561                   else
4562                   {
4563                     item.setEnabled(true);
4564                   }
4565                 }
4566               } catch (Exception e)
4567               {
4568                 Cache.log
4569                         .debug("Exception during web service menu building process.",
4570                                 e);
4571               }
4572             }
4573           });
4574         } catch (Exception e)
4575         {
4576         }
4577         buildingMenu = false;
4578       }
4579     }).start();
4580
4581   }
4582
4583   /**
4584    * construct any groupURL type service menu entries.
4585    *
4586    * @param webService
4587    */
4588   private void build_urlServiceMenu(JMenu webService)
4589   {
4590     // TODO: remove this code when 2.7 is released
4591     // DEBUG - alignmentView
4592     /*
4593      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4594      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4595      *
4596      * @Override public void actionPerformed(ActionEvent e) {
4597      * jalview.datamodel.AlignmentView
4598      * .testSelectionViews(af.viewport.getAlignment(),
4599      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4600      *
4601      * }); webService.add(testAlView);
4602      */
4603     // TODO: refactor to RestClient discoverer and merge menu entries for
4604     // rest-style services with other types of analysis/calculation service
4605     // SHmmr test client - still being implemented.
4606     // DEBUG - alignmentView
4607
4608     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4609             .getRestClients())
4610     {
4611       client.attachWSMenuEntry(
4612               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4613               this);
4614     }
4615   }
4616
4617   /**
4618    * Searches the alignment sequences for xRefs and builds the Show
4619    * Cross-References menu (formerly called Show Products), with database
4620    * sources for which cross-references are found (protein sources for a
4621    * nucleotide alignment and vice versa)
4622    *
4623    * @return true if Show Cross-references menu should be enabled
4624    */
4625   public boolean canShowProducts()
4626   {
4627     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4628     AlignmentI dataset = viewport.getAlignment().getDataset();
4629     boolean showp = false;
4630     try
4631     {
4632       showProducts.removeAll();
4633       final boolean dna = viewport.getAlignment().isNucleotide();
4634       List<String> ptypes = (seqs == null || seqs.length == 0) ? null
4635               : new CrossRef(seqs, dataset)
4636                       .findXrefSourcesForSequences(dna);
4637
4638       for (final String source : ptypes)
4639       {
4640         showp = true;
4641         final AlignFrame af = this;
4642         JMenuItem xtype = new JMenuItem(source);
4643         xtype.addActionListener(new ActionListener()
4644         {
4645           @Override
4646           public void actionPerformed(ActionEvent e)
4647           {
4648             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4649           }
4650         });
4651         showProducts.add(xtype);
4652       }
4653       showProducts.setVisible(showp);
4654       showProducts.setEnabled(showp);
4655     } catch (Exception e)
4656     {
4657       Cache.log
4658               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4659                       e);
4660       return false;
4661     }
4662     return showp;
4663   }
4664
4665   /**
4666    * Finds and displays cross-references for the selected sequences (protein
4667    * products for nucleotide sequences, dna coding sequences for peptides).
4668    *
4669    * @param sel
4670    *          the sequences to show cross-references for
4671    * @param dna
4672    *          true if from a nucleotide alignment (so showing proteins)
4673    * @param source
4674    *          the database to show cross-references for
4675    */
4676   protected void showProductsFor(final SequenceI[] sel,
4677           final boolean _odna, final String source)
4678   {
4679     Runnable foo = new Runnable()
4680     {
4681
4682       @Override
4683       public void run()
4684       {
4685         final long sttime = System.currentTimeMillis();
4686         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4687                 "status.searching_for_sequences_from",
4688                 new Object[] { source }), sttime);
4689         try
4690         {
4691           AlignmentI alignment = AlignFrame.this.getViewport()
4692                   .getAlignment();
4693           AlignmentI dataset = alignment.getDataset() == null ? alignment
4694                   : alignment.getDataset();
4695           boolean dna = alignment.isNucleotide();
4696           if (_odna != dna)
4697           {
4698             System.err
4699                     .println("Conflict: showProducts for alignment originally "
4700                             + "thought to be "
4701                             + (_odna ? "DNA" : "Protein")
4702                             + " now searching for "
4703                             + (dna ? "DNA" : "Protein") + " Context.");
4704           }
4705           AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
4706                   source, dna);
4707           if (xrefs == null)
4708           {
4709             return;
4710           }
4711           /*
4712            * get display scheme (if any) to apply to features
4713            */
4714           FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4715                   .getFeatureColourScheme(source);
4716
4717           AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
4718                   xrefs);
4719           if (!dna)
4720           {
4721             xrefsAlignment = AlignmentUtils.makeCdsAlignment(
4722                     xrefsAlignment.getSequencesArray(), dataset, sel);
4723             xrefsAlignment.alignAs(alignment);
4724           }
4725
4726           /*
4727            * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
4728            * sequences). If we are DNA, drop introns and update mappings
4729            */
4730           AlignmentI copyAlignment = null;
4731
4732           if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4733           {
4734             boolean copyAlignmentIsAligned = false;
4735             if (dna)
4736             {
4737               copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
4738                       xrefsAlignment.getSequencesArray());
4739               if (copyAlignment.getHeight() == 0)
4740               {
4741                 JOptionPane.showMessageDialog(AlignFrame.this,
4742                         MessageManager.getString("label.cant_map_cds"),
4743                         MessageManager.getString("label.operation_failed"),
4744                         JOptionPane.OK_OPTION);
4745                 System.err.println("Failed to make CDS alignment");
4746               }
4747
4748               /*
4749                * pending getting Embl transcripts to 'align',
4750                * we are only doing this for Ensembl
4751                */
4752               // TODO proper criteria for 'can align as cdna'
4753               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4754                       || AlignmentUtils.looksLikeEnsembl(alignment))
4755               {
4756                 copyAlignment.alignAs(alignment);
4757                 copyAlignmentIsAligned = true;
4758               }
4759             }
4760             else
4761             {
4762               copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
4763                       xrefs.getSequencesArray(), dataset);
4764             }
4765             copyAlignment.setGapCharacter(AlignFrame.this.viewport
4766                     .getGapCharacter());
4767
4768             StructureSelectionManager ssm = StructureSelectionManager
4769                     .getStructureSelectionManager(Desktop.instance);
4770
4771             /*
4772              * register any new mappings for sequence mouseover etc
4773              * (will not duplicate any previously registered mappings)
4774              */
4775             ssm.registerMappings(dataset.getCodonFrames());
4776
4777             if (copyAlignment.getHeight() <= 0)
4778             {
4779               System.err.println("No Sequences generated for xRef type "
4780                       + source);
4781               return;
4782             }
4783             /*
4784              * align protein to dna
4785              */
4786             if (dna && copyAlignmentIsAligned)
4787             {
4788               xrefsAlignment.alignAs(copyAlignment);
4789             }
4790             else
4791             {
4792               /*
4793                * align cdna to protein - currently only if
4794                * fetching and aligning Ensembl transcripts!
4795                */
4796               // TODO: generalise for other sources of locus/transcript/cds data
4797               if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4798               {
4799                 copyAlignment.alignAs(xrefsAlignment);
4800               }
4801             }
4802           }
4803           /*
4804            * build AlignFrame(s) according to available alignment data
4805            */
4806           AlignFrame newFrame = new AlignFrame(xrefsAlignment,
4807                   DEFAULT_WIDTH, DEFAULT_HEIGHT);
4808           if (Cache.getDefault("HIDE_INTRONS", true))
4809           {
4810             newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
4811           }
4812           String newtitle = String.format("%s %s %s",
4813                   dna ? MessageManager.getString("label.proteins")
4814                           : MessageManager.getString("label.nucleotides"),
4815                   MessageManager.getString("label.for"), getTitle());
4816           newFrame.setTitle(newtitle);
4817
4818           if (copyAlignment == null)
4819           {
4820             /*
4821              * split frame display is turned off in preferences file
4822              */
4823             Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4824                     DEFAULT_HEIGHT);
4825             return; // via finally clause
4826           }
4827           AlignFrame copyThis = new AlignFrame(copyAlignment,
4828                   AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4829           copyThis.setTitle(AlignFrame.this.getTitle());
4830
4831           boolean showSequenceFeatures = viewport.isShowSequenceFeatures();
4832           newFrame.setShowSeqFeatures(showSequenceFeatures);
4833           copyThis.setShowSeqFeatures(showSequenceFeatures);
4834           FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4835                   .getFeatureRenderer();
4836
4837           /*
4838            * copy feature rendering settings to split frame
4839            */
4840           newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4841                   .transferSettings(myFeatureStyling);
4842           copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4843                   .transferSettings(myFeatureStyling);
4844
4845           /*
4846            * apply 'database source' feature configuration
4847            * if any was found
4848            */
4849           // TODO is this the feature colouring for the original
4850           // alignment or the fetched xrefs? either could be Ensembl
4851           newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4852           copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4853
4854           SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4855                   dna ? newFrame : copyThis);
4856           newFrame.setVisible(true);
4857           copyThis.setVisible(true);
4858           String linkedTitle = MessageManager
4859                   .getString("label.linked_view_title");
4860           Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4861           sf.adjustDivider();
4862         } catch (OutOfMemoryError e)
4863         {
4864           new OOMWarning("whilst fetching crossreferences", e);
4865         } catch (Throwable e)
4866         {
4867           Cache.log.error("Error when finding crossreferences", e);
4868         } finally
4869         {
4870           AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4871                   "status.finished_searching_for_sequences_from",
4872                   new Object[] { source }), sttime);
4873         }
4874       }
4875
4876       /**
4877        * Makes an alignment containing the given sequences, and adds them to the
4878        * given dataset, which is also set as the dataset for the new alignment
4879        *
4880        * TODO: refactor to DatasetI method
4881        *
4882        * @param dataset
4883        * @param seqs
4884        * @return
4885        */
4886       protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4887               AlignmentI seqs)
4888       {
4889         SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4890         for (int s = 0; s < sprods.length; s++)
4891         {
4892           sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4893           if (dataset.getSequences() == null
4894                   || !dataset.getSequences().contains(
4895                           sprods[s].getDatasetSequence()))
4896           {
4897             dataset.addSequence(sprods[s].getDatasetSequence());
4898           }
4899           sprods[s].updatePDBIds();
4900         }
4901         Alignment al = new Alignment(sprods);
4902         al.setDataset(dataset);
4903         return al;
4904       }
4905
4906     };
4907     Thread frunner = new Thread(foo);
4908     frunner.start();
4909   }
4910
4911   /**
4912    * Construct and display a new frame containing the translation of this
4913    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4914    */
4915   @Override
4916   public void showTranslation_actionPerformed(ActionEvent e)
4917   {
4918     AlignmentI al = null;
4919     try
4920     {
4921       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4922
4923       al = dna.translateCdna();
4924     } catch (Exception ex)
4925     {
4926       jalview.bin.Cache.log.error(
4927               "Exception during translation. Please report this !", ex);
4928       final String msg = MessageManager
4929               .getString("label.error_when_translating_sequences_submit_bug_report");
4930       final String errorTitle = MessageManager
4931               .getString("label.implementation_error")
4932               + MessageManager.getString("label.translation_failed");
4933       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4934               JOptionPane.ERROR_MESSAGE);
4935       return;
4936     }
4937     if (al == null || al.getHeight() == 0)
4938     {
4939       final String msg = MessageManager
4940               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4941       final String errorTitle = MessageManager
4942               .getString("label.translation_failed");
4943       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4944               JOptionPane.WARNING_MESSAGE);
4945     }
4946     else
4947     {
4948       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4949       af.setFileFormat(this.currentFileFormat);
4950       final String newTitle = MessageManager.formatMessage(
4951               "label.translation_of_params",
4952               new Object[] { this.getTitle() });
4953       af.setTitle(newTitle);
4954       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4955       {
4956         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4957         viewport.openSplitFrame(af, new Alignment(seqs));
4958       }
4959       else
4960       {
4961         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4962                 DEFAULT_HEIGHT);
4963       }
4964     }
4965   }
4966
4967   /**
4968    * Set the file format
4969    *
4970    * @param fileFormat
4971    */
4972   public void setFileFormat(String fileFormat)
4973   {
4974     this.currentFileFormat = fileFormat;
4975   }
4976
4977   /**
4978    * Try to load a features file onto the alignment.
4979    *
4980    * @param file
4981    *          contents or path to retrieve file
4982    * @param type
4983    *          access mode of file (see jalview.io.AlignFile)
4984    * @return true if features file was parsed correctly.
4985    */
4986   public boolean parseFeaturesFile(String file, String type)
4987   {
4988     return avc.parseFeaturesFile(file, type,
4989             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4990
4991   }
4992
4993   @Override
4994   public void refreshFeatureUI(boolean enableIfNecessary)
4995   {
4996     // note - currently this is only still here rather than in the controller
4997     // because of the featureSettings hard reference that is yet to be
4998     // abstracted
4999     if (enableIfNecessary)
5000     {
5001       viewport.setShowSequenceFeatures(true);
5002       showSeqFeatures.setSelected(true);
5003     }
5004
5005   }
5006
5007   @Override
5008   public void dragEnter(DropTargetDragEvent evt)
5009   {
5010   }
5011
5012   @Override
5013   public void dragExit(DropTargetEvent evt)
5014   {
5015   }
5016
5017   @Override
5018   public void dragOver(DropTargetDragEvent evt)
5019   {
5020   }
5021
5022   @Override
5023   public void dropActionChanged(DropTargetDragEvent evt)
5024   {
5025   }
5026
5027   @Override
5028   public void drop(DropTargetDropEvent evt)
5029   {
5030     Transferable t = evt.getTransferable();
5031     java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
5032
5033     try
5034     {
5035       Desktop.transferFromDropTarget(files, protocols, evt, t);
5036     } catch (Exception e)
5037     {
5038       e.printStackTrace();
5039     }
5040     if (files != null)
5041     {
5042       try
5043       {
5044         // check to see if any of these files have names matching sequences in
5045         // the alignment
5046         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5047                 .getAlignment().getSequencesArray());
5048         /**
5049          * Object[] { String,SequenceI}
5050          */
5051         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5052         ArrayList<String> filesnotmatched = new ArrayList<String>();
5053         for (int i = 0; i < files.size(); i++)
5054         {
5055           String file = files.get(i).toString();
5056           String pdbfn = "";
5057           String protocol = FormatAdapter.checkProtocol(file);
5058           if (protocol == jalview.io.FormatAdapter.FILE)
5059           {
5060             File fl = new File(file);
5061             pdbfn = fl.getName();
5062           }
5063           else if (protocol == jalview.io.FormatAdapter.URL)
5064           {
5065             URL url = new URL(file);
5066             pdbfn = url.getFile();
5067           }
5068           if (pdbfn.length() > 0)
5069           {
5070             // attempt to find a match in the alignment
5071             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5072             int l = 0, c = pdbfn.indexOf(".");
5073             while (mtch == null && c != -1)
5074             {
5075               do
5076               {
5077                 l = c;
5078               } while ((c = pdbfn.indexOf(".", l)) > l);
5079               if (l > -1)
5080               {
5081                 pdbfn = pdbfn.substring(0, l);
5082               }
5083               mtch = idm.findAllIdMatches(pdbfn);
5084             }
5085             if (mtch != null)
5086             {
5087               String type = null;
5088               try
5089               {
5090                 type = new IdentifyFile().identify(file, protocol);
5091               } catch (Exception ex)
5092               {
5093                 type = null;
5094               }
5095               if (type != null)
5096               {
5097                 if (type.equalsIgnoreCase("PDB"))
5098                 {
5099                   filesmatched.add(new Object[] { file, protocol, mtch });
5100                   continue;
5101                 }
5102               }
5103             }
5104             // File wasn't named like one of the sequences or wasn't a PDB file.
5105             filesnotmatched.add(file);
5106           }
5107         }
5108         int assocfiles = 0;
5109         if (filesmatched.size() > 0)
5110         {
5111           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5112                   || JOptionPane
5113                           .showConfirmDialog(
5114                                   this,
5115                                   MessageManager
5116                                           .formatMessage(
5117                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5118                                                   new Object[] { Integer
5119                                                           .valueOf(
5120                                                                   filesmatched
5121                                                                           .size())
5122                                                           .toString() }),
5123                                   MessageManager
5124                                           .getString("label.automatically_associate_pdb_files_by_name"),
5125                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5126
5127           {
5128             for (Object[] fm : filesmatched)
5129             {
5130               // try and associate
5131               // TODO: may want to set a standard ID naming formalism for
5132               // associating PDB files which have no IDs.
5133               for (SequenceI toassoc : (SequenceI[]) fm[2])
5134               {
5135                 PDBEntry pe = new AssociatePdbFileWithSeq()
5136                         .associatePdbWithSeq((String) fm[0],
5137                                 (String) fm[1], toassoc, false,
5138                                 Desktop.instance);
5139                 if (pe != null)
5140                 {
5141                   System.err.println("Associated file : "
5142                           + ((String) fm[0]) + " with "
5143                           + toassoc.getDisplayId(true));
5144                   assocfiles++;
5145                 }
5146               }
5147               alignPanel.paintAlignment(true);
5148             }
5149           }
5150         }
5151         if (filesnotmatched.size() > 0)
5152         {
5153           if (assocfiles > 0
5154                   && (Cache.getDefault(
5155                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5156                           .showConfirmDialog(
5157                                   this,
5158                                   "<html>"
5159                                           + MessageManager
5160                                                   .formatMessage(
5161                                                           "label.ignore_unmatched_dropped_files_info",
5162                                                           new Object[] { Integer
5163                                                                   .valueOf(
5164                                                                           filesnotmatched
5165                                                                                   .size())
5166                                                                   .toString() })
5167                                           + "</html>",
5168                                   MessageManager
5169                                           .getString("label.ignore_unmatched_dropped_files"),
5170                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5171           {
5172             return;
5173           }
5174           for (String fn : filesnotmatched)
5175           {
5176             loadJalviewDataFile(fn, null, null, null);
5177           }
5178
5179         }
5180       } catch (Exception ex)
5181       {
5182         ex.printStackTrace();
5183       }
5184     }
5185   }
5186
5187   /**
5188    * Attempt to load a "dropped" file or URL string: First by testing whether
5189    * it's an Annotation file, then a JNet file, and finally a features file. If
5190    * all are false then the user may have dropped an alignment file onto this
5191    * AlignFrame.
5192    *
5193    * @param file
5194    *          either a filename or a URL string.
5195    */
5196   public void loadJalviewDataFile(String file, String protocol,
5197           String format, SequenceI assocSeq)
5198   {
5199     try
5200     {
5201       if (protocol == null)
5202       {
5203         protocol = FormatAdapter.checkProtocol(file);
5204       }
5205       // if the file isn't identified, or not positively identified as some
5206       // other filetype (PFAM is default unidentified alignment file type) then
5207       // try to parse as annotation.
5208       boolean isAnnotation = (format == null || format
5209               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5210               .annotateAlignmentView(viewport, file, protocol) : false;
5211
5212       if (!isAnnotation)
5213       {
5214         // first see if its a T-COFFEE score file
5215         TCoffeeScoreFile tcf = null;
5216         try
5217         {
5218           tcf = new TCoffeeScoreFile(file, protocol);
5219           if (tcf.isValid())
5220           {
5221             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5222             {
5223               tcoffeeColour.setEnabled(true);
5224               tcoffeeColour.setSelected(true);
5225               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5226               isAnnotation = true;
5227               statusBar
5228                       .setText(MessageManager
5229                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5230             }
5231             else
5232             {
5233               // some problem - if no warning its probable that the ID matching
5234               // process didn't work
5235               JOptionPane
5236                       .showMessageDialog(
5237                               Desktop.desktop,
5238                               tcf.getWarningMessage() == null ? MessageManager
5239                                       .getString("label.check_file_matches_sequence_ids_alignment")
5240                                       : tcf.getWarningMessage(),
5241                               MessageManager
5242                                       .getString("label.problem_reading_tcoffee_score_file"),
5243                               JOptionPane.WARNING_MESSAGE);
5244             }
5245           }
5246           else
5247           {
5248             tcf = null;
5249           }
5250         } catch (Exception x)
5251         {
5252           Cache.log
5253                   .debug("Exception when processing data source as T-COFFEE score file",
5254                           x);
5255           tcf = null;
5256         }
5257         if (tcf == null)
5258         {
5259           // try to see if its a JNet 'concise' style annotation file *before*
5260           // we
5261           // try to parse it as a features file
5262           if (format == null)
5263           {
5264             format = new IdentifyFile().identify(file, protocol);
5265           }
5266           if (format.equalsIgnoreCase("JnetFile"))
5267           {
5268             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5269                     file, protocol);
5270             new JnetAnnotationMaker();
5271             JnetAnnotationMaker.add_annotation(predictions,
5272                     viewport.getAlignment(), 0, false);
5273             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5274             viewport.getAlignment().setSeqrep(repseq);
5275             ColumnSelection cs = new ColumnSelection();
5276             cs.hideInsertionsFor(repseq);
5277             viewport.setColumnSelection(cs);
5278             isAnnotation = true;
5279           }
5280           else if (IdentifyFile.FeaturesFile.equals(format))
5281           {
5282             if (parseFeaturesFile(file, protocol))
5283             {
5284               alignPanel.paintAlignment(true);
5285             }
5286           }
5287           else
5288           {
5289             new FileLoader().LoadFile(viewport, file, protocol, format);
5290           }
5291         }
5292       }
5293       if (isAnnotation)
5294       {
5295
5296         alignPanel.adjustAnnotationHeight();
5297         viewport.updateSequenceIdColours();
5298         buildSortByAnnotationScoresMenu();
5299         alignPanel.paintAlignment(true);
5300       }
5301     } catch (Exception ex)
5302     {
5303       ex.printStackTrace();
5304     } catch (OutOfMemoryError oom)
5305     {
5306       try
5307       {
5308         System.gc();
5309       } catch (Exception x)
5310       {
5311       }
5312       new OOMWarning(
5313               "loading data "
5314                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5315                               : "using " + protocol + " from " + file)
5316                               : ".")
5317                       + (format != null ? "(parsing as '" + format
5318                               + "' file)" : ""), oom, Desktop.desktop);
5319     }
5320   }
5321
5322   /**
5323    * Method invoked by the ChangeListener on the tabbed pane, in other words
5324    * when a different tabbed pane is selected by the user or programmatically.
5325    */
5326   @Override
5327   public void tabSelectionChanged(int index)
5328   {
5329     if (index > -1)
5330     {
5331       alignPanel = alignPanels.get(index);
5332       viewport = alignPanel.av;
5333       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5334       setMenusFromViewport(viewport);
5335     }
5336
5337     /*
5338      * If there is a frame linked to this one in a SplitPane, switch it to the
5339      * same view tab index. No infinite recursion of calls should happen, since
5340      * tabSelectionChanged() should not get invoked on setting the selected
5341      * index to an unchanged value. Guard against setting an invalid index
5342      * before the new view peer tab has been created.
5343      */
5344     final AlignViewportI peer = viewport.getCodingComplement();
5345     if (peer != null)
5346     {
5347       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5348       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5349       {
5350         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5351       }
5352     }
5353   }
5354
5355   /**
5356    * On right mouse click on view tab, prompt for and set new view name.
5357    */
5358   @Override
5359   public void tabbedPane_mousePressed(MouseEvent e)
5360   {
5361     if (e.isPopupTrigger())
5362     {
5363       String msg = MessageManager.getString("label.enter_view_name");
5364       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5365               JOptionPane.QUESTION_MESSAGE);
5366
5367       if (reply != null)
5368       {
5369         viewport.viewName = reply;
5370         // TODO warn if reply is in getExistingViewNames()?
5371         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5372       }
5373     }
5374   }
5375
5376   public AlignViewport getCurrentView()
5377   {
5378     return viewport;
5379   }
5380
5381   /**
5382    * Open the dialog for regex description parsing.
5383    */
5384   @Override
5385   protected void extractScores_actionPerformed(ActionEvent e)
5386   {
5387     ParseProperties pp = new jalview.analysis.ParseProperties(
5388             viewport.getAlignment());
5389     // TODO: verify regex and introduce GUI dialog for version 2.5
5390     // if (pp.getScoresFromDescription("col", "score column ",
5391     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5392     // true)>0)
5393     if (pp.getScoresFromDescription("description column",
5394             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5395     {
5396       buildSortByAnnotationScoresMenu();
5397     }
5398   }
5399
5400   /*
5401    * (non-Javadoc)
5402    *
5403    * @see
5404    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5405    * )
5406    */
5407   @Override
5408   protected void showDbRefs_actionPerformed(ActionEvent e)
5409   {
5410     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5411   }
5412
5413   /*
5414    * (non-Javadoc)
5415    *
5416    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5417    * ActionEvent)
5418    */
5419   @Override
5420   protected void showNpFeats_actionPerformed(ActionEvent e)
5421   {
5422     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5423   }
5424
5425   /**
5426    * find the viewport amongst the tabs in this alignment frame and close that
5427    * tab
5428    *
5429    * @param av
5430    */
5431   public boolean closeView(AlignViewportI av)
5432   {
5433     if (viewport == av)
5434     {
5435       this.closeMenuItem_actionPerformed(false);
5436       return true;
5437     }
5438     Component[] comp = tabbedPane.getComponents();
5439     for (int i = 0; comp != null && i < comp.length; i++)
5440     {
5441       if (comp[i] instanceof AlignmentPanel)
5442       {
5443         if (((AlignmentPanel) comp[i]).av == av)
5444         {
5445           // close the view.
5446           closeView((AlignmentPanel) comp[i]);
5447           return true;
5448         }
5449       }
5450     }
5451     return false;
5452   }
5453
5454   protected void build_fetchdbmenu(JMenu webService)
5455   {
5456     // Temporary hack - DBRef Fetcher always top level ws entry.
5457     // TODO We probably want to store a sequence database checklist in
5458     // preferences and have checkboxes.. rather than individual sources selected
5459     // here
5460     final JMenu rfetch = new JMenu(
5461             MessageManager.getString("action.fetch_db_references"));
5462     rfetch.setToolTipText(MessageManager
5463             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5464     webService.add(rfetch);
5465
5466     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5467             MessageManager.getString("option.trim_retrieved_seqs"));
5468     trimrs.setToolTipText(MessageManager
5469             .getString("label.trim_retrieved_sequences"));
5470     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5471     trimrs.addActionListener(new ActionListener()
5472     {
5473       @Override
5474       public void actionPerformed(ActionEvent e)
5475       {
5476         trimrs.setSelected(trimrs.isSelected());
5477         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5478                 Boolean.valueOf(trimrs.isSelected()).toString());
5479       };
5480     });
5481     rfetch.add(trimrs);
5482     JMenuItem fetchr = new JMenuItem(
5483             MessageManager.getString("label.standard_databases"));
5484     fetchr.setToolTipText(MessageManager
5485             .getString("label.fetch_embl_uniprot"));
5486     fetchr.addActionListener(new ActionListener()
5487     {
5488
5489       @Override
5490       public void actionPerformed(ActionEvent e)
5491       {
5492         new Thread(new Runnable()
5493         {
5494           @Override
5495           public void run()
5496           {
5497             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5498                     .getAlignment().isNucleotide();
5499             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5500                     .getSequenceSelection(), alignPanel.alignFrame, null,
5501                     alignPanel.alignFrame.featureSettings, isNucleotide);
5502             dbRefFetcher.addListener(new FetchFinishedListenerI()
5503             {
5504               @Override
5505               public void finished()
5506               {
5507                 AlignFrame.this.setMenusForViewport();
5508               }
5509             });
5510             dbRefFetcher.fetchDBRefs(false);
5511           }
5512         }).start();
5513
5514       }
5515
5516     });
5517     rfetch.add(fetchr);
5518     final AlignFrame me = this;
5519     new Thread(new Runnable()
5520     {
5521       @Override
5522       public void run()
5523       {
5524         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5525                 .getSequenceFetcherSingleton(me);
5526         javax.swing.SwingUtilities.invokeLater(new Runnable()
5527         {
5528           @Override
5529           public void run()
5530           {
5531             String[] dbclasses = sf.getOrderedSupportedSources();
5532             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5533             // jalview.util.QuickSort.sort(otherdb, otherdb);
5534             List<DbSourceProxy> otherdb;
5535             JMenu dfetch = new JMenu();
5536             JMenu ifetch = new JMenu();
5537             JMenuItem fetchr = null;
5538             int comp = 0, icomp = 0, mcomp = 15;
5539             String mname = null;
5540             int dbi = 0;
5541             for (String dbclass : dbclasses)
5542             {
5543               otherdb = sf.getSourceProxy(dbclass);
5544               // add a single entry for this class, or submenu allowing 'fetch
5545               // all' or pick one
5546               if (otherdb == null || otherdb.size() < 1)
5547               {
5548                 continue;
5549               }
5550               // List<DbSourceProxy> dbs=otherdb;
5551               // otherdb=new ArrayList<DbSourceProxy>();
5552               // for (DbSourceProxy db:dbs)
5553               // {
5554               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5555               // }
5556               if (mname == null)
5557               {
5558                 mname = "From " + dbclass;
5559               }
5560               if (otherdb.size() == 1)
5561               {
5562                 final DbSourceProxy[] dassource = otherdb
5563                         .toArray(new DbSourceProxy[0]);
5564                 DbSourceProxy src = otherdb.get(0);
5565                 fetchr = new JMenuItem(src.getDbSource());
5566                 fetchr.addActionListener(new ActionListener()
5567                 {
5568
5569                   @Override
5570                   public void actionPerformed(ActionEvent e)
5571                   {
5572                     new Thread(new Runnable()
5573                     {
5574
5575                       @Override
5576                       public void run()
5577                       {
5578                         boolean isNucleotide = alignPanel.alignFrame
5579                                 .getViewport().getAlignment()
5580                                 .isNucleotide();
5581                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5582                                 alignPanel.av.getSequenceSelection(),
5583                                 alignPanel.alignFrame, dassource,
5584                                 alignPanel.alignFrame.featureSettings,
5585                                 isNucleotide);
5586                         dbRefFetcher
5587                                 .addListener(new FetchFinishedListenerI()
5588                                 {
5589                                   @Override
5590                                   public void finished()
5591                                   {
5592                                     AlignFrame.this.setMenusForViewport();
5593                                   }
5594                                 });
5595                         dbRefFetcher.fetchDBRefs(false);
5596                       }
5597                     }).start();
5598                   }
5599
5600                 });
5601                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5602                         MessageManager.formatMessage(
5603                                 "label.fetch_retrieve_from",
5604                                 new Object[] { src.getDbName() })));
5605                 dfetch.add(fetchr);
5606                 comp++;
5607               }
5608               else
5609               {
5610                 final DbSourceProxy[] dassource = otherdb
5611                         .toArray(new DbSourceProxy[0]);
5612                 // fetch all entry
5613                 DbSourceProxy src = otherdb.get(0);
5614                 fetchr = new JMenuItem(MessageManager.formatMessage(
5615                         "label.fetch_all_param",
5616                         new Object[] { src.getDbSource() }));
5617                 fetchr.addActionListener(new ActionListener()
5618                 {
5619                   @Override
5620                   public void actionPerformed(ActionEvent e)
5621                   {
5622                     new Thread(new Runnable()
5623                     {
5624
5625                       @Override
5626                       public void run()
5627                       {
5628                         boolean isNucleotide = alignPanel.alignFrame
5629                                 .getViewport().getAlignment()
5630                                 .isNucleotide();
5631                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5632                                 alignPanel.av.getSequenceSelection(),
5633                                 alignPanel.alignFrame, dassource,
5634                                 alignPanel.alignFrame.featureSettings,
5635                                 isNucleotide);
5636                         dbRefFetcher
5637                                 .addListener(new FetchFinishedListenerI()
5638                                 {
5639                                   @Override
5640                                   public void finished()
5641                                   {
5642                                     AlignFrame.this.setMenusForViewport();
5643                                   }
5644                                 });
5645                         dbRefFetcher.fetchDBRefs(false);
5646                       }
5647                     }).start();
5648                   }
5649                 });
5650
5651                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5652                         MessageManager.formatMessage(
5653                                 "label.fetch_retrieve_from_all_sources",
5654                                 new Object[] {
5655                                     Integer.valueOf(otherdb.size())
5656                                             .toString(), src.getDbSource(),
5657                                     src.getDbName() })));
5658                 dfetch.add(fetchr);
5659                 comp++;
5660                 // and then build the rest of the individual menus
5661                 ifetch = new JMenu(MessageManager.formatMessage(
5662                         "label.source_from_db_source",
5663                         new Object[] { src.getDbSource() }));
5664                 icomp = 0;
5665                 String imname = null;
5666                 int i = 0;
5667                 for (DbSourceProxy sproxy : otherdb)
5668                 {
5669                   String dbname = sproxy.getDbName();
5670                   String sname = dbname.length() > 5 ? dbname.substring(0,
5671                           5) + "..." : dbname;
5672                   String msname = dbname.length() > 10 ? dbname.substring(
5673                           0, 10) + "..." : dbname;
5674                   if (imname == null)
5675                   {
5676                     imname = MessageManager.formatMessage(
5677                             "label.from_msname", new Object[] { sname });
5678                   }
5679                   fetchr = new JMenuItem(msname);
5680                   final DbSourceProxy[] dassrc = { sproxy };
5681                   fetchr.addActionListener(new ActionListener()
5682                   {
5683
5684                     @Override
5685                     public void actionPerformed(ActionEvent e)
5686                     {
5687                       new Thread(new Runnable()
5688                       {
5689
5690                         @Override
5691                         public void run()
5692                         {
5693                           boolean isNucleotide = alignPanel.alignFrame
5694                                   .getViewport().getAlignment()
5695                                   .isNucleotide();
5696                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5697                                   alignPanel.av.getSequenceSelection(),
5698                                   alignPanel.alignFrame, dassrc,
5699                                   alignPanel.alignFrame.featureSettings,
5700                                   isNucleotide);
5701                           dbRefFetcher
5702                                   .addListener(new FetchFinishedListenerI()
5703                                   {
5704                                     @Override
5705                                     public void finished()
5706                                     {
5707                                       AlignFrame.this.setMenusForViewport();
5708                                     }
5709                                   });
5710                           dbRefFetcher.fetchDBRefs(false);
5711                         }
5712                       }).start();
5713                     }
5714
5715                   });
5716                   fetchr.setToolTipText("<html>"
5717                           + MessageManager.formatMessage(
5718                                   "label.fetch_retrieve_from", new Object[]
5719                                   { dbname }));
5720                   ifetch.add(fetchr);
5721                   ++i;
5722                   if (++icomp >= mcomp || i == (otherdb.size()))
5723                   {
5724                     ifetch.setText(MessageManager.formatMessage(
5725                             "label.source_to_target", imname, sname));
5726                     dfetch.add(ifetch);
5727                     ifetch = new JMenu();
5728                     imname = null;
5729                     icomp = 0;
5730                     comp++;
5731                   }
5732                 }
5733               }
5734               ++dbi;
5735               if (comp >= mcomp || dbi >= (dbclasses.length))
5736               {
5737                 dfetch.setText(MessageManager.formatMessage(
5738                         "label.source_to_target", mname, dbclass));
5739                 rfetch.add(dfetch);
5740                 dfetch = new JMenu();
5741                 mname = null;
5742                 comp = 0;
5743               }
5744             }
5745           }
5746         });
5747       }
5748     }).start();
5749
5750   }
5751
5752   /**
5753    * Left justify the whole alignment.
5754    */
5755   @Override
5756   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5757   {
5758     AlignmentI al = viewport.getAlignment();
5759     al.justify(false);
5760     viewport.firePropertyChange("alignment", null, al);
5761   }
5762
5763   /**
5764    * Right justify the whole alignment.
5765    */
5766   @Override
5767   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5768   {
5769     AlignmentI al = viewport.getAlignment();
5770     al.justify(true);
5771     viewport.firePropertyChange("alignment", null, al);
5772   }
5773
5774   @Override
5775   public void setShowSeqFeatures(boolean b)
5776   {
5777     showSeqFeatures.setSelected(b);
5778     viewport.setShowSequenceFeatures(b);
5779   }
5780
5781   /*
5782    * (non-Javadoc)
5783    *
5784    * @see
5785    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5786    * awt.event.ActionEvent)
5787    */
5788   @Override
5789   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5790   {
5791     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5792     alignPanel.paintAlignment(true);
5793   }
5794
5795   /*
5796    * (non-Javadoc)
5797    *
5798    * @see
5799    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5800    * .ActionEvent)
5801    */
5802   @Override
5803   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5804   {
5805     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5806     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5807
5808   }
5809
5810   /*
5811    * (non-Javadoc)
5812    *
5813    * @see
5814    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5815    * .event.ActionEvent)
5816    */
5817   @Override
5818   protected void showGroupConservation_actionPerformed(ActionEvent e)
5819   {
5820     viewport.setShowGroupConservation(showGroupConservation.getState());
5821     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5822   }
5823
5824   /*
5825    * (non-Javadoc)
5826    *
5827    * @see
5828    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5829    * .event.ActionEvent)
5830    */
5831   @Override
5832   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5833   {
5834     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5835     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5836   }
5837
5838   /*
5839    * (non-Javadoc)
5840    *
5841    * @see
5842    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5843    * .event.ActionEvent)
5844    */
5845   @Override
5846   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5847   {
5848     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5849     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5850   }
5851
5852   @Override
5853   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5854   {
5855     showSequenceLogo.setState(true);
5856     viewport.setShowSequenceLogo(true);
5857     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5858     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5859   }
5860
5861   @Override
5862   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5863   {
5864     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5865   }
5866
5867   /*
5868    * (non-Javadoc)
5869    *
5870    * @see
5871    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5872    * .event.ActionEvent)
5873    */
5874   @Override
5875   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5876   {
5877     if (avc.makeGroupsFromSelection())
5878     {
5879       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5880       alignPanel.updateAnnotation();
5881       alignPanel.paintAlignment(true);
5882     }
5883   }
5884
5885   public void clearAlignmentSeqRep()
5886   {
5887     // TODO refactor alignmentseqrep to controller
5888     if (viewport.getAlignment().hasSeqrep())
5889     {
5890       viewport.getAlignment().setSeqrep(null);
5891       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5892       alignPanel.updateAnnotation();
5893       alignPanel.paintAlignment(true);
5894     }
5895   }
5896
5897   @Override
5898   protected void createGroup_actionPerformed(ActionEvent e)
5899   {
5900     if (avc.createGroup())
5901     {
5902       alignPanel.alignmentChanged();
5903     }
5904   }
5905
5906   @Override
5907   protected void unGroup_actionPerformed(ActionEvent e)
5908   {
5909     if (avc.unGroup())
5910     {
5911       alignPanel.alignmentChanged();
5912     }
5913   }
5914
5915   /**
5916    * make the given alignmentPanel the currently selected tab
5917    *
5918    * @param alignmentPanel
5919    */
5920   public void setDisplayedView(AlignmentPanel alignmentPanel)
5921   {
5922     if (!viewport.getSequenceSetId().equals(
5923             alignmentPanel.av.getSequenceSetId()))
5924     {
5925       throw new Error(
5926               MessageManager
5927                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5928     }
5929     if (tabbedPane != null
5930             && tabbedPane.getTabCount() > 0
5931             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5932                     .getSelectedIndex())
5933     {
5934       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5935     }
5936   }
5937
5938   /**
5939    * Action on selection of menu options to Show or Hide annotations.
5940    *
5941    * @param visible
5942    * @param forSequences
5943    *          update sequence-related annotations
5944    * @param forAlignment
5945    *          update non-sequence-related annotations
5946    */
5947   @Override
5948   protected void setAnnotationsVisibility(boolean visible,
5949           boolean forSequences, boolean forAlignment)
5950   {
5951     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5952             .getAlignmentAnnotation();
5953     if (anns == null)
5954     {
5955       return;
5956     }
5957     for (AlignmentAnnotation aa : anns)
5958     {
5959       /*
5960        * don't display non-positional annotations on an alignment
5961        */
5962       if (aa.annotations == null)
5963       {
5964         continue;
5965       }
5966       boolean apply = (aa.sequenceRef == null && forAlignment)
5967               || (aa.sequenceRef != null && forSequences);
5968       if (apply)
5969       {
5970         aa.visible = visible;
5971       }
5972     }
5973     alignPanel.validateAnnotationDimensions(true);
5974     alignPanel.alignmentChanged();
5975   }
5976
5977   /**
5978    * Store selected annotation sort order for the view and repaint.
5979    */
5980   @Override
5981   protected void sortAnnotations_actionPerformed()
5982   {
5983     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5984     this.alignPanel.av
5985             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5986     alignPanel.paintAlignment(true);
5987   }
5988
5989   /**
5990    *
5991    * @return alignment panels in this alignment frame
5992    */
5993   public List<? extends AlignmentViewPanel> getAlignPanels()
5994   {
5995     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5996   }
5997
5998   /**
5999    * Open a new alignment window, with the cDNA associated with this (protein)
6000    * alignment, aligned as is the protein.
6001    */
6002   protected void viewAsCdna_actionPerformed()
6003   {
6004     // TODO no longer a menu action - refactor as required
6005     final AlignmentI alignment = getViewport().getAlignment();
6006     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6007     if (mappings == null)
6008     {
6009       return;
6010     }
6011     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6012     for (SequenceI aaSeq : alignment.getSequences())
6013     {
6014       for (AlignedCodonFrame acf : mappings)
6015       {
6016         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6017         if (dnaSeq != null)
6018         {
6019           /*
6020            * There is a cDNA mapping for this protein sequence - add to new
6021            * alignment. It will share the same dataset sequence as other mapped
6022            * cDNA (no new mappings need to be created).
6023            */
6024           final Sequence newSeq = new Sequence(dnaSeq);
6025           newSeq.setDatasetSequence(dnaSeq);
6026           cdnaSeqs.add(newSeq);
6027         }
6028       }
6029     }
6030     if (cdnaSeqs.size() == 0)
6031     {
6032       // show a warning dialog no mapped cDNA
6033       return;
6034     }
6035     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6036             .size()]));
6037     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6038             AlignFrame.DEFAULT_HEIGHT);
6039     cdna.alignAs(alignment);
6040     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6041             + this.title;
6042     Desktop.addInternalFrame(alignFrame, newtitle,
6043             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6044   }
6045
6046   /**
6047    * Set visibility of dna/protein complement view (available when shown in a
6048    * split frame).
6049    *
6050    * @param show
6051    */
6052   @Override
6053   protected void showComplement_actionPerformed(boolean show)
6054   {
6055     SplitContainerI sf = getSplitViewContainer();
6056     if (sf != null)
6057     {
6058       sf.setComplementVisible(this, show);
6059     }
6060   }
6061
6062   /**
6063    * Generate the reverse (optionally complemented) of the selected sequences,
6064    * and add them to the alignment
6065    */
6066   @Override
6067   protected void showReverse_actionPerformed(boolean complement)
6068   {
6069     AlignmentI al = null;
6070     try
6071     {
6072       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6073       al = dna.reverseCdna(complement);
6074       viewport.addAlignment(al, "");
6075       addHistoryItem(new EditCommand(
6076               MessageManager.getString("label.add_sequences"),
6077               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
6078               viewport.getAlignment()));
6079     } catch (Exception ex)
6080     {
6081       System.err.println(ex.getMessage());
6082       return;
6083     }
6084   }
6085
6086   /**
6087    * Try to run a script in the Groovy console, having first ensured that this
6088    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
6089    * be targeted at this alignment.
6090    */
6091   @Override
6092   protected void runGroovy_actionPerformed()
6093   {
6094     Jalview.setCurrentAlignFrame(this);
6095     groovy.ui.Console console = Desktop.getGroovyConsole();
6096     if (console != null)
6097     {
6098       try
6099       {
6100         console.runScript();
6101       } catch (Exception ex)
6102       {
6103         System.err.println((ex.toString()));
6104         JOptionPane
6105                 .showInternalMessageDialog(Desktop.desktop, MessageManager
6106                         .getString("label.couldnt_run_groovy_script"),
6107                         MessageManager
6108                                 .getString("label.groovy_support_failed"),
6109                         JOptionPane.ERROR_MESSAGE);
6110       }
6111     }
6112     else
6113     {
6114       System.err.println("Can't run Groovy script as console not found");
6115     }
6116   }
6117
6118   /**
6119    * Hides columns containing (or not containing) a specified feature, provided
6120    * that would not leave all columns hidden
6121    *
6122    * @param featureType
6123    * @param columnsContaining
6124    * @return
6125    */
6126   public boolean hideFeatureColumns(String featureType,
6127           boolean columnsContaining)
6128   {
6129     boolean notForHiding = avc.markColumnsContainingFeatures(
6130             columnsContaining, false, false, featureType);
6131     if (notForHiding)
6132     {
6133       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
6134               false, featureType))
6135       {
6136         getViewport().hideSelectedColumns();
6137         return true;
6138       }
6139     }
6140     return false;
6141   }
6142 }
6143
6144 class PrintThread extends Thread
6145 {
6146   AlignmentPanel ap;
6147
6148   public PrintThread(AlignmentPanel ap)
6149   {
6150     this.ap = ap;
6151   }
6152
6153   static PageFormat pf;
6154
6155   @Override
6156   public void run()
6157   {
6158     PrinterJob printJob = PrinterJob.getPrinterJob();
6159
6160     if (pf != null)
6161     {
6162       printJob.setPrintable(ap, pf);
6163     }
6164     else
6165     {
6166       printJob.setPrintable(ap);
6167     }
6168
6169     if (printJob.printDialog())
6170     {
6171       try
6172       {
6173         printJob.print();
6174       } catch (Exception PrintException)
6175       {
6176         PrintException.printStackTrace();
6177       }
6178     }
6179   }
6180 }