src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.FeatureSettingsI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.ScoreModelI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.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.jbgui.GAlignFrame;
  78 import jalview.schemes.Blosum62ColourScheme;
  79 import jalview.schemes.BuriedColourScheme;
  80 import jalview.schemes.ClustalxColourScheme;
  81 import jalview.schemes.ColourSchemeI;
  82 import jalview.schemes.ColourSchemeProperty;
  83 import jalview.schemes.HelixColourScheme;
  84 import jalview.schemes.HydrophobicColourScheme;
  85 import jalview.schemes.NucleotideColourScheme;
  86 import jalview.schemes.PIDColourScheme;
  87 import jalview.schemes.PurinePyrimidineColourScheme;
  88 import jalview.schemes.RNAHelicesColourChooser;
  89 import jalview.schemes.ResidueProperties;
  90 import jalview.schemes.StrandColourScheme;
  91 import jalview.schemes.TCoffeeColourScheme;
  92 import jalview.schemes.TaylorColourScheme;
  93 import jalview.schemes.TurnColourScheme;
  94 import jalview.schemes.UserColourScheme;
  95 import jalview.schemes.ZappoColourScheme;
  96 import jalview.structure.StructureSelectionManager;
  97 import jalview.util.MessageManager;
  98 import jalview.viewmodel.AlignmentViewport;
  99 import jalview.ws.SequenceFetcher;
 100 import jalview.ws.jws1.Discoverer;
 101 import jalview.ws.jws2.Jws2Discoverer;
 102 import jalview.ws.jws2.jabaws2.Jws2Instance;
 103 import jalview.ws.seqfetcher.ASequenceFetcher;
 104 import jalview.ws.seqfetcher.DbSourceProxy;
 105
 106 import java.awt.BorderLayout;
 107 import java.awt.Component;
 108 import java.awt.Rectangle;
 109 import java.awt.Toolkit;
 110 import java.awt.datatransfer.Clipboard;
 111 import java.awt.datatransfer.DataFlavor;
 112 import java.awt.datatransfer.StringSelection;
 113 import java.awt.datatransfer.Transferable;
 114 import java.awt.dnd.DnDConstants;
 115 import java.awt.dnd.DropTargetDragEvent;
 116 import java.awt.dnd.DropTargetDropEvent;
 117 import java.awt.dnd.DropTargetEvent;
 118 import java.awt.dnd.DropTargetListener;
 119 import java.awt.event.ActionEvent;
 120 import java.awt.event.ActionListener;
 121 import java.awt.event.ItemEvent;
 122 import java.awt.event.ItemListener;
 123 import java.awt.event.KeyAdapter;
 124 import java.awt.event.KeyEvent;
 125 import java.awt.event.MouseAdapter;
 126 import java.awt.event.MouseEvent;
 127 import java.awt.print.PageFormat;
 128 import java.awt.print.PrinterJob;
 129 import java.beans.PropertyChangeEvent;
 130 import java.io.File;
 131 import java.net.URL;
 132 import java.util.ArrayList;
 133 import java.util.Arrays;
 134 import java.util.Deque;
 135 import java.util.Enumeration;
 136 import java.util.Hashtable;
 137 import java.util.List;
 138 import java.util.Vector;
 139
 140 import javax.swing.JCheckBoxMenuItem;
 141 import javax.swing.JEditorPane;
 142 import javax.swing.JInternalFrame;
 143 import javax.swing.JLayeredPane;
 144 import javax.swing.JMenu;
 145 import javax.swing.JMenuItem;
 146 import javax.swing.JOptionPane;
 147 import javax.swing.JRadioButtonMenuItem;
 148 import javax.swing.JScrollPane;
 149 import javax.swing.SwingUtilities;
 150
 151 /**
 152  * DOCUMENT ME!
 153  *
 154  * @author $author$
 155  * @version $Revision$
 156  */
 157 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 158         IProgressIndicator, AlignViewControllerGuiI
 159 {
 160
 161   public static final int DEFAULT_WIDTH = 700;
 162
 163   public static final int DEFAULT_HEIGHT = 500;
 164
 165   /*
 166    * The currently displayed panel (selected tabbed view if more than one)
 167    */
 168   public AlignmentPanel alignPanel;
 169
 170   AlignViewport viewport;
 171
 172   public AlignViewControllerI avc;
 173
 174   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 175
 176   /**
 177    * Last format used to load or save alignments in this window
 178    */
 179   String currentFileFormat = null;
 180
 181   /**
 182    * Current filename for this alignment
 183    */
 184   String fileName = null;
 185
 186   /**
 187    * Creates a new AlignFrame object with specific width and height.
 188    *
 189    * @param al
 190    * @param width
 191    * @param height
 192    */
 193   public AlignFrame(AlignmentI al, int width, int height)
 194   {
 195     this(al, null, width, height);
 196   }
 197
 198   /**
 199    * Creates a new AlignFrame object with specific width, height and
 200    * sequenceSetId
 201    *
 202    * @param al
 203    * @param width
 204    * @param height
 205    * @param sequenceSetId
 206    */
 207   public AlignFrame(AlignmentI al, int width, int height,
 208           String sequenceSetId)
 209   {
 210     this(al, null, width, height, sequenceSetId);
 211   }
 212
 213   /**
 214    * Creates a new AlignFrame object with specific width, height and
 215    * sequenceSetId
 216    *
 217    * @param al
 218    * @param width
 219    * @param height
 220    * @param sequenceSetId
 221    * @param viewId
 222    */
 223   public AlignFrame(AlignmentI al, int width, int height,
 224           String sequenceSetId, String viewId)
 225   {
 226     this(al, null, width, height, sequenceSetId, viewId);
 227   }
 228
 229   /**
 230    * new alignment window with hidden columns
 231    *
 232    * @param al
 233    *          AlignmentI
 234    * @param hiddenColumns
 235    *          ColumnSelection or null
 236    * @param width
 237    *          Width of alignment frame
 238    * @param height
 239    *          height of frame.
 240    */
 241   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 242           int width, int height)
 243   {
 244     this(al, hiddenColumns, width, height, null);
 245   }
 246
 247   /**
 248    * Create alignment frame for al with hiddenColumns, a specific width and
 249    * height, and specific sequenceId
 250    *
 251    * @param al
 252    * @param hiddenColumns
 253    * @param width
 254    * @param height
 255    * @param sequenceSetId
 256    *          (may be null)
 257    */
 258   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 259           int width, int height, String sequenceSetId)
 260   {
 261     this(al, hiddenColumns, width, height, sequenceSetId, null);
 262   }
 263
 264   /**
 265    * Create alignment frame for al with hiddenColumns, a specific width and
 266    * height, and specific sequenceId
 267    *
 268    * @param al
 269    * @param hiddenColumns
 270    * @param width
 271    * @param height
 272    * @param sequenceSetId
 273    *          (may be null)
 274    * @param viewId
 275    *          (may be null)
 276    */
 277   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 278           int width, int height, String sequenceSetId, String viewId)
 279   {
 280     setSize(width, height);
 281
 282     if (al.getDataset() == null)
 283     {
 284       al.setDataset(null);
 285     }
 286
 287     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 288
 289     alignPanel = new AlignmentPanel(this, viewport);
 290
 291     addAlignmentPanel(alignPanel, true);
 292     init();
 293   }
 294
 295   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 296           ColumnSelection hiddenColumns, int width, int height)
 297   {
 298     setSize(width, height);
 299
 300     if (al.getDataset() == null)
 301     {
 302       al.setDataset(null);
 303     }
 304
 305     viewport = new AlignViewport(al, hiddenColumns);
 306
 307     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 308     {
 309       viewport.hideSequence(hiddenSeqs);
 310     }
 311     alignPanel = new AlignmentPanel(this, viewport);
 312     addAlignmentPanel(alignPanel, true);
 313     init();
 314   }
 315
 316   /**
 317    * Make a new AlignFrame from existing alignmentPanels
 318    *
 319    * @param ap
 320    *          AlignmentPanel
 321    * @param av
 322    *          AlignViewport
 323    */
 324   public AlignFrame(AlignmentPanel ap)
 325   {
 326     viewport = ap.av;
 327     alignPanel = ap;
 328     addAlignmentPanel(ap, false);
 329     init();
 330   }
 331
 332   /**
 333    * initalise the alignframe from the underlying viewport data and the
 334    * configurations
 335    */
 336   void init()
 337   {
 338     if (!Jalview.isHeadlessMode())
 339     {
 340       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 341     }
 342
 343     avc = new jalview.controller.AlignViewController(this, viewport,
 344             alignPanel);
 345     if (viewport.getAlignmentConservationAnnotation() == null)
 346     {
 347       BLOSUM62Colour.setEnabled(false);
 348       conservationMenuItem.setEnabled(false);
 349       modifyConservation.setEnabled(false);
 350       // PIDColour.setEnabled(false);
 351       // abovePIDThreshold.setEnabled(false);
 352       // modifyPID.setEnabled(false);
 353     }
 354
 355     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 356             "No sort");
 357
 358     if (sortby.equals("Id"))
 359     {
 360       sortIDMenuItem_actionPerformed(null);
 361     }
 362     else if (sortby.equals("Pairwise Identity"))
 363     {
 364       sortPairwiseMenuItem_actionPerformed(null);
 365     }
 366
 367     if (Desktop.desktop != null)
 368     {
 369       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 370       addServiceListeners();
 371       setGUINucleotide(viewport.getAlignment().isNucleotide());
 372     }
 373
 374     this.alignPanel.av
 375             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 376
 377     setMenusFromViewport(viewport);
 378     buildSortByAnnotationScoresMenu();
 379     buildTreeMenu();
 380
 381     if (viewport.getWrapAlignment())
 382     {
 383       wrapMenuItem_actionPerformed(null);
 384     }
 385
 386     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 387     {
 388       this.overviewMenuItem_actionPerformed(null);
 389     }
 390
 391     addKeyListener();
 392
 393     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 394     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 395     final String menuLabel = MessageManager
 396             .getString("label.copy_format_from");
 397     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 398             new ViewSetProvider()
 399             {
 400
 401               @Override
 402               public AlignmentPanel[] getAllAlignmentPanels()
 403               {
 404                 origview.clear();
 405                 origview.add(alignPanel);
 406                 // make an array of all alignment panels except for this one
 407                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 408                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 409                 aps.remove(AlignFrame.this.alignPanel);
 410                 return aps.toArray(new AlignmentPanel[aps.size()]);
 411               }
 412             }, selviews, new ItemListener()
 413             {
 414
 415               @Override
 416               public void itemStateChanged(ItemEvent e)
 417               {
 418                 if (origview.size() > 0)
 419                 {
 420                   final AlignmentPanel ap = origview.get(0);
 421
 422                   /*
 423                    * Copy the ViewStyle of the selected panel to 'this one'.
 424                    * Don't change value of 'scaleProteinAsCdna' unless copying
 425                    * from a SplitFrame.
 426                    */
 427                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 428                           .getViewStyle();
 429                   boolean fromSplitFrame = selviews.get(0)
 430                           .getAlignViewport().getCodingComplement() != null;
 431                   if (!fromSplitFrame)
 432                   {
 433                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 434                             .getViewStyle().isScaleProteinAsCdna());
 435                   }
 436                   ap.getAlignViewport().setViewStyle(vs);
 437
 438                   /*
 439                    * Also rescale ViewStyle of SplitFrame complement if there is
 440                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 441                    * the whole ViewStyle (allow cDNA protein to have different
 442                    * fonts)
 443                    */
 444                   AlignViewportI complement = ap.getAlignViewport()
 445                           .getCodingComplement();
 446                   if (complement != null && vs.isScaleProteinAsCdna())
 447                   {
 448                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 449                     ((SplitFrame) af.getSplitViewContainer())
 450                             .adjustLayout();
 451                     af.setMenusForViewport();
 452                   }
 453
 454                   ap.updateLayout();
 455                   ap.setSelected(true);
 456                   ap.alignFrame.setMenusForViewport();
 457
 458                 }
 459               }
 460             });
 461     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 462             .indexOf("devel") > -1
 463             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 464                     .indexOf("test") > -1)
 465     {
 466       formatMenu.add(vsel);
 467     }
 468
 469   }
 470
 471   /**
 472    * Change the filename and format for the alignment, and enable the 'reload'
 473    * button functionality.
 474    *
 475    * @param file
 476    *          valid filename
 477    * @param format
 478    *          format of file
 479    */
 480   public void setFileName(String file, String format)
 481   {
 482     fileName = file;
 483     setFileFormat(format);
 484     reload.setEnabled(true);
 485   }
 486
 487   /**
 488    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 489    * events
 490    */
 491   void addKeyListener()
 492   {
 493     addKeyListener(new KeyAdapter()
 494     {
 495       @Override
 496       public void keyPressed(KeyEvent evt)
 497       {
 498         if (viewport.cursorMode
 499                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 500                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 501                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 502                 && Character.isDigit(evt.getKeyChar()))
 503         {
 504           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 505         }
 506
 507         switch (evt.getKeyCode())
 508         {
 509
 510         case 27: // escape key
 511           deselectAllSequenceMenuItem_actionPerformed(null);
 512
 513           break;
 514
 515         case KeyEvent.VK_DOWN:
 516           if (evt.isAltDown() || !viewport.cursorMode)
 517           {
 518             moveSelectedSequences(false);
 519           }
 520           if (viewport.cursorMode)
 521           {
 522             alignPanel.getSeqPanel().moveCursor(0, 1);
 523           }
 524           break;
 525
 526         case KeyEvent.VK_UP:
 527           if (evt.isAltDown() || !viewport.cursorMode)
 528           {
 529             moveSelectedSequences(true);
 530           }
 531           if (viewport.cursorMode)
 532           {
 533             alignPanel.getSeqPanel().moveCursor(0, -1);
 534           }
 535
 536           break;
 537
 538         case KeyEvent.VK_LEFT:
 539           if (evt.isAltDown() || !viewport.cursorMode)
 540           {
 541             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 542           }
 543           else
 544           {
 545             alignPanel.getSeqPanel().moveCursor(-1, 0);
 546           }
 547
 548           break;
 549
 550         case KeyEvent.VK_RIGHT:
 551           if (evt.isAltDown() || !viewport.cursorMode)
 552           {
 553             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 554           }
 555           else
 556           {
 557             alignPanel.getSeqPanel().moveCursor(1, 0);
 558           }
 559           break;
 560
 561         case KeyEvent.VK_SPACE:
 562           if (viewport.cursorMode)
 563           {
 564             alignPanel.getSeqPanel().insertGapAtCursor(
 565                     evt.isControlDown() || evt.isShiftDown()
 566                             || evt.isAltDown());
 567           }
 568           break;
 569
 570         // case KeyEvent.VK_A:
 571         // if (viewport.cursorMode)
 572         // {
 573         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 574         // //System.out.println("A");
 575         // }
 576         // break;
 577         /*
 578          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 579          * System.out.println("closing bracket"); } break;
 580          */
 581         case KeyEvent.VK_DELETE:
 582         case KeyEvent.VK_BACK_SPACE:
 583           if (!viewport.cursorMode)
 584           {
 585             cut_actionPerformed(null);
 586           }
 587           else
 588           {
 589             alignPanel.getSeqPanel().deleteGapAtCursor(
 590                     evt.isControlDown() || evt.isShiftDown()
 591                             || evt.isAltDown());
 592           }
 593
 594           break;
 595
 596         case KeyEvent.VK_S:
 597           if (viewport.cursorMode)
 598           {
 599             alignPanel.getSeqPanel().setCursorRow();
 600           }
 601           break;
 602         case KeyEvent.VK_C:
 603           if (viewport.cursorMode && !evt.isControlDown())
 604           {
 605             alignPanel.getSeqPanel().setCursorColumn();
 606           }
 607           break;
 608         case KeyEvent.VK_P:
 609           if (viewport.cursorMode)
 610           {
 611             alignPanel.getSeqPanel().setCursorPosition();
 612           }
 613           break;
 614
 615         case KeyEvent.VK_ENTER:
 616         case KeyEvent.VK_COMMA:
 617           if (viewport.cursorMode)
 618           {
 619             alignPanel.getSeqPanel().setCursorRowAndColumn();
 620           }
 621           break;
 622
 623         case KeyEvent.VK_Q:
 624           if (viewport.cursorMode)
 625           {
 626             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 627           }
 628           break;
 629         case KeyEvent.VK_M:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 633           }
 634           break;
 635
 636         case KeyEvent.VK_F2:
 637           viewport.cursorMode = !viewport.cursorMode;
 638           statusBar.setText(MessageManager.formatMessage(
 639                   "label.keyboard_editing_mode",
 640                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 641           if (viewport.cursorMode)
 642           {
 643             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 644             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 645           }
 646           alignPanel.getSeqPanel().seqCanvas.repaint();
 647           break;
 648
 649         case KeyEvent.VK_F1:
 650           try
 651           {
 652             Help.showHelpWindow();
 653           } catch (Exception ex)
 654           {
 655             ex.printStackTrace();
 656           }
 657           break;
 658         case KeyEvent.VK_H:
 659         {
 660           boolean toggleSeqs = !evt.isControlDown();
 661           boolean toggleCols = !evt.isShiftDown();
 662           toggleHiddenRegions(toggleSeqs, toggleCols);
 663           break;
 664         }
 665         case KeyEvent.VK_PAGE_UP:
 666           if (viewport.getWrapAlignment())
 667           {
 668             alignPanel.scrollUp(true);
 669           }
 670           else
 671           {
 672             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 673                     - viewport.endSeq + viewport.startSeq);
 674           }
 675           break;
 676         case KeyEvent.VK_PAGE_DOWN:
 677           if (viewport.getWrapAlignment())
 678           {
 679             alignPanel.scrollUp(false);
 680           }
 681           else
 682           {
 683             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 684                     + viewport.endSeq - viewport.startSeq);
 685           }
 686           break;
 687         }
 688       }
 689
 690       @Override
 691       public void keyReleased(KeyEvent evt)
 692       {
 693         switch (evt.getKeyCode())
 694         {
 695         case KeyEvent.VK_LEFT:
 696           if (evt.isAltDown() || !viewport.cursorMode)
 697           {
 698             viewport.firePropertyChange("alignment", null, viewport
 699                     .getAlignment().getSequences());
 700           }
 701           break;
 702
 703         case KeyEvent.VK_RIGHT:
 704           if (evt.isAltDown() || !viewport.cursorMode)
 705           {
 706             viewport.firePropertyChange("alignment", null, viewport
 707                     .getAlignment().getSequences());
 708           }
 709           break;
 710         }
 711       }
 712     });
 713   }
 714
 715   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 716   {
 717     ap.alignFrame = this;
 718     avc = new jalview.controller.AlignViewController(this, viewport,
 719             alignPanel);
 720
 721     alignPanels.add(ap);
 722
 723     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 724
 725     int aSize = alignPanels.size();
 726
 727     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 728
 729     if (aSize == 1 && ap.av.viewName == null)
 730     {
 731       this.getContentPane().add(ap, BorderLayout.CENTER);
 732     }
 733     else
 734     {
 735       if (aSize == 2)
 736       {
 737         setInitialTabVisible();
 738       }
 739
 740       expandViews.setEnabled(true);
 741       gatherViews.setEnabled(true);
 742       tabbedPane.addTab(ap.av.viewName, ap);
 743
 744       ap.setVisible(false);
 745     }
 746
 747     if (newPanel)
 748     {
 749       if (ap.av.isPadGaps())
 750       {
 751         ap.av.getAlignment().padGaps();
 752       }
 753       ap.av.updateConservation(ap);
 754       ap.av.updateConsensus(ap);
 755       ap.av.updateStrucConsensus(ap);
 756     }
 757   }
 758
 759   public void setInitialTabVisible()
 760   {
 761     expandViews.setEnabled(true);
 762     gatherViews.setEnabled(true);
 763     tabbedPane.setVisible(true);
 764     AlignmentPanel first = alignPanels.get(0);
 765     tabbedPane.addTab(first.av.viewName, first);
 766     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 767   }
 768
 769   public AlignViewport getViewport()
 770   {
 771     return viewport;
 772   }
 773
 774   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 775   private void addServiceListeners()
 776   {
 777     final java.beans.PropertyChangeListener thisListener;
 778     Desktop.instance.addJalviewPropertyChangeListener("services",
 779             thisListener = new java.beans.PropertyChangeListener()
 780             {
 781               @Override
 782               public void propertyChange(PropertyChangeEvent evt)
 783               {
 784                 // // System.out.println("Discoverer property change.");
 785                 // if (evt.getPropertyName().equals("services"))
 786                 {
 787                   SwingUtilities.invokeLater(new Runnable()
 788                   {
 789
 790                     @Override
 791                     public void run()
 792                     {
 793                       System.err
 794                               .println("Rebuild WS Menu for service change");
 795                       BuildWebServiceMenu();
 796                     }
 797
 798                   });
 799                 }
 800               }
 801             });
 802     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 803     {
 804       @Override
 805       public void internalFrameClosed(
 806               javax.swing.event.InternalFrameEvent evt)
 807       {
 808         // System.out.println("deregistering discoverer listener");
 809         Desktop.instance.removeJalviewPropertyChangeListener("services",
 810                 thisListener);
 811         closeMenuItem_actionPerformed(true);
 812       };
 813     });
 814     // Finally, build the menu once to get current service state
 815     new Thread(new Runnable()
 816     {
 817       @Override
 818       public void run()
 819       {
 820         BuildWebServiceMenu();
 821       }
 822     }).start();
 823   }
 824
 825   /**
 826    * Configure menu items that vary according to whether the alignment is
 827    * nucleotide or protein
 828    *
 829    * @param nucleotide
 830    */
 831   public void setGUINucleotide(boolean nucleotide)
 832   {
 833     showTranslation.setVisible(nucleotide);
 834     showReverse.setVisible(nucleotide);
 835     showReverseComplement.setVisible(nucleotide);
 836     conservationMenuItem.setEnabled(!nucleotide);
 837     modifyConservation.setEnabled(!nucleotide);
 838     showGroupConservation.setEnabled(!nucleotide);
 839     rnahelicesColour.setEnabled(nucleotide);
 840     purinePyrimidineColour.setEnabled(nucleotide);
 841     showComplementMenuItem.setText(MessageManager
 842             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 843     setColourSelected(jalview.bin.Cache.getDefault(
 844             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 845                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 846   }
 847
 848   /**
 849    * set up menus for the current viewport. This may be called after any
 850    * operation that affects the data in the current view (selection changed,
 851    * etc) to update the menus to reflect the new state.
 852    */
 853   @Override
 854   public void setMenusForViewport()
 855   {
 856     setMenusFromViewport(viewport);
 857   }
 858
 859   /**
 860    * Need to call this method when tabs are selected for multiple views, or when
 861    * loading from Jalview2XML.java
 862    *
 863    * @param av
 864    *          AlignViewport
 865    */
 866   void setMenusFromViewport(AlignViewport av)
 867   {
 868     padGapsMenuitem.setSelected(av.isPadGaps());
 869     colourTextMenuItem.setSelected(av.isShowColourText());
 870     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 871     conservationMenuItem.setSelected(av.getConservationSelected());
 872     seqLimits.setSelected(av.getShowJVSuffix());
 873     idRightAlign.setSelected(av.isRightAlignIds());
 874     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 875     renderGapsMenuItem.setSelected(av.isRenderGaps());
 876     wrapMenuItem.setSelected(av.getWrapAlignment());
 877     scaleAbove.setVisible(av.getWrapAlignment());
 878     scaleLeft.setVisible(av.getWrapAlignment());
 879     scaleRight.setVisible(av.getWrapAlignment());
 880     annotationPanelMenuItem.setState(av.isShowAnnotation());
 881     /*
 882      * Show/hide annotations only enabled if annotation panel is shown
 883      */
 884     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 885     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 886     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 887     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 888     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 889     viewTextMenuItem.setSelected(av.getShowText());
 890     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 891     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 892     showGroupConservation.setSelected(av.isShowGroupConservation());
 893     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 894     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 895     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 896
 897     setColourSelected(ColourSchemeProperty.getColourName(av
 898             .getGlobalColourScheme()));
 899
 900     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 901     hiddenMarkers.setState(av.getShowHiddenMarkers());
 902     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 903     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 904     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 905     autoCalculate.setSelected(av.autoCalculateConsensus);
 906     sortByTree.setSelected(av.sortByTree);
 907     listenToViewSelections.setSelected(av.followSelection);
 908     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 909     rnahelicesColour
 910             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 911
 912     showProducts.setEnabled(canShowProducts());
 913
 914     updateEditMenuBar();
 915   }
 916
 917   private IProgressIndicator progressBar;
 918
 919   /*
 920    * (non-Javadoc)
 921    *
 922    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 923    */
 924   @Override
 925   public void setProgressBar(String message, long id)
 926   {
 927     progressBar.setProgressBar(message, id);
 928   }
 929
 930   @Override
 931   public void registerHandler(final long id,
 932           final IProgressIndicatorHandler handler)
 933   {
 934     progressBar.registerHandler(id, handler);
 935   }
 936
 937   /**
 938    *
 939    * @return true if any progress bars are still active
 940    */
 941   @Override
 942   public boolean operationInProgress()
 943   {
 944     return progressBar.operationInProgress();
 945   }
 946
 947   @Override
 948   public void setStatus(String text)
 949   {
 950     statusBar.setText(text);
 951   }
 952
 953   /*
 954    * Added so Castor Mapping file can obtain Jalview Version
 955    */
 956   public String getVersion()
 957   {
 958     return jalview.bin.Cache.getProperty("VERSION");
 959   }
 960
 961   public FeatureRenderer getFeatureRenderer()
 962   {
 963     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 964   }
 965
 966   @Override
 967   public void fetchSequence_actionPerformed(ActionEvent e)
 968   {
 969     new jalview.gui.SequenceFetcher(this);
 970   }
 971
 972   @Override
 973   public void addFromFile_actionPerformed(ActionEvent e)
 974   {
 975     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 976   }
 977
 978   @Override
 979   public void reload_actionPerformed(ActionEvent e)
 980   {
 981     if (fileName != null)
 982     {
 983       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 984       // originating file's format
 985       // TODO: work out how to recover feature settings for correct view(s) when
 986       // file is reloaded.
 987       if (currentFileFormat.equals("Jalview"))
 988       {
 989         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 990         for (int i = 0; i < frames.length; i++)
 991         {
 992           if (frames[i] instanceof AlignFrame && frames[i] != this
 993                   && ((AlignFrame) frames[i]).fileName != null
 994                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 995           {
 996             try
 997             {
 998               frames[i].setSelected(true);
 999               Desktop.instance.closeAssociatedWindows();
1000             } catch (java.beans.PropertyVetoException ex)
1001             {
1002             }
1003           }
1004
1005         }
1006         Desktop.instance.closeAssociatedWindows();
1007
1008         FileLoader loader = new FileLoader();
1009         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1010         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1011       }
1012       else
1013       {
1014         Rectangle bounds = this.getBounds();
1015
1016         FileLoader loader = new FileLoader();
1017         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1018         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1019                 protocol, currentFileFormat);
1020
1021         newframe.setBounds(bounds);
1022         if (featureSettings != null && featureSettings.isShowing())
1023         {
1024           final Rectangle fspos = featureSettings.frame.getBounds();
1025           // TODO: need a 'show feature settings' function that takes bounds -
1026           // need to refactor Desktop.addFrame
1027           newframe.featureSettings_actionPerformed(null);
1028           final FeatureSettings nfs = newframe.featureSettings;
1029           SwingUtilities.invokeLater(new Runnable()
1030           {
1031             @Override
1032             public void run()
1033             {
1034               nfs.frame.setBounds(fspos);
1035             }
1036           });
1037           this.featureSettings.close();
1038           this.featureSettings = null;
1039         }
1040         this.closeMenuItem_actionPerformed(true);
1041       }
1042     }
1043   }
1044
1045   @Override
1046   public void addFromText_actionPerformed(ActionEvent e)
1047   {
1048     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1049             .getAlignPanel());
1050   }
1051
1052   @Override
1053   public void addFromURL_actionPerformed(ActionEvent e)
1054   {
1055     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1056   }
1057
1058   @Override
1059   public void save_actionPerformed(ActionEvent e)
1060   {
1061     if (fileName == null
1062             || (currentFileFormat == null || !jalview.io.FormatAdapter
1063                     .isValidIOFormat(currentFileFormat, true))
1064             || fileName.startsWith("http"))
1065     {
1066       saveAs_actionPerformed(null);
1067     }
1068     else
1069     {
1070       saveAlignment(fileName, currentFileFormat);
1071     }
1072   }
1073
1074   /**
1075    * DOCUMENT ME!
1076    *
1077    * @param e
1078    *          DOCUMENT ME!
1079    */
1080   @Override
1081   public void saveAs_actionPerformed(ActionEvent e)
1082   {
1083     JalviewFileChooser chooser = new JalviewFileChooser(
1084             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1085             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1086             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1087             currentFileFormat, false);
1088
1089     chooser.setFileView(new JalviewFileView());
1090     chooser.setDialogTitle(MessageManager
1091             .getString("label.save_alignment_to_file"));
1092     chooser.setToolTipText(MessageManager.getString("action.save"));
1093
1094     int value = chooser.showSaveDialog(this);
1095
1096     if (value == JalviewFileChooser.APPROVE_OPTION)
1097     {
1098       currentFileFormat = chooser.getSelectedFormat();
1099       while (currentFileFormat == null)
1100       {
1101         JOptionPane
1102                 .showInternalMessageDialog(
1103                         Desktop.desktop,
1104                         MessageManager
1105                                 .getString("label.select_file_format_before_saving"),
1106                         MessageManager
1107                                 .getString("label.file_format_not_specified"),
1108                         JOptionPane.WARNING_MESSAGE);
1109         currentFileFormat = chooser.getSelectedFormat();
1110         value = chooser.showSaveDialog(this);
1111         if (value != JalviewFileChooser.APPROVE_OPTION)
1112         {
1113           return;
1114         }
1115       }
1116
1117       fileName = chooser.getSelectedFile().getPath();
1118
1119       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1120               currentFileFormat);
1121
1122       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1123       if (currentFileFormat.indexOf(" ") > -1)
1124       {
1125         currentFileFormat = currentFileFormat.substring(0,
1126                 currentFileFormat.indexOf(" "));
1127       }
1128       saveAlignment(fileName, currentFileFormat);
1129     }
1130   }
1131
1132   public boolean saveAlignment(String file, String format)
1133   {
1134     boolean success = true;
1135
1136     if (format.equalsIgnoreCase("Jalview"))
1137     {
1138       String shortName = title;
1139
1140       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1141       {
1142         shortName = shortName.substring(shortName
1143                 .lastIndexOf(java.io.File.separatorChar) + 1);
1144       }
1145
1146       success = new Jalview2XML().saveAlignment(this, file, shortName);
1147
1148       statusBar.setText(MessageManager.formatMessage(
1149               "label.successfully_saved_to_file_in_format", new Object[] {
1150                   fileName, format }));
1151
1152     }
1153     else
1154     {
1155       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1156       {
1157         warningMessage("Cannot save file " + fileName + " using format "
1158                 + format, "Alignment output format not supported");
1159         if (!Jalview.isHeadlessMode())
1160         {
1161           saveAs_actionPerformed(null);
1162         }
1163         return false;
1164       }
1165
1166       AlignmentExportData exportData = getAlignmentForExport(format,
1167               viewport, null);
1168       if (exportData.getSettings().isCancelled())
1169       {
1170         return false;
1171       }
1172       FormatAdapter f = new FormatAdapter(alignPanel,
1173               exportData.getSettings());
1174       String output = f.formatSequences(
1175               format,
1176               exportData.getAlignment(), // class cast exceptions will
1177               // occur in the distant future
1178               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1179               f.getCacheSuffixDefault(format),
1180               viewport.getColumnSelection());
1181
1182       if (output == null)
1183       {
1184         success = false;
1185       }
1186       else
1187       {
1188         try
1189         {
1190           java.io.PrintWriter out = new java.io.PrintWriter(
1191                   new java.io.FileWriter(file));
1192
1193           out.print(output);
1194           out.close();
1195           this.setTitle(file);
1196           statusBar.setText(MessageManager.formatMessage(
1197                   "label.successfully_saved_to_file_in_format",
1198                   new Object[] { fileName, format }));
1199         } catch (Exception ex)
1200         {
1201           success = false;
1202           ex.printStackTrace();
1203         }
1204       }
1205     }
1206
1207     if (!success)
1208     {
1209       JOptionPane.showInternalMessageDialog(this, MessageManager
1210               .formatMessage("label.couldnt_save_file",
1211                       new Object[] { fileName }), MessageManager
1212               .getString("label.error_saving_file"),
1213               JOptionPane.WARNING_MESSAGE);
1214     }
1215
1216     return success;
1217   }
1218
1219   private void warningMessage(String warning, String title)
1220   {
1221     if (new jalview.util.Platform().isHeadless())
1222     {
1223       System.err.println("Warning: " + title + "\nWarning: " + warning);
1224
1225     }
1226     else
1227     {
1228       JOptionPane.showInternalMessageDialog(this, warning, title,
1229               JOptionPane.WARNING_MESSAGE);
1230     }
1231     return;
1232   }
1233
1234   /**
1235    * DOCUMENT ME!
1236    *
1237    * @param e
1238    *          DOCUMENT ME!
1239    */
1240   @Override
1241   protected void outputText_actionPerformed(ActionEvent e)
1242   {
1243
1244     AlignmentExportData exportData = getAlignmentForExport(
1245             e.getActionCommand(), viewport, null);
1246     if (exportData.getSettings().isCancelled())
1247     {
1248       return;
1249     }
1250     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1251     cap.setForInput(null);
1252     try
1253     {
1254       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1255               .formatSequences(e.getActionCommand(),
1256                       exportData.getAlignment(),
1257                       exportData.getOmitHidden(),
1258                       exportData.getStartEndPostions(),
1259                       viewport.getColumnSelection()));
1260       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1261               "label.alignment_output_command",
1262               new Object[] { e.getActionCommand() }), 600, 500);
1263     } catch (OutOfMemoryError oom)
1264     {
1265       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1266       cap.dispose();
1267     }
1268
1269   }
1270
1271   public static AlignmentExportData getAlignmentForExport(
1272           String exportFormat, AlignViewportI viewport,
1273           AlignExportSettingI exportSettings)
1274   {
1275     AlignmentI alignmentToExport = null;
1276     AlignExportSettingI settings = exportSettings;
1277     String[] omitHidden = null;
1278     int[] alignmentStartEnd = new int[2];
1279
1280     HiddenSequences hiddenSeqs = viewport.getAlignment()
1281             .getHiddenSequences();
1282
1283     alignmentToExport = viewport.getAlignment();
1284     alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1285
1286     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1287     if (settings == null)
1288     {
1289       settings = new AlignExportSettings(hasHiddenSeqs,
1290               viewport.hasHiddenColumns(), exportFormat);
1291     }
1292     // settings.isExportAnnotations();
1293
1294     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1295     {
1296       omitHidden = viewport.getViewAsString(false);
1297     }
1298
1299     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1300     {
1301       alignmentToExport = hiddenSeqs.getFullAlignment();
1302     }
1303     else
1304     {
1305       alignmentToExport = viewport.getAlignment();
1306       alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1307               .getColumnSelection().getHiddenColumns());
1308     }
1309     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1310             omitHidden, alignmentStartEnd, settings);
1311     return ed;
1312   }
1313
1314   public static int[] getStartEnd(int[] aligmentStartEnd,
1315           List<int[]> hiddenCols)
1316   {
1317     int startPos = aligmentStartEnd[0];
1318     int endPos = aligmentStartEnd[1];
1319
1320     int[] lowestRange = new int[] { -1, -1 };
1321     int[] higestRange = new int[] { -1, -1 };
1322
1323     for (int[] hiddenCol : hiddenCols)
1324     {
1325       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1326       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1327     }
1328
1329     if (lowestRange[0] == -1 && lowestRange[1] == -1)
1330     {
1331       startPos = aligmentStartEnd[0];
1332     }
1333     else
1334     {
1335       startPos = lowestRange[1] + 1;
1336     }
1337
1338     if (higestRange[0] == -1 && higestRange[1] == -1)
1339     {
1340       endPos = aligmentStartEnd[1];
1341     }
1342     else
1343     {
1344       endPos = higestRange[0] - 1;
1345     }
1346
1347     // System.out.println("Export range : " + startPos + " - " + endPos);
1348     return new int[] { startPos, endPos };
1349   }
1350
1351   public static void main(String[] args)
1352   {
1353     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1354     hiddenCols.add(new int[] { 0, 0 });
1355     hiddenCols.add(new int[] { 6, 9 });
1356     hiddenCols.add(new int[] { 11, 12 });
1357     hiddenCols.add(new int[] { 33, 33 });
1358     hiddenCols.add(new int[] { 50, 50 });
1359
1360     int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1361     // System.out.println("Export range : " + x[0] + " - " + x[1]);
1362   }
1363
1364   /**
1365    * DOCUMENT ME!
1366    *
1367    * @param e
1368    *          DOCUMENT ME!
1369    */
1370   @Override
1371   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1372   {
1373     new HtmlSvgOutput(null, alignPanel);
1374   }
1375
1376   @Override
1377   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1378   {
1379     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1380     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1381   }
1382
1383   public void createImageMap(File file, String image)
1384   {
1385     alignPanel.makePNGImageMap(file, image);
1386   }
1387
1388   /**
1389    * DOCUMENT ME!
1390    *
1391    * @param e
1392    *          DOCUMENT ME!
1393    */
1394   @Override
1395   public void createPNG(File f)
1396   {
1397     alignPanel.makePNG(f);
1398   }
1399
1400   /**
1401    * DOCUMENT ME!
1402    *
1403    * @param e
1404    *          DOCUMENT ME!
1405    */
1406   @Override
1407   public void createEPS(File f)
1408   {
1409     alignPanel.makeEPS(f);
1410   }
1411
1412   @Override
1413   public void createSVG(File f)
1414   {
1415     alignPanel.makeSVG(f);
1416   }
1417
1418   @Override
1419   public void pageSetup_actionPerformed(ActionEvent e)
1420   {
1421     PrinterJob printJob = PrinterJob.getPrinterJob();
1422     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1423   }
1424
1425   /**
1426    * DOCUMENT ME!
1427    *
1428    * @param e
1429    *          DOCUMENT ME!
1430    */
1431   @Override
1432   public void printMenuItem_actionPerformed(ActionEvent e)
1433   {
1434     // Putting in a thread avoids Swing painting problems
1435     PrintThread thread = new PrintThread(alignPanel);
1436     thread.start();
1437   }
1438
1439   @Override
1440   public void exportFeatures_actionPerformed(ActionEvent e)
1441   {
1442     new AnnotationExporter().exportFeatures(alignPanel);
1443   }
1444
1445   @Override
1446   public void exportAnnotations_actionPerformed(ActionEvent e)
1447   {
1448     new AnnotationExporter().exportAnnotations(alignPanel);
1449   }
1450
1451   @Override
1452   public void associatedData_actionPerformed(ActionEvent e)
1453   {
1454     // Pick the tree file
1455     JalviewFileChooser chooser = new JalviewFileChooser(
1456             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1457     chooser.setFileView(new JalviewFileView());
1458     chooser.setDialogTitle(MessageManager
1459             .getString("label.load_jalview_annotations"));
1460     chooser.setToolTipText(MessageManager
1461             .getString("label.load_jalview_annotations"));
1462
1463     int value = chooser.showOpenDialog(null);
1464
1465     if (value == JalviewFileChooser.APPROVE_OPTION)
1466     {
1467       String choice = chooser.getSelectedFile().getPath();
1468       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1469       loadJalviewDataFile(choice, null, null, null);
1470     }
1471
1472   }
1473
1474   /**
1475    * Close the current view or all views in the alignment frame. If the frame
1476    * only contains one view then the alignment will be removed from memory.
1477    *
1478    * @param closeAllTabs
1479    */
1480   @Override
1481   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1482   {
1483     if (alignPanels != null && alignPanels.size() < 2)
1484     {
1485       closeAllTabs = true;
1486     }
1487
1488     try
1489     {
1490       if (alignPanels != null)
1491       {
1492         if (closeAllTabs)
1493         {
1494           if (this.isClosed())
1495           {
1496             // really close all the windows - otherwise wait till
1497             // setClosed(true) is called
1498             for (int i = 0; i < alignPanels.size(); i++)
1499             {
1500               AlignmentPanel ap = alignPanels.get(i);
1501               ap.closePanel();
1502             }
1503           }
1504         }
1505         else
1506         {
1507           closeView(alignPanel);
1508         }
1509       }
1510
1511       if (closeAllTabs)
1512       {
1513         /*
1514          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1515          * be called recursively, with the frame now in 'closed' state
1516          */
1517         this.setClosed(true);
1518       }
1519     } catch (Exception ex)
1520     {
1521       ex.printStackTrace();
1522     }
1523   }
1524
1525   /**
1526    * Close the specified panel and close up tabs appropriately.
1527    *
1528    * @param panelToClose
1529    */
1530   public void closeView(AlignmentPanel panelToClose)
1531   {
1532     int index = tabbedPane.getSelectedIndex();
1533     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1534     alignPanels.remove(panelToClose);
1535     panelToClose.closePanel();
1536     panelToClose = null;
1537
1538     tabbedPane.removeTabAt(closedindex);
1539     tabbedPane.validate();
1540
1541     if (index > closedindex || index == tabbedPane.getTabCount())
1542     {
1543       // modify currently selected tab index if necessary.
1544       index--;
1545     }
1546
1547     this.tabSelectionChanged(index);
1548   }
1549
1550   /**
1551    * DOCUMENT ME!
1552    */
1553   void updateEditMenuBar()
1554   {
1555
1556     if (viewport.getHistoryList().size() > 0)
1557     {
1558       undoMenuItem.setEnabled(true);
1559       CommandI command = viewport.getHistoryList().peek();
1560       undoMenuItem.setText(MessageManager.formatMessage(
1561               "label.undo_command",
1562               new Object[] { command.getDescription() }));
1563     }
1564     else
1565     {
1566       undoMenuItem.setEnabled(false);
1567       undoMenuItem.setText(MessageManager.getString("action.undo"));
1568     }
1569
1570     if (viewport.getRedoList().size() > 0)
1571     {
1572       redoMenuItem.setEnabled(true);
1573
1574       CommandI command = viewport.getRedoList().peek();
1575       redoMenuItem.setText(MessageManager.formatMessage(
1576               "label.redo_command",
1577               new Object[] { command.getDescription() }));
1578     }
1579     else
1580     {
1581       redoMenuItem.setEnabled(false);
1582       redoMenuItem.setText(MessageManager.getString("action.redo"));
1583     }
1584   }
1585
1586   @Override
1587   public void addHistoryItem(CommandI command)
1588   {
1589     if (command.getSize() > 0)
1590     {
1591       viewport.addToHistoryList(command);
1592       viewport.clearRedoList();
1593       updateEditMenuBar();
1594       viewport.updateHiddenColumns();
1595       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1596       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1597       // viewport.getColumnSelection()
1598       // .getHiddenColumns().size() > 0);
1599     }
1600   }
1601
1602   /**
1603    *
1604    * @return alignment objects for all views
1605    */
1606   AlignmentI[] getViewAlignments()
1607   {
1608     if (alignPanels != null)
1609     {
1610       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1611       int i = 0;
1612       for (AlignmentPanel ap : alignPanels)
1613       {
1614         als[i++] = ap.av.getAlignment();
1615       }
1616       return als;
1617     }
1618     if (viewport != null)
1619     {
1620       return new AlignmentI[] { viewport.getAlignment() };
1621     }
1622     return null;
1623   }
1624
1625   /**
1626    * DOCUMENT ME!
1627    *
1628    * @param e
1629    *          DOCUMENT ME!
1630    */
1631   @Override
1632   protected void undoMenuItem_actionPerformed(ActionEvent e)
1633   {
1634     if (viewport.getHistoryList().isEmpty())
1635     {
1636       return;
1637     }
1638     CommandI command = viewport.getHistoryList().pop();
1639     viewport.addToRedoList(command);
1640     command.undoCommand(getViewAlignments());
1641
1642     AlignmentViewport originalSource = getOriginatingSource(command);
1643     updateEditMenuBar();
1644
1645     if (originalSource != null)
1646     {
1647       if (originalSource != viewport)
1648       {
1649         Cache.log
1650                 .warn("Implementation worry: mismatch of viewport origin for undo");
1651       }
1652       originalSource.updateHiddenColumns();
1653       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1654       // null
1655       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1656       // viewport.getColumnSelection()
1657       // .getHiddenColumns().size() > 0);
1658       originalSource.firePropertyChange("alignment", null, originalSource
1659               .getAlignment().getSequences());
1660     }
1661   }
1662
1663   /**
1664    * DOCUMENT ME!
1665    *
1666    * @param e
1667    *          DOCUMENT ME!
1668    */
1669   @Override
1670   protected void redoMenuItem_actionPerformed(ActionEvent e)
1671   {
1672     if (viewport.getRedoList().size() < 1)
1673     {
1674       return;
1675     }
1676
1677     CommandI command = viewport.getRedoList().pop();
1678     viewport.addToHistoryList(command);
1679     command.doCommand(getViewAlignments());
1680
1681     AlignmentViewport originalSource = getOriginatingSource(command);
1682     updateEditMenuBar();
1683
1684     if (originalSource != null)
1685     {
1686
1687       if (originalSource != viewport)
1688       {
1689         Cache.log
1690                 .warn("Implementation worry: mismatch of viewport origin for redo");
1691       }
1692       originalSource.updateHiddenColumns();
1693       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1694       // null
1695       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1696       // viewport.getColumnSelection()
1697       // .getHiddenColumns().size() > 0);
1698       originalSource.firePropertyChange("alignment", null, originalSource
1699               .getAlignment().getSequences());
1700     }
1701   }
1702
1703   AlignmentViewport getOriginatingSource(CommandI command)
1704   {
1705     AlignmentViewport originalSource = null;
1706     // For sequence removal and addition, we need to fire
1707     // the property change event FROM the viewport where the
1708     // original alignment was altered
1709     AlignmentI al = null;
1710     if (command instanceof EditCommand)
1711     {
1712       EditCommand editCommand = (EditCommand) command;
1713       al = editCommand.getAlignment();
1714       List<Component> comps = PaintRefresher.components.get(viewport
1715               .getSequenceSetId());
1716
1717       for (Component comp : comps)
1718       {
1719         if (comp instanceof AlignmentPanel)
1720         {
1721           if (al == ((AlignmentPanel) comp).av.getAlignment())
1722           {
1723             originalSource = ((AlignmentPanel) comp).av;
1724             break;
1725           }
1726         }
1727       }
1728     }
1729
1730     if (originalSource == null)
1731     {
1732       // The original view is closed, we must validate
1733       // the current view against the closed view first
1734       if (al != null)
1735       {
1736         PaintRefresher.validateSequences(al, viewport.getAlignment());
1737       }
1738
1739       originalSource = viewport;
1740     }
1741
1742     return originalSource;
1743   }
1744
1745   /**
1746    * DOCUMENT ME!
1747    *
1748    * @param up
1749    *          DOCUMENT ME!
1750    */
1751   public void moveSelectedSequences(boolean up)
1752   {
1753     SequenceGroup sg = viewport.getSelectionGroup();
1754
1755     if (sg == null)
1756     {
1757       return;
1758     }
1759     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1760             viewport.getHiddenRepSequences(), up);
1761     alignPanel.paintAlignment(true);
1762   }
1763
1764   synchronized void slideSequences(boolean right, int size)
1765   {
1766     List<SequenceI> sg = new ArrayList<SequenceI>();
1767     if (viewport.cursorMode)
1768     {
1769       sg.add(viewport.getAlignment().getSequenceAt(
1770               alignPanel.getSeqPanel().seqCanvas.cursorY));
1771     }
1772     else if (viewport.getSelectionGroup() != null
1773             && viewport.getSelectionGroup().getSize() != viewport
1774                     .getAlignment().getHeight())
1775     {
1776       sg = viewport.getSelectionGroup().getSequences(
1777               viewport.getHiddenRepSequences());
1778     }
1779
1780     if (sg.size() < 1)
1781     {
1782       return;
1783     }
1784
1785     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1786
1787     for (SequenceI seq : viewport.getAlignment().getSequences())
1788     {
1789       if (!sg.contains(seq))
1790       {
1791         invertGroup.add(seq);
1792       }
1793     }
1794
1795     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1796
1797     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1798     for (int i = 0; i < invertGroup.size(); i++)
1799     {
1800       seqs2[i] = invertGroup.get(i);
1801     }
1802
1803     SlideSequencesCommand ssc;
1804     if (right)
1805     {
1806       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1807               size, viewport.getGapCharacter());
1808     }
1809     else
1810     {
1811       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1812               size, viewport.getGapCharacter());
1813     }
1814
1815     int groupAdjustment = 0;
1816     if (ssc.getGapsInsertedBegin() && right)
1817     {
1818       if (viewport.cursorMode)
1819       {
1820         alignPanel.getSeqPanel().moveCursor(size, 0);
1821       }
1822       else
1823       {
1824         groupAdjustment = size;
1825       }
1826     }
1827     else if (!ssc.getGapsInsertedBegin() && !right)
1828     {
1829       if (viewport.cursorMode)
1830       {
1831         alignPanel.getSeqPanel().moveCursor(-size, 0);
1832       }
1833       else
1834       {
1835         groupAdjustment = -size;
1836       }
1837     }
1838
1839     if (groupAdjustment != 0)
1840     {
1841       viewport.getSelectionGroup().setStartRes(
1842               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1843       viewport.getSelectionGroup().setEndRes(
1844               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1845     }
1846
1847     /*
1848      * just extend the last slide command if compatible; but not if in
1849      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1850      */
1851     boolean appendHistoryItem = false;
1852     Deque<CommandI> historyList = viewport.getHistoryList();
1853     boolean inSplitFrame = getSplitViewContainer() != null;
1854     if (!inSplitFrame && historyList != null && historyList.size() > 0
1855             && historyList.peek() instanceof SlideSequencesCommand)
1856     {
1857       appendHistoryItem = ssc
1858               .appendSlideCommand((SlideSequencesCommand) historyList
1859                       .peek());
1860     }
1861
1862     if (!appendHistoryItem)
1863     {
1864       addHistoryItem(ssc);
1865     }
1866
1867     repaint();
1868   }
1869
1870   /**
1871    * DOCUMENT ME!
1872    *
1873    * @param e
1874    *          DOCUMENT ME!
1875    */
1876   @Override
1877   protected void copy_actionPerformed(ActionEvent e)
1878   {
1879     System.gc();
1880     if (viewport.getSelectionGroup() == null)
1881     {
1882       return;
1883     }
1884     // TODO: preserve the ordering of displayed alignment annotation in any
1885     // internal paste (particularly sequence associated annotation)
1886     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1887     String[] omitHidden = null;
1888
1889     if (viewport.hasHiddenColumns())
1890     {
1891       omitHidden = viewport.getViewAsString(true);
1892     }
1893
1894     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1895             omitHidden, null);
1896
1897     StringSelection ss = new StringSelection(output);
1898
1899     try
1900     {
1901       jalview.gui.Desktop.internalCopy = true;
1902       // Its really worth setting the clipboard contents
1903       // to empty before setting the large StringSelection!!
1904       Toolkit.getDefaultToolkit().getSystemClipboard()
1905               .setContents(new StringSelection(""), null);
1906
1907       Toolkit.getDefaultToolkit().getSystemClipboard()
1908               .setContents(ss, Desktop.instance);
1909     } catch (OutOfMemoryError er)
1910     {
1911       new OOMWarning("copying region", er);
1912       return;
1913     }
1914
1915     ArrayList<int[]> hiddenColumns = null;
1916     if (viewport.hasHiddenColumns())
1917     {
1918       hiddenColumns = new ArrayList<int[]>();
1919       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1920               .getSelectionGroup().getEndRes();
1921       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1922       {
1923         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1924         {
1925           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1926               region[1] - hiddenOffset });
1927         }
1928       }
1929     }
1930
1931     Desktop.jalviewClipboard = new Object[] { seqs,
1932         viewport.getAlignment().getDataset(), hiddenColumns };
1933     statusBar.setText(MessageManager.formatMessage(
1934             "label.copied_sequences_to_clipboard", new Object[] { Integer
1935                     .valueOf(seqs.length).toString() }));
1936   }
1937
1938   /**
1939    * DOCUMENT ME!
1940    *
1941    * @param e
1942    *          DOCUMENT ME!
1943    */
1944   @Override
1945   protected void pasteNew_actionPerformed(ActionEvent e)
1946   {
1947     paste(true);
1948   }
1949
1950   /**
1951    * DOCUMENT ME!
1952    *
1953    * @param e
1954    *          DOCUMENT ME!
1955    */
1956   @Override
1957   protected void pasteThis_actionPerformed(ActionEvent e)
1958   {
1959     paste(false);
1960   }
1961
1962   /**
1963    * Paste contents of Jalview clipboard
1964    *
1965    * @param newAlignment
1966    *          true to paste to a new alignment, otherwise add to this.
1967    */
1968   void paste(boolean newAlignment)
1969   {
1970     boolean externalPaste = true;
1971     try
1972     {
1973       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1974       Transferable contents = c.getContents(this);
1975
1976       if (contents == null)
1977       {
1978         return;
1979       }
1980
1981       String str, format;
1982       try
1983       {
1984         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1985         if (str.length() < 1)
1986         {
1987           return;
1988         }
1989
1990         format = new IdentifyFile().identify(str, "Paste");
1991
1992       } catch (OutOfMemoryError er)
1993       {
1994         new OOMWarning("Out of memory pasting sequences!!", er);
1995         return;
1996       }
1997
1998       SequenceI[] sequences;
1999       boolean annotationAdded = false;
2000       AlignmentI alignment = null;
2001
2002       if (Desktop.jalviewClipboard != null)
2003       {
2004         // The clipboard was filled from within Jalview, we must use the
2005         // sequences
2006         // And dataset from the copied alignment
2007         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2008         // be doubly sure that we create *new* sequence objects.
2009         sequences = new SequenceI[newseq.length];
2010         for (int i = 0; i < newseq.length; i++)
2011         {
2012           sequences[i] = new Sequence(newseq[i]);
2013         }
2014         alignment = new Alignment(sequences);
2015         externalPaste = false;
2016       }
2017       else
2018       {
2019         // parse the clipboard as an alignment.
2020         alignment = new FormatAdapter().readFile(str, "Paste", format);
2021         sequences = alignment.getSequencesArray();
2022       }
2023
2024       int alwidth = 0;
2025       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2026       int fgroup = -1;
2027
2028       if (newAlignment)
2029       {
2030
2031         if (Desktop.jalviewClipboard != null)
2032         {
2033           // dataset is inherited
2034           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2035         }
2036         else
2037         {
2038           // new dataset is constructed
2039           alignment.setDataset(null);
2040         }
2041         alwidth = alignment.getWidth() + 1;
2042       }
2043       else
2044       {
2045         AlignmentI pastedal = alignment; // preserve pasted alignment object
2046         // Add pasted sequences and dataset into existing alignment.
2047         alignment = viewport.getAlignment();
2048         alwidth = alignment.getWidth() + 1;
2049         // decide if we need to import sequences from an existing dataset
2050         boolean importDs = Desktop.jalviewClipboard != null
2051                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2052         // importDs==true instructs us to copy over new dataset sequences from
2053         // an existing alignment
2054         Vector newDs = (importDs) ? new Vector() : null; // used to create
2055         // minimum dataset set
2056
2057         for (int i = 0; i < sequences.length; i++)
2058         {
2059           if (importDs)
2060           {
2061             newDs.addElement(null);
2062           }
2063           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2064           // paste
2065           if (importDs && ds != null)
2066           {
2067             if (!newDs.contains(ds))
2068             {
2069               newDs.setElementAt(ds, i);
2070               ds = new Sequence(ds);
2071               // update with new dataset sequence
2072               sequences[i].setDatasetSequence(ds);
2073             }
2074             else
2075             {
2076               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2077             }
2078           }
2079           else
2080           {
2081             // copy and derive new dataset sequence
2082             sequences[i] = sequences[i].deriveSequence();
2083             alignment.getDataset().addSequence(
2084                     sequences[i].getDatasetSequence());
2085             // TODO: avoid creation of duplicate dataset sequences with a
2086             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2087           }
2088           alignment.addSequence(sequences[i]); // merges dataset
2089         }
2090         if (newDs != null)
2091         {
2092           newDs.clear(); // tidy up
2093         }
2094         if (alignment.getAlignmentAnnotation() != null)
2095         {
2096           for (AlignmentAnnotation alan : alignment
2097                   .getAlignmentAnnotation())
2098           {
2099             if (alan.graphGroup > fgroup)
2100             {
2101               fgroup = alan.graphGroup;
2102             }
2103           }
2104         }
2105         if (pastedal.getAlignmentAnnotation() != null)
2106         {
2107           // Add any annotation attached to alignment.
2108           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2109           for (int i = 0; i < alann.length; i++)
2110           {
2111             annotationAdded = true;
2112             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2113             {
2114               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2115               if (newann.graphGroup > -1)
2116               {
2117                 if (newGraphGroups.size() <= newann.graphGroup
2118                         || newGraphGroups.get(newann.graphGroup) == null)
2119                 {
2120                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2121                   {
2122                     newGraphGroups.add(q, null);
2123                   }
2124                   newGraphGroups.set(newann.graphGroup, new Integer(
2125                           ++fgroup));
2126                 }
2127                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2128                         .intValue();
2129               }
2130
2131               newann.padAnnotation(alwidth);
2132               alignment.addAnnotation(newann);
2133             }
2134           }
2135         }
2136       }
2137       if (!newAlignment)
2138       {
2139         // /////
2140         // ADD HISTORY ITEM
2141         //
2142         addHistoryItem(new EditCommand(
2143                 MessageManager.getString("label.add_sequences"),
2144                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2145       }
2146       // Add any annotations attached to sequences
2147       for (int i = 0; i < sequences.length; i++)
2148       {
2149         if (sequences[i].getAnnotation() != null)
2150         {
2151           AlignmentAnnotation newann;
2152           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2153           {
2154             annotationAdded = true;
2155             newann = sequences[i].getAnnotation()[a];
2156             newann.adjustForAlignment();
2157             newann.padAnnotation(alwidth);
2158             if (newann.graphGroup > -1)
2159             {
2160               if (newann.graphGroup > -1)
2161               {
2162                 if (newGraphGroups.size() <= newann.graphGroup
2163                         || newGraphGroups.get(newann.graphGroup) == null)
2164                 {
2165                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2166                   {
2167                     newGraphGroups.add(q, null);
2168                   }
2169                   newGraphGroups.set(newann.graphGroup, new Integer(
2170                           ++fgroup));
2171                 }
2172                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2173                         .intValue();
2174               }
2175             }
2176             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2177             // was
2178             // duplicated
2179             // earlier
2180             alignment
2181                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2182           }
2183         }
2184       }
2185       if (!newAlignment)
2186       {
2187
2188         // propagate alignment changed.
2189         viewport.setEndSeq(alignment.getHeight());
2190         if (annotationAdded)
2191         {
2192           // Duplicate sequence annotation in all views.
2193           AlignmentI[] alview = this.getViewAlignments();
2194           for (int i = 0; i < sequences.length; i++)
2195           {
2196             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2197             if (sann == null)
2198             {
2199               continue;
2200             }
2201             for (int avnum = 0; avnum < alview.length; avnum++)
2202             {
2203               if (alview[avnum] != alignment)
2204               {
2205                 // duplicate in a view other than the one with input focus
2206                 int avwidth = alview[avnum].getWidth() + 1;
2207                 // this relies on sann being preserved after we
2208                 // modify the sequence's annotation array for each duplication
2209                 for (int a = 0; a < sann.length; a++)
2210                 {
2211                   AlignmentAnnotation newann = new AlignmentAnnotation(
2212                           sann[a]);
2213                   sequences[i].addAlignmentAnnotation(newann);
2214                   newann.padAnnotation(avwidth);
2215                   alview[avnum].addAnnotation(newann); // annotation was
2216                   // duplicated earlier
2217                   // TODO JAL-1145 graphGroups are not updated for sequence
2218                   // annotation added to several views. This may cause
2219                   // strangeness
2220                   alview[avnum].setAnnotationIndex(newann, a);
2221                 }
2222               }
2223             }
2224           }
2225           buildSortByAnnotationScoresMenu();
2226         }
2227         viewport.firePropertyChange("alignment", null,
2228                 alignment.getSequences());
2229         if (alignPanels != null)
2230         {
2231           for (AlignmentPanel ap : alignPanels)
2232           {
2233             ap.validateAnnotationDimensions(false);
2234           }
2235         }
2236         else
2237         {
2238           alignPanel.validateAnnotationDimensions(false);
2239         }
2240
2241       }
2242       else
2243       {
2244         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2245                 DEFAULT_HEIGHT);
2246         String newtitle = new String("Copied sequences");
2247
2248         if (Desktop.jalviewClipboard != null
2249                 && Desktop.jalviewClipboard[2] != null)
2250         {
2251           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2252           for (int[] region : hc)
2253           {
2254             af.viewport.hideColumns(region[0], region[1]);
2255           }
2256         }
2257
2258         // >>>This is a fix for the moment, until a better solution is
2259         // found!!<<<
2260         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2261                 .transferSettings(
2262                         alignPanel.getSeqPanel().seqCanvas
2263                                 .getFeatureRenderer());
2264
2265         // TODO: maintain provenance of an alignment, rather than just make the
2266         // title a concatenation of operations.
2267         if (!externalPaste)
2268         {
2269           if (title.startsWith("Copied sequences"))
2270           {
2271             newtitle = title;
2272           }
2273           else
2274           {
2275             newtitle = newtitle.concat("- from " + title);
2276           }
2277         }
2278         else
2279         {
2280           newtitle = new String("Pasted sequences");
2281         }
2282
2283         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2284                 DEFAULT_HEIGHT);
2285
2286       }
2287
2288     } catch (Exception ex)
2289     {
2290       ex.printStackTrace();
2291       System.out.println("Exception whilst pasting: " + ex);
2292       // could be anything being pasted in here
2293     }
2294
2295   }
2296
2297   @Override
2298   protected void expand_newalign(ActionEvent e)
2299   {
2300     try
2301     {
2302       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2303               .getAlignment(), -1);
2304       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2305               DEFAULT_HEIGHT);
2306       String newtitle = new String("Flanking alignment");
2307
2308       if (Desktop.jalviewClipboard != null
2309               && Desktop.jalviewClipboard[2] != null)
2310       {
2311         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2312         for (int region[] : hc)
2313         {
2314           af.viewport.hideColumns(region[0], region[1]);
2315         }
2316       }
2317
2318       // >>>This is a fix for the moment, until a better solution is
2319       // found!!<<<
2320       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2321               .transferSettings(
2322                       alignPanel.getSeqPanel().seqCanvas
2323                               .getFeatureRenderer());
2324
2325       // TODO: maintain provenance of an alignment, rather than just make the
2326       // title a concatenation of operations.
2327       {
2328         if (title.startsWith("Copied sequences"))
2329         {
2330           newtitle = title;
2331         }
2332         else
2333         {
2334           newtitle = newtitle.concat("- from " + title);
2335         }
2336       }
2337
2338       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2339
2340     } catch (Exception ex)
2341     {
2342       ex.printStackTrace();
2343       System.out.println("Exception whilst pasting: " + ex);
2344       // could be anything being pasted in here
2345     } catch (OutOfMemoryError oom)
2346     {
2347       new OOMWarning("Viewing flanking region of alignment", oom);
2348     }
2349   }
2350
2351   /**
2352    * DOCUMENT ME!
2353    *
2354    * @param e
2355    *          DOCUMENT ME!
2356    */
2357   @Override
2358   protected void cut_actionPerformed(ActionEvent e)
2359   {
2360     copy_actionPerformed(null);
2361     delete_actionPerformed(null);
2362   }
2363
2364   /**
2365    * DOCUMENT ME!
2366    *
2367    * @param e
2368    *          DOCUMENT ME!
2369    */
2370   @Override
2371   protected void delete_actionPerformed(ActionEvent evt)
2372   {
2373
2374     SequenceGroup sg = viewport.getSelectionGroup();
2375     if (sg == null)
2376     {
2377       return;
2378     }
2379
2380     /*
2381      * If the cut affects all sequences, warn, remove highlighted columns
2382      */
2383     if (sg.getSize() == viewport.getAlignment().getHeight())
2384     {
2385       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2386               .getAlignment().getWidth()) ? true : false;
2387       if (isEntireAlignWidth)
2388       {
2389         int confirm = JOptionPane.showConfirmDialog(this,
2390                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2391                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2392                 JOptionPane.OK_CANCEL_OPTION);
2393
2394         if (confirm == JOptionPane.CANCEL_OPTION
2395                 || confirm == JOptionPane.CLOSED_OPTION)
2396         {
2397           return;
2398         }
2399       }
2400       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2401               sg.getEndRes() + 1);
2402     }
2403     SequenceI[] cut = sg.getSequences()
2404             .toArray(new SequenceI[sg.getSize()]);
2405
2406     addHistoryItem(new EditCommand(
2407             MessageManager.getString("label.cut_sequences"), Action.CUT,
2408             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2409             viewport.getAlignment()));
2410
2411     viewport.setSelectionGroup(null);
2412     viewport.sendSelection();
2413     viewport.getAlignment().deleteGroup(sg);
2414
2415     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2416             .getSequences());
2417     if (viewport.getAlignment().getHeight() < 1)
2418     {
2419       try
2420       {
2421         this.setClosed(true);
2422       } catch (Exception ex)
2423       {
2424       }
2425     }
2426   }
2427
2428   /**
2429    * DOCUMENT ME!
2430    *
2431    * @param e
2432    *          DOCUMENT ME!
2433    */
2434   @Override
2435   protected void deleteGroups_actionPerformed(ActionEvent e)
2436   {
2437     if (avc.deleteGroups())
2438     {
2439       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2440       alignPanel.updateAnnotation();
2441       alignPanel.paintAlignment(true);
2442     }
2443   }
2444
2445   /**
2446    * DOCUMENT ME!
2447    *
2448    * @param e
2449    *          DOCUMENT ME!
2450    */
2451   @Override
2452   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2453   {
2454     SequenceGroup sg = new SequenceGroup();
2455
2456     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2457     {
2458       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2459     }
2460
2461     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2462     viewport.setSelectionGroup(sg);
2463     viewport.sendSelection();
2464     alignPanel.paintAlignment(true);
2465     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2466   }
2467
2468   /**
2469    * DOCUMENT ME!
2470    *
2471    * @param e
2472    *          DOCUMENT ME!
2473    */
2474   @Override
2475   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2476   {
2477     if (viewport.cursorMode)
2478     {
2479       alignPanel.getSeqPanel().keyboardNo1 = null;
2480       alignPanel.getSeqPanel().keyboardNo2 = null;
2481     }
2482     viewport.setSelectionGroup(null);
2483     viewport.getColumnSelection().clear();
2484     viewport.setSelectionGroup(null);
2485     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2486     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2487     alignPanel.paintAlignment(true);
2488     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2489     viewport.sendSelection();
2490   }
2491
2492   /**
2493    * DOCUMENT ME!
2494    *
2495    * @param e
2496    *          DOCUMENT ME!
2497    */
2498   @Override
2499   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2500   {
2501     SequenceGroup sg = viewport.getSelectionGroup();
2502
2503     if (sg == null)
2504     {
2505       selectAllSequenceMenuItem_actionPerformed(null);
2506
2507       return;
2508     }
2509
2510     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2511     {
2512       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2513     }
2514
2515     alignPanel.paintAlignment(true);
2516     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2517     viewport.sendSelection();
2518   }
2519
2520   @Override
2521   public void invertColSel_actionPerformed(ActionEvent e)
2522   {
2523     viewport.invertColumnSelection();
2524     alignPanel.paintAlignment(true);
2525     viewport.sendSelection();
2526   }
2527
2528   /**
2529    * DOCUMENT ME!
2530    *
2531    * @param e
2532    *          DOCUMENT ME!
2533    */
2534   @Override
2535   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2536   {
2537     trimAlignment(true);
2538   }
2539
2540   /**
2541    * DOCUMENT ME!
2542    *
2543    * @param e
2544    *          DOCUMENT ME!
2545    */
2546   @Override
2547   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2548   {
2549     trimAlignment(false);
2550   }
2551
2552   void trimAlignment(boolean trimLeft)
2553   {
2554     ColumnSelection colSel = viewport.getColumnSelection();
2555     int column;
2556
2557     if (!colSel.isEmpty())
2558     {
2559       if (trimLeft)
2560       {
2561         column = colSel.getMin();
2562       }
2563       else
2564       {
2565         column = colSel.getMax();
2566       }
2567
2568       SequenceI[] seqs;
2569       if (viewport.getSelectionGroup() != null)
2570       {
2571         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2572                 viewport.getHiddenRepSequences());
2573       }
2574       else
2575       {
2576         seqs = viewport.getAlignment().getSequencesArray();
2577       }
2578
2579       TrimRegionCommand trimRegion;
2580       if (trimLeft)
2581       {
2582         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2583                 column, viewport.getAlignment());
2584         viewport.setStartRes(0);
2585       }
2586       else
2587       {
2588         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2589                 column, viewport.getAlignment());
2590       }
2591
2592       statusBar.setText(MessageManager.formatMessage(
2593               "label.removed_columns",
2594               new String[] { Integer.valueOf(trimRegion.getSize())
2595                       .toString() }));
2596
2597       addHistoryItem(trimRegion);
2598
2599       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2600       {
2601         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2602                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2603         {
2604           viewport.getAlignment().deleteGroup(sg);
2605         }
2606       }
2607
2608       viewport.firePropertyChange("alignment", null, viewport
2609               .getAlignment().getSequences());
2610     }
2611   }
2612
2613   /**
2614    * DOCUMENT ME!
2615    *
2616    * @param e
2617    *          DOCUMENT ME!
2618    */
2619   @Override
2620   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2621   {
2622     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2623
2624     SequenceI[] seqs;
2625     if (viewport.getSelectionGroup() != null)
2626     {
2627       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2628               viewport.getHiddenRepSequences());
2629       start = viewport.getSelectionGroup().getStartRes();
2630       end = viewport.getSelectionGroup().getEndRes();
2631     }
2632     else
2633     {
2634       seqs = viewport.getAlignment().getSequencesArray();
2635     }
2636
2637     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2638             "Remove Gapped Columns", seqs, start, end,
2639             viewport.getAlignment());
2640
2641     addHistoryItem(removeGapCols);
2642
2643     statusBar.setText(MessageManager.formatMessage(
2644             "label.removed_empty_columns",
2645             new Object[] { Integer.valueOf(removeGapCols.getSize())
2646                     .toString() }));
2647
2648     // This is to maintain viewport position on first residue
2649     // of first sequence
2650     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2651     int startRes = seq.findPosition(viewport.startRes);
2652     // ShiftList shifts;
2653     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2654     // edit.alColumnChanges=shifts.getInverse();
2655     // if (viewport.hasHiddenColumns)
2656     // viewport.getColumnSelection().compensateForEdits(shifts);
2657     viewport.setStartRes(seq.findIndex(startRes) - 1);
2658     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2659             .getSequences());
2660
2661   }
2662
2663   /**
2664    * DOCUMENT ME!
2665    *
2666    * @param e
2667    *          DOCUMENT ME!
2668    */
2669   @Override
2670   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2671   {
2672     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2673
2674     SequenceI[] seqs;
2675     if (viewport.getSelectionGroup() != null)
2676     {
2677       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2678               viewport.getHiddenRepSequences());
2679       start = viewport.getSelectionGroup().getStartRes();
2680       end = viewport.getSelectionGroup().getEndRes();
2681     }
2682     else
2683     {
2684       seqs = viewport.getAlignment().getSequencesArray();
2685     }
2686
2687     // This is to maintain viewport position on first residue
2688     // of first sequence
2689     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2690     int startRes = seq.findPosition(viewport.startRes);
2691
2692     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2693             viewport.getAlignment()));
2694
2695     viewport.setStartRes(seq.findIndex(startRes) - 1);
2696
2697     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2698             .getSequences());
2699
2700   }
2701
2702   /**
2703    * DOCUMENT ME!
2704    *
2705    * @param e
2706    *          DOCUMENT ME!
2707    */
2708   @Override
2709   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2710   {
2711     viewport.setPadGaps(padGapsMenuitem.isSelected());
2712     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2713             .getSequences());
2714   }
2715
2716   /**
2717    * DOCUMENT ME!
2718    *
2719    * @param e
2720    *          DOCUMENT ME!
2721    */
2722   @Override
2723   public void findMenuItem_actionPerformed(ActionEvent e)
2724   {
2725     new Finder();
2726   }
2727
2728   /**
2729    * Create a new view of the current alignment.
2730    */
2731   @Override
2732   public void newView_actionPerformed(ActionEvent e)
2733   {
2734     newView(null, true);
2735   }
2736
2737   /**
2738    * Creates and shows a new view of the current alignment.
2739    *
2740    * @param viewTitle
2741    *          title of newly created view; if null, one will be generated
2742    * @param copyAnnotation
2743    *          if true then duplicate all annnotation, groups and settings
2744    * @return new alignment panel, already displayed.
2745    */
2746   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2747   {
2748     /*
2749      * Create a new AlignmentPanel (with its own, new Viewport)
2750      */
2751     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2752             true);
2753     if (!copyAnnotation)
2754     {
2755       /*
2756        * remove all groups and annotation except for the automatic stuff
2757        */
2758       newap.av.getAlignment().deleteAllGroups();
2759       newap.av.getAlignment().deleteAllAnnotations(false);
2760     }
2761
2762     newap.av.setGatherViewsHere(false);
2763
2764     if (viewport.viewName == null)
2765     {
2766       viewport.viewName = MessageManager
2767               .getString("label.view_name_original");
2768     }
2769
2770     /*
2771      * Views share the same edits undo and redo stacks
2772      */
2773     newap.av.setHistoryList(viewport.getHistoryList());
2774     newap.av.setRedoList(viewport.getRedoList());
2775
2776     /*
2777      * Views share the same mappings; need to deregister any new mappings
2778      * created by copyAlignPanel, and register the new reference to the shared
2779      * mappings
2780      */
2781     newap.av.replaceMappings(viewport.getAlignment());
2782
2783     newap.av.viewName = getNewViewName(viewTitle);
2784
2785     addAlignmentPanel(newap, true);
2786     newap.alignmentChanged();
2787
2788     if (alignPanels.size() == 2)
2789     {
2790       viewport.setGatherViewsHere(true);
2791     }
2792     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2793     return newap;
2794   }
2795
2796   /**
2797    * Make a new name for the view, ensuring it is unique within the current
2798    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2799    * these now use viewId. Unique view names are still desirable for usability.)
2800    *
2801    * @param viewTitle
2802    * @return
2803    */
2804   protected String getNewViewName(String viewTitle)
2805   {
2806     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2807     boolean addFirstIndex = false;
2808     if (viewTitle == null || viewTitle.trim().length() == 0)
2809     {
2810       viewTitle = MessageManager.getString("action.view");
2811       addFirstIndex = true;
2812     }
2813     else
2814     {
2815       index = 1;// we count from 1 if given a specific name
2816     }
2817     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2818
2819     List<Component> comps = PaintRefresher.components.get(viewport
2820             .getSequenceSetId());
2821
2822     List<String> existingNames = getExistingViewNames(comps);
2823
2824     while (existingNames.contains(newViewName))
2825     {
2826       newViewName = viewTitle + " " + (++index);
2827     }
2828     return newViewName;
2829   }
2830
2831   /**
2832    * Returns a list of distinct view names found in the given list of
2833    * components. View names are held on the viewport of an AlignmentPanel.
2834    *
2835    * @param comps
2836    * @return
2837    */
2838   protected List<String> getExistingViewNames(List<Component> comps)
2839   {
2840     List<String> existingNames = new ArrayList<String>();
2841     for (Component comp : comps)
2842     {
2843       if (comp instanceof AlignmentPanel)
2844       {
2845         AlignmentPanel ap = (AlignmentPanel) comp;
2846         if (!existingNames.contains(ap.av.viewName))
2847         {
2848           existingNames.add(ap.av.viewName);
2849         }
2850       }
2851     }
2852     return existingNames;
2853   }
2854
2855   /**
2856    * Explode tabbed views into separate windows.
2857    */
2858   @Override
2859   public void expandViews_actionPerformed(ActionEvent e)
2860   {
2861     Desktop.instance.explodeViews(this);
2862   }
2863
2864   /**
2865    * Gather views in separate windows back into a tabbed presentation.
2866    */
2867   @Override
2868   public void gatherViews_actionPerformed(ActionEvent e)
2869   {
2870     Desktop.instance.gatherViews(this);
2871   }
2872
2873   /**
2874    * DOCUMENT ME!
2875    *
2876    * @param e
2877    *          DOCUMENT ME!
2878    */
2879   @Override
2880   public void font_actionPerformed(ActionEvent e)
2881   {
2882     new FontChooser(alignPanel);
2883   }
2884
2885   /**
2886    * DOCUMENT ME!
2887    *
2888    * @param e
2889    *          DOCUMENT ME!
2890    */
2891   @Override
2892   protected void seqLimit_actionPerformed(ActionEvent e)
2893   {
2894     viewport.setShowJVSuffix(seqLimits.isSelected());
2895
2896     alignPanel.getIdPanel().getIdCanvas()
2897             .setPreferredSize(alignPanel.calculateIdWidth());
2898     alignPanel.paintAlignment(true);
2899   }
2900
2901   @Override
2902   public void idRightAlign_actionPerformed(ActionEvent e)
2903   {
2904     viewport.setRightAlignIds(idRightAlign.isSelected());
2905     alignPanel.paintAlignment(true);
2906   }
2907
2908   @Override
2909   public void centreColumnLabels_actionPerformed(ActionEvent e)
2910   {
2911     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2912     alignPanel.paintAlignment(true);
2913   }
2914
2915   /*
2916    * (non-Javadoc)
2917    *
2918    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2919    */
2920   @Override
2921   protected void followHighlight_actionPerformed()
2922   {
2923     /*
2924      * Set the 'follow' flag on the Viewport (and scroll to position if now
2925      * true).
2926      */
2927     final boolean state = this.followHighlightMenuItem.getState();
2928     viewport.setFollowHighlight(state);
2929     if (state)
2930     {
2931       alignPanel.scrollToPosition(
2932               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2933     }
2934   }
2935
2936   /**
2937    * DOCUMENT ME!
2938    *
2939    * @param e
2940    *          DOCUMENT ME!
2941    */
2942   @Override
2943   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2944   {
2945     viewport.setColourText(colourTextMenuItem.isSelected());
2946     alignPanel.paintAlignment(true);
2947   }
2948
2949   /**
2950    * DOCUMENT ME!
2951    *
2952    * @param e
2953    *          DOCUMENT ME!
2954    */
2955   @Override
2956   public void wrapMenuItem_actionPerformed(ActionEvent e)
2957   {
2958     scaleAbove.setVisible(wrapMenuItem.isSelected());
2959     scaleLeft.setVisible(wrapMenuItem.isSelected());
2960     scaleRight.setVisible(wrapMenuItem.isSelected());
2961     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2962     alignPanel.updateLayout();
2963   }
2964
2965   @Override
2966   public void showAllSeqs_actionPerformed(ActionEvent e)
2967   {
2968     viewport.showAllHiddenSeqs();
2969   }
2970
2971   @Override
2972   public void showAllColumns_actionPerformed(ActionEvent e)
2973   {
2974     viewport.showAllHiddenColumns();
2975     repaint();
2976     viewport.sendSelection();
2977   }
2978
2979   @Override
2980   public void hideSelSequences_actionPerformed(ActionEvent e)
2981   {
2982     viewport.hideAllSelectedSeqs();
2983     // alignPanel.paintAlignment(true);
2984   }
2985
2986   /**
2987    * called by key handler and the hide all/show all menu items
2988    *
2989    * @param toggleSeqs
2990    * @param toggleCols
2991    */
2992   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2993   {
2994
2995     boolean hide = false;
2996     SequenceGroup sg = viewport.getSelectionGroup();
2997     if (!toggleSeqs && !toggleCols)
2998     {
2999       // Hide everything by the current selection - this is a hack - we do the
3000       // invert and then hide
3001       // first check that there will be visible columns after the invert.
3002       if ((viewport.getColumnSelection() != null
3003               && viewport.getColumnSelection().getSelected() != null && viewport
3004               .getColumnSelection().getSelected().size() > 0)
3005               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3006                       .getEndRes()))
3007       {
3008         // now invert the sequence set, if required - empty selection implies
3009         // that no hiding is required.
3010         if (sg != null)
3011         {
3012           invertSequenceMenuItem_actionPerformed(null);
3013           sg = viewport.getSelectionGroup();
3014           toggleSeqs = true;
3015
3016         }
3017         viewport.expandColSelection(sg, true);
3018         // finally invert the column selection and get the new sequence
3019         // selection.
3020         invertColSel_actionPerformed(null);
3021         toggleCols = true;
3022       }
3023     }
3024
3025     if (toggleSeqs)
3026     {
3027       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3028       {
3029         hideSelSequences_actionPerformed(null);
3030         hide = true;
3031       }
3032       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3033               .size() > 0))
3034       {
3035         showAllSeqs_actionPerformed(null);
3036       }
3037     }
3038
3039     if (toggleCols)
3040     {
3041       if (viewport.getColumnSelection().getSelected().size() > 0)
3042       {
3043         hideSelColumns_actionPerformed(null);
3044         if (!toggleSeqs)
3045         {
3046           viewport.setSelectionGroup(sg);
3047         }
3048       }
3049       else if (!hide)
3050       {
3051         showAllColumns_actionPerformed(null);
3052       }
3053     }
3054   }
3055
3056   /*
3057    * (non-Javadoc)
3058    *
3059    * @see
3060    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3061    * event.ActionEvent)
3062    */
3063   @Override
3064   public void hideAllButSelection_actionPerformed(ActionEvent e)
3065   {
3066     toggleHiddenRegions(false, false);
3067     viewport.sendSelection();
3068   }
3069
3070   /*
3071    * (non-Javadoc)
3072    *
3073    * @see
3074    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3075    * .ActionEvent)
3076    */
3077   @Override
3078   public void hideAllSelection_actionPerformed(ActionEvent e)
3079   {
3080     SequenceGroup sg = viewport.getSelectionGroup();
3081     viewport.expandColSelection(sg, false);
3082     viewport.hideAllSelectedSeqs();
3083     viewport.hideSelectedColumns();
3084     alignPanel.paintAlignment(true);
3085     viewport.sendSelection();
3086   }
3087
3088   /*
3089    * (non-Javadoc)
3090    *
3091    * @see
3092    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3093    * ActionEvent)
3094    */
3095   @Override
3096   public void showAllhidden_actionPerformed(ActionEvent e)
3097   {
3098     viewport.showAllHiddenColumns();
3099     viewport.showAllHiddenSeqs();
3100     alignPanel.paintAlignment(true);
3101     viewport.sendSelection();
3102   }
3103
3104   @Override
3105   public void hideSelColumns_actionPerformed(ActionEvent e)
3106   {
3107     viewport.hideSelectedColumns();
3108     alignPanel.paintAlignment(true);
3109     viewport.sendSelection();
3110   }
3111
3112   @Override
3113   public void hiddenMarkers_actionPerformed(ActionEvent e)
3114   {
3115     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3116     repaint();
3117   }
3118
3119   /**
3120    * DOCUMENT ME!
3121    *
3122    * @param e
3123    *          DOCUMENT ME!
3124    */
3125   @Override
3126   protected void scaleAbove_actionPerformed(ActionEvent e)
3127   {
3128     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3129     alignPanel.paintAlignment(true);
3130   }
3131
3132   /**
3133    * DOCUMENT ME!
3134    *
3135    * @param e
3136    *          DOCUMENT ME!
3137    */
3138   @Override
3139   protected void scaleLeft_actionPerformed(ActionEvent e)
3140   {
3141     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3142     alignPanel.paintAlignment(true);
3143   }
3144
3145   /**
3146    * DOCUMENT ME!
3147    *
3148    * @param e
3149    *          DOCUMENT ME!
3150    */
3151   @Override
3152   protected void scaleRight_actionPerformed(ActionEvent e)
3153   {
3154     viewport.setScaleRightWrapped(scaleRight.isSelected());
3155     alignPanel.paintAlignment(true);
3156   }
3157
3158   /**
3159    * DOCUMENT ME!
3160    *
3161    * @param e
3162    *          DOCUMENT ME!
3163    */
3164   @Override
3165   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3166   {
3167     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3168     alignPanel.paintAlignment(true);
3169   }
3170
3171   /**
3172    * DOCUMENT ME!
3173    *
3174    * @param e
3175    *          DOCUMENT ME!
3176    */
3177   @Override
3178   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3179   {
3180     viewport.setShowText(viewTextMenuItem.isSelected());
3181     alignPanel.paintAlignment(true);
3182   }
3183
3184   /**
3185    * DOCUMENT ME!
3186    *
3187    * @param e
3188    *          DOCUMENT ME!
3189    */
3190   @Override
3191   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3192   {
3193     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3194     alignPanel.paintAlignment(true);
3195   }
3196
3197   public FeatureSettings featureSettings;
3198
3199   @Override
3200   public FeatureSettingsControllerI getFeatureSettingsUI()
3201   {
3202     return featureSettings;
3203   }
3204
3205   @Override
3206   public void featureSettings_actionPerformed(ActionEvent e)
3207   {
3208     if (featureSettings != null)
3209     {
3210       featureSettings.close();
3211       featureSettings = null;
3212     }
3213     if (!showSeqFeatures.isSelected())
3214     {
3215       // make sure features are actually displayed
3216       showSeqFeatures.setSelected(true);
3217       showSeqFeatures_actionPerformed(null);
3218     }
3219     featureSettings = new FeatureSettings(this);
3220   }
3221
3222   /**
3223    * Set or clear 'Show Sequence Features'
3224    *
3225    * @param evt
3226    *          DOCUMENT ME!
3227    */
3228   @Override
3229   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3230   {
3231     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3232     alignPanel.paintAlignment(true);
3233     if (alignPanel.getOverviewPanel() != null)
3234     {
3235       alignPanel.getOverviewPanel().updateOverviewImage();
3236     }
3237   }
3238
3239   /**
3240    * Set or clear 'Show Sequence Features'
3241    *
3242    * @param evt
3243    *          DOCUMENT ME!
3244    */
3245   @Override
3246   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3247   {
3248     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3249             .isSelected());
3250     if (viewport.isShowSequenceFeaturesHeight())
3251     {
3252       // ensure we're actually displaying features
3253       viewport.setShowSequenceFeatures(true);
3254       showSeqFeatures.setSelected(true);
3255     }
3256     alignPanel.paintAlignment(true);
3257     if (alignPanel.getOverviewPanel() != null)
3258     {
3259       alignPanel.getOverviewPanel().updateOverviewImage();
3260     }
3261   }
3262
3263   /**
3264    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3265    * the annotations panel as a whole.
3266    *
3267    * The options to show/hide all annotations should be enabled when the panel
3268    * is shown, and disabled when the panel is hidden.
3269    *
3270    * @param e
3271    */
3272   @Override
3273   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3274   {
3275     final boolean setVisible = annotationPanelMenuItem.isSelected();
3276     viewport.setShowAnnotation(setVisible);
3277     this.showAllSeqAnnotations.setEnabled(setVisible);
3278     this.hideAllSeqAnnotations.setEnabled(setVisible);
3279     this.showAllAlAnnotations.setEnabled(setVisible);
3280     this.hideAllAlAnnotations.setEnabled(setVisible);
3281     alignPanel.updateLayout();
3282   }
3283
3284   @Override
3285   public void alignmentProperties()
3286   {
3287     JEditorPane editPane = new JEditorPane("text/html", "");
3288     editPane.setEditable(false);
3289     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3290             .formatAsHtml();
3291     editPane.setText(MessageManager.formatMessage("label.html_content",
3292             new Object[] { contents.toString() }));
3293     JInternalFrame frame = new JInternalFrame();
3294     frame.getContentPane().add(new JScrollPane(editPane));
3295
3296     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3297             "label.alignment_properties", new Object[] { getTitle() }),
3298             500, 400);
3299   }
3300
3301   /**
3302    * DOCUMENT ME!
3303    *
3304    * @param e
3305    *          DOCUMENT ME!
3306    */
3307   @Override
3308   public void overviewMenuItem_actionPerformed(ActionEvent e)
3309   {
3310     if (alignPanel.overviewPanel != null)
3311     {
3312       return;
3313     }
3314
3315     JInternalFrame frame = new JInternalFrame();
3316     OverviewPanel overview = new OverviewPanel(alignPanel);
3317     frame.setContentPane(overview);
3318     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3319             "label.overview_params", new Object[] { this.getTitle() }),
3320             frame.getWidth(), frame.getHeight());
3321     frame.pack();
3322     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3323     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3324     {
3325       @Override
3326       public void internalFrameClosed(
3327               javax.swing.event.InternalFrameEvent evt)
3328       {
3329         alignPanel.setOverviewPanel(null);
3330       };
3331     });
3332
3333     alignPanel.setOverviewPanel(overview);
3334   }
3335
3336   @Override
3337   public void textColour_actionPerformed(ActionEvent e)
3338   {
3339     new TextColourChooser().chooseColour(alignPanel, null);
3340   }
3341
3342   /**
3343    * DOCUMENT ME!
3344    *
3345    * @param e
3346    *          DOCUMENT ME!
3347    */
3348   @Override
3349   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3350   {
3351     changeColour(null);
3352   }
3353
3354   /**
3355    * DOCUMENT ME!
3356    *
3357    * @param e
3358    *          DOCUMENT ME!
3359    */
3360   @Override
3361   public void clustalColour_actionPerformed(ActionEvent e)
3362   {
3363     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3364             viewport.getHiddenRepSequences()));
3365   }
3366
3367   /**
3368    * DOCUMENT ME!
3369    *
3370    * @param e
3371    *          DOCUMENT ME!
3372    */
3373   @Override
3374   public void zappoColour_actionPerformed(ActionEvent e)
3375   {
3376     changeColour(new ZappoColourScheme());
3377   }
3378
3379   /**
3380    * DOCUMENT ME!
3381    *
3382    * @param e
3383    *          DOCUMENT ME!
3384    */
3385   @Override
3386   public void taylorColour_actionPerformed(ActionEvent e)
3387   {
3388     changeColour(new TaylorColourScheme());
3389   }
3390
3391   /**
3392    * DOCUMENT ME!
3393    *
3394    * @param e
3395    *          DOCUMENT ME!
3396    */
3397   @Override
3398   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3399   {
3400     changeColour(new HydrophobicColourScheme());
3401   }
3402
3403   /**
3404    * DOCUMENT ME!
3405    *
3406    * @param e
3407    *          DOCUMENT ME!
3408    */
3409   @Override
3410   public void helixColour_actionPerformed(ActionEvent e)
3411   {
3412     changeColour(new HelixColourScheme());
3413   }
3414
3415   /**
3416    * DOCUMENT ME!
3417    *
3418    * @param e
3419    *          DOCUMENT ME!
3420    */
3421   @Override
3422   public void strandColour_actionPerformed(ActionEvent e)
3423   {
3424     changeColour(new StrandColourScheme());
3425   }
3426
3427   /**
3428    * DOCUMENT ME!
3429    *
3430    * @param e
3431    *          DOCUMENT ME!
3432    */
3433   @Override
3434   public void turnColour_actionPerformed(ActionEvent e)
3435   {
3436     changeColour(new TurnColourScheme());
3437   }
3438
3439   /**
3440    * DOCUMENT ME!
3441    *
3442    * @param e
3443    *          DOCUMENT ME!
3444    */
3445   @Override
3446   public void buriedColour_actionPerformed(ActionEvent e)
3447   {
3448     changeColour(new BuriedColourScheme());
3449   }
3450
3451   /**
3452    * DOCUMENT ME!
3453    *
3454    * @param e
3455    *          DOCUMENT ME!
3456    */
3457   @Override
3458   public void nucleotideColour_actionPerformed(ActionEvent e)
3459   {
3460     changeColour(new NucleotideColourScheme());
3461   }
3462
3463   @Override
3464   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3465   {
3466     changeColour(new PurinePyrimidineColourScheme());
3467   }
3468
3469   /*
3470    * public void covariationColour_actionPerformed(ActionEvent e) {
3471    * changeColour(new
3472    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3473    * ()[0])); }
3474    */
3475   @Override
3476   public void annotationColour_actionPerformed(ActionEvent e)
3477   {
3478     new AnnotationColourChooser(viewport, alignPanel);
3479   }
3480
3481   @Override
3482   public void annotationColumn_actionPerformed(ActionEvent e)
3483   {
3484     new AnnotationColumnChooser(viewport, alignPanel);
3485   }
3486
3487   @Override
3488   public void rnahelicesColour_actionPerformed(ActionEvent e)
3489   {
3490     new RNAHelicesColourChooser(viewport, alignPanel);
3491   }
3492
3493   /**
3494    * DOCUMENT ME!
3495    *
3496    * @param e
3497    *          DOCUMENT ME!
3498    */
3499   @Override
3500   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3501   {
3502     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3503   }
3504
3505   /**
3506    * DOCUMENT ME!
3507    *
3508    * @param cs
3509    *          DOCUMENT ME!
3510    */
3511   @Override
3512   public void changeColour(ColourSchemeI cs)
3513   {
3514     // TODO: pull up to controller method
3515
3516     if (cs != null)
3517     {
3518       // Make sure viewport is up to date w.r.t. any sliders
3519       if (viewport.getAbovePIDThreshold())
3520       {
3521         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3522                 "Background");
3523         viewport.setThreshold(threshold);
3524       }
3525
3526       if (viewport.getConservationSelected())
3527       {
3528         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3529                 cs, "Background"));
3530       }
3531       if (cs instanceof TCoffeeColourScheme)
3532       {
3533         tcoffeeColour.setEnabled(true);
3534         tcoffeeColour.setSelected(true);
3535       }
3536     }
3537
3538     viewport.setGlobalColourScheme(cs);
3539
3540     alignPanel.paintAlignment(true);
3541   }
3542
3543   /**
3544    * DOCUMENT ME!
3545    *
3546    * @param e
3547    *          DOCUMENT ME!
3548    */
3549   @Override
3550   protected void modifyPID_actionPerformed(ActionEvent e)
3551   {
3552     if (viewport.getAbovePIDThreshold()
3553             && viewport.getGlobalColourScheme() != null)
3554     {
3555       SliderPanel.setPIDSliderSource(alignPanel,
3556               viewport.getGlobalColourScheme(), "Background");
3557       SliderPanel.showPIDSlider();
3558     }
3559   }
3560
3561   /**
3562    * DOCUMENT ME!
3563    *
3564    * @param e
3565    *          DOCUMENT ME!
3566    */
3567   @Override
3568   protected void modifyConservation_actionPerformed(ActionEvent e)
3569   {
3570     if (viewport.getConservationSelected()
3571             && viewport.getGlobalColourScheme() != null)
3572     {
3573       SliderPanel.setConservationSlider(alignPanel,
3574               viewport.getGlobalColourScheme(), "Background");
3575       SliderPanel.showConservationSlider();
3576     }
3577   }
3578
3579   /**
3580    * DOCUMENT ME!
3581    *
3582    * @param e
3583    *          DOCUMENT ME!
3584    */
3585   @Override
3586   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3587   {
3588     viewport.setConservationSelected(conservationMenuItem.isSelected());
3589
3590     viewport.setAbovePIDThreshold(false);
3591     abovePIDThreshold.setSelected(false);
3592
3593     changeColour(viewport.getGlobalColourScheme());
3594
3595     modifyConservation_actionPerformed(null);
3596   }
3597
3598   /**
3599    * DOCUMENT ME!
3600    *
3601    * @param e
3602    *          DOCUMENT ME!
3603    */
3604   @Override
3605   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3606   {
3607     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3608
3609     conservationMenuItem.setSelected(false);
3610     viewport.setConservationSelected(false);
3611
3612     changeColour(viewport.getGlobalColourScheme());
3613
3614     modifyPID_actionPerformed(null);
3615   }
3616
3617   /**
3618    * DOCUMENT ME!
3619    *
3620    * @param e
3621    *          DOCUMENT ME!
3622    */
3623   @Override
3624   public void userDefinedColour_actionPerformed(ActionEvent e)
3625   {
3626     if (e.getActionCommand().equals(
3627             MessageManager.getString("action.user_defined")))
3628     {
3629       new UserDefinedColours(alignPanel, null);
3630     }
3631     else
3632     {
3633       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3634               .getUserColourSchemes().get(e.getActionCommand());
3635
3636       changeColour(udc);
3637     }
3638   }
3639
3640   public void updateUserColourMenu()
3641   {
3642
3643     Component[] menuItems = colourMenu.getMenuComponents();
3644     int iSize = menuItems.length;
3645     for (int i = 0; i < iSize; i++)
3646     {
3647       if (menuItems[i].getName() != null
3648               && menuItems[i].getName().equals("USER_DEFINED"))
3649       {
3650         colourMenu.remove(menuItems[i]);
3651         iSize--;
3652       }
3653     }
3654     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3655     {
3656       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3657               .getUserColourSchemes().keys();
3658
3659       while (userColours.hasMoreElements())
3660       {
3661         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3662                 userColours.nextElement().toString());
3663         radioItem.setName("USER_DEFINED");
3664         radioItem.addMouseListener(new MouseAdapter()
3665         {
3666           @Override
3667           public void mousePressed(MouseEvent evt)
3668           {
3669             if (evt.isControlDown()
3670                     || SwingUtilities.isRightMouseButton(evt))
3671             {
3672               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3673
3674               int option = JOptionPane.showInternalConfirmDialog(
3675                       jalview.gui.Desktop.desktop,
3676                       MessageManager
3677                               .getString("label.remove_from_default_list"),
3678                       MessageManager
3679                               .getString("label.remove_user_defined_colour"),
3680                       JOptionPane.YES_NO_OPTION);
3681               if (option == JOptionPane.YES_OPTION)
3682               {
3683                 jalview.gui.UserDefinedColours
3684                         .removeColourFromDefaults(radioItem.getText());
3685                 colourMenu.remove(radioItem);
3686               }
3687               else
3688               {
3689                 radioItem.addActionListener(new ActionListener()
3690                 {
3691                   @Override
3692                   public void actionPerformed(ActionEvent evt)
3693                   {
3694                     userDefinedColour_actionPerformed(evt);
3695                   }
3696                 });
3697               }
3698             }
3699           }
3700         });
3701         radioItem.addActionListener(new ActionListener()
3702         {
3703           @Override
3704           public void actionPerformed(ActionEvent evt)
3705           {
3706             userDefinedColour_actionPerformed(evt);
3707           }
3708         });
3709
3710         colourMenu.insert(radioItem, 15);
3711         colours.add(radioItem);
3712       }
3713     }
3714   }
3715
3716   /**
3717    * DOCUMENT ME!
3718    *
3719    * @param e
3720    *          DOCUMENT ME!
3721    */
3722   @Override
3723   public void PIDColour_actionPerformed(ActionEvent e)
3724   {
3725     changeColour(new PIDColourScheme());
3726   }
3727
3728   /**
3729    * DOCUMENT ME!
3730    *
3731    * @param e
3732    *          DOCUMENT ME!
3733    */
3734   @Override
3735   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3736   {
3737     changeColour(new Blosum62ColourScheme());
3738   }
3739
3740   /**
3741    * DOCUMENT ME!
3742    *
3743    * @param e
3744    *          DOCUMENT ME!
3745    */
3746   @Override
3747   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3748   {
3749     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3750     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3751             .getAlignment().getSequenceAt(0), null);
3752     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3753             viewport.getAlignment()));
3754     alignPanel.paintAlignment(true);
3755   }
3756
3757   /**
3758    * DOCUMENT ME!
3759    *
3760    * @param e
3761    *          DOCUMENT ME!
3762    */
3763   @Override
3764   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3765   {
3766     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3767     AlignmentSorter.sortByID(viewport.getAlignment());
3768     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3769             viewport.getAlignment()));
3770     alignPanel.paintAlignment(true);
3771   }
3772
3773   /**
3774    * DOCUMENT ME!
3775    *
3776    * @param e
3777    *          DOCUMENT ME!
3778    */
3779   @Override
3780   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3781   {
3782     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3783     AlignmentSorter.sortByLength(viewport.getAlignment());
3784     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3785             viewport.getAlignment()));
3786     alignPanel.paintAlignment(true);
3787   }
3788
3789   /**
3790    * DOCUMENT ME!
3791    *
3792    * @param e
3793    *          DOCUMENT ME!
3794    */
3795   @Override
3796   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3797   {
3798     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3799     AlignmentSorter.sortByGroup(viewport.getAlignment());
3800     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3801             viewport.getAlignment()));
3802
3803     alignPanel.paintAlignment(true);
3804   }
3805
3806   /**
3807    * DOCUMENT ME!
3808    *
3809    * @param e
3810    *          DOCUMENT ME!
3811    */
3812   @Override
3813   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3814   {
3815     new RedundancyPanel(alignPanel, this);
3816   }
3817
3818   /**
3819    * DOCUMENT ME!
3820    *
3821    * @param e
3822    *          DOCUMENT ME!
3823    */
3824   @Override
3825   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3826   {
3827     if ((viewport.getSelectionGroup() == null)
3828             || (viewport.getSelectionGroup().getSize() < 2))
3829     {
3830       JOptionPane.showInternalMessageDialog(this, MessageManager
3831               .getString("label.you_must_select_least_two_sequences"),
3832               MessageManager.getString("label.invalid_selection"),
3833               JOptionPane.WARNING_MESSAGE);
3834     }
3835     else
3836     {
3837       JInternalFrame frame = new JInternalFrame();
3838       frame.setContentPane(new PairwiseAlignPanel(viewport));
3839       Desktop.addInternalFrame(frame,
3840               MessageManager.getString("action.pairwise_alignment"), 600,
3841               500);
3842     }
3843   }
3844
3845   /**
3846    * DOCUMENT ME!
3847    *
3848    * @param e
3849    *          DOCUMENT ME!
3850    */
3851   @Override
3852   public void PCAMenuItem_actionPerformed(ActionEvent e)
3853   {
3854     if (((viewport.getSelectionGroup() != null)
3855             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3856             .getSelectionGroup().getSize() > 0))
3857             || (viewport.getAlignment().getHeight() < 4))
3858     {
3859       JOptionPane
3860               .showInternalMessageDialog(
3861                       this,
3862                       MessageManager
3863                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3864                       MessageManager
3865                               .getString("label.sequence_selection_insufficient"),
3866                       JOptionPane.WARNING_MESSAGE);
3867
3868       return;
3869     }
3870
3871     new PCAPanel(alignPanel);
3872   }
3873
3874   @Override
3875   public void autoCalculate_actionPerformed(ActionEvent e)
3876   {
3877     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3878     if (viewport.autoCalculateConsensus)
3879     {
3880       viewport.firePropertyChange("alignment", null, viewport
3881               .getAlignment().getSequences());
3882     }
3883   }
3884
3885   @Override
3886   public void sortByTreeOption_actionPerformed(ActionEvent e)
3887   {
3888     viewport.sortByTree = sortByTree.isSelected();
3889   }
3890
3891   @Override
3892   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3893   {
3894     viewport.followSelection = listenToViewSelections.isSelected();
3895   }
3896
3897   /**
3898    * DOCUMENT ME!
3899    *
3900    * @param e
3901    *          DOCUMENT ME!
3902    */
3903   @Override
3904   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3905   {
3906     newTreePanel("AV", "PID", "Average distance tree using PID");
3907   }
3908
3909   /**
3910    * DOCUMENT ME!
3911    *
3912    * @param e
3913    *          DOCUMENT ME!
3914    */
3915   @Override
3916   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3917   {
3918     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3919   }
3920
3921   /**
3922    * DOCUMENT ME!
3923    *
3924    * @param e
3925    *          DOCUMENT ME!
3926    */
3927   @Override
3928   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3929   {
3930     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3931   }
3932
3933   /**
3934    * DOCUMENT ME!
3935    *
3936    * @param e
3937    *          DOCUMENT ME!
3938    */
3939   @Override
3940   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3941   {
3942     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3943   }
3944
3945   /**
3946    * DOCUMENT ME!
3947    *
3948    * @param type
3949    *          DOCUMENT ME!
3950    * @param pwType
3951    *          DOCUMENT ME!
3952    * @param title
3953    *          DOCUMENT ME!
3954    */
3955   void newTreePanel(String type, String pwType, String title)
3956   {
3957     TreePanel tp;
3958
3959     if (viewport.getSelectionGroup() != null
3960             && viewport.getSelectionGroup().getSize() > 0)
3961     {
3962       if (viewport.getSelectionGroup().getSize() < 3)
3963       {
3964         JOptionPane
3965                 .showMessageDialog(
3966                         Desktop.desktop,
3967                         MessageManager
3968                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3969                         MessageManager
3970                                 .getString("label.not_enough_sequences"),
3971                         JOptionPane.WARNING_MESSAGE);
3972         return;
3973       }
3974
3975       SequenceGroup sg = viewport.getSelectionGroup();
3976
3977       /* Decide if the selection is a column region */
3978       for (SequenceI _s : sg.getSequences())
3979       {
3980         if (_s.getLength() < sg.getEndRes())
3981         {
3982           JOptionPane
3983                   .showMessageDialog(
3984                           Desktop.desktop,
3985                           MessageManager
3986                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3987                           MessageManager
3988                                   .getString("label.sequences_selection_not_aligned"),
3989                           JOptionPane.WARNING_MESSAGE);
3990
3991           return;
3992         }
3993       }
3994
3995       title = title + " on region";
3996       tp = new TreePanel(alignPanel, type, pwType);
3997     }
3998     else
3999     {
4000       // are the visible sequences aligned?
4001       if (!viewport.getAlignment().isAligned(false))
4002       {
4003         JOptionPane
4004                 .showMessageDialog(
4005                         Desktop.desktop,
4006                         MessageManager
4007                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4008                         MessageManager
4009                                 .getString("label.sequences_not_aligned"),
4010                         JOptionPane.WARNING_MESSAGE);
4011
4012         return;
4013       }
4014
4015       if (viewport.getAlignment().getHeight() < 2)
4016       {
4017         return;
4018       }
4019
4020       tp = new TreePanel(alignPanel, type, pwType);
4021     }
4022
4023     title += " from ";
4024
4025     if (viewport.viewName != null)
4026     {
4027       title += viewport.viewName + " of ";
4028     }
4029
4030     title += this.title;
4031
4032     Desktop.addInternalFrame(tp, title, 600, 500);
4033   }
4034
4035   /**
4036    * DOCUMENT ME!
4037    *
4038    * @param title
4039    *          DOCUMENT ME!
4040    * @param order
4041    *          DOCUMENT ME!
4042    */
4043   public void addSortByOrderMenuItem(String title,
4044           final AlignmentOrder order)
4045   {
4046     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4047             "action.by_title_param", new Object[] { title }));
4048     sort.add(item);
4049     item.addActionListener(new java.awt.event.ActionListener()
4050     {
4051       @Override
4052       public void actionPerformed(ActionEvent e)
4053       {
4054         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4055
4056         // TODO: JBPNote - have to map order entries to curent SequenceI
4057         // pointers
4058         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4059
4060         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4061                 .getAlignment()));
4062
4063         alignPanel.paintAlignment(true);
4064       }
4065     });
4066   }
4067
4068   /**
4069    * Add a new sort by annotation score menu item
4070    *
4071    * @param sort
4072    *          the menu to add the option to
4073    * @param scoreLabel
4074    *          the label used to retrieve scores for each sequence on the
4075    *          alignment
4076    */
4077   public void addSortByAnnotScoreMenuItem(JMenu sort,
4078           final String scoreLabel)
4079   {
4080     final JMenuItem item = new JMenuItem(scoreLabel);
4081     sort.add(item);
4082     item.addActionListener(new java.awt.event.ActionListener()
4083     {
4084       @Override
4085       public void actionPerformed(ActionEvent e)
4086       {
4087         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4088         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4089                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4090         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4091                 viewport.getAlignment()));
4092         alignPanel.paintAlignment(true);
4093       }
4094     });
4095   }
4096
4097   /**
4098    * last hash for alignment's annotation array - used to minimise cost of
4099    * rebuild.
4100    */
4101   protected int _annotationScoreVectorHash;
4102
4103   /**
4104    * search the alignment and rebuild the sort by annotation score submenu the
4105    * last alignment annotation vector hash is stored to minimize cost of
4106    * rebuilding in subsequence calls.
4107    *
4108    */
4109   @Override
4110   public void buildSortByAnnotationScoresMenu()
4111   {
4112     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4113     {
4114       return;
4115     }
4116
4117     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4118     {
4119       sortByAnnotScore.removeAll();
4120       // almost certainly a quicker way to do this - but we keep it simple
4121       Hashtable scoreSorts = new Hashtable();
4122       AlignmentAnnotation aann[];
4123       for (SequenceI sqa : viewport.getAlignment().getSequences())
4124       {
4125         aann = sqa.getAnnotation();
4126         for (int i = 0; aann != null && i < aann.length; i++)
4127         {
4128           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4129           {
4130             scoreSorts.put(aann[i].label, aann[i].label);
4131           }
4132         }
4133       }
4134       Enumeration labels = scoreSorts.keys();
4135       while (labels.hasMoreElements())
4136       {
4137         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4138                 (String) labels.nextElement());
4139       }
4140       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4141       scoreSorts.clear();
4142
4143       _annotationScoreVectorHash = viewport.getAlignment()
4144               .getAlignmentAnnotation().hashCode();
4145     }
4146   }
4147
4148   /**
4149    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4150    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4151    * call. Listeners are added to remove the menu item when the treePanel is
4152    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4153    * modified.
4154    *
4155    * @param treePanel
4156    *          Displayed tree window.
4157    * @param title
4158    *          SortBy menu item title.
4159    */
4160   @Override
4161   public void buildTreeMenu()
4162   {
4163     calculateTree.removeAll();
4164     // build the calculate menu
4165
4166     for (final String type : new String[] { "NJ", "AV" })
4167     {
4168       String treecalcnm = MessageManager.getString("label.tree_calc_"
4169               + type.toLowerCase());
4170       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4171       {
4172         JMenuItem tm = new JMenuItem();
4173         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4174         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4175         {
4176           String smn = MessageManager.getStringOrReturn(
4177                   "label.score_model_", sm.getName());
4178           final String title = MessageManager.formatMessage(
4179                   "label.treecalc_title", treecalcnm, smn);
4180           tm.setText(title);//
4181           tm.addActionListener(new java.awt.event.ActionListener()
4182           {
4183             @Override
4184             public void actionPerformed(ActionEvent e)
4185             {
4186               newTreePanel(type, pwtype, title);
4187             }
4188           });
4189           calculateTree.add(tm);
4190         }
4191
4192       }
4193     }
4194     sortByTreeMenu.removeAll();
4195
4196     List<Component> comps = PaintRefresher.components.get(viewport
4197             .getSequenceSetId());
4198     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4199     for (Component comp : comps)
4200     {
4201       if (comp instanceof TreePanel)
4202       {
4203         treePanels.add((TreePanel) comp);
4204       }
4205     }
4206
4207     if (treePanels.size() < 1)
4208     {
4209       sortByTreeMenu.setVisible(false);
4210       return;
4211     }
4212
4213     sortByTreeMenu.setVisible(true);
4214
4215     for (final TreePanel tp : treePanels)
4216     {
4217       final JMenuItem item = new JMenuItem(tp.getTitle());
4218       item.addActionListener(new java.awt.event.ActionListener()
4219       {
4220         @Override
4221         public void actionPerformed(ActionEvent e)
4222         {
4223           tp.sortByTree_actionPerformed();
4224           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4225
4226         }
4227       });
4228
4229       sortByTreeMenu.add(item);
4230     }
4231   }
4232
4233   public boolean sortBy(AlignmentOrder alorder, String undoname)
4234   {
4235     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4236     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4237     if (undoname != null)
4238     {
4239       addHistoryItem(new OrderCommand(undoname, oldOrder,
4240               viewport.getAlignment()));
4241     }
4242     alignPanel.paintAlignment(true);
4243     return true;
4244   }
4245
4246   /**
4247    * Work out whether the whole set of sequences or just the selected set will
4248    * be submitted for multiple alignment.
4249    *
4250    */
4251   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4252   {
4253     // Now, check we have enough sequences
4254     AlignmentView msa = null;
4255
4256     if ((viewport.getSelectionGroup() != null)
4257             && (viewport.getSelectionGroup().getSize() > 1))
4258     {
4259       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4260       // some common interface!
4261       /*
4262        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4263        * SequenceI[sz = seqs.getSize(false)];
4264        *
4265        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4266        * seqs.getSequenceAt(i); }
4267        */
4268       msa = viewport.getAlignmentView(true);
4269     }
4270     else if (viewport.getSelectionGroup() != null
4271             && viewport.getSelectionGroup().getSize() == 1)
4272     {
4273       int option = JOptionPane.showConfirmDialog(this,
4274               MessageManager.getString("warn.oneseq_msainput_selection"),
4275               MessageManager.getString("label.invalid_selection"),
4276               JOptionPane.OK_CANCEL_OPTION);
4277       if (option == JOptionPane.OK_OPTION)
4278       {
4279         msa = viewport.getAlignmentView(false);
4280       }
4281     }
4282     else
4283     {
4284       msa = viewport.getAlignmentView(false);
4285     }
4286     return msa;
4287   }
4288
4289   /**
4290    * Decides what is submitted to a secondary structure prediction service: the
4291    * first sequence in the alignment, or in the current selection, or, if the
4292    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4293    * region or the whole alignment. (where the first sequence in the set is the
4294    * one that the prediction will be for).
4295    */
4296   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4297   {
4298     AlignmentView seqs = null;
4299
4300     if ((viewport.getSelectionGroup() != null)
4301             && (viewport.getSelectionGroup().getSize() > 0))
4302     {
4303       seqs = viewport.getAlignmentView(true);
4304     }
4305     else
4306     {
4307       seqs = viewport.getAlignmentView(false);
4308     }
4309     // limit sequences - JBPNote in future - could spawn multiple prediction
4310     // jobs
4311     // TODO: viewport.getAlignment().isAligned is a global state - the local
4312     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4313     if (!viewport.getAlignment().isAligned(false))
4314     {
4315       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4316       // TODO: if seqs.getSequences().length>1 then should really have warned
4317       // user!
4318
4319     }
4320     return seqs;
4321   }
4322
4323   /**
4324    * DOCUMENT ME!
4325    *
4326    * @param e
4327    *          DOCUMENT ME!
4328    */
4329   @Override
4330   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4331   {
4332     // Pick the tree file
4333     JalviewFileChooser chooser = new JalviewFileChooser(
4334             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4335     chooser.setFileView(new JalviewFileView());
4336     chooser.setDialogTitle(MessageManager
4337             .getString("label.select_newick_like_tree_file"));
4338     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4339
4340     int value = chooser.showOpenDialog(null);
4341
4342     if (value == JalviewFileChooser.APPROVE_OPTION)
4343     {
4344       String choice = chooser.getSelectedFile().getPath();
4345       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4346       jalview.io.NewickFile fin = null;
4347       try
4348       {
4349         fin = new jalview.io.NewickFile(choice, "File");
4350         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4351       } catch (Exception ex)
4352       {
4353         JOptionPane
4354                 .showMessageDialog(
4355                         Desktop.desktop,
4356                         ex.getMessage(),
4357                         MessageManager
4358                                 .getString("label.problem_reading_tree_file"),
4359                         JOptionPane.WARNING_MESSAGE);
4360         ex.printStackTrace();
4361       }
4362       if (fin != null && fin.hasWarningMessage())
4363       {
4364         JOptionPane.showMessageDialog(Desktop.desktop, fin
4365                 .getWarningMessage(), MessageManager
4366                 .getString("label.possible_problem_with_tree_file"),
4367                 JOptionPane.WARNING_MESSAGE);
4368       }
4369     }
4370   }
4371
4372   @Override
4373   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4374   {
4375     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4376   }
4377
4378   public TreePanel ShowNewickTree(NewickFile nf, String title)
4379   {
4380     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4381   }
4382
4383   public TreePanel ShowNewickTree(NewickFile nf, String title,
4384           AlignmentView input)
4385   {
4386     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4387   }
4388
4389   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4390           int h, int x, int y)
4391   {
4392     return ShowNewickTree(nf, title, null, w, h, x, y);
4393   }
4394
4395   /**
4396    * Add a treeviewer for the tree extracted from a newick file object to the
4397    * current alignment view
4398    *
4399    * @param nf
4400    *          the tree
4401    * @param title
4402    *          tree viewer title
4403    * @param input
4404    *          Associated alignment input data (or null)
4405    * @param w
4406    *          width
4407    * @param h
4408    *          height
4409    * @param x
4410    *          position
4411    * @param y
4412    *          position
4413    * @return TreePanel handle
4414    */
4415   public TreePanel ShowNewickTree(NewickFile nf, String title,
4416           AlignmentView input, int w, int h, int x, int y)
4417   {
4418     TreePanel tp = null;
4419
4420     try
4421     {
4422       nf.parse();
4423
4424       if (nf.getTree() != null)
4425       {
4426         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4427
4428         tp.setSize(w, h);
4429
4430         if (x > 0 && y > 0)
4431         {
4432           tp.setLocation(x, y);
4433         }
4434
4435         Desktop.addInternalFrame(tp, title, w, h);
4436       }
4437     } catch (Exception ex)
4438     {
4439       ex.printStackTrace();
4440     }
4441
4442     return tp;
4443   }
4444
4445   private boolean buildingMenu = false;
4446
4447   /**
4448    * Generates menu items and listener event actions for web service clients
4449    *
4450    */
4451   public void BuildWebServiceMenu()
4452   {
4453     while (buildingMenu)
4454     {
4455       try
4456       {
4457         System.err.println("Waiting for building menu to finish.");
4458         Thread.sleep(10);
4459       } catch (Exception e)
4460       {
4461       }
4462     }
4463     final AlignFrame me = this;
4464     buildingMenu = true;
4465     new Thread(new Runnable()
4466     {
4467       @Override
4468       public void run()
4469       {
4470         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4471         try
4472         {
4473           // System.err.println("Building ws menu again "
4474           // + Thread.currentThread());
4475           // TODO: add support for context dependent disabling of services based
4476           // on
4477           // alignment and current selection
4478           // TODO: add additional serviceHandle parameter to specify abstract
4479           // handler
4480           // class independently of AbstractName
4481           // TODO: add in rediscovery GUI function to restart discoverer
4482           // TODO: group services by location as well as function and/or
4483           // introduce
4484           // object broker mechanism.
4485           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4486           final IProgressIndicator af = me;
4487           final JMenu msawsmenu = new JMenu("Alignment");
4488           final JMenu secstrmenu = new JMenu(
4489                   "Secondary Structure Prediction");
4490           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4491           final JMenu analymenu = new JMenu("Analysis");
4492           final JMenu dismenu = new JMenu("Protein Disorder");
4493           // final JMenu msawsmenu = new
4494           // JMenu(MessageManager.getString("label.alignment"));
4495           // final JMenu secstrmenu = new
4496           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4497           // final JMenu seqsrchmenu = new
4498           // JMenu(MessageManager.getString("label.sequence_database_search"));
4499           // final JMenu analymenu = new
4500           // JMenu(MessageManager.getString("label.analysis"));
4501           // final JMenu dismenu = new
4502           // JMenu(MessageManager.getString("label.protein_disorder"));
4503           // JAL-940 - only show secondary structure prediction services from
4504           // the legacy server
4505           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4506               // &&
4507           Discoverer.services != null && (Discoverer.services.size() > 0))
4508           {
4509             // TODO: refactor to allow list of AbstractName/Handler bindings to
4510             // be
4511             // stored or retrieved from elsewhere
4512             // No MSAWS used any more:
4513             // Vector msaws = null; // (Vector)
4514             // Discoverer.services.get("MsaWS");
4515             Vector secstrpr = (Vector) Discoverer.services
4516                     .get("SecStrPred");
4517             if (secstrpr != null)
4518             {
4519               // Add any secondary structure prediction services
4520               for (int i = 0, j = secstrpr.size(); i < j; i++)
4521               {
4522                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4523                         .get(i);
4524                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4525                         .getServiceClient(sh);
4526                 int p = secstrmenu.getItemCount();
4527                 impl.attachWSMenuEntry(secstrmenu, me);
4528                 int q = secstrmenu.getItemCount();
4529                 for (int litm = p; litm < q; litm++)
4530                 {
4531                   legacyItems.add(secstrmenu.getItem(litm));
4532                 }
4533               }
4534             }
4535           }
4536
4537           // Add all submenus in the order they should appear on the web
4538           // services menu
4539           wsmenu.add(msawsmenu);
4540           wsmenu.add(secstrmenu);
4541           wsmenu.add(dismenu);
4542           wsmenu.add(analymenu);
4543           // No search services yet
4544           // wsmenu.add(seqsrchmenu);
4545
4546           javax.swing.SwingUtilities.invokeLater(new Runnable()
4547           {
4548             @Override
4549             public void run()
4550             {
4551               try
4552               {
4553                 webService.removeAll();
4554                 // first, add discovered services onto the webservices menu
4555                 if (wsmenu.size() > 0)
4556                 {
4557                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4558                   {
4559                     webService.add(wsmenu.get(i));
4560                   }
4561                 }
4562                 else
4563                 {
4564                   webService.add(me.webServiceNoServices);
4565                 }
4566                 // TODO: move into separate menu builder class.
4567                 boolean new_sspred = false;
4568                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4569                 {
4570                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4571                   if (jws2servs != null)
4572                   {
4573                     if (jws2servs.hasServices())
4574                     {
4575                       jws2servs.attachWSMenuEntry(webService, me);
4576                       for (Jws2Instance sv : jws2servs.getServices())
4577                       {
4578                         if (sv.description.toLowerCase().contains("jpred"))
4579                         {
4580                           for (JMenuItem jmi : legacyItems)
4581                           {
4582                             jmi.setVisible(false);
4583                           }
4584                         }
4585                       }
4586
4587                     }
4588                     if (jws2servs.isRunning())
4589                     {
4590                       JMenuItem tm = new JMenuItem(
4591                               "Still discovering JABA Services");
4592                       tm.setEnabled(false);
4593                       webService.add(tm);
4594                     }
4595                   }
4596                 }
4597                 build_urlServiceMenu(me.webService);
4598                 build_fetchdbmenu(webService);
4599                 for (JMenu item : wsmenu)
4600                 {
4601                   if (item.getItemCount() == 0)
4602                   {
4603                     item.setEnabled(false);
4604                   }
4605                   else
4606                   {
4607                     item.setEnabled(true);
4608                   }
4609                 }
4610               } catch (Exception e)
4611               {
4612                 Cache.log
4613                         .debug("Exception during web service menu building process.",
4614                                 e);
4615               }
4616             }
4617           });
4618         } catch (Exception e)
4619         {
4620         }
4621         buildingMenu = false;
4622       }
4623     }).start();
4624
4625   }
4626
4627   /**
4628    * construct any groupURL type service menu entries.
4629    *
4630    * @param webService
4631    */
4632   private void build_urlServiceMenu(JMenu webService)
4633   {
4634     // TODO: remove this code when 2.7 is released
4635     // DEBUG - alignmentView
4636     /*
4637      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4638      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4639      *
4640      * @Override public void actionPerformed(ActionEvent e) {
4641      * jalview.datamodel.AlignmentView
4642      * .testSelectionViews(af.viewport.getAlignment(),
4643      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4644      *
4645      * }); webService.add(testAlView);
4646      */
4647     // TODO: refactor to RestClient discoverer and merge menu entries for
4648     // rest-style services with other types of analysis/calculation service
4649     // SHmmr test client - still being implemented.
4650     // DEBUG - alignmentView
4651
4652     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4653             .getRestClients())
4654     {
4655       client.attachWSMenuEntry(
4656               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4657               this);
4658     }
4659   }
4660
4661   /**
4662    * Searches selected sequences for xRef products and builds the Show
4663    * Cross-References menu (formerly called Show Products)
4664    *
4665    * @return true if Show Cross-references menu should be enabled.
4666    */
4667   public boolean canShowProducts()
4668   {
4669     SequenceI[] selection = viewport.getSequenceSelection();
4670     AlignmentI dataset = viewport.getAlignment().getDataset();
4671     boolean showp = false;
4672     try
4673     {
4674       showProducts.removeAll();
4675       final boolean dna = viewport.getAlignment().isNucleotide();
4676       String[] ptypes = (selection == null || selection.length == 0) ? null
4677               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4678
4679       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4680       {
4681         showp = true;
4682         final AlignFrame af = this;
4683         final String source = ptypes[t];
4684         JMenuItem xtype = new JMenuItem(ptypes[t]);
4685         xtype.addActionListener(new ActionListener()
4686         {
4687
4688           @Override
4689           public void actionPerformed(ActionEvent e)
4690           {
4691             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4692           }
4693
4694         });
4695         showProducts.add(xtype);
4696       }
4697       showProducts.setVisible(showp);
4698       showProducts.setEnabled(showp);
4699     } catch (Exception e)
4700     {
4701       jalview.bin.Cache.log
4702               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4703                       e);
4704       return false;
4705     }
4706     return showp;
4707   }
4708
4709   protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4710           final String source)
4711   {
4712     Runnable foo = new Runnable()
4713     {
4714
4715       @Override
4716       public void run()
4717       {
4718         final long sttime = System.currentTimeMillis();
4719         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4720                 "status.searching_for_sequences_from",
4721                 new Object[] { source }), sttime);
4722         try
4723         {
4724           /*
4725            * 'peer' sequences are any to add to this alignment, for example
4726            * alternative protein products for my protein's gene
4727            */
4728           List<SequenceI> addedPeers = new ArrayList<SequenceI>();
4729           AlignmentI alignment = AlignFrame.this.getViewport()
4730                   .getAlignment();
4731           Alignment xrefs = CrossRef.findXrefSequences(sel, dna, source,
4732                   alignment, addedPeers);
4733           if (xrefs != null)
4734           {
4735             /*
4736              * figure out colour scheme if any to apply to features
4737              */
4738             ASequenceFetcher sftch = new SequenceFetcher();
4739             List<DbSourceProxy> proxies = sftch.getSourceProxy(source);
4740             FeatureSettingsI featureColourScheme = null;
4741             for (DbSourceProxy proxy : proxies)
4742             {
4743               FeatureSettingsI preferredColours = proxy
4744                       .getFeatureColourScheme();
4745               if (preferredColours != null)
4746               {
4747                 featureColourScheme = preferredColours;
4748                 break;
4749               }
4750             }
4751             Alignment al = makeCrossReferencesAlignment(
4752                     alignment.getDataset(), xrefs);
4753
4754             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4755                     DEFAULT_HEIGHT);
4756             String newtitle = String.format("%s %s %s",
4757                     MessageManager.getString(dna ? "label.proteins"
4758                             : "label.nucleotides"), MessageManager
4759                             .getString("label.for"), getTitle());
4760             newFrame.setTitle(newtitle);
4761
4762             boolean asSplitFrame = Cache.getDefault(
4763                     Preferences.ENABLE_SPLIT_FRAME, true);
4764             if (asSplitFrame)
4765             {
4766               /*
4767                * Make a copy of this alignment (sharing the same dataset
4768                * sequences). If we are DNA, drop introns and update mappings
4769                */
4770               AlignmentI copyAlignment = null;
4771               final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4772                       .getSequenceSelection();
4773               List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4774               if (dna)
4775               {
4776                 copyAlignment = AlignmentUtils.makeCdsAlignment(
4777                         sequenceSelection, cf, alignment);
4778                 if (copyAlignment.getHeight() == 0)
4779                 {
4780                   System.err.println("Failed to make CDS alignment");
4781                 }
4782                 al.getCodonFrames().clear();
4783                 al.getCodonFrames().addAll(cf);
4784               }
4785               else
4786               {
4787                 copyAlignment = new Alignment(new Alignment(
4788                         sequenceSelection));
4789                 copyAlignment.getCodonFrames().addAll(cf);
4790               }
4791               copyAlignment.setGapCharacter(AlignFrame.this.viewport
4792                       .getGapCharacter());
4793               StructureSelectionManager ssm = StructureSelectionManager
4794                       .getStructureSelectionManager(Desktop.instance);
4795               ssm.registerMappings(cf);
4796
4797               /*
4798                * add in any extra 'peer' sequences discovered
4799                * (e.g. alternative protein products)
4800                */
4801               for (SequenceI peer : addedPeers)
4802               {
4803                 copyAlignment.addSequence(peer);
4804               }
4805
4806               if (copyAlignment.getHeight() > 0)
4807               {
4808                 /*
4809                  * align protein to dna
4810                  */
4811                 // FIXME what if the dna is not aligned :-O
4812                 if (dna)
4813                 {
4814                   al.alignAs(copyAlignment);
4815                 }
4816                 else
4817                 {
4818                   /*
4819                    * align cdna to protein - currently only if
4820                    * fetching and aligning Ensembl transcripts!
4821                    */
4822                   if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4823                   {
4824                     copyAlignment.alignAs(al);
4825                   }
4826                 }
4827
4828                 AlignFrame copyThis = new AlignFrame(copyAlignment,
4829                         AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4830                 copyThis.setTitle(AlignFrame.this.getTitle());
4831
4832                 boolean showSequenceFeatures = viewport
4833                         .isShowSequenceFeatures();
4834                 newFrame.setShowSeqFeatures(showSequenceFeatures);
4835                 copyThis.setShowSeqFeatures(showSequenceFeatures);
4836                 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4837                         .getFeatureRenderer();
4838
4839                 /*
4840                  * copy feature rendering settings to split frame
4841                  */
4842                 newFrame.alignPanel.getSeqPanel().seqCanvas
4843                         .getFeatureRenderer().transferSettings(
4844                                 myFeatureStyling);
4845                 copyThis.alignPanel.getSeqPanel().seqCanvas
4846                         .getFeatureRenderer().transferSettings(
4847                                 myFeatureStyling);
4848
4849                 /*
4850                  * apply 'database source' feature configuration
4851                  * if any was found
4852                  */
4853                 // TODO is this the feature colouring for the original
4854                 // alignment or the fetched xrefs? either could be Ensembl
4855                 newFrame.getViewport().applyFeaturesStyle(
4856                         featureColourScheme);
4857                 copyThis.getViewport().applyFeaturesStyle(
4858                         featureColourScheme);
4859
4860                 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4861                         dna ? newFrame : copyThis);
4862                 newFrame.setVisible(true);
4863                 copyThis.setVisible(true);
4864                 String linkedTitle = MessageManager
4865                         .getString("label.linked_view_title");
4866                 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4867                 sf.adjustDivider();
4868               }
4869             }
4870             else
4871             {
4872               Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4873                       DEFAULT_HEIGHT);
4874             }
4875           }
4876           else
4877           {
4878             System.err.println("No Sequences generated for xRef type "
4879                     + source);
4880           }
4881         } catch (Exception e)
4882         {
4883           jalview.bin.Cache.log.error(
4884                   "Exception when finding crossreferences", e);
4885         } catch (OutOfMemoryError e)
4886         {
4887           new OOMWarning("whilst fetching crossreferences", e);
4888         } catch (Error e)
4889         {
4890           jalview.bin.Cache.log.error("Error when finding crossreferences",
4891                   e);
4892         }
4893         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4894                 "status.finished_searching_for_sequences_from",
4895                 new Object[] { source }), sttime);
4896       }
4897
4898       /**
4899        * Makes an alignment containing the given sequences; the sequences are
4900        * added to the given alignment dataset, and the dataset is set on (shared
4901        * by) the new alignment
4902        *
4903        * @param dataset
4904        * @param seqs
4905        * @return
4906        */
4907       protected Alignment makeCrossReferencesAlignment(Alignment dataset,
4908               Alignment seqs)
4909       {
4910         SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4911         for (int s = 0; s < sprods.length; s++)
4912         {
4913           sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4914           if (dataset.getSequences() == null
4915                   || !dataset.getSequences().contains(
4916                           sprods[s].getDatasetSequence()))
4917           {
4918             dataset.addSequence(sprods[s].getDatasetSequence());
4919           }
4920           sprods[s].updatePDBIds();
4921         }
4922         Alignment al = new Alignment(sprods);
4923         al.setDataset(dataset);
4924         return al;
4925       }
4926
4927     };
4928     Thread frunner = new Thread(foo);
4929     frunner.start();
4930   }
4931
4932   public boolean canShowTranslationProducts(SequenceI[] selection,
4933           AlignmentI alignment)
4934   {
4935     // old way
4936     try
4937     {
4938       return (jalview.analysis.Dna.canTranslate(selection,
4939               viewport.getViewAsVisibleContigs(true)));
4940     } catch (Exception e)
4941     {
4942       jalview.bin.Cache.log
4943               .warn("canTranslate threw an exception - please report to help@jalview.org",
4944                       e);
4945       return false;
4946     }
4947   }
4948
4949   /**
4950    * Construct and display a new frame containing the translation of this
4951    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4952    */
4953   @Override
4954   public void showTranslation_actionPerformed(ActionEvent e)
4955   {
4956     AlignmentI al = null;
4957     try
4958     {
4959       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4960
4961       al = dna.translateCdna();
4962     } catch (Exception ex)
4963     {
4964       jalview.bin.Cache.log.error(
4965               "Exception during translation. Please report this !", ex);
4966       final String msg = MessageManager
4967               .getString("label.error_when_translating_sequences_submit_bug_report");
4968       final String errorTitle = MessageManager
4969               .getString("label.implementation_error")
4970               + MessageManager.getString("translation_failed");
4971       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4972               JOptionPane.ERROR_MESSAGE);
4973       return;
4974     }
4975     if (al == null || al.getHeight() == 0)
4976     {
4977       final String msg = MessageManager
4978               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4979       final String errorTitle = MessageManager
4980               .getString("label.translation_failed");
4981       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4982               JOptionPane.WARNING_MESSAGE);
4983     }
4984     else
4985     {
4986       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4987       af.setFileFormat(this.currentFileFormat);
4988       final String newTitle = MessageManager.formatMessage(
4989               "label.translation_of_params",
4990               new Object[] { this.getTitle() });
4991       af.setTitle(newTitle);
4992       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4993       {
4994         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4995         viewport.openSplitFrame(af, new Alignment(seqs));
4996       }
4997       else
4998       {
4999         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
5000                 DEFAULT_HEIGHT);
5001       }
5002     }
5003   }
5004
5005   /**
5006    * Set the file format
5007    *
5008    * @param fileFormat
5009    */
5010   public void setFileFormat(String fileFormat)
5011   {
5012     this.currentFileFormat = fileFormat;
5013   }
5014
5015   /**
5016    * Try to load a features file onto the alignment.
5017    *
5018    * @param file
5019    *          contents or path to retrieve file
5020    * @param type
5021    *          access mode of file (see jalview.io.AlignFile)
5022    * @return true if features file was parsed correctly.
5023    */
5024   public boolean parseFeaturesFile(String file, String type)
5025   {
5026     return avc.parseFeaturesFile(file, type,
5027             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5028
5029   }
5030
5031   @Override
5032   public void refreshFeatureUI(boolean enableIfNecessary)
5033   {
5034     // note - currently this is only still here rather than in the controller
5035     // because of the featureSettings hard reference that is yet to be
5036     // abstracted
5037     if (enableIfNecessary)
5038     {
5039       viewport.setShowSequenceFeatures(true);
5040       showSeqFeatures.setSelected(true);
5041     }
5042
5043   }
5044
5045   @Override
5046   public void dragEnter(DropTargetDragEvent evt)
5047   {
5048   }
5049
5050   @Override
5051   public void dragExit(DropTargetEvent evt)
5052   {
5053   }
5054
5055   @Override
5056   public void dragOver(DropTargetDragEvent evt)
5057   {
5058   }
5059
5060   @Override
5061   public void dropActionChanged(DropTargetDragEvent evt)
5062   {
5063   }
5064
5065   @Override
5066   public void drop(DropTargetDropEvent evt)
5067   {
5068     Transferable t = evt.getTransferable();
5069     java.util.List files = null;
5070
5071     try
5072     {
5073       DataFlavor uriListFlavor = new DataFlavor(
5074               "text/uri-list;class=java.lang.String");
5075       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5076       {
5077         // Works on Windows and MacOSX
5078         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5079         files = (java.util.List) t
5080                 .getTransferData(DataFlavor.javaFileListFlavor);
5081       }
5082       else if (t.isDataFlavorSupported(uriListFlavor))
5083       {
5084         // This is used by Unix drag system
5085         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5086         String data = (String) t.getTransferData(uriListFlavor);
5087         files = new java.util.ArrayList(1);
5088         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5089                 data, "\r\n"); st.hasMoreTokens();)
5090         {
5091           String s = st.nextToken();
5092           if (s.startsWith("#"))
5093           {
5094             // the line is a comment (as per the RFC 2483)
5095             continue;
5096           }
5097
5098           java.net.URI uri = new java.net.URI(s);
5099           // check to see if we can handle this kind of URI
5100           if (uri.getScheme().toLowerCase().startsWith("http"))
5101           {
5102             files.add(uri.toString());
5103           }
5104           else
5105           {
5106             // otherwise preserve old behaviour: catch all for file objects
5107             java.io.File file = new java.io.File(uri);
5108             files.add(file.toString());
5109           }
5110         }
5111       }
5112     } catch (Exception e)
5113     {
5114       e.printStackTrace();
5115     }
5116     if (files != null)
5117     {
5118       try
5119       {
5120         // check to see if any of these files have names matching sequences in
5121         // the alignment
5122         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5123                 .getAlignment().getSequencesArray());
5124         /**
5125          * Object[] { String,SequenceI}
5126          */
5127         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5128         ArrayList<String> filesnotmatched = new ArrayList<String>();
5129         for (int i = 0; i < files.size(); i++)
5130         {
5131           String file = files.get(i).toString();
5132           String pdbfn = "";
5133           String protocol = FormatAdapter.checkProtocol(file);
5134           if (protocol == jalview.io.FormatAdapter.FILE)
5135           {
5136             File fl = new File(file);
5137             pdbfn = fl.getName();
5138           }
5139           else if (protocol == jalview.io.FormatAdapter.URL)
5140           {
5141             URL url = new URL(file);
5142             pdbfn = url.getFile();
5143           }
5144           if (pdbfn.length() > 0)
5145           {
5146             // attempt to find a match in the alignment
5147             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5148             int l = 0, c = pdbfn.indexOf(".");
5149             while (mtch == null && c != -1)
5150             {
5151               do
5152               {
5153                 l = c;
5154               } while ((c = pdbfn.indexOf(".", l)) > l);
5155               if (l > -1)
5156               {
5157                 pdbfn = pdbfn.substring(0, l);
5158               }
5159               mtch = idm.findAllIdMatches(pdbfn);
5160             }
5161             if (mtch != null)
5162             {
5163               String type = null;
5164               try
5165               {
5166                 type = new IdentifyFile().identify(file, protocol);
5167               } catch (Exception ex)
5168               {
5169                 type = null;
5170               }
5171               if (type != null)
5172               {
5173                 if (type.equalsIgnoreCase("PDB"))
5174                 {
5175                   filesmatched.add(new Object[] { file, protocol, mtch });
5176                   continue;
5177                 }
5178               }
5179             }
5180             // File wasn't named like one of the sequences or wasn't a PDB file.
5181             filesnotmatched.add(file);
5182           }
5183         }
5184         int assocfiles = 0;
5185         if (filesmatched.size() > 0)
5186         {
5187           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5188                   || JOptionPane
5189                           .showConfirmDialog(
5190                                   this,
5191                                   MessageManager
5192                                           .formatMessage(
5193                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5194                                                   new Object[] { Integer
5195                                                           .valueOf(
5196                                                                   filesmatched
5197                                                                           .size())
5198                                                           .toString() }),
5199                                   MessageManager
5200                                           .getString("label.automatically_associate_pdb_files_by_name"),
5201                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5202
5203           {
5204             for (Object[] fm : filesmatched)
5205             {
5206               // try and associate
5207               // TODO: may want to set a standard ID naming formalism for
5208               // associating PDB files which have no IDs.
5209               for (SequenceI toassoc : (SequenceI[]) fm[2])
5210               {
5211                 PDBEntry pe = new AssociatePdbFileWithSeq()
5212                         .associatePdbWithSeq((String) fm[0],
5213                                 (String) fm[1], toassoc, false,
5214                                 Desktop.instance);
5215                 if (pe != null)
5216                 {
5217                   System.err.println("Associated file : "
5218                           + ((String) fm[0]) + " with "
5219                           + toassoc.getDisplayId(true));
5220                   assocfiles++;
5221                 }
5222               }
5223               alignPanel.paintAlignment(true);
5224             }
5225           }
5226         }
5227         if (filesnotmatched.size() > 0)
5228         {
5229           if (assocfiles > 0
5230                   && (Cache.getDefault(
5231                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5232                           .showConfirmDialog(
5233                                   this,
5234                                   "<html>"
5235                                           + MessageManager
5236                                                   .formatMessage(
5237                                                           "label.ignore_unmatched_dropped_files_info",
5238                                                           new Object[] { Integer
5239                                                                   .valueOf(
5240                                                                           filesnotmatched
5241                                                                                   .size())
5242                                                                   .toString() })
5243                                           + "</html>",
5244                                   MessageManager
5245                                           .getString("label.ignore_unmatched_dropped_files"),
5246                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5247           {
5248             return;
5249           }
5250           for (String fn : filesnotmatched)
5251           {
5252             loadJalviewDataFile(fn, null, null, null);
5253           }
5254
5255         }
5256       } catch (Exception ex)
5257       {
5258         ex.printStackTrace();
5259       }
5260     }
5261   }
5262
5263   /**
5264    * Attempt to load a "dropped" file or URL string: First by testing whether
5265    * it's an Annotation file, then a JNet file, and finally a features file. If
5266    * all are false then the user may have dropped an alignment file onto this
5267    * AlignFrame.
5268    *
5269    * @param file
5270    *          either a filename or a URL string.
5271    */
5272   public void loadJalviewDataFile(String file, String protocol,
5273           String format, SequenceI assocSeq)
5274   {
5275     try
5276     {
5277       if (protocol == null)
5278       {
5279         protocol = FormatAdapter.checkProtocol(file);
5280       }
5281       // if the file isn't identified, or not positively identified as some
5282       // other filetype (PFAM is default unidentified alignment file type) then
5283       // try to parse as annotation.
5284       boolean isAnnotation = (format == null || format
5285               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5286               .annotateAlignmentView(viewport, file, protocol) : false;
5287
5288       if (!isAnnotation)
5289       {
5290         // first see if its a T-COFFEE score file
5291         TCoffeeScoreFile tcf = null;
5292         try
5293         {
5294           tcf = new TCoffeeScoreFile(file, protocol);
5295           if (tcf.isValid())
5296           {
5297             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5298             {
5299               tcoffeeColour.setEnabled(true);
5300               tcoffeeColour.setSelected(true);
5301               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5302               isAnnotation = true;
5303               statusBar
5304                       .setText(MessageManager
5305                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5306             }
5307             else
5308             {
5309               // some problem - if no warning its probable that the ID matching
5310               // process didn't work
5311               JOptionPane
5312                       .showMessageDialog(
5313                               Desktop.desktop,
5314                               tcf.getWarningMessage() == null ? MessageManager
5315                                       .getString("label.check_file_matches_sequence_ids_alignment")
5316                                       : tcf.getWarningMessage(),
5317                               MessageManager
5318                                       .getString("label.problem_reading_tcoffee_score_file"),
5319                               JOptionPane.WARNING_MESSAGE);
5320             }
5321           }
5322           else
5323           {
5324             tcf = null;
5325           }
5326         } catch (Exception x)
5327         {
5328           Cache.log
5329                   .debug("Exception when processing data source as T-COFFEE score file",
5330                           x);
5331           tcf = null;
5332         }
5333         if (tcf == null)
5334         {
5335           // try to see if its a JNet 'concise' style annotation file *before*
5336           // we
5337           // try to parse it as a features file
5338           if (format == null)
5339           {
5340             format = new IdentifyFile().identify(file, protocol);
5341           }
5342           if (format.equalsIgnoreCase("JnetFile"))
5343           {
5344             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5345                     file, protocol);
5346             new JnetAnnotationMaker();
5347             JnetAnnotationMaker.add_annotation(predictions,
5348                     viewport.getAlignment(), 0, false);
5349             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5350             viewport.getAlignment().setSeqrep(repseq);
5351             ColumnSelection cs = new ColumnSelection();
5352             cs.hideInsertionsFor(repseq);
5353             viewport.setColumnSelection(cs);
5354             isAnnotation = true;
5355           }
5356           else if (IdentifyFile.FeaturesFile.equals(format))
5357           {
5358             if (parseFeaturesFile(file, protocol))
5359             {
5360               alignPanel.paintAlignment(true);
5361             }
5362           }
5363           else
5364           {
5365             new FileLoader().LoadFile(viewport, file, protocol, format);
5366           }
5367         }
5368       }
5369       if (isAnnotation)
5370       {
5371
5372         alignPanel.adjustAnnotationHeight();
5373         viewport.updateSequenceIdColours();
5374         buildSortByAnnotationScoresMenu();
5375         alignPanel.paintAlignment(true);
5376       }
5377     } catch (Exception ex)
5378     {
5379       ex.printStackTrace();
5380     } catch (OutOfMemoryError oom)
5381     {
5382       try
5383       {
5384         System.gc();
5385       } catch (Exception x)
5386       {
5387       }
5388       new OOMWarning(
5389               "loading data "
5390                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5391                               : "using " + protocol + " from " + file)
5392                               : ".")
5393                       + (format != null ? "(parsing as '" + format
5394                               + "' file)" : ""), oom, Desktop.desktop);
5395     }
5396   }
5397
5398   /**
5399    * Method invoked by the ChangeListener on the tabbed pane, in other words
5400    * when a different tabbed pane is selected by the user or programmatically.
5401    */
5402   @Override
5403   public void tabSelectionChanged(int index)
5404   {
5405     if (index > -1)
5406     {
5407       alignPanel = alignPanels.get(index);
5408       viewport = alignPanel.av;
5409       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5410       setMenusFromViewport(viewport);
5411     }
5412
5413     /*
5414      * If there is a frame linked to this one in a SplitPane, switch it to the
5415      * same view tab index. No infinite recursion of calls should happen, since
5416      * tabSelectionChanged() should not get invoked on setting the selected
5417      * index to an unchanged value. Guard against setting an invalid index
5418      * before the new view peer tab has been created.
5419      */
5420     final AlignViewportI peer = viewport.getCodingComplement();
5421     if (peer != null)
5422     {
5423       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5424       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5425       {
5426         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5427       }
5428     }
5429   }
5430
5431   /**
5432    * On right mouse click on view tab, prompt for and set new view name.
5433    */
5434   @Override
5435   public void tabbedPane_mousePressed(MouseEvent e)
5436   {
5437     if (SwingUtilities.isRightMouseButton(e))
5438     {
5439       String msg = MessageManager.getString("label.enter_view_name");
5440       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5441               JOptionPane.QUESTION_MESSAGE);
5442
5443       if (reply != null)
5444       {
5445         viewport.viewName = reply;
5446         // TODO warn if reply is in getExistingViewNames()?
5447         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5448       }
5449     }
5450   }
5451
5452   public AlignViewport getCurrentView()
5453   {
5454     return viewport;
5455   }
5456
5457   /**
5458    * Open the dialog for regex description parsing.
5459    */
5460   @Override
5461   protected void extractScores_actionPerformed(ActionEvent e)
5462   {
5463     ParseProperties pp = new jalview.analysis.ParseProperties(
5464             viewport.getAlignment());
5465     // TODO: verify regex and introduce GUI dialog for version 2.5
5466     // if (pp.getScoresFromDescription("col", "score column ",
5467     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5468     // true)>0)
5469     if (pp.getScoresFromDescription("description column",
5470             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5471     {
5472       buildSortByAnnotationScoresMenu();
5473     }
5474   }
5475
5476   /*
5477    * (non-Javadoc)
5478    *
5479    * @see
5480    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5481    * )
5482    */
5483   @Override
5484   protected void showDbRefs_actionPerformed(ActionEvent e)
5485   {
5486     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5487   }
5488
5489   /*
5490    * (non-Javadoc)
5491    *
5492    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5493    * ActionEvent)
5494    */
5495   @Override
5496   protected void showNpFeats_actionPerformed(ActionEvent e)
5497   {
5498     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5499   }
5500
5501   /**
5502    * find the viewport amongst the tabs in this alignment frame and close that
5503    * tab
5504    *
5505    * @param av
5506    */
5507   public boolean closeView(AlignViewportI av)
5508   {
5509     if (viewport == av)
5510     {
5511       this.closeMenuItem_actionPerformed(false);
5512       return true;
5513     }
5514     Component[] comp = tabbedPane.getComponents();
5515     for (int i = 0; comp != null && i < comp.length; i++)
5516     {
5517       if (comp[i] instanceof AlignmentPanel)
5518       {
5519         if (((AlignmentPanel) comp[i]).av == av)
5520         {
5521           // close the view.
5522           closeView((AlignmentPanel) comp[i]);
5523           return true;
5524         }
5525       }
5526     }
5527     return false;
5528   }
5529
5530   protected void build_fetchdbmenu(JMenu webService)
5531   {
5532     // Temporary hack - DBRef Fetcher always top level ws entry.
5533     // TODO We probably want to store a sequence database checklist in
5534     // preferences and have checkboxes.. rather than individual sources selected
5535     // here
5536     final JMenu rfetch = new JMenu(
5537             MessageManager.getString("action.fetch_db_references"));
5538     rfetch.setToolTipText(MessageManager
5539             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5540     webService.add(rfetch);
5541
5542     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5543             MessageManager.getString("option.trim_retrieved_seqs"));
5544     trimrs.setToolTipText(MessageManager
5545             .getString("label.trim_retrieved_sequences"));
5546     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5547     trimrs.addActionListener(new ActionListener()
5548     {
5549       @Override
5550       public void actionPerformed(ActionEvent e)
5551       {
5552         trimrs.setSelected(trimrs.isSelected());
5553         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5554                 Boolean.valueOf(trimrs.isSelected()).toString());
5555       };
5556     });
5557     rfetch.add(trimrs);
5558     JMenuItem fetchr = new JMenuItem(
5559             MessageManager.getString("label.standard_databases"));
5560     fetchr.setToolTipText(MessageManager
5561             .getString("label.fetch_embl_uniprot"));
5562     fetchr.addActionListener(new ActionListener()
5563     {
5564
5565       @Override
5566       public void actionPerformed(ActionEvent e)
5567       {
5568         new Thread(new Runnable()
5569         {
5570
5571           @Override
5572           public void run()
5573           {
5574             boolean isNuclueotide = alignPanel.alignFrame.getViewport()
5575                     .getAlignment().isNucleotide();
5576             new jalview.ws.DBRefFetcher(alignPanel.av
5577                     .getSequenceSelection(), alignPanel.alignFrame, null,
5578                     alignPanel.alignFrame.featureSettings, isNuclueotide)
5579                     .fetchDBRefs(false);
5580           }
5581         }).start();
5582
5583       }
5584
5585     });
5586     rfetch.add(fetchr);
5587     final AlignFrame me = this;
5588     new Thread(new Runnable()
5589     {
5590       @Override
5591       public void run()
5592       {
5593         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5594                 .getSequenceFetcherSingleton(me);
5595         javax.swing.SwingUtilities.invokeLater(new Runnable()
5596         {
5597           @Override
5598           public void run()
5599           {
5600             String[] dbclasses = sf.getOrderedSupportedSources();
5601             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5602             // jalview.util.QuickSort.sort(otherdb, otherdb);
5603             List<DbSourceProxy> otherdb;
5604             JMenu dfetch = new JMenu();
5605             JMenu ifetch = new JMenu();
5606             JMenuItem fetchr = null;
5607             int comp = 0, icomp = 0, mcomp = 15;
5608             String mname = null;
5609             int dbi = 0;
5610             for (String dbclass : dbclasses)
5611             {
5612               otherdb = sf.getSourceProxy(dbclass);
5613               // add a single entry for this class, or submenu allowing 'fetch
5614               // all' or pick one
5615               if (otherdb == null || otherdb.size() < 1)
5616               {
5617                 continue;
5618               }
5619               // List<DbSourceProxy> dbs=otherdb;
5620               // otherdb=new ArrayList<DbSourceProxy>();
5621               // for (DbSourceProxy db:dbs)
5622               // {
5623               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5624               // }
5625               if (mname == null)
5626               {
5627                 mname = "From " + dbclass;
5628               }
5629               if (otherdb.size() == 1)
5630               {
5631                 final DbSourceProxy[] dassource = otherdb
5632                         .toArray(new DbSourceProxy[0]);
5633                 DbSourceProxy src = otherdb.get(0);
5634                 fetchr = new JMenuItem(src.getDbSource());
5635                 fetchr.addActionListener(new ActionListener()
5636                 {
5637
5638                   @Override
5639                   public void actionPerformed(ActionEvent e)
5640                   {
5641                     new Thread(new Runnable()
5642                     {
5643
5644                       @Override
5645                       public void run()
5646                       {
5647                         boolean isNuclueotide = alignPanel.alignFrame
5648                                 .getViewport().getAlignment()
5649                                 .isNucleotide();
5650                         new jalview.ws.DBRefFetcher(alignPanel.av
5651                                 .getSequenceSelection(),
5652                                 alignPanel.alignFrame, dassource,
5653                                 alignPanel.alignFrame.featureSettings,
5654                                 isNuclueotide).fetchDBRefs(false);
5655                       }
5656                     }).start();
5657                   }
5658
5659                 });
5660                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5661                         MessageManager.formatMessage(
5662                                 "label.fetch_retrieve_from",
5663                                 new Object[] { src.getDbName() })));
5664                 dfetch.add(fetchr);
5665                 comp++;
5666               }
5667               else
5668               {
5669                 final DbSourceProxy[] dassource = otherdb
5670                         .toArray(new DbSourceProxy[0]);
5671                 // fetch all entry
5672                 DbSourceProxy src = otherdb.get(0);
5673                 fetchr = new JMenuItem(MessageManager.formatMessage(
5674                         "label.fetch_all_param",
5675                         new Object[] { src.getDbSource() }));
5676                 fetchr.addActionListener(new ActionListener()
5677                 {
5678                   @Override
5679                   public void actionPerformed(ActionEvent e)
5680                   {
5681                     new Thread(new Runnable()
5682                     {
5683
5684                       @Override
5685                       public void run()
5686                       {
5687                         boolean isNuclueotide = alignPanel.alignFrame
5688                                 .getViewport().getAlignment()
5689                                 .isNucleotide();
5690                         new jalview.ws.DBRefFetcher(alignPanel.av
5691                                 .getSequenceSelection(),
5692                                 alignPanel.alignFrame, dassource,
5693                                 alignPanel.alignFrame.featureSettings,
5694                                 isNuclueotide).fetchDBRefs(false);
5695                       }
5696                     }).start();
5697                   }
5698                 });
5699
5700                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5701                         MessageManager.formatMessage(
5702                                 "label.fetch_retrieve_from_all_sources",
5703                                 new Object[] {
5704                                     Integer.valueOf(otherdb.size())
5705                                             .toString(), src.getDbSource(),
5706                                     src.getDbName() })));
5707                 dfetch.add(fetchr);
5708                 comp++;
5709                 // and then build the rest of the individual menus
5710                 ifetch = new JMenu(MessageManager.formatMessage(
5711                         "label.source_from_db_source",
5712                         new Object[] { src.getDbSource() }));
5713                 icomp = 0;
5714                 String imname = null;
5715                 int i = 0;
5716                 for (DbSourceProxy sproxy : otherdb)
5717                 {
5718                   String dbname = sproxy.getDbName();
5719                   String sname = dbname.length() > 5 ? dbname.substring(0,
5720                           5) + "..." : dbname;
5721                   String msname = dbname.length() > 10 ? dbname.substring(
5722                           0, 10) + "..." : dbname;
5723                   if (imname == null)
5724                   {
5725                     imname = MessageManager.formatMessage(
5726                             "label.from_msname", new Object[] { sname });
5727                   }
5728                   fetchr = new JMenuItem(msname);
5729                   final DbSourceProxy[] dassrc = { sproxy };
5730                   fetchr.addActionListener(new ActionListener()
5731                   {
5732
5733                     @Override
5734                     public void actionPerformed(ActionEvent e)
5735                     {
5736                       new Thread(new Runnable()
5737                       {
5738
5739                         @Override
5740                         public void run()
5741                         {
5742                           boolean isNuclueotide = alignPanel.alignFrame
5743                                   .getViewport().getAlignment()
5744                                   .isNucleotide();
5745                           new jalview.ws.DBRefFetcher(alignPanel.av
5746                                   .getSequenceSelection(),
5747                                   alignPanel.alignFrame, dassrc,
5748                                   alignPanel.alignFrame.featureSettings,
5749                                   isNuclueotide).fetchDBRefs(false);
5750                         }
5751                       }).start();
5752                     }
5753
5754                   });
5755                   fetchr.setToolTipText("<html>"
5756                           + MessageManager.formatMessage(
5757                                   "label.fetch_retrieve_from", new Object[]
5758                                   { dbname }));
5759                   ifetch.add(fetchr);
5760                   ++i;
5761                   if (++icomp >= mcomp || i == (otherdb.size()))
5762                   {
5763                     ifetch.setText(MessageManager.formatMessage(
5764                             "label.source_to_target", imname, sname));
5765                     dfetch.add(ifetch);
5766                     ifetch = new JMenu();
5767                     imname = null;
5768                     icomp = 0;
5769                     comp++;
5770                   }
5771                 }
5772               }
5773               ++dbi;
5774               if (comp >= mcomp || dbi >= (dbclasses.length))
5775               {
5776                 dfetch.setText(MessageManager.formatMessage(
5777                         "label.source_to_target", mname, dbclass));
5778                 rfetch.add(dfetch);
5779                 dfetch = new JMenu();
5780                 mname = null;
5781                 comp = 0;
5782               }
5783             }
5784           }
5785         });
5786       }
5787     }).start();
5788
5789   }
5790
5791   /**
5792    * Left justify the whole alignment.
5793    */
5794   @Override
5795   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5796   {
5797     AlignmentI al = viewport.getAlignment();
5798     al.justify(false);
5799     viewport.firePropertyChange("alignment", null, al);
5800   }
5801
5802   /**
5803    * Right justify the whole alignment.
5804    */
5805   @Override
5806   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5807   {
5808     AlignmentI al = viewport.getAlignment();
5809     al.justify(true);
5810     viewport.firePropertyChange("alignment", null, al);
5811   }
5812
5813   @Override
5814   public void setShowSeqFeatures(boolean b)
5815   {
5816     showSeqFeatures.setSelected(b);
5817     viewport.setShowSequenceFeatures(b);
5818   }
5819
5820   /*
5821    * (non-Javadoc)
5822    *
5823    * @see
5824    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5825    * awt.event.ActionEvent)
5826    */
5827   @Override
5828   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5829   {
5830     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5831     alignPanel.paintAlignment(true);
5832   }
5833
5834   /*
5835    * (non-Javadoc)
5836    *
5837    * @see
5838    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5839    * .ActionEvent)
5840    */
5841   @Override
5842   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5843   {
5844     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5845     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5846
5847   }
5848
5849   /*
5850    * (non-Javadoc)
5851    *
5852    * @see
5853    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5854    * .event.ActionEvent)
5855    */
5856   @Override
5857   protected void showGroupConservation_actionPerformed(ActionEvent e)
5858   {
5859     viewport.setShowGroupConservation(showGroupConservation.getState());
5860     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5861   }
5862
5863   /*
5864    * (non-Javadoc)
5865    *
5866    * @see
5867    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5868    * .event.ActionEvent)
5869    */
5870   @Override
5871   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5872   {
5873     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5874     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5875   }
5876
5877   /*
5878    * (non-Javadoc)
5879    *
5880    * @see
5881    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5882    * .event.ActionEvent)
5883    */
5884   @Override
5885   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5886   {
5887     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5888     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5889   }
5890
5891   @Override
5892   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5893   {
5894     showSequenceLogo.setState(true);
5895     viewport.setShowSequenceLogo(true);
5896     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5897     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5898   }
5899
5900   @Override
5901   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5902   {
5903     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5904   }
5905
5906   /*
5907    * (non-Javadoc)
5908    *
5909    * @see
5910    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5911    * .event.ActionEvent)
5912    */
5913   @Override
5914   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5915   {
5916     if (avc.makeGroupsFromSelection())
5917     {
5918       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5919       alignPanel.updateAnnotation();
5920       alignPanel.paintAlignment(true);
5921     }
5922   }
5923
5924   public void clearAlignmentSeqRep()
5925   {
5926     // TODO refactor alignmentseqrep to controller
5927     if (viewport.getAlignment().hasSeqrep())
5928     {
5929       viewport.getAlignment().setSeqrep(null);
5930       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5931       alignPanel.updateAnnotation();
5932       alignPanel.paintAlignment(true);
5933     }
5934   }
5935
5936   @Override
5937   protected void createGroup_actionPerformed(ActionEvent e)
5938   {
5939     if (avc.createGroup())
5940     {
5941       alignPanel.alignmentChanged();
5942     }
5943   }
5944
5945   @Override
5946   protected void unGroup_actionPerformed(ActionEvent e)
5947   {
5948     if (avc.unGroup())
5949     {
5950       alignPanel.alignmentChanged();
5951     }
5952   }
5953
5954   /**
5955    * make the given alignmentPanel the currently selected tab
5956    *
5957    * @param alignmentPanel
5958    */
5959   public void setDisplayedView(AlignmentPanel alignmentPanel)
5960   {
5961     if (!viewport.getSequenceSetId().equals(
5962             alignmentPanel.av.getSequenceSetId()))
5963     {
5964       throw new Error(
5965               MessageManager
5966                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5967     }
5968     if (tabbedPane != null
5969             && tabbedPane.getTabCount() > 0
5970             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5971                     .getSelectedIndex())
5972     {
5973       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5974     }
5975   }
5976
5977   /**
5978    * Action on selection of menu options to Show or Hide annotations.
5979    *
5980    * @param visible
5981    * @param forSequences
5982    *          update sequence-related annotations
5983    * @param forAlignment
5984    *          update non-sequence-related annotations
5985    */
5986   @Override
5987   protected void setAnnotationsVisibility(boolean visible,
5988           boolean forSequences, boolean forAlignment)
5989   {
5990     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5991             .getAlignmentAnnotation())
5992     {
5993       /*
5994        * don't display non-positional annotations on an alignment
5995        */
5996       if (aa.annotations == null)
5997       {
5998         continue;
5999       }
6000       boolean apply = (aa.sequenceRef == null && forAlignment)
6001               || (aa.sequenceRef != null && forSequences);
6002       if (apply)
6003       {
6004         aa.visible = visible;
6005       }
6006     }
6007     alignPanel.validateAnnotationDimensions(true);
6008     alignPanel.alignmentChanged();
6009   }
6010
6011   /**
6012    * Store selected annotation sort order for the view and repaint.
6013    */
6014   @Override
6015   protected void sortAnnotations_actionPerformed()
6016   {
6017     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6018     this.alignPanel.av
6019             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6020     alignPanel.paintAlignment(true);
6021   }
6022
6023   /**
6024    *
6025    * @return alignment panels in this alignment frame
6026    */
6027   public List<? extends AlignmentViewPanel> getAlignPanels()
6028   {
6029     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6030   }
6031
6032   /**
6033    * Open a new alignment window, with the cDNA associated with this (protein)
6034    * alignment, aligned as is the protein.
6035    */
6036   protected void viewAsCdna_actionPerformed()
6037   {
6038     // TODO no longer a menu action - refactor as required
6039     final AlignmentI alignment = getViewport().getAlignment();
6040     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6041     if (mappings == null)
6042     {
6043       return;
6044     }
6045     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6046     for (SequenceI aaSeq : alignment.getSequences())
6047     {
6048       for (AlignedCodonFrame acf : mappings)
6049       {
6050         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6051         if (dnaSeq != null)
6052         {
6053           /*
6054            * There is a cDNA mapping for this protein sequence - add to new
6055            * alignment. It will share the same dataset sequence as other mapped
6056            * cDNA (no new mappings need to be created).
6057            */
6058           final Sequence newSeq = new Sequence(dnaSeq);
6059           newSeq.setDatasetSequence(dnaSeq);
6060           cdnaSeqs.add(newSeq);
6061         }
6062       }
6063     }
6064     if (cdnaSeqs.size() == 0)
6065     {
6066       // show a warning dialog no mapped cDNA
6067       return;
6068     }
6069     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6070             .size()]));
6071     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6072             AlignFrame.DEFAULT_HEIGHT);
6073     cdna.alignAs(alignment);
6074     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6075             + this.title;
6076     Desktop.addInternalFrame(alignFrame, newtitle,
6077             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6078   }
6079
6080   /**
6081    * Set visibility of dna/protein complement view (available when shown in a
6082    * split frame).
6083    *
6084    * @param show
6085    */
6086   @Override
6087   protected void showComplement_actionPerformed(boolean show)
6088   {
6089     SplitContainerI sf = getSplitViewContainer();
6090     if (sf != null)
6091     {
6092       sf.setComplementVisible(this, show);
6093     }
6094   }
6095
6096   /**
6097    * Generate the reverse (optionally complemented) of the selected sequences,
6098    * and add them to the alignment
6099    */
6100   @Override
6101   protected void showReverse_actionPerformed(boolean complement)
6102   {
6103     AlignmentI al = null;
6104     try
6105     {
6106       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6107
6108       al = dna.reverseCdna(complement);
6109       viewport.addAlignment(al, "");
6110     } catch (Exception ex)
6111     {
6112       System.err.println(ex.getMessage());
6113       return;
6114     }
6115   }
6116 }
6117
6118 class PrintThread extends Thread
6119 {
6120   AlignmentPanel ap;
6121
6122   public PrintThread(AlignmentPanel ap)
6123   {
6124     this.ap = ap;
6125   }
6126
6127   static PageFormat pf;
6128
6129   @Override
6130   public void run()
6131   {
6132     PrinterJob printJob = PrinterJob.getPrinterJob();
6133
6134     if (pf != null)
6135     {
6136       printJob.setPrintable(ap, pf);
6137     }
6138     else
6139     {
6140       printJob.setPrintable(ap);
6141     }
6142
6143     if (printJob.printDialog())
6144     {
6145       try
6146       {
6147         printJob.print();
6148       } catch (Exception PrintException)
6149       {
6150         PrintException.printStackTrace();
6151       }
6152     }
6153   }
6154 }