src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.AAFrequency;
  24 import jalview.analysis.AlignmentSorter;
  25 import jalview.analysis.AlignmentUtils;
  26 import jalview.analysis.Conservation;
  27 import jalview.analysis.CrossRef;
  28 import jalview.analysis.NJTree;
  29 import jalview.analysis.ParseProperties;
  30 import jalview.analysis.SequenceIdMatcher;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.analysis.ScoreModelI;
  35 import jalview.bin.Cache;
  36 import jalview.commands.CommandI;
  37 import jalview.commands.EditCommand;
  38 import jalview.commands.EditCommand.Action;
  39 import jalview.commands.OrderCommand;
  40 import jalview.commands.RemoveGapColCommand;
  41 import jalview.commands.RemoveGapsCommand;
  42 import jalview.commands.SlideSequencesCommand;
  43 import jalview.commands.TrimRegionCommand;
  44 import jalview.datamodel.AlignedCodonFrame;
  45 import jalview.datamodel.Alignment;
  46 import jalview.datamodel.AlignmentAnnotation;
  47 import jalview.datamodel.AlignmentI;
  48 import jalview.datamodel.AlignmentOrder;
  49 import jalview.datamodel.AlignmentView;
  50 import jalview.datamodel.ColumnSelection;
  51 import jalview.datamodel.PDBEntry;
  52 import jalview.datamodel.SeqCigar;
  53 import jalview.datamodel.Sequence;
  54 import jalview.datamodel.SequenceGroup;
  55 import jalview.datamodel.SequenceI;
  56 import jalview.io.AlignmentProperties;
  57 import jalview.io.AnnotationFile;
  58 import jalview.io.FeaturesFile;
  59 import jalview.io.FileLoader;
  60 import jalview.io.FormatAdapter;
  61 import jalview.io.HTMLOutput;
  62 import jalview.io.IdentifyFile;
  63 import jalview.io.JalviewFileChooser;
  64 import jalview.io.JalviewFileView;
  65 import jalview.io.JnetAnnotationMaker;
  66 import jalview.io.NewickFile;
  67 import jalview.io.TCoffeeScoreFile;
  68 import jalview.jbgui.GAlignFrame;
  69 import jalview.schemes.Blosum62ColourScheme;
  70 import jalview.schemes.BuriedColourScheme;
  71 import jalview.schemes.ClustalxColourScheme;
  72 import jalview.schemes.ColourSchemeI;
  73 import jalview.schemes.ColourSchemeProperty;
  74 import jalview.schemes.HelixColourScheme;
  75 import jalview.schemes.HydrophobicColourScheme;
  76 import jalview.schemes.NucleotideColourScheme;
  77 import jalview.schemes.PIDColourScheme;
  78 import jalview.schemes.PurinePyrimidineColourScheme;
  79 import jalview.schemes.RNAHelicesColourChooser;
  80 import jalview.schemes.ResidueProperties;
  81 import jalview.schemes.StrandColourScheme;
  82 import jalview.schemes.TCoffeeColourScheme;
  83 import jalview.schemes.TaylorColourScheme;
  84 import jalview.schemes.TurnColourScheme;
  85 import jalview.schemes.UserColourScheme;
  86 import jalview.schemes.ZappoColourScheme;
  87 import jalview.structure.StructureSelectionManager;
  88 import jalview.util.MessageManager;
  89 import jalview.ws.jws1.Discoverer;
  90 import jalview.ws.jws2.Jws2Discoverer;
  91 import jalview.ws.jws2.jabaws2.Jws2Instance;
  92 import jalview.ws.seqfetcher.DbSourceProxy;
  93
  94 import java.awt.BorderLayout;
  95 import java.awt.Component;
  96 import java.awt.GridLayout;
  97 import java.awt.Rectangle;
  98 import java.awt.Toolkit;
  99 import java.awt.datatransfer.Clipboard;
 100 import java.awt.datatransfer.DataFlavor;
 101 import java.awt.datatransfer.StringSelection;
 102 import java.awt.datatransfer.Transferable;
 103 import java.awt.dnd.DnDConstants;
 104 import java.awt.dnd.DropTargetDragEvent;
 105 import java.awt.dnd.DropTargetDropEvent;
 106 import java.awt.dnd.DropTargetEvent;
 107 import java.awt.dnd.DropTargetListener;
 108 import java.awt.event.ActionEvent;
 109 import java.awt.event.ActionListener;
 110 import java.awt.event.KeyAdapter;
 111 import java.awt.event.KeyEvent;
 112 import java.awt.event.MouseAdapter;
 113 import java.awt.event.MouseEvent;
 114 import java.awt.print.PageFormat;
 115 import java.awt.print.PrinterJob;
 116 import java.beans.PropertyChangeEvent;
 117 import java.io.File;
 118 import java.net.URL;
 119 import java.util.ArrayList;
 120 import java.util.Arrays;
 121 import java.util.Enumeration;
 122 import java.util.Hashtable;
 123 import java.util.List;
 124 import java.util.Vector;
 125
 126 import javax.swing.JButton;
 127 import javax.swing.JCheckBoxMenuItem;
 128 import javax.swing.JEditorPane;
 129 import javax.swing.JInternalFrame;
 130 import javax.swing.JLabel;
 131 import javax.swing.JLayeredPane;
 132 import javax.swing.JMenu;
 133 import javax.swing.JMenuItem;
 134 import javax.swing.JOptionPane;
 135 import javax.swing.JPanel;
 136 import javax.swing.JProgressBar;
 137 import javax.swing.JRadioButtonMenuItem;
 138 import javax.swing.JScrollPane;
 139 import javax.swing.SwingUtilities;
 140
 141 /**
 142  * DOCUMENT ME!
 143  *
 144  * @author $author$
 145  * @version $Revision$
 146  */
 147 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 148         IProgressIndicator, AlignViewControllerGuiI
 149 {
 150
 151   /** DOCUMENT ME!! */
 152   public static final int DEFAULT_WIDTH = 700;
 153
 154   /** DOCUMENT ME!! */
 155   public static final int DEFAULT_HEIGHT = 500;
 156
 157   public AlignmentPanel alignPanel;
 158
 159   AlignViewport viewport;
 160
 161   public AlignViewControllerI avc;
 162
 163   Vector alignPanels = new Vector();
 164
 165   /**
 166    * Last format used to load or save alignments in this window
 167    */
 168   String currentFileFormat = null;
 169
 170   /**
 171    * Current filename for this alignment
 172    */
 173   String fileName = null;
 174
 175   /**
 176    * Creates a new AlignFrame object with specific width and height.
 177    *
 178    * @param al
 179    * @param width
 180    * @param height
 181    */
 182   public AlignFrame(AlignmentI al, int width, int height)
 183   {
 184     this(al, null, width, height);
 185   }
 186
 187   /**
 188    * Creates a new AlignFrame object with specific width, height and
 189    * sequenceSetId
 190    *
 191    * @param al
 192    * @param width
 193    * @param height
 194    * @param sequenceSetId
 195    */
 196   public AlignFrame(AlignmentI al, int width, int height,
 197           String sequenceSetId)
 198   {
 199     this(al, null, width, height, sequenceSetId);
 200   }
 201
 202   /**
 203    * Creates a new AlignFrame object with specific width, height and
 204    * sequenceSetId
 205    *
 206    * @param al
 207    * @param width
 208    * @param height
 209    * @param sequenceSetId
 210    * @param viewId
 211    */
 212   public AlignFrame(AlignmentI al, int width, int height,
 213           String sequenceSetId, String viewId)
 214   {
 215     this(al, null, width, height, sequenceSetId, viewId);
 216   }
 217
 218   /**
 219    * new alignment window with hidden columns
 220    *
 221    * @param al
 222    *          AlignmentI
 223    * @param hiddenColumns
 224    *          ColumnSelection or null
 225    * @param width
 226    *          Width of alignment frame
 227    * @param height
 228    *          height of frame.
 229    */
 230   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 231           int width, int height)
 232   {
 233     this(al, hiddenColumns, width, height, null);
 234   }
 235
 236   /**
 237    * Create alignment frame for al with hiddenColumns, a specific width and
 238    * height, and specific sequenceId
 239    *
 240    * @param al
 241    * @param hiddenColumns
 242    * @param width
 243    * @param height
 244    * @param sequenceSetId
 245    *          (may be null)
 246    */
 247   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 248           int width, int height, String sequenceSetId)
 249   {
 250     this(al, hiddenColumns, width, height, sequenceSetId, null);
 251   }
 252
 253   /**
 254    * Create alignment frame for al with hiddenColumns, a specific width and
 255    * height, and specific sequenceId
 256    *
 257    * @param al
 258    * @param hiddenColumns
 259    * @param width
 260    * @param height
 261    * @param sequenceSetId
 262    *          (may be null)
 263    * @param viewId
 264    *          (may be null)
 265    */
 266   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 267           int width, int height, String sequenceSetId, String viewId)
 268   {
 269     setSize(width, height);
 270
 271     if (al.getDataset() == null)
 272     {
 273       al.setDataset(null);
 274     }
 275
 276     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 277
 278     alignPanel = new AlignmentPanel(this, viewport);
 279
 280
 281     addAlignmentPanel(alignPanel, true);
 282     init();
 283   }
 284
 285   /**
 286    * Make a new AlignFrame from existing alignmentPanels
 287    *
 288    * @param ap
 289    *          AlignmentPanel
 290    * @param av
 291    *          AlignViewport
 292    */
 293   public AlignFrame(AlignmentPanel ap)
 294   {
 295     viewport = ap.av;
 296     alignPanel = ap;
 297     addAlignmentPanel(ap, false);
 298     init();
 299   }
 300
 301   /**
 302    * initalise the alignframe from the underlying viewport data and the
 303    * configurations
 304    */
 305   void init()
 306   {
 307     avc = new jalview.controller.AlignViewController(this, viewport,
 308             alignPanel);
 309     if (viewport.getAlignmentConservationAnnotation() == null)
 310     {
 311       BLOSUM62Colour.setEnabled(false);
 312       conservationMenuItem.setEnabled(false);
 313       modifyConservation.setEnabled(false);
 314       // PIDColour.setEnabled(false);
 315       // abovePIDThreshold.setEnabled(false);
 316       // modifyPID.setEnabled(false);
 317     }
 318
 319     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 320             "No sort");
 321
 322     if (sortby.equals("Id"))
 323     {
 324       sortIDMenuItem_actionPerformed(null);
 325     }
 326     else if (sortby.equals("Pairwise Identity"))
 327     {
 328       sortPairwiseMenuItem_actionPerformed(null);
 329     }
 330
 331     if (Desktop.desktop != null)
 332     {
 333       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 334       addServiceListeners();
 335       setGUINucleotide(viewport.getAlignment().isNucleotide());
 336     }
 337
 338     setMenusFromViewport(viewport);
 339     buildSortByAnnotationScoresMenu();
 340     buildTreeMenu();
 341
 342     if (viewport.wrapAlignment)
 343     {
 344       wrapMenuItem_actionPerformed(null);
 345     }
 346
 347     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 348     {
 349       this.overviewMenuItem_actionPerformed(null);
 350     }
 351
 352     addKeyListener();
 353
 354   }
 355
 356   /**
 357    * Change the filename and format for the alignment, and enable the 'reload'
 358    * button functionality.
 359    *
 360    * @param file
 361    *          valid filename
 362    * @param format
 363    *          format of file
 364    */
 365   public void setFileName(String file, String format)
 366   {
 367     fileName = file;
 368     currentFileFormat = format;
 369     reload.setEnabled(true);
 370   }
 371
 372   void addKeyListener()
 373   {
 374     addKeyListener(new KeyAdapter()
 375     {
 376       @Override
 377       public void keyPressed(KeyEvent evt)
 378       {
 379         if (viewport.cursorMode
 380                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 381                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 382                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 383                 && Character.isDigit(evt.getKeyChar()))
 384         {
 385           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 386         }
 387
 388         switch (evt.getKeyCode())
 389         {
 390
 391         case 27: // escape key
 392           deselectAllSequenceMenuItem_actionPerformed(null);
 393
 394           break;
 395
 396         case KeyEvent.VK_DOWN:
 397           if (evt.isAltDown() || !viewport.cursorMode)
 398           {
 399             moveSelectedSequences(false);
 400           }
 401           if (viewport.cursorMode)
 402           {
 403             alignPanel.seqPanel.moveCursor(0, 1);
 404           }
 405           break;
 406
 407         case KeyEvent.VK_UP:
 408           if (evt.isAltDown() || !viewport.cursorMode)
 409           {
 410             moveSelectedSequences(true);
 411           }
 412           if (viewport.cursorMode)
 413           {
 414             alignPanel.seqPanel.moveCursor(0, -1);
 415           }
 416
 417           break;
 418
 419         case KeyEvent.VK_LEFT:
 420           if (evt.isAltDown() || !viewport.cursorMode)
 421           {
 422             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 423           }
 424           else
 425           {
 426             alignPanel.seqPanel.moveCursor(-1, 0);
 427           }
 428
 429           break;
 430
 431         case KeyEvent.VK_RIGHT:
 432           if (evt.isAltDown() || !viewport.cursorMode)
 433           {
 434             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 435           }
 436           else
 437           {
 438             alignPanel.seqPanel.moveCursor(1, 0);
 439           }
 440           break;
 441
 442         case KeyEvent.VK_SPACE:
 443           if (viewport.cursorMode)
 444           {
 445             alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 446                     || evt.isShiftDown() || evt.isAltDown());
 447           }
 448           break;
 449
 450         // case KeyEvent.VK_A:
 451         // if (viewport.cursorMode)
 452         // {
 453         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 454         // //System.out.println("A");
 455         // }
 456         // break;
 457         /*
 458          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 459          * System.out.println("closing bracket"); } break;
 460          */
 461         case KeyEvent.VK_DELETE:
 462         case KeyEvent.VK_BACK_SPACE:
 463           if (!viewport.cursorMode)
 464           {
 465             cut_actionPerformed(null);
 466           }
 467           else
 468           {
 469             alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 470                     || evt.isShiftDown() || evt.isAltDown());
 471           }
 472
 473           break;
 474
 475         case KeyEvent.VK_S:
 476           if (viewport.cursorMode)
 477           {
 478             alignPanel.seqPanel.setCursorRow();
 479           }
 480           break;
 481         case KeyEvent.VK_C:
 482           if (viewport.cursorMode && !evt.isControlDown())
 483           {
 484             alignPanel.seqPanel.setCursorColumn();
 485           }
 486           break;
 487         case KeyEvent.VK_P:
 488           if (viewport.cursorMode)
 489           {
 490             alignPanel.seqPanel.setCursorPosition();
 491           }
 492           break;
 493
 494         case KeyEvent.VK_ENTER:
 495         case KeyEvent.VK_COMMA:
 496           if (viewport.cursorMode)
 497           {
 498             alignPanel.seqPanel.setCursorRowAndColumn();
 499           }
 500           break;
 501
 502         case KeyEvent.VK_Q:
 503           if (viewport.cursorMode)
 504           {
 505             alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 506           }
 507           break;
 508         case KeyEvent.VK_M:
 509           if (viewport.cursorMode)
 510           {
 511             alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 512           }
 513           break;
 514
 515         case KeyEvent.VK_F2:
 516           viewport.cursorMode = !viewport.cursorMode;
 517           statusBar.setText(MessageManager.formatMessage(
 518                   "label.keyboard_editing_mode", new String[]
 519                   { (viewport.cursorMode ? "on" : "off") }));
 520           if (viewport.cursorMode)
 521           {
 522             alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 523             alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 524           }
 525           alignPanel.seqPanel.seqCanvas.repaint();
 526           break;
 527
 528         case KeyEvent.VK_F1:
 529           try
 530           {
 531             Help.showHelpWindow();
 532           } catch (Exception ex)
 533           {
 534             ex.printStackTrace();
 535           }
 536           break;
 537         case KeyEvent.VK_H:
 538         {
 539           boolean toggleSeqs = !evt.isControlDown();
 540           boolean toggleCols = !evt.isShiftDown();
 541           toggleHiddenRegions(toggleSeqs, toggleCols);
 542           break;
 543         }
 544         case KeyEvent.VK_PAGE_UP:
 545           if (viewport.wrapAlignment)
 546           {
 547             alignPanel.scrollUp(true);
 548           }
 549           else
 550           {
 551             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 552                     - viewport.endSeq + viewport.startSeq);
 553           }
 554           break;
 555         case KeyEvent.VK_PAGE_DOWN:
 556           if (viewport.wrapAlignment)
 557           {
 558             alignPanel.scrollUp(false);
 559           }
 560           else
 561           {
 562             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 563                     + viewport.endSeq - viewport.startSeq);
 564           }
 565           break;
 566         }
 567       }
 568
 569       @Override
 570       public void keyReleased(KeyEvent evt)
 571       {
 572         switch (evt.getKeyCode())
 573         {
 574         case KeyEvent.VK_LEFT:
 575           if (evt.isAltDown() || !viewport.cursorMode)
 576           {
 577             viewport.firePropertyChange("alignment", null, viewport
 578                     .getAlignment().getSequences());
 579           }
 580           break;
 581
 582         case KeyEvent.VK_RIGHT:
 583           if (evt.isAltDown() || !viewport.cursorMode)
 584           {
 585             viewport.firePropertyChange("alignment", null, viewport
 586                     .getAlignment().getSequences());
 587           }
 588           break;
 589         }
 590       }
 591     });
 592   }
 593
 594   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 595   {
 596     ap.alignFrame = this;
 597     avc = new jalview.controller.AlignViewController(this, viewport,
 598             alignPanel);
 599
 600     alignPanels.addElement(ap);
 601
 602     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 603
 604     int aSize = alignPanels.size();
 605
 606     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 607
 608     if (aSize == 1 && ap.av.viewName == null)
 609     {
 610       this.getContentPane().add(ap, BorderLayout.CENTER);
 611     }
 612     else
 613     {
 614       if (aSize == 2)
 615       {
 616         setInitialTabVisible();
 617       }
 618
 619       expandViews.setEnabled(true);
 620       gatherViews.setEnabled(true);
 621       tabbedPane.addTab(ap.av.viewName, ap);
 622
 623       ap.setVisible(false);
 624     }
 625
 626     if (newPanel)
 627     {
 628       if (ap.av.isPadGaps())
 629       {
 630         ap.av.getAlignment().padGaps();
 631       }
 632       ap.av.updateConservation(ap);
 633       ap.av.updateConsensus(ap);
 634       ap.av.updateStrucConsensus(ap);
 635     }
 636   }
 637
 638   public void setInitialTabVisible()
 639   {
 640     expandViews.setEnabled(true);
 641     gatherViews.setEnabled(true);
 642     tabbedPane.setVisible(true);
 643     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
 644     tabbedPane.addTab(first.av.viewName, first);
 645     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 646   }
 647
 648   public AlignViewport getViewport()
 649   {
 650     return viewport;
 651   }
 652
 653   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 654   private void addServiceListeners()
 655   {
 656     final java.beans.PropertyChangeListener thisListener;
 657     Desktop.instance.addJalviewPropertyChangeListener("services",
 658             thisListener = new java.beans.PropertyChangeListener()
 659             {
 660               @Override
 661               public void propertyChange(PropertyChangeEvent evt)
 662               {
 663                 // // System.out.println("Discoverer property change.");
 664                 // if (evt.getPropertyName().equals("services"))
 665                 {
 666                   SwingUtilities.invokeLater(new Runnable()
 667                   {
 668
 669                     @Override
 670                     public void run()
 671                     {
 672                       System.err
 673                               .println("Rebuild WS Menu for service change");
 674                       BuildWebServiceMenu();
 675                     }
 676
 677                   });
 678                 }
 679               }
 680             });
 681     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 682     {
 683       @Override
 684       public void internalFrameClosed(
 685               javax.swing.event.InternalFrameEvent evt)
 686       {
 687         System.out.println("deregistering discoverer listener");
 688         Desktop.instance.removeJalviewPropertyChangeListener("services",
 689                 thisListener);
 690         closeMenuItem_actionPerformed(true);
 691       };
 692     });
 693     // Finally, build the menu once to get current service state
 694     new Thread(new Runnable()
 695     {
 696       @Override
 697       public void run()
 698       {
 699         BuildWebServiceMenu();
 700       }
 701     }).start();
 702   }
 703
 704   public void setGUINucleotide(boolean nucleotide)
 705   {
 706     showTranslation.setVisible(nucleotide);
 707     cdna.setVisible(!nucleotide);
 708     conservationMenuItem.setEnabled(!nucleotide);
 709     modifyConservation.setEnabled(!nucleotide);
 710     showGroupConservation.setEnabled(!nucleotide);
 711     rnahelicesColour.setEnabled(nucleotide);
 712     purinePyrimidineColour.setEnabled(nucleotide);
 713   }
 714
 715   /**
 716    * Builds codon mappings from this (protein) alignment to any compatible
 717    * nucleotide alignments. Mappings are built between sequences with the same
 718    * name and compatible lengths. Also makes the cDNA alignment a
 719    * CommandListener for the protein alignment so that edits are mirrored.
 720    */
 721   @Override
 722   protected void linkCdna_actionPerformed()
 723   {
 724     int linkedCount = 0;
 725     int alreadyLinkedCount = 0;
 726     final AlignmentI thisAlignment = this.alignPanel.getAlignment();
 727
 728     for (AlignFrame af : Desktop.getAlignframes())
 729     {
 730       if (af.alignPanel != null)
 731       {
 732         final AlignmentI thatAlignment = af.alignPanel.getAlignment();
 733         if (thatAlignment.isNucleotide())
 734         {
 735           // TODO exclude an AlignFrame which is already mapped to this one
 736           // temporary version: exclude if already a CommandListener (should
 737           // cover most cases but not all)
 738           final boolean alreadyMapped = this.viewport
 739                   .getStructureSelectionManager().hasCommandListener(
 740                           af.viewport);
 741           if (alreadyMapped)
 742           {
 743             alreadyLinkedCount++;
 744           }
 745           else
 746           {
 747             boolean mapped = AlignmentUtils.mapProteinToCdna(thisAlignment,
 748                     thatAlignment);
 749             if (mapped)
 750             {
 751               final StructureSelectionManager ssm = StructureSelectionManager
 752                       .getStructureSelectionManager(Desktop.instance);
 753               ssm.addMappings(thisAlignment.getCodonFrames());
 754               ssm.addCommandListener(af.getViewport());
 755               linkedCount++;
 756             }
 757           }
 758         }
 759       }
 760     }
 761     String msg = "";
 762     if (linkedCount == 0 && alreadyLinkedCount == 0)
 763     {
 764       msg = MessageManager.getString("label.no_cdna");
 765     }
 766     else if (linkedCount > 0)
 767     {
 768       msg = MessageManager.formatMessage("label.linked_cdna", linkedCount);
 769     }
 770     else
 771     {
 772       msg = MessageManager.formatMessage("label.cdna_all_linked",
 773               alreadyLinkedCount);
 774     }
 775     setStatus(msg);
 776   }
 777
 778   /**
 779    * Align any linked cDNA to match the alignment of this (protein) alignment.
 780    * Any mapped sequence regions will be realigned, unmapped sequences are not
 781    * affected.
 782    */
 783   @Override
 784   protected void alignCdna_actionPerformed()
 785   {
 786     int seqCount = 0;
 787     int alignCount = 0;
 788     final AlignmentI thisAlignment = this.alignPanel.getAlignment();
 789     for (AlignFrame af : Desktop.getAlignframes())
 790     {
 791       if (af.alignPanel != null)
 792       {
 793         final AlignmentI thatAlignment = af.alignPanel.getAlignment();
 794         if (thatAlignment.isNucleotide())
 795         {
 796           int seqsAligned = thatAlignment.alignAs(thisAlignment);
 797           seqCount += seqsAligned;
 798           if (seqsAligned > 0)
 799           {
 800             af.viewport.alignmentChanged(af.alignPanel);
 801             alignCount++;
 802           }
 803         }
 804       }
 805     }
 806     setStatus(MessageManager.formatMessage("label.cdna_aligned", seqCount,
 807             alignCount));
 808   }
 809   /**
 810    * set up menus for the current viewport. This may be called after any
 811    * operation that affects the data in the current view (selection changed,
 812    * etc) to update the menus to reflect the new state.
 813    */
 814   public void setMenusForViewport()
 815   {
 816     setMenusFromViewport(viewport);
 817   }
 818
 819   /**
 820    * Need to call this method when tabs are selected for multiple views, or when
 821    * loading from Jalview2XML.java
 822    *
 823    * @param av
 824    *          AlignViewport
 825    */
 826   void setMenusFromViewport(AlignViewport av)
 827   {
 828     padGapsMenuitem.setSelected(av.isPadGaps());
 829     colourTextMenuItem.setSelected(av.showColourText);
 830     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 831     conservationMenuItem.setSelected(av.getConservationSelected());
 832     seqLimits.setSelected(av.getShowJVSuffix());
 833     idRightAlign.setSelected(av.rightAlignIds);
 834     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
 835     renderGapsMenuItem.setSelected(av.renderGaps);
 836     wrapMenuItem.setSelected(av.wrapAlignment);
 837     scaleAbove.setVisible(av.wrapAlignment);
 838     scaleLeft.setVisible(av.wrapAlignment);
 839     scaleRight.setVisible(av.wrapAlignment);
 840     annotationPanelMenuItem.setState(av.showAnnotation);
 841     /*
 842      * Show/hide annotations only enabled if annotation panel is shown
 843      */
 844     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 845     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 846     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 847     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 848     viewBoxesMenuItem.setSelected(av.showBoxes);
 849     viewTextMenuItem.setSelected(av.showText);
 850     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 851     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 852     showGroupConservation.setSelected(av.isShowGroupConservation());
 853     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 854     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 855     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 856
 857     setColourSelected(ColourSchemeProperty.getColourName(av
 858             .getGlobalColourScheme()));
 859
 860     showSeqFeatures.setSelected(av.showSequenceFeatures);
 861     hiddenMarkers.setState(av.showHiddenMarkers);
 862     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 863     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
 864     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
 865     autoCalculate.setSelected(av.autoCalculateConsensus);
 866     sortByTree.setSelected(av.sortByTree);
 867     listenToViewSelections.setSelected(av.followSelection);
 868     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 869     rnahelicesColour
 870             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 871     setShowProductsEnabled();
 872     updateEditMenuBar();
 873   }
 874
 875   // methods for implementing IProgressIndicator
 876   // need to refactor to a reusable stub class
 877   Hashtable progressBars, progressBarHandlers;
 878
 879   /*
 880    * (non-Javadoc)
 881    *
 882    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 883    */
 884   @Override
 885   public void setProgressBar(String message, long id)
 886   {
 887     if (progressBars == null)
 888     {
 889       progressBars = new Hashtable();
 890       progressBarHandlers = new Hashtable();
 891     }
 892
 893     JPanel progressPanel;
 894     Long lId = new Long(id);
 895     GridLayout layout = (GridLayout) statusPanel.getLayout();
 896     if (progressBars.get(lId) != null)
 897     {
 898       progressPanel = (JPanel) progressBars.get(new Long(id));
 899       statusPanel.remove(progressPanel);
 900       progressBars.remove(lId);
 901       progressPanel = null;
 902       if (message != null)
 903       {
 904         statusBar.setText(message);
 905       }
 906       if (progressBarHandlers.contains(lId))
 907       {
 908         progressBarHandlers.remove(lId);
 909       }
 910       layout.setRows(layout.getRows() - 1);
 911     }
 912     else
 913     {
 914       progressPanel = new JPanel(new BorderLayout(10, 5));
 915
 916       JProgressBar progressBar = new JProgressBar();
 917       progressBar.setIndeterminate(true);
 918
 919       progressPanel.add(new JLabel(message), BorderLayout.WEST);
 920       progressPanel.add(progressBar, BorderLayout.CENTER);
 921
 922       layout.setRows(layout.getRows() + 1);
 923       statusPanel.add(progressPanel);
 924
 925       progressBars.put(lId, progressPanel);
 926     }
 927     // update GUI
 928     // setMenusForViewport();
 929     validate();
 930   }
 931
 932   @Override
 933   public void registerHandler(final long id,
 934           final IProgressIndicatorHandler handler)
 935   {
 936     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
 937     {
 938       throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
 939     }
 940     progressBarHandlers.put(new Long(id), handler);
 941     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
 942     if (handler.canCancel())
 943     {
 944       JButton cancel = new JButton(
 945               MessageManager.getString("action.cancel"));
 946       final IProgressIndicator us = this;
 947       cancel.addActionListener(new ActionListener()
 948       {
 949
 950         @Override
 951         public void actionPerformed(ActionEvent e)
 952         {
 953           handler.cancelActivity(id);
 954           us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
 955         }
 956       });
 957       progressPanel.add(cancel, BorderLayout.EAST);
 958     }
 959   }
 960
 961   /**
 962    *
 963    * @return true if any progress bars are still active
 964    */
 965   @Override
 966   public boolean operationInProgress()
 967   {
 968     if (progressBars != null && progressBars.size() > 0)
 969     {
 970       return true;
 971     }
 972     return false;
 973   }
 974
 975   @Override
 976   public void setStatus(String text)
 977   {
 978     statusBar.setText(text);
 979   };
 980
 981   /*
 982    * Added so Castor Mapping file can obtain Jalview Version
 983    */
 984   public String getVersion()
 985   {
 986     return jalview.bin.Cache.getProperty("VERSION");
 987   }
 988
 989   public FeatureRenderer getFeatureRenderer()
 990   {
 991     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
 992   }
 993
 994   @Override
 995   public void fetchSequence_actionPerformed(ActionEvent e)
 996   {
 997     new SequenceFetcher(this);
 998   }
 999
1000   @Override
1001   public void addFromFile_actionPerformed(ActionEvent e)
1002   {
1003     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1004   }
1005
1006   @Override
1007   public void reload_actionPerformed(ActionEvent e)
1008   {
1009     if (fileName != null)
1010     {
1011       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1012       // originating file's format
1013       // TODO: work out how to recover feature settings for correct view(s) when
1014       // file is reloaded.
1015       if (currentFileFormat.equals("Jalview"))
1016       {
1017         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1018         for (int i = 0; i < frames.length; i++)
1019         {
1020           if (frames[i] instanceof AlignFrame && frames[i] != this
1021                   && ((AlignFrame) frames[i]).fileName != null
1022                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1023           {
1024             try
1025             {
1026               frames[i].setSelected(true);
1027               Desktop.instance.closeAssociatedWindows();
1028             } catch (java.beans.PropertyVetoException ex)
1029             {
1030             }
1031           }
1032
1033         }
1034         Desktop.instance.closeAssociatedWindows();
1035
1036         FileLoader loader = new FileLoader();
1037         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1038         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1039       }
1040       else
1041       {
1042         Rectangle bounds = this.getBounds();
1043
1044         FileLoader loader = new FileLoader();
1045         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1046         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1047                 protocol, currentFileFormat);
1048
1049         newframe.setBounds(bounds);
1050         if (featureSettings != null && featureSettings.isShowing())
1051         {
1052           final Rectangle fspos = featureSettings.frame.getBounds();
1053           // TODO: need a 'show feature settings' function that takes bounds -
1054           // need to refactor Desktop.addFrame
1055           newframe.featureSettings_actionPerformed(null);
1056           final FeatureSettings nfs = newframe.featureSettings;
1057           SwingUtilities.invokeLater(new Runnable()
1058           {
1059             @Override
1060             public void run()
1061             {
1062               nfs.frame.setBounds(fspos);
1063             }
1064           });
1065           this.featureSettings.close();
1066           this.featureSettings = null;
1067         }
1068         this.closeMenuItem_actionPerformed(true);
1069       }
1070     }
1071   }
1072
1073   @Override
1074   public void addFromText_actionPerformed(ActionEvent e)
1075   {
1076     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
1077   }
1078
1079   @Override
1080   public void addFromURL_actionPerformed(ActionEvent e)
1081   {
1082     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1083   }
1084
1085   @Override
1086   public void save_actionPerformed(ActionEvent e)
1087   {
1088     if (fileName == null
1089             || (currentFileFormat == null || !jalview.io.FormatAdapter
1090                     .isValidIOFormat(currentFileFormat, true))
1091             || fileName.startsWith("http"))
1092     {
1093       saveAs_actionPerformed(null);
1094     }
1095     else
1096     {
1097       saveAlignment(fileName, currentFileFormat);
1098     }
1099   }
1100
1101   /**
1102    * DOCUMENT ME!
1103    *
1104    * @param e
1105    *          DOCUMENT ME!
1106    */
1107   @Override
1108   public void saveAs_actionPerformed(ActionEvent e)
1109   {
1110     JalviewFileChooser chooser = new JalviewFileChooser(
1111             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1112             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1113             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1114             currentFileFormat, false);
1115
1116     chooser.setFileView(new JalviewFileView());
1117     chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1118     chooser.setToolTipText(MessageManager.getString("action.save"));
1119
1120     int value = chooser.showSaveDialog(this);
1121
1122     if (value == JalviewFileChooser.APPROVE_OPTION)
1123     {
1124       currentFileFormat = chooser.getSelectedFormat();
1125       if (currentFileFormat == null)
1126       {
1127         JOptionPane
1128                 .showInternalMessageDialog(
1129                         Desktop.desktop,
1130                         MessageManager
1131                                 .getString("label.select_file_format_before_saving"),
1132                         MessageManager
1133                                 .getString("label.file_format_not_specified"),
1134                         JOptionPane.WARNING_MESSAGE);
1135         value = chooser.showSaveDialog(this);
1136         return;
1137       }
1138
1139       fileName = chooser.getSelectedFile().getPath();
1140
1141       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1142               currentFileFormat);
1143
1144       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1145       if (currentFileFormat.indexOf(" ") > -1)
1146       {
1147         currentFileFormat = currentFileFormat.substring(0,
1148                 currentFileFormat.indexOf(" "));
1149       }
1150       saveAlignment(fileName, currentFileFormat);
1151     }
1152   }
1153
1154   public boolean saveAlignment(String file, String format)
1155   {
1156     boolean success = true;
1157
1158     if (format.equalsIgnoreCase("Jalview"))
1159     {
1160       String shortName = title;
1161
1162       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1163       {
1164         shortName = shortName.substring(shortName
1165                 .lastIndexOf(java.io.File.separatorChar) + 1);
1166       }
1167
1168       success = new Jalview2XML().SaveAlignment(this, file, shortName);
1169
1170       statusBar.setText(MessageManager.formatMessage(
1171               "label.successfully_saved_to_file_in_format", new String[]
1172               { fileName, format }));
1173
1174     }
1175     else
1176     {
1177       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1178       {
1179         warningMessage("Cannot save file " + fileName + " using format "
1180                 + format, "Alignment output format not supported");
1181         saveAs_actionPerformed(null);
1182         // JBPNote need to have a raise_gui flag here
1183         return false;
1184       }
1185
1186       String[] omitHidden = null;
1187
1188       if (viewport.hasHiddenColumns())
1189       {
1190         int reply = JOptionPane
1191                 .showInternalConfirmDialog(
1192                         Desktop.desktop,
1193                         MessageManager
1194                                 .getString("label.alignment_contains_hidden_columns"),
1195                         MessageManager
1196                                 .getString("action.save_omit_hidden_columns"),
1197                         JOptionPane.YES_NO_OPTION,
1198                         JOptionPane.QUESTION_MESSAGE);
1199
1200         if (reply == JOptionPane.YES_OPTION)
1201         {
1202           omitHidden = viewport.getViewAsString(false);
1203         }
1204       }
1205       FormatAdapter f = new FormatAdapter();
1206       String output = f.formatSequences(format,
1207               viewport.getAlignment(), // class cast exceptions will
1208               // occur in the distant future
1209               omitHidden, f.getCacheSuffixDefault(format),
1210               viewport.getColumnSelection());
1211
1212       if (output == null)
1213       {
1214         success = false;
1215       }
1216       else
1217       {
1218         try
1219         {
1220           java.io.PrintWriter out = new java.io.PrintWriter(
1221                   new java.io.FileWriter(file));
1222
1223           out.print(output);
1224           out.close();
1225           this.setTitle(file);
1226           statusBar.setText(MessageManager.formatMessage(
1227                   "label.successfully_saved_to_file_in_format",
1228                   new String[]
1229                   { fileName, format }));
1230         } catch (Exception ex)
1231         {
1232           success = false;
1233           ex.printStackTrace();
1234         }
1235       }
1236     }
1237
1238     if (!success)
1239     {
1240       JOptionPane.showInternalMessageDialog(this, MessageManager
1241               .formatMessage("label.couldnt_save_file", new String[]
1242               { fileName }), MessageManager
1243               .getString("label.error_saving_file"),
1244               JOptionPane.WARNING_MESSAGE);
1245     }
1246
1247     return success;
1248   }
1249
1250   private void warningMessage(String warning, String title)
1251   {
1252     if (new jalview.util.Platform().isHeadless())
1253     {
1254       System.err.println("Warning: " + title + "\nWarning: " + warning);
1255
1256     }
1257     else
1258     {
1259       JOptionPane.showInternalMessageDialog(this, warning, title,
1260               JOptionPane.WARNING_MESSAGE);
1261     }
1262     return;
1263   }
1264
1265   /**
1266    * DOCUMENT ME!
1267    *
1268    * @param e
1269    *          DOCUMENT ME!
1270    */
1271   @Override
1272   protected void outputText_actionPerformed(ActionEvent e)
1273   {
1274     String[] omitHidden = null;
1275
1276     if (viewport.hasHiddenColumns())
1277     {
1278       int reply = JOptionPane
1279               .showInternalConfirmDialog(
1280                       Desktop.desktop,
1281                       MessageManager
1282                               .getString("label.alignment_contains_hidden_columns"),
1283                       MessageManager
1284                               .getString("action.save_omit_hidden_columns"),
1285                       JOptionPane.YES_NO_OPTION,
1286                       JOptionPane.QUESTION_MESSAGE);
1287
1288       if (reply == JOptionPane.YES_OPTION)
1289       {
1290         omitHidden = viewport.getViewAsString(false);
1291       }
1292     }
1293
1294     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1295     cap.setForInput(null);
1296
1297     try
1298     {
1299       cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1300               viewport.getAlignment(), omitHidden,
1301               viewport.getColumnSelection()));
1302       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1303               "label.alignment_output_command", new String[]
1304               { e.getActionCommand() }), 600, 500);
1305     } catch (OutOfMemoryError oom)
1306     {
1307       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1308       cap.dispose();
1309     }
1310
1311   }
1312
1313   /**
1314    * DOCUMENT ME!
1315    *
1316    * @param e
1317    *          DOCUMENT ME!
1318    */
1319   @Override
1320   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1321   {
1322     new HTMLOutput(alignPanel,
1323             alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1324             alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1325   }
1326
1327   public void createImageMap(File file, String image)
1328   {
1329     alignPanel.makePNGImageMap(file, image);
1330   }
1331
1332   /**
1333    * DOCUMENT ME!
1334    *
1335    * @param e
1336    *          DOCUMENT ME!
1337    */
1338   @Override
1339   public void createPNG(File f)
1340   {
1341     alignPanel.makePNG(f);
1342   }
1343
1344   /**
1345    * DOCUMENT ME!
1346    *
1347    * @param e
1348    *          DOCUMENT ME!
1349    */
1350   @Override
1351   public void createEPS(File f)
1352   {
1353     alignPanel.makeEPS(f);
1354   }
1355
1356   public void createSVG(File f)
1357   {
1358     alignPanel.makeSVG(f);
1359   }
1360   @Override
1361   public void pageSetup_actionPerformed(ActionEvent e)
1362   {
1363     PrinterJob printJob = PrinterJob.getPrinterJob();
1364     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1365   }
1366
1367   /**
1368    * DOCUMENT ME!
1369    *
1370    * @param e
1371    *          DOCUMENT ME!
1372    */
1373   @Override
1374   public void printMenuItem_actionPerformed(ActionEvent e)
1375   {
1376     // Putting in a thread avoids Swing painting problems
1377     PrintThread thread = new PrintThread(alignPanel);
1378     thread.start();
1379   }
1380
1381   @Override
1382   public void exportFeatures_actionPerformed(ActionEvent e)
1383   {
1384     new AnnotationExporter().exportFeatures(alignPanel);
1385   }
1386
1387   @Override
1388   public void exportAnnotations_actionPerformed(ActionEvent e)
1389   {
1390     new AnnotationExporter().exportAnnotations(alignPanel,
1391             viewport.showAnnotation ? viewport.getAlignment()
1392                     .getAlignmentAnnotation() : null, viewport
1393                     .getAlignment().getGroups(), ((Alignment) viewport
1394                     .getAlignment()).alignmentProperties);
1395   }
1396
1397   @Override
1398   public void associatedData_actionPerformed(ActionEvent e)
1399   {
1400     // Pick the tree file
1401     JalviewFileChooser chooser = new JalviewFileChooser(
1402             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1403     chooser.setFileView(new JalviewFileView());
1404     chooser.setDialogTitle(MessageManager
1405             .getString("label.load_jalview_annotations"));
1406     chooser.setToolTipText(MessageManager
1407             .getString("label.load_jalview_annotations"));
1408
1409     int value = chooser.showOpenDialog(null);
1410
1411     if (value == JalviewFileChooser.APPROVE_OPTION)
1412     {
1413       String choice = chooser.getSelectedFile().getPath();
1414       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1415       loadJalviewDataFile(choice, null, null, null);
1416     }
1417
1418   }
1419
1420   /**
1421    * Close the current view or all views in the alignment frame. If the frame
1422    * only contains one view then the alignment will be removed from memory.
1423    *
1424    * @param closeAllTabs
1425    */
1426   @Override
1427   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1428   {
1429     if (alignPanels != null && alignPanels.size() < 2)
1430     {
1431       closeAllTabs = true;
1432     }
1433
1434     try
1435     {
1436       if (alignPanels != null)
1437       {
1438         if (closeAllTabs)
1439         {
1440           if (this.isClosed())
1441           {
1442             // really close all the windows - otherwise wait till
1443             // setClosed(true) is called
1444             for (int i = 0; i < alignPanels.size(); i++)
1445             {
1446               AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1447               ap.closePanel();
1448             }
1449           }
1450         }
1451         else
1452         {
1453           closeView(alignPanel);
1454         }
1455       }
1456
1457       if (closeAllTabs)
1458       {
1459         this.setClosed(true);
1460       }
1461     } catch (Exception ex)
1462     {
1463       ex.printStackTrace();
1464     }
1465   }
1466
1467   /**
1468    * close alignPanel2 and shuffle tabs appropriately.
1469    *
1470    * @param alignPanel2
1471    */
1472   public void closeView(AlignmentPanel alignPanel2)
1473   {
1474     int index = tabbedPane.getSelectedIndex();
1475     int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1476     alignPanels.removeElement(alignPanel2);
1477     // Unnecessary
1478     // if (viewport == alignPanel2.av)
1479     // {
1480     // viewport = null;
1481     // }
1482     alignPanel2.closePanel();
1483     alignPanel2 = null;
1484
1485     tabbedPane.removeTabAt(closedindex);
1486     tabbedPane.validate();
1487
1488     if (index > closedindex || index == tabbedPane.getTabCount())
1489     {
1490       // modify currently selected tab index if necessary.
1491       index--;
1492     }
1493
1494     this.tabSelectionChanged(index);
1495   }
1496
1497   /**
1498    * DOCUMENT ME!
1499    */
1500   void updateEditMenuBar()
1501   {
1502
1503     if (viewport.getHistoryList().size() > 0)
1504     {
1505       undoMenuItem.setEnabled(true);
1506       CommandI command = viewport.getHistoryList().peek();
1507       undoMenuItem.setText(MessageManager.formatMessage(
1508               "label.undo_command", new String[]
1509               { command.getDescription() }));
1510     }
1511     else
1512     {
1513       undoMenuItem.setEnabled(false);
1514       undoMenuItem.setText(MessageManager.getString("action.undo"));
1515     }
1516
1517     if (viewport.getRedoList().size() > 0)
1518     {
1519       redoMenuItem.setEnabled(true);
1520
1521       CommandI command = viewport.getRedoList().peek();
1522       redoMenuItem.setText(MessageManager.formatMessage(
1523               "label.redo_command", new String[]
1524               { command.getDescription() }));
1525     }
1526     else
1527     {
1528       redoMenuItem.setEnabled(false);
1529       redoMenuItem.setText(MessageManager.getString("action.redo"));
1530     }
1531   }
1532
1533   public void addHistoryItem(CommandI command)
1534   {
1535     if (command.getSize() > 0)
1536     {
1537       viewport.addToHistoryList(command);
1538       viewport.clearRedoList();
1539       updateEditMenuBar();
1540       viewport.updateHiddenColumns();
1541       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1542       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1543       // viewport.getColumnSelection()
1544       // .getHiddenColumns().size() > 0);
1545     }
1546   }
1547
1548   /**
1549    *
1550    * @return alignment objects for all views
1551    */
1552   AlignmentI[] getViewAlignments()
1553   {
1554     if (alignPanels != null)
1555     {
1556       Enumeration e = alignPanels.elements();
1557       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1558       for (int i = 0; e.hasMoreElements(); i++)
1559       {
1560         als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1561       }
1562       return als;
1563     }
1564     if (viewport != null)
1565     {
1566       return new AlignmentI[]
1567       { viewport.getAlignment() };
1568     }
1569     return null;
1570   }
1571
1572   /**
1573    * DOCUMENT ME!
1574    *
1575    * @param e
1576    *          DOCUMENT ME!
1577    */
1578   @Override
1579   protected void undoMenuItem_actionPerformed(ActionEvent e)
1580   {
1581     if (viewport.getHistoryList().isEmpty())
1582     {
1583       return;
1584     }
1585     CommandI command = viewport.getHistoryList().pop();
1586     viewport.addToRedoList(command);
1587     // TODO: execute command before adding to redo list / broadcasting?
1588     command.undoCommand(getViewAlignments());
1589
1590     AlignViewport originalSource = getOriginatingSource(command);
1591     updateEditMenuBar();
1592
1593     if (originalSource != null)
1594     {
1595       if (originalSource != viewport)
1596       {
1597         Cache.log
1598                 .warn("Implementation worry: mismatch of viewport origin for undo");
1599       }
1600       originalSource.updateHiddenColumns();
1601       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1602       // null
1603       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1604       // viewport.getColumnSelection()
1605       // .getHiddenColumns().size() > 0);
1606       originalSource.firePropertyChange("alignment", null, originalSource
1607               .getAlignment().getSequences());
1608     }
1609   }
1610
1611   /**
1612    * DOCUMENT ME!
1613    *
1614    * @param e
1615    *          DOCUMENT ME!
1616    */
1617   @Override
1618   protected void redoMenuItem_actionPerformed(ActionEvent e)
1619   {
1620     if (viewport.getRedoList().size() < 1)
1621     {
1622       return;
1623     }
1624
1625     CommandI command = viewport.getRedoList().pop();
1626     viewport.addToHistoryList(command);
1627     command.doCommand(getViewAlignments());
1628
1629     AlignViewport originalSource = getOriginatingSource(command);
1630     updateEditMenuBar();
1631
1632     if (originalSource != null)
1633     {
1634
1635       if (originalSource != viewport)
1636       {
1637         Cache.log
1638                 .warn("Implementation worry: mismatch of viewport origin for redo");
1639       }
1640       originalSource.updateHiddenColumns();
1641       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1642       // null
1643       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1644       // viewport.getColumnSelection()
1645       // .getHiddenColumns().size() > 0);
1646       originalSource.firePropertyChange("alignment", null, originalSource
1647               .getAlignment().getSequences());
1648     }
1649   }
1650
1651   AlignViewport getOriginatingSource(CommandI command)
1652   {
1653     AlignViewport originalSource = null;
1654     // For sequence removal and addition, we need to fire
1655     // the property change event FROM the viewport where the
1656     // original alignment was altered
1657     AlignmentI al = null;
1658     if (command instanceof EditCommand)
1659     {
1660       EditCommand editCommand = (EditCommand) command;
1661       al = editCommand.getAlignment();
1662       Vector comps = (Vector) PaintRefresher.components.get(viewport
1663               .getSequenceSetId());
1664
1665       for (int i = 0; i < comps.size(); i++)
1666       {
1667         if (comps.elementAt(i) instanceof AlignmentPanel)
1668         {
1669           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1670           {
1671             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1672             break;
1673           }
1674         }
1675       }
1676     }
1677
1678     if (originalSource == null)
1679     {
1680       // The original view is closed, we must validate
1681       // the current view against the closed view first
1682       if (al != null)
1683       {
1684         PaintRefresher.validateSequences(al, viewport.getAlignment());
1685       }
1686
1687       originalSource = viewport;
1688     }
1689
1690     return originalSource;
1691   }
1692
1693   /**
1694    * DOCUMENT ME!
1695    *
1696    * @param up
1697    *          DOCUMENT ME!
1698    */
1699   public void moveSelectedSequences(boolean up)
1700   {
1701     SequenceGroup sg = viewport.getSelectionGroup();
1702
1703     if (sg == null)
1704     {
1705       return;
1706     }
1707     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1708             viewport.getHiddenRepSequences(), up);
1709     alignPanel.paintAlignment(true);
1710   }
1711
1712   synchronized void slideSequences(boolean right, int size)
1713   {
1714     List<SequenceI> sg = new Vector();
1715     if (viewport.cursorMode)
1716     {
1717       sg.add(viewport.getAlignment().getSequenceAt(
1718               alignPanel.seqPanel.seqCanvas.cursorY));
1719     }
1720     else if (viewport.getSelectionGroup() != null
1721             && viewport.getSelectionGroup().getSize() != viewport
1722                     .getAlignment().getHeight())
1723     {
1724       sg = viewport.getSelectionGroup().getSequences(
1725               viewport.getHiddenRepSequences());
1726     }
1727
1728     if (sg.size() < 1)
1729     {
1730       return;
1731     }
1732
1733     Vector invertGroup = new Vector();
1734
1735     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1736     {
1737       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1738       {
1739         invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1740       }
1741     }
1742
1743     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1744
1745     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1746     for (int i = 0; i < invertGroup.size(); i++)
1747     {
1748       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1749     }
1750
1751     SlideSequencesCommand ssc;
1752     if (right)
1753     {
1754       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1755               size, viewport.getGapCharacter());
1756     }
1757     else
1758     {
1759       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1760               size, viewport.getGapCharacter());
1761     }
1762
1763     int groupAdjustment = 0;
1764     if (ssc.getGapsInsertedBegin() && right)
1765     {
1766       if (viewport.cursorMode)
1767       {
1768         alignPanel.seqPanel.moveCursor(size, 0);
1769       }
1770       else
1771       {
1772         groupAdjustment = size;
1773       }
1774     }
1775     else if (!ssc.getGapsInsertedBegin() && !right)
1776     {
1777       if (viewport.cursorMode)
1778       {
1779         alignPanel.seqPanel.moveCursor(-size, 0);
1780       }
1781       else
1782       {
1783         groupAdjustment = -size;
1784       }
1785     }
1786
1787     if (groupAdjustment != 0)
1788     {
1789       viewport.getSelectionGroup().setStartRes(
1790               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1791       viewport.getSelectionGroup().setEndRes(
1792               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1793     }
1794
1795     boolean appendHistoryItem = false;
1796     if (viewport.getHistoryList() != null
1797             && viewport.getHistoryList().size() > 0
1798             && viewport.getHistoryList().peek() instanceof SlideSequencesCommand)
1799     {
1800       appendHistoryItem = ssc
1801               .appendSlideCommand((SlideSequencesCommand) viewport
1802                       .getHistoryList()
1803                       .peek());
1804     }
1805
1806     if (!appendHistoryItem)
1807     {
1808       addHistoryItem(ssc);
1809     }
1810
1811     repaint();
1812   }
1813
1814   /**
1815    * DOCUMENT ME!
1816    *
1817    * @param e
1818    *          DOCUMENT ME!
1819    */
1820   @Override
1821   protected void copy_actionPerformed(ActionEvent e)
1822   {
1823     System.gc();
1824     if (viewport.getSelectionGroup() == null)
1825     {
1826       return;
1827     }
1828     // TODO: preserve the ordering of displayed alignment annotation in any
1829     // internal paste (particularly sequence associated annotation)
1830     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1831     String[] omitHidden = null;
1832
1833     if (viewport.hasHiddenColumns())
1834     {
1835       omitHidden = viewport.getViewAsString(true);
1836     }
1837
1838     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1839             omitHidden);
1840
1841     StringSelection ss = new StringSelection(output);
1842
1843     try
1844     {
1845       jalview.gui.Desktop.internalCopy = true;
1846       // Its really worth setting the clipboard contents
1847       // to empty before setting the large StringSelection!!
1848       Toolkit.getDefaultToolkit().getSystemClipboard()
1849               .setContents(new StringSelection(""), null);
1850
1851       Toolkit.getDefaultToolkit().getSystemClipboard()
1852               .setContents(ss, Desktop.instance);
1853     } catch (OutOfMemoryError er)
1854     {
1855       new OOMWarning("copying region", er);
1856       return;
1857     }
1858
1859     Vector hiddenColumns = null;
1860     if (viewport.hasHiddenColumns())
1861     {
1862       hiddenColumns = new Vector();
1863       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1864               .getSelectionGroup().getEndRes();
1865       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1866               .size(); i++)
1867       {
1868         int[] region = (int[]) viewport.getColumnSelection()
1869                 .getHiddenColumns().elementAt(i);
1870         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1871         {
1872           hiddenColumns.addElement(new int[]
1873           { region[0] - hiddenOffset, region[1] - hiddenOffset });
1874         }
1875       }
1876     }
1877
1878     Desktop.jalviewClipboard = new Object[]
1879     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1880     statusBar.setText(MessageManager.formatMessage(
1881             "label.copied_sequences_to_clipboard", new String[]
1882             { Integer.valueOf(seqs.length).toString() }));
1883   }
1884
1885   /**
1886    * DOCUMENT ME!
1887    *
1888    * @param e
1889    *          DOCUMENT ME!
1890    */
1891   @Override
1892   protected void pasteNew_actionPerformed(ActionEvent e)
1893   {
1894     paste(true);
1895   }
1896
1897   /**
1898    * DOCUMENT ME!
1899    *
1900    * @param e
1901    *          DOCUMENT ME!
1902    */
1903   @Override
1904   protected void pasteThis_actionPerformed(ActionEvent e)
1905   {
1906     paste(false);
1907   }
1908
1909   /**
1910    * Paste contents of Jalview clipboard
1911    *
1912    * @param newAlignment
1913    *          true to paste to a new alignment, otherwise add to this.
1914    */
1915   void paste(boolean newAlignment)
1916   {
1917     boolean externalPaste = true;
1918     try
1919     {
1920       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1921       Transferable contents = c.getContents(this);
1922
1923       if (contents == null)
1924       {
1925         return;
1926       }
1927
1928       String str, format;
1929       try
1930       {
1931         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1932         if (str.length() < 1)
1933         {
1934           return;
1935         }
1936
1937         format = new IdentifyFile().Identify(str, "Paste");
1938
1939       } catch (OutOfMemoryError er)
1940       {
1941         new OOMWarning("Out of memory pasting sequences!!", er);
1942         return;
1943       }
1944
1945       SequenceI[] sequences;
1946       boolean annotationAdded = false;
1947       AlignmentI alignment = null;
1948
1949       if (Desktop.jalviewClipboard != null)
1950       {
1951         // The clipboard was filled from within Jalview, we must use the
1952         // sequences
1953         // And dataset from the copied alignment
1954         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1955         // be doubly sure that we create *new* sequence objects.
1956         sequences = new SequenceI[newseq.length];
1957         for (int i = 0; i < newseq.length; i++)
1958         {
1959           sequences[i] = new Sequence(newseq[i]);
1960         }
1961         alignment = new Alignment(sequences);
1962         externalPaste = false;
1963       }
1964       else
1965       {
1966         // parse the clipboard as an alignment.
1967         alignment = new FormatAdapter().readFile(str, "Paste", format);
1968         sequences = alignment.getSequencesArray();
1969       }
1970
1971       int alwidth = 0;
1972       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1973       int fgroup = -1;
1974
1975       if (newAlignment)
1976       {
1977
1978         if (Desktop.jalviewClipboard != null)
1979         {
1980           // dataset is inherited
1981           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1982         }
1983         else
1984         {
1985           // new dataset is constructed
1986           alignment.setDataset(null);
1987         }
1988         alwidth = alignment.getWidth() + 1;
1989       }
1990       else
1991       {
1992         AlignmentI pastedal = alignment; // preserve pasted alignment object
1993         // Add pasted sequences and dataset into existing alignment.
1994         alignment = viewport.getAlignment();
1995         alwidth = alignment.getWidth() + 1;
1996         // decide if we need to import sequences from an existing dataset
1997         boolean importDs = Desktop.jalviewClipboard != null
1998                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1999         // importDs==true instructs us to copy over new dataset sequences from
2000         // an existing alignment
2001         Vector newDs = (importDs) ? new Vector() : null; // used to create
2002         // minimum dataset set
2003
2004         for (int i = 0; i < sequences.length; i++)
2005         {
2006           if (importDs)
2007           {
2008             newDs.addElement(null);
2009           }
2010           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2011           // paste
2012           if (importDs && ds != null)
2013           {
2014             if (!newDs.contains(ds))
2015             {
2016               newDs.setElementAt(ds, i);
2017               ds = new Sequence(ds);
2018               // update with new dataset sequence
2019               sequences[i].setDatasetSequence(ds);
2020             }
2021             else
2022             {
2023               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2024             }
2025           }
2026           else
2027           {
2028             // copy and derive new dataset sequence
2029             sequences[i] = sequences[i].deriveSequence();
2030             alignment.getDataset().addSequence(
2031                     sequences[i].getDatasetSequence());
2032             // TODO: avoid creation of duplicate dataset sequences with a
2033             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2034           }
2035           alignment.addSequence(sequences[i]); // merges dataset
2036         }
2037         if (newDs != null)
2038         {
2039           newDs.clear(); // tidy up
2040         }
2041         if (alignment.getAlignmentAnnotation() != null)
2042         {
2043           for (AlignmentAnnotation alan : alignment
2044                   .getAlignmentAnnotation())
2045           {
2046             if (alan.graphGroup > fgroup)
2047             {
2048               fgroup = alan.graphGroup;
2049             }
2050           }
2051         }
2052         if (pastedal.getAlignmentAnnotation() != null)
2053         {
2054           // Add any annotation attached to alignment.
2055           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2056           for (int i = 0; i < alann.length; i++)
2057           {
2058             annotationAdded = true;
2059             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2060             {
2061               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2062               if (newann.graphGroup > -1)
2063               {
2064                 if (newGraphGroups.size() <= newann.graphGroup
2065                         || newGraphGroups.get(newann.graphGroup) == null)
2066                 {
2067                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2068                   {
2069                     newGraphGroups.add(q, null);
2070                   }
2071                   newGraphGroups.set(newann.graphGroup, new Integer(
2072                           ++fgroup));
2073                 }
2074                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2075                         .intValue();
2076               }
2077
2078               newann.padAnnotation(alwidth);
2079               alignment.addAnnotation(newann);
2080             }
2081           }
2082         }
2083       }
2084       if (!newAlignment)
2085       {
2086         // /////
2087         // ADD HISTORY ITEM
2088         //
2089         addHistoryItem(new EditCommand(
2090                 MessageManager.getString("label.add_sequences"),
2091                 Action.PASTE,
2092                 sequences, 0, alignment.getWidth(), alignment));
2093       }
2094       // Add any annotations attached to sequences
2095       for (int i = 0; i < sequences.length; i++)
2096       {
2097         if (sequences[i].getAnnotation() != null)
2098         {
2099           AlignmentAnnotation newann;
2100           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2101           {
2102             annotationAdded = true;
2103             newann = sequences[i].getAnnotation()[a];
2104             newann.adjustForAlignment();
2105             newann.padAnnotation(alwidth);
2106             if (newann.graphGroup > -1)
2107             {
2108               if (newann.graphGroup > -1)
2109               {
2110                 if (newGraphGroups.size() <= newann.graphGroup
2111                         || newGraphGroups.get(newann.graphGroup) == null)
2112                 {
2113                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2114                   {
2115                     newGraphGroups.add(q, null);
2116                   }
2117                   newGraphGroups.set(newann.graphGroup, new Integer(
2118                           ++fgroup));
2119                 }
2120                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2121                         .intValue();
2122               }
2123             }
2124             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2125             // was
2126             // duplicated
2127             // earlier
2128             alignment
2129                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2130           }
2131         }
2132       }
2133       if (!newAlignment)
2134       {
2135
2136         // propagate alignment changed.
2137         viewport.setEndSeq(alignment.getHeight());
2138         if (annotationAdded)
2139         {
2140           // Duplicate sequence annotation in all views.
2141           AlignmentI[] alview = this.getViewAlignments();
2142           for (int i = 0; i < sequences.length; i++)
2143           {
2144             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2145             if (sann == null)
2146             {
2147               continue;
2148             }
2149             for (int avnum = 0; avnum < alview.length; avnum++)
2150             {
2151               if (alview[avnum] != alignment)
2152               {
2153                 // duplicate in a view other than the one with input focus
2154                 int avwidth = alview[avnum].getWidth() + 1;
2155                 // this relies on sann being preserved after we
2156                 // modify the sequence's annotation array for each duplication
2157                 for (int a = 0; a < sann.length; a++)
2158                 {
2159                   AlignmentAnnotation newann = new AlignmentAnnotation(
2160                           sann[a]);
2161                   sequences[i].addAlignmentAnnotation(newann);
2162                   newann.padAnnotation(avwidth);
2163                   alview[avnum].addAnnotation(newann); // annotation was
2164                   // duplicated earlier
2165                   // TODO JAL-1145 graphGroups are not updated for sequence
2166                   // annotation added to several views. This may cause
2167                   // strangeness
2168                   alview[avnum].setAnnotationIndex(newann, a);
2169                 }
2170               }
2171             }
2172           }
2173           buildSortByAnnotationScoresMenu();
2174         }
2175         viewport.firePropertyChange("alignment", null,
2176                 alignment.getSequences());
2177         if (alignPanels != null)
2178         {
2179           for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2180           {
2181             ap.validateAnnotationDimensions(false);
2182           }
2183         }
2184         else
2185         {
2186           alignPanel.validateAnnotationDimensions(false);
2187         }
2188
2189       }
2190       else
2191       {
2192         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2193                 DEFAULT_HEIGHT);
2194         String newtitle = new String("Copied sequences");
2195
2196         if (Desktop.jalviewClipboard != null
2197                 && Desktop.jalviewClipboard[2] != null)
2198         {
2199           Vector hc = (Vector) Desktop.jalviewClipboard[2];
2200           for (int i = 0; i < hc.size(); i++)
2201           {
2202             int[] region = (int[]) hc.elementAt(i);
2203             af.viewport.hideColumns(region[0], region[1]);
2204           }
2205         }
2206
2207         // >>>This is a fix for the moment, until a better solution is
2208         // found!!<<<
2209         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2210                 .transferSettings(
2211                         alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2212
2213         // TODO: maintain provenance of an alignment, rather than just make the
2214         // title a concatenation of operations.
2215         if (!externalPaste)
2216         {
2217           if (title.startsWith("Copied sequences"))
2218           {
2219             newtitle = title;
2220           }
2221           else
2222           {
2223             newtitle = newtitle.concat("- from " + title);
2224           }
2225         }
2226         else
2227         {
2228           newtitle = new String("Pasted sequences");
2229         }
2230
2231         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2232                 DEFAULT_HEIGHT);
2233
2234       }
2235
2236     } catch (Exception ex)
2237     {
2238       ex.printStackTrace();
2239       System.out.println("Exception whilst pasting: " + ex);
2240       // could be anything being pasted in here
2241     }
2242
2243   }
2244
2245   @Override
2246   protected void expand_newalign(ActionEvent e)
2247   {
2248     try
2249     {
2250       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2251               .getAlignment(), -1);
2252       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2253               DEFAULT_HEIGHT);
2254       String newtitle = new String("Flanking alignment");
2255
2256       if (Desktop.jalviewClipboard != null
2257               && Desktop.jalviewClipboard[2] != null)
2258       {
2259         Vector hc = (Vector) Desktop.jalviewClipboard[2];
2260         for (int i = 0; i < hc.size(); i++)
2261         {
2262           int[] region = (int[]) hc.elementAt(i);
2263           af.viewport.hideColumns(region[0], region[1]);
2264         }
2265       }
2266
2267       // >>>This is a fix for the moment, until a better solution is
2268       // found!!<<<
2269       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2270               .transferSettings(
2271                       alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2272
2273       // TODO: maintain provenance of an alignment, rather than just make the
2274       // title a concatenation of operations.
2275       {
2276         if (title.startsWith("Copied sequences"))
2277         {
2278           newtitle = title;
2279         }
2280         else
2281         {
2282           newtitle = newtitle.concat("- from " + title);
2283         }
2284       }
2285
2286       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
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     } catch (OutOfMemoryError oom)
2294     {
2295       new OOMWarning("Viewing flanking region of alignment", oom);
2296     }
2297   }
2298
2299   /**
2300    * DOCUMENT ME!
2301    *
2302    * @param e
2303    *          DOCUMENT ME!
2304    */
2305   @Override
2306   protected void cut_actionPerformed(ActionEvent e)
2307   {
2308     copy_actionPerformed(null);
2309     delete_actionPerformed(null);
2310   }
2311
2312   /**
2313    * DOCUMENT ME!
2314    *
2315    * @param e
2316    *          DOCUMENT ME!
2317    */
2318   @Override
2319   protected void delete_actionPerformed(ActionEvent evt)
2320   {
2321
2322     SequenceGroup sg = viewport.getSelectionGroup();
2323     if (sg == null)
2324     {
2325       return;
2326     }
2327
2328     List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2329     SequenceI seq;
2330     for (int i = 0; i < sg.getSize(); i++)
2331     {
2332       seq = sg.getSequenceAt(i);
2333       seqs.add(seq);
2334     }
2335
2336     // If the cut affects all sequences, warn, remove highlighted columns
2337     if (sg.getSize() == viewport.getAlignment().getHeight())
2338     {
2339       int confirm = JOptionPane.showConfirmDialog(this,
2340               MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2341               MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2342               JOptionPane.OK_CANCEL_OPTION);
2343
2344       if (confirm == JOptionPane.CANCEL_OPTION
2345               || confirm == JOptionPane.CLOSED_OPTION)
2346       {
2347         return;
2348       }
2349       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2350               sg.getEndRes() + 1);
2351     }
2352
2353     SequenceI[] cut = new SequenceI[seqs.size()];
2354     for (int i = 0; i < seqs.size(); i++)
2355     {
2356       cut[i] = seqs.get(i);
2357     }
2358
2359     /*
2360      * //ADD HISTORY ITEM
2361      */
2362     addHistoryItem(new EditCommand(
2363             MessageManager.getString("label.cut_sequences"), Action.CUT,
2364             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2365             viewport.getAlignment()));
2366
2367     viewport.setSelectionGroup(null);
2368     viewport.sendSelection();
2369     viewport.getAlignment().deleteGroup(sg);
2370
2371     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2372             .getSequences());
2373     if (viewport.getAlignment().getHeight() < 1)
2374     {
2375       try
2376       {
2377         this.setClosed(true);
2378       } catch (Exception ex)
2379       {
2380       }
2381     }
2382   }
2383
2384   /**
2385    * DOCUMENT ME!
2386    *
2387    * @param e
2388    *          DOCUMENT ME!
2389    */
2390   @Override
2391   protected void deleteGroups_actionPerformed(ActionEvent e)
2392   {
2393     if (avc.deleteGroups())
2394     {
2395       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2396       alignPanel.updateAnnotation();
2397       alignPanel.paintAlignment(true);
2398     }
2399   }
2400
2401   /**
2402    * DOCUMENT ME!
2403    *
2404    * @param e
2405    *          DOCUMENT ME!
2406    */
2407   @Override
2408   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2409   {
2410     SequenceGroup sg = new SequenceGroup();
2411
2412     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2413     {
2414       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2415     }
2416
2417     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2418     viewport.setSelectionGroup(sg);
2419     viewport.sendSelection();
2420     alignPanel.paintAlignment(true);
2421     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2422   }
2423
2424   /**
2425    * DOCUMENT ME!
2426    *
2427    * @param e
2428    *          DOCUMENT ME!
2429    */
2430   @Override
2431   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2432   {
2433     if (viewport.cursorMode)
2434     {
2435       alignPanel.seqPanel.keyboardNo1 = null;
2436       alignPanel.seqPanel.keyboardNo2 = null;
2437     }
2438     viewport.setSelectionGroup(null);
2439     viewport.getColumnSelection().clear();
2440     viewport.setSelectionGroup(null);
2441     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2442     alignPanel.idPanel.idCanvas.searchResults = null;
2443     alignPanel.paintAlignment(true);
2444     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2445     viewport.sendSelection();
2446   }
2447
2448   /**
2449    * DOCUMENT ME!
2450    *
2451    * @param e
2452    *          DOCUMENT ME!
2453    */
2454   @Override
2455   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2456   {
2457     SequenceGroup sg = viewport.getSelectionGroup();
2458
2459     if (sg == null)
2460     {
2461       selectAllSequenceMenuItem_actionPerformed(null);
2462
2463       return;
2464     }
2465
2466     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2467     {
2468       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2469     }
2470
2471     alignPanel.paintAlignment(true);
2472     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2473     viewport.sendSelection();
2474   }
2475
2476   @Override
2477   public void invertColSel_actionPerformed(ActionEvent e)
2478   {
2479     viewport.invertColumnSelection();
2480     alignPanel.paintAlignment(true);
2481     viewport.sendSelection();
2482   }
2483
2484   /**
2485    * DOCUMENT ME!
2486    *
2487    * @param e
2488    *          DOCUMENT ME!
2489    */
2490   @Override
2491   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2492   {
2493     trimAlignment(true);
2494   }
2495
2496   /**
2497    * DOCUMENT ME!
2498    *
2499    * @param e
2500    *          DOCUMENT ME!
2501    */
2502   @Override
2503   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2504   {
2505     trimAlignment(false);
2506   }
2507
2508   void trimAlignment(boolean trimLeft)
2509   {
2510     ColumnSelection colSel = viewport.getColumnSelection();
2511     int column;
2512
2513     if (colSel.size() > 0)
2514     {
2515       if (trimLeft)
2516       {
2517         column = colSel.getMin();
2518       }
2519       else
2520       {
2521         column = colSel.getMax();
2522       }
2523
2524       SequenceI[] seqs;
2525       if (viewport.getSelectionGroup() != null)
2526       {
2527         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2528                 viewport.getHiddenRepSequences());
2529       }
2530       else
2531       {
2532         seqs = viewport.getAlignment().getSequencesArray();
2533       }
2534
2535       TrimRegionCommand trimRegion;
2536       if (trimLeft)
2537       {
2538         trimRegion = new TrimRegionCommand("Remove Left",
2539                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2540                 viewport.getAlignment(), viewport.getColumnSelection(),
2541                 viewport.getSelectionGroup());
2542         viewport.setStartRes(0);
2543       }
2544       else
2545       {
2546         trimRegion = new TrimRegionCommand("Remove Right",
2547                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2548                 viewport.getAlignment(), viewport.getColumnSelection(),
2549                 viewport.getSelectionGroup());
2550       }
2551
2552       statusBar.setText(MessageManager.formatMessage(
2553               "label.removed_columns", new String[]
2554               { Integer.valueOf(trimRegion.getSize()).toString() }));
2555
2556       addHistoryItem(trimRegion);
2557
2558       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2559       {
2560         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2561                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2562         {
2563           viewport.getAlignment().deleteGroup(sg);
2564         }
2565       }
2566
2567       viewport.firePropertyChange("alignment", null, viewport
2568               .getAlignment().getSequences());
2569     }
2570   }
2571
2572   /**
2573    * DOCUMENT ME!
2574    *
2575    * @param e
2576    *          DOCUMENT ME!
2577    */
2578   @Override
2579   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2580   {
2581     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2582
2583     SequenceI[] seqs;
2584     if (viewport.getSelectionGroup() != null)
2585     {
2586       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2587               viewport.getHiddenRepSequences());
2588       start = viewport.getSelectionGroup().getStartRes();
2589       end = viewport.getSelectionGroup().getEndRes();
2590     }
2591     else
2592     {
2593       seqs = viewport.getAlignment().getSequencesArray();
2594     }
2595
2596     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2597             "Remove Gapped Columns", seqs, start, end,
2598             viewport.getAlignment());
2599
2600     addHistoryItem(removeGapCols);
2601
2602     statusBar.setText(MessageManager.formatMessage(
2603             "label.removed_empty_columns", new String[]
2604             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2605
2606     // This is to maintain viewport position on first residue
2607     // of first sequence
2608     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2609     int startRes = seq.findPosition(viewport.startRes);
2610     // ShiftList shifts;
2611     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2612     // edit.alColumnChanges=shifts.getInverse();
2613     // if (viewport.hasHiddenColumns)
2614     // viewport.getColumnSelection().compensateForEdits(shifts);
2615     viewport.setStartRes(seq.findIndex(startRes) - 1);
2616     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2617             .getSequences());
2618
2619   }
2620
2621   /**
2622    * DOCUMENT ME!
2623    *
2624    * @param e
2625    *          DOCUMENT ME!
2626    */
2627   @Override
2628   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2629   {
2630     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2631
2632     SequenceI[] seqs;
2633     if (viewport.getSelectionGroup() != null)
2634     {
2635       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2636               viewport.getHiddenRepSequences());
2637       start = viewport.getSelectionGroup().getStartRes();
2638       end = viewport.getSelectionGroup().getEndRes();
2639     }
2640     else
2641     {
2642       seqs = viewport.getAlignment().getSequencesArray();
2643     }
2644
2645     // This is to maintain viewport position on first residue
2646     // of first sequence
2647     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2648     int startRes = seq.findPosition(viewport.startRes);
2649
2650     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2651             viewport.getAlignment()));
2652
2653     viewport.setStartRes(seq.findIndex(startRes) - 1);
2654
2655     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2656             .getSequences());
2657
2658   }
2659
2660   /**
2661    * DOCUMENT ME!
2662    *
2663    * @param e
2664    *          DOCUMENT ME!
2665    */
2666   @Override
2667   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2668   {
2669     viewport.setPadGaps(padGapsMenuitem.isSelected());
2670     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2671             .getSequences());
2672   }
2673
2674   // else
2675   {
2676     // if (justifySeqs>0)
2677     {
2678       // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2679     }
2680   }
2681
2682   // }
2683
2684   /**
2685    * DOCUMENT ME!
2686    *
2687    * @param e
2688    *          DOCUMENT ME!
2689    */
2690   @Override
2691   public void findMenuItem_actionPerformed(ActionEvent e)
2692   {
2693     new Finder();
2694   }
2695
2696   /**
2697    * Create a new view of the current alignment.
2698    */
2699   @Override
2700   public void newView_actionPerformed(ActionEvent e)
2701   {
2702     newView(true);
2703   }
2704
2705   /**
2706    *
2707    * @param copyAnnotation
2708    *          if true then duplicate all annnotation, groups and settings
2709    * @return new alignment panel, already displayed.
2710    */
2711   public AlignmentPanel newView(boolean copyAnnotation)
2712   {
2713     return newView(null, copyAnnotation);
2714   }
2715
2716   /**
2717    *
2718    * @param viewTitle
2719    *          title of newly created view
2720    * @return new alignment panel, already displayed.
2721    */
2722   public AlignmentPanel newView(String viewTitle)
2723   {
2724     return newView(viewTitle, true);
2725   }
2726
2727   /**
2728    *
2729    * @param viewTitle
2730    *          title of newly created view
2731    * @param copyAnnotation
2732    *          if true then duplicate all annnotation, groups and settings
2733    * @return new alignment panel, already displayed.
2734    */
2735   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2736   {
2737     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2738             true);
2739     if (!copyAnnotation)
2740     {
2741       // just remove all the current annotation except for the automatic stuff
2742       newap.av.getAlignment().deleteAllGroups();
2743       for (AlignmentAnnotation alan : newap.av.getAlignment()
2744               .getAlignmentAnnotation())
2745       {
2746         if (!alan.autoCalculated)
2747         {
2748           newap.av.getAlignment().deleteAnnotation(alan);
2749         }
2750         ;
2751       }
2752     }
2753
2754     newap.av.gatherViewsHere = false;
2755
2756     if (viewport.viewName == null)
2757     {
2758       viewport.viewName = "Original";
2759     }
2760
2761     newap.av.setHistoryList(viewport.getHistoryList());
2762     newap.av.setRedoList(viewport.getRedoList());
2763
2764     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2765     // make sure the new view has a unique name - this is essential for Jalview
2766     // 2 archives
2767     boolean addFirstIndex = false;
2768     if (viewTitle == null || viewTitle.trim().length() == 0)
2769     {
2770       viewTitle = MessageManager.getString("action.view");
2771       addFirstIndex = true;
2772     }
2773     else
2774     {
2775       index = 1;// we count from 1 if given a specific name
2776     }
2777     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2778     Vector comps = (Vector) PaintRefresher.components.get(viewport
2779             .getSequenceSetId());
2780     Vector existingNames = new Vector();
2781     for (int i = 0; i < comps.size(); i++)
2782     {
2783       if (comps.elementAt(i) instanceof AlignmentPanel)
2784       {
2785         AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2786         if (!existingNames.contains(ap.av.viewName))
2787         {
2788           existingNames.addElement(ap.av.viewName);
2789         }
2790       }
2791     }
2792
2793     while (existingNames.contains(newViewName))
2794     {
2795       newViewName = viewTitle + " " + (++index);
2796     }
2797
2798     newap.av.viewName = newViewName;
2799
2800     addAlignmentPanel(newap, true);
2801     newap.alignmentChanged();
2802
2803     if (alignPanels.size() == 2)
2804     {
2805       viewport.gatherViewsHere = true;
2806     }
2807     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2808     return newap;
2809   }
2810
2811   @Override
2812   public void expandViews_actionPerformed(ActionEvent e)
2813   {
2814     Desktop.instance.explodeViews(this);
2815   }
2816
2817   @Override
2818   public void gatherViews_actionPerformed(ActionEvent e)
2819   {
2820     Desktop.instance.gatherViews(this);
2821   }
2822
2823   /**
2824    * DOCUMENT ME!
2825    *
2826    * @param e
2827    *          DOCUMENT ME!
2828    */
2829   @Override
2830   public void font_actionPerformed(ActionEvent e)
2831   {
2832     new FontChooser(alignPanel);
2833   }
2834
2835   /**
2836    * DOCUMENT ME!
2837    *
2838    * @param e
2839    *          DOCUMENT ME!
2840    */
2841   @Override
2842   protected void seqLimit_actionPerformed(ActionEvent e)
2843   {
2844     viewport.setShowJVSuffix(seqLimits.isSelected());
2845
2846     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2847             .calculateIdWidth());
2848     alignPanel.paintAlignment(true);
2849   }
2850
2851   @Override
2852   public void idRightAlign_actionPerformed(ActionEvent e)
2853   {
2854     viewport.rightAlignIds = idRightAlign.isSelected();
2855     alignPanel.paintAlignment(true);
2856   }
2857
2858   @Override
2859   public void centreColumnLabels_actionPerformed(ActionEvent e)
2860   {
2861     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2862     alignPanel.paintAlignment(true);
2863   }
2864
2865   /*
2866    * (non-Javadoc)
2867    *
2868    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2869    */
2870   @Override
2871   protected void followHighlight_actionPerformed()
2872   {
2873     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2874     {
2875       alignPanel.scrollToPosition(
2876               alignPanel.seqPanel.seqCanvas.searchResults, false);
2877     }
2878   }
2879
2880   /**
2881    * DOCUMENT ME!
2882    *
2883    * @param e
2884    *          DOCUMENT ME!
2885    */
2886   @Override
2887   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2888   {
2889     viewport.setColourText(colourTextMenuItem.isSelected());
2890     alignPanel.paintAlignment(true);
2891   }
2892
2893   /**
2894    * DOCUMENT ME!
2895    *
2896    * @param e
2897    *          DOCUMENT ME!
2898    */
2899   @Override
2900   public void wrapMenuItem_actionPerformed(ActionEvent e)
2901   {
2902     scaleAbove.setVisible(wrapMenuItem.isSelected());
2903     scaleLeft.setVisible(wrapMenuItem.isSelected());
2904     scaleRight.setVisible(wrapMenuItem.isSelected());
2905     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2906     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2907   }
2908
2909   @Override
2910   public void showAllSeqs_actionPerformed(ActionEvent e)
2911   {
2912     viewport.showAllHiddenSeqs();
2913   }
2914
2915   @Override
2916   public void showAllColumns_actionPerformed(ActionEvent e)
2917   {
2918     viewport.showAllHiddenColumns();
2919     repaint();
2920   }
2921
2922   @Override
2923   public void hideSelSequences_actionPerformed(ActionEvent e)
2924   {
2925     viewport.hideAllSelectedSeqs();
2926     alignPanel.paintAlignment(true);
2927   }
2928
2929   /**
2930    * called by key handler and the hide all/show all menu items
2931    *
2932    * @param toggleSeqs
2933    * @param toggleCols
2934    */
2935   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2936   {
2937
2938     boolean hide = false;
2939     SequenceGroup sg = viewport.getSelectionGroup();
2940     if (!toggleSeqs && !toggleCols)
2941     {
2942       // Hide everything by the current selection - this is a hack - we do the
2943       // invert and then hide
2944       // first check that there will be visible columns after the invert.
2945       if ((viewport.getColumnSelection() != null
2946               && viewport.getColumnSelection().getSelected() != null && viewport
2947               .getColumnSelection().getSelected().size() > 0)
2948               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2949                       .getEndRes()))
2950       {
2951         // now invert the sequence set, if required - empty selection implies
2952         // that no hiding is required.
2953         if (sg != null)
2954         {
2955           invertSequenceMenuItem_actionPerformed(null);
2956           sg = viewport.getSelectionGroup();
2957           toggleSeqs = true;
2958
2959         }
2960         viewport.expandColSelection(sg, true);
2961         // finally invert the column selection and get the new sequence
2962         // selection.
2963         invertColSel_actionPerformed(null);
2964         toggleCols = true;
2965       }
2966     }
2967
2968     if (toggleSeqs)
2969     {
2970       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2971       {
2972         hideSelSequences_actionPerformed(null);
2973         hide = true;
2974       }
2975       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2976               .size() > 0))
2977       {
2978         showAllSeqs_actionPerformed(null);
2979       }
2980     }
2981
2982     if (toggleCols)
2983     {
2984       if (viewport.getColumnSelection().getSelected().size() > 0)
2985       {
2986         hideSelColumns_actionPerformed(null);
2987         if (!toggleSeqs)
2988         {
2989           viewport.setSelectionGroup(sg);
2990         }
2991       }
2992       else if (!hide)
2993       {
2994         showAllColumns_actionPerformed(null);
2995       }
2996     }
2997   }
2998
2999   /*
3000    * (non-Javadoc)
3001    *
3002    * @see
3003    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3004    * event.ActionEvent)
3005    */
3006   @Override
3007   public void hideAllButSelection_actionPerformed(ActionEvent e)
3008   {
3009     toggleHiddenRegions(false, false);
3010   }
3011
3012   /*
3013    * (non-Javadoc)
3014    *
3015    * @see
3016    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3017    * .ActionEvent)
3018    */
3019   @Override
3020   public void hideAllSelection_actionPerformed(ActionEvent e)
3021   {
3022     SequenceGroup sg = viewport.getSelectionGroup();
3023     viewport.expandColSelection(sg, false);
3024     viewport.hideAllSelectedSeqs();
3025     viewport.hideSelectedColumns();
3026     alignPanel.paintAlignment(true);
3027   }
3028
3029   /*
3030    * (non-Javadoc)
3031    *
3032    * @see
3033    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3034    * ActionEvent)
3035    */
3036   @Override
3037   public void showAllhidden_actionPerformed(ActionEvent e)
3038   {
3039     viewport.showAllHiddenColumns();
3040     viewport.showAllHiddenSeqs();
3041     alignPanel.paintAlignment(true);
3042   }
3043
3044   @Override
3045   public void hideSelColumns_actionPerformed(ActionEvent e)
3046   {
3047     viewport.hideSelectedColumns();
3048     alignPanel.paintAlignment(true);
3049   }
3050
3051   @Override
3052   public void hiddenMarkers_actionPerformed(ActionEvent e)
3053   {
3054     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3055     repaint();
3056   }
3057
3058   /**
3059    * DOCUMENT ME!
3060    *
3061    * @param e
3062    *          DOCUMENT ME!
3063    */
3064   @Override
3065   protected void scaleAbove_actionPerformed(ActionEvent e)
3066   {
3067     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3068     alignPanel.paintAlignment(true);
3069   }
3070
3071   /**
3072    * DOCUMENT ME!
3073    *
3074    * @param e
3075    *          DOCUMENT ME!
3076    */
3077   @Override
3078   protected void scaleLeft_actionPerformed(ActionEvent e)
3079   {
3080     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3081     alignPanel.paintAlignment(true);
3082   }
3083
3084   /**
3085    * DOCUMENT ME!
3086    *
3087    * @param e
3088    *          DOCUMENT ME!
3089    */
3090   @Override
3091   protected void scaleRight_actionPerformed(ActionEvent e)
3092   {
3093     viewport.setScaleRightWrapped(scaleRight.isSelected());
3094     alignPanel.paintAlignment(true);
3095   }
3096
3097   /**
3098    * DOCUMENT ME!
3099    *
3100    * @param e
3101    *          DOCUMENT ME!
3102    */
3103   @Override
3104   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3105   {
3106     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3107     alignPanel.paintAlignment(true);
3108   }
3109
3110   /**
3111    * DOCUMENT ME!
3112    *
3113    * @param e
3114    *          DOCUMENT ME!
3115    */
3116   @Override
3117   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3118   {
3119     viewport.setShowText(viewTextMenuItem.isSelected());
3120     alignPanel.paintAlignment(true);
3121   }
3122
3123   /**
3124    * DOCUMENT ME!
3125    *
3126    * @param e
3127    *          DOCUMENT ME!
3128    */
3129   @Override
3130   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3131   {
3132     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3133     alignPanel.paintAlignment(true);
3134   }
3135
3136   public FeatureSettings featureSettings;
3137
3138   @Override
3139   public void featureSettings_actionPerformed(ActionEvent e)
3140   {
3141     if (featureSettings != null)
3142     {
3143       featureSettings.close();
3144       featureSettings = null;
3145     }
3146     if (!showSeqFeatures.isSelected())
3147     {
3148       // make sure features are actually displayed
3149       showSeqFeatures.setSelected(true);
3150       showSeqFeatures_actionPerformed(null);
3151     }
3152     featureSettings = new FeatureSettings(this);
3153   }
3154
3155   /**
3156    * Set or clear 'Show Sequence Features'
3157    *
3158    * @param evt
3159    *          DOCUMENT ME!
3160    */
3161   @Override
3162   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3163   {
3164     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3165     alignPanel.paintAlignment(true);
3166     if (alignPanel.getOverviewPanel() != null)
3167     {
3168       alignPanel.getOverviewPanel().updateOverviewImage();
3169     }
3170   }
3171
3172   /**
3173    * Set or clear 'Show Sequence Features'
3174    *
3175    * @param evt
3176    *          DOCUMENT ME!
3177    */
3178   @Override
3179   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3180   {
3181     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3182             .isSelected());
3183     if (viewport.getShowSequenceFeaturesHeight())
3184     {
3185       // ensure we're actually displaying features
3186       viewport.setShowSequenceFeatures(true);
3187       showSeqFeatures.setSelected(true);
3188     }
3189     alignPanel.paintAlignment(true);
3190     if (alignPanel.getOverviewPanel() != null)
3191     {
3192       alignPanel.getOverviewPanel().updateOverviewImage();
3193     }
3194   }
3195
3196   /**
3197    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3198    * the annotations panel as a whole.
3199    *
3200    * The options to show/hide all annotations should be enabled when the panel
3201    * is shown, and disabled when the panel is hidden.
3202    *
3203    * @param e
3204    */
3205   @Override
3206   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3207   {
3208     final boolean setVisible = annotationPanelMenuItem.isSelected();
3209     viewport.setShowAnnotation(setVisible);
3210     alignPanel.setAnnotationVisible(setVisible);
3211     this.showAllSeqAnnotations.setEnabled(setVisible);
3212     this.hideAllSeqAnnotations.setEnabled(setVisible);
3213     this.showAllAlAnnotations.setEnabled(setVisible);
3214     this.hideAllAlAnnotations.setEnabled(setVisible);
3215   }
3216
3217   @Override
3218   public void alignmentProperties()
3219   {
3220     JEditorPane editPane = new JEditorPane("text/html", "");
3221     editPane.setEditable(false);
3222     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3223             .formatAsHtml();
3224     editPane.setText(MessageManager.formatMessage("label.html_content",
3225             new String[]
3226             { contents.toString() }));
3227     JInternalFrame frame = new JInternalFrame();
3228     frame.getContentPane().add(new JScrollPane(editPane));
3229
3230     Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3231             "label.alignment_properties", new String[]
3232             { getTitle() }), 500, 400);
3233   }
3234
3235   /**
3236    * DOCUMENT ME!
3237    *
3238    * @param e
3239    *          DOCUMENT ME!
3240    */
3241   @Override
3242   public void overviewMenuItem_actionPerformed(ActionEvent e)
3243   {
3244     if (alignPanel.overviewPanel != null)
3245     {
3246       return;
3247     }
3248
3249     JInternalFrame frame = new JInternalFrame();
3250     OverviewPanel overview = new OverviewPanel(alignPanel);
3251     frame.setContentPane(overview);
3252     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3253             "label.overview_params", new String[]
3254             { this.getTitle() }), frame.getWidth(), frame.getHeight());
3255     frame.pack();
3256     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3257     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3258     {
3259       @Override
3260       public void internalFrameClosed(
3261               javax.swing.event.InternalFrameEvent evt)
3262       {
3263         alignPanel.setOverviewPanel(null);
3264       };
3265     });
3266
3267     alignPanel.setOverviewPanel(overview);
3268   }
3269
3270   @Override
3271   public void textColour_actionPerformed(ActionEvent e)
3272   {
3273     new TextColourChooser().chooseColour(alignPanel, null);
3274   }
3275
3276   /**
3277    * DOCUMENT ME!
3278    *
3279    * @param e
3280    *          DOCUMENT ME!
3281    */
3282   @Override
3283   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3284   {
3285     changeColour(null);
3286   }
3287
3288   /**
3289    * DOCUMENT ME!
3290    *
3291    * @param e
3292    *          DOCUMENT ME!
3293    */
3294   @Override
3295   public void clustalColour_actionPerformed(ActionEvent e)
3296   {
3297     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3298             viewport.getHiddenRepSequences()));
3299   }
3300
3301   /**
3302    * DOCUMENT ME!
3303    *
3304    * @param e
3305    *          DOCUMENT ME!
3306    */
3307   @Override
3308   public void zappoColour_actionPerformed(ActionEvent e)
3309   {
3310     changeColour(new ZappoColourScheme());
3311   }
3312
3313   /**
3314    * DOCUMENT ME!
3315    *
3316    * @param e
3317    *          DOCUMENT ME!
3318    */
3319   @Override
3320   public void taylorColour_actionPerformed(ActionEvent e)
3321   {
3322     changeColour(new TaylorColourScheme());
3323   }
3324
3325   /**
3326    * DOCUMENT ME!
3327    *
3328    * @param e
3329    *          DOCUMENT ME!
3330    */
3331   @Override
3332   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3333   {
3334     changeColour(new HydrophobicColourScheme());
3335   }
3336
3337   /**
3338    * DOCUMENT ME!
3339    *
3340    * @param e
3341    *          DOCUMENT ME!
3342    */
3343   @Override
3344   public void helixColour_actionPerformed(ActionEvent e)
3345   {
3346     changeColour(new HelixColourScheme());
3347   }
3348
3349   /**
3350    * DOCUMENT ME!
3351    *
3352    * @param e
3353    *          DOCUMENT ME!
3354    */
3355   @Override
3356   public void strandColour_actionPerformed(ActionEvent e)
3357   {
3358     changeColour(new StrandColourScheme());
3359   }
3360
3361   /**
3362    * DOCUMENT ME!
3363    *
3364    * @param e
3365    *          DOCUMENT ME!
3366    */
3367   @Override
3368   public void turnColour_actionPerformed(ActionEvent e)
3369   {
3370     changeColour(new TurnColourScheme());
3371   }
3372
3373   /**
3374    * DOCUMENT ME!
3375    *
3376    * @param e
3377    *          DOCUMENT ME!
3378    */
3379   @Override
3380   public void buriedColour_actionPerformed(ActionEvent e)
3381   {
3382     changeColour(new BuriedColourScheme());
3383   }
3384
3385   /**
3386    * DOCUMENT ME!
3387    *
3388    * @param e
3389    *          DOCUMENT ME!
3390    */
3391   @Override
3392   public void nucleotideColour_actionPerformed(ActionEvent e)
3393   {
3394     changeColour(new NucleotideColourScheme());
3395   }
3396
3397   @Override
3398   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3399   {
3400     changeColour(new PurinePyrimidineColourScheme());
3401   }
3402
3403   /*
3404    * public void covariationColour_actionPerformed(ActionEvent e) {
3405    * changeColour(new
3406    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3407    * ()[0])); }
3408    */
3409   @Override
3410   public void annotationColour_actionPerformed(ActionEvent e)
3411   {
3412     new AnnotationColourChooser(viewport, alignPanel);
3413   }
3414
3415   @Override
3416   public void rnahelicesColour_actionPerformed(ActionEvent e)
3417   {
3418     new RNAHelicesColourChooser(viewport, alignPanel);
3419   }
3420
3421   /**
3422    * DOCUMENT ME!
3423    *
3424    * @param e
3425    *          DOCUMENT ME!
3426    */
3427   @Override
3428   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3429   {
3430     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3431   }
3432
3433   /**
3434    * DOCUMENT ME!
3435    *
3436    * @param cs
3437    *          DOCUMENT ME!
3438    */
3439   public void changeColour(ColourSchemeI cs)
3440   {
3441     // TODO: compare with applet and pull up to model method
3442     int threshold = 0;
3443
3444     if (cs != null)
3445     {
3446       if (viewport.getAbovePIDThreshold())
3447       {
3448         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3449                 "Background");
3450         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3451       }
3452       else
3453       {
3454         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3455       }
3456
3457       if (viewport.getConservationSelected())
3458       {
3459
3460         Alignment al = (Alignment) viewport.getAlignment();
3461         Conservation c = new Conservation("All",
3462                 ResidueProperties.propHash, 3, al.getSequences(), 0,
3463                 al.getWidth() - 1);
3464
3465         c.calculate();
3466         c.verdict(false, viewport.getConsPercGaps());
3467
3468         cs.setConservation(c);
3469
3470         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3471                 cs, "Background"));
3472       }
3473       else
3474       {
3475         cs.setConservation(null);
3476       }
3477
3478       cs.setConsensus(viewport.getSequenceConsensusHash());
3479     }
3480
3481     viewport.setGlobalColourScheme(cs);
3482
3483     if (viewport.getColourAppliesToAllGroups())
3484     {
3485
3486       for (SequenceGroup sg : viewport.getAlignment().getGroups())
3487       {
3488         if (cs == null)
3489         {
3490           sg.cs = null;
3491           continue;
3492         }
3493
3494         if (cs instanceof ClustalxColourScheme)
3495         {
3496           sg.cs = new ClustalxColourScheme(sg,
3497                   viewport.getHiddenRepSequences());
3498         }
3499         else if (cs instanceof UserColourScheme)
3500         {
3501           sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3502         }
3503         else
3504         {
3505           try
3506           {
3507             sg.cs = cs.getClass().newInstance();
3508           } catch (Exception ex)
3509           {
3510           }
3511         }
3512
3513         if (viewport.getAbovePIDThreshold()
3514                 || cs instanceof PIDColourScheme
3515                 || cs instanceof Blosum62ColourScheme)
3516         {
3517           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3518
3519           sg.cs.setConsensus(AAFrequency.calculate(
3520                   sg.getSequences(viewport.getHiddenRepSequences()),
3521                   sg.getStartRes(), sg.getEndRes() + 1));
3522         }
3523         else
3524         {
3525           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3526         }
3527
3528         if (viewport.getConservationSelected())
3529         {
3530           Conservation c = new Conservation("Group",
3531                   ResidueProperties.propHash, 3, sg.getSequences(viewport
3532                           .getHiddenRepSequences()), sg.getStartRes(),
3533                   sg.getEndRes() + 1);
3534           c.calculate();
3535           c.verdict(false, viewport.getConsPercGaps());
3536           sg.cs.setConservation(c);
3537         }
3538         else
3539         {
3540           sg.cs.setConservation(null);
3541         }
3542       }
3543     }
3544
3545     if (alignPanel.getOverviewPanel() != null)
3546     {
3547       alignPanel.getOverviewPanel().updateOverviewImage();
3548     }
3549
3550     alignPanel.paintAlignment(true);
3551   }
3552
3553   /**
3554    * DOCUMENT ME!
3555    *
3556    * @param e
3557    *          DOCUMENT ME!
3558    */
3559   @Override
3560   protected void modifyPID_actionPerformed(ActionEvent e)
3561   {
3562     if (viewport.getAbovePIDThreshold()
3563             && viewport.getGlobalColourScheme() != null)
3564     {
3565       SliderPanel.setPIDSliderSource(alignPanel,
3566               viewport.getGlobalColourScheme(), "Background");
3567       SliderPanel.showPIDSlider();
3568     }
3569   }
3570
3571   /**
3572    * DOCUMENT ME!
3573    *
3574    * @param e
3575    *          DOCUMENT ME!
3576    */
3577   @Override
3578   protected void modifyConservation_actionPerformed(ActionEvent e)
3579   {
3580     if (viewport.getConservationSelected()
3581             && viewport.getGlobalColourScheme() != null)
3582     {
3583       SliderPanel.setConservationSlider(alignPanel,
3584               viewport.getGlobalColourScheme(), "Background");
3585       SliderPanel.showConservationSlider();
3586     }
3587   }
3588
3589   /**
3590    * DOCUMENT ME!
3591    *
3592    * @param e
3593    *          DOCUMENT ME!
3594    */
3595   @Override
3596   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3597   {
3598     viewport.setConservationSelected(conservationMenuItem.isSelected());
3599
3600     viewport.setAbovePIDThreshold(false);
3601     abovePIDThreshold.setSelected(false);
3602
3603     changeColour(viewport.getGlobalColourScheme());
3604
3605     modifyConservation_actionPerformed(null);
3606   }
3607
3608   /**
3609    * DOCUMENT ME!
3610    *
3611    * @param e
3612    *          DOCUMENT ME!
3613    */
3614   @Override
3615   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3616   {
3617     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3618
3619     conservationMenuItem.setSelected(false);
3620     viewport.setConservationSelected(false);
3621
3622     changeColour(viewport.getGlobalColourScheme());
3623
3624     modifyPID_actionPerformed(null);
3625   }
3626
3627   /**
3628    * DOCUMENT ME!
3629    *
3630    * @param e
3631    *          DOCUMENT ME!
3632    */
3633   @Override
3634   public void userDefinedColour_actionPerformed(ActionEvent e)
3635   {
3636     if (e.getActionCommand().equals(
3637             MessageManager.getString("action.user_defined")))
3638     {
3639       new UserDefinedColours(alignPanel, null);
3640     }
3641     else
3642     {
3643       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3644               .getUserColourSchemes().get(e.getActionCommand());
3645
3646       changeColour(udc);
3647     }
3648   }
3649
3650   public void updateUserColourMenu()
3651   {
3652
3653     Component[] menuItems = colourMenu.getMenuComponents();
3654     int i, iSize = menuItems.length;
3655     for (i = 0; i < iSize; i++)
3656     {
3657       if (menuItems[i].getName() != null
3658               && menuItems[i].getName().equals("USER_DEFINED"))
3659       {
3660         colourMenu.remove(menuItems[i]);
3661         iSize--;
3662       }
3663     }
3664     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3665     {
3666       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3667               .getUserColourSchemes().keys();
3668
3669       while (userColours.hasMoreElements())
3670       {
3671         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3672                 userColours.nextElement().toString());
3673         radioItem.setName("USER_DEFINED");
3674         radioItem.addMouseListener(new MouseAdapter()
3675         {
3676           @Override
3677           public void mousePressed(MouseEvent evt)
3678           {
3679             if (evt.isControlDown()
3680                     || SwingUtilities.isRightMouseButton(evt))
3681             {
3682               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3683
3684               int option = JOptionPane.showInternalConfirmDialog(
3685                       jalview.gui.Desktop.desktop,
3686                       MessageManager
3687                               .getString("label.remove_from_default_list"),
3688                       MessageManager
3689                               .getString("label.remove_user_defined_colour"),
3690                       JOptionPane.YES_NO_OPTION);
3691               if (option == JOptionPane.YES_OPTION)
3692               {
3693                 jalview.gui.UserDefinedColours
3694                         .removeColourFromDefaults(radioItem.getText());
3695                 colourMenu.remove(radioItem);
3696               }
3697               else
3698               {
3699                 radioItem.addActionListener(new ActionListener()
3700                 {
3701                   @Override
3702                   public void actionPerformed(ActionEvent evt)
3703                   {
3704                     userDefinedColour_actionPerformed(evt);
3705                   }
3706                 });
3707               }
3708             }
3709           }
3710         });
3711         radioItem.addActionListener(new ActionListener()
3712         {
3713           @Override
3714           public void actionPerformed(ActionEvent evt)
3715           {
3716             userDefinedColour_actionPerformed(evt);
3717           }
3718         });
3719
3720         colourMenu.insert(radioItem, 15);
3721         colours.add(radioItem);
3722       }
3723     }
3724   }
3725
3726   /**
3727    * DOCUMENT ME!
3728    *
3729    * @param e
3730    *          DOCUMENT ME!
3731    */
3732   @Override
3733   public void PIDColour_actionPerformed(ActionEvent e)
3734   {
3735     changeColour(new PIDColourScheme());
3736   }
3737
3738   /**
3739    * DOCUMENT ME!
3740    *
3741    * @param e
3742    *          DOCUMENT ME!
3743    */
3744   @Override
3745   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3746   {
3747     changeColour(new Blosum62ColourScheme());
3748   }
3749
3750   /**
3751    * DOCUMENT ME!
3752    *
3753    * @param e
3754    *          DOCUMENT ME!
3755    */
3756   @Override
3757   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3758   {
3759     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3760     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3761             .getAlignment().getSequenceAt(0), null);
3762     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3763             viewport.getAlignment()));
3764     alignPanel.paintAlignment(true);
3765   }
3766
3767   /**
3768    * DOCUMENT ME!
3769    *
3770    * @param e
3771    *          DOCUMENT ME!
3772    */
3773   @Override
3774   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3775   {
3776     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3777     AlignmentSorter.sortByID(viewport.getAlignment());
3778     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3779             viewport.getAlignment()));
3780     alignPanel.paintAlignment(true);
3781   }
3782
3783   /**
3784    * DOCUMENT ME!
3785    *
3786    * @param e
3787    *          DOCUMENT ME!
3788    */
3789   @Override
3790   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3791   {
3792     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3793     AlignmentSorter.sortByLength(viewport.getAlignment());
3794     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3795             viewport.getAlignment()));
3796     alignPanel.paintAlignment(true);
3797   }
3798
3799   /**
3800    * DOCUMENT ME!
3801    *
3802    * @param e
3803    *          DOCUMENT ME!
3804    */
3805   @Override
3806   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3807   {
3808     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3809     AlignmentSorter.sortByGroup(viewport.getAlignment());
3810     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3811             viewport.getAlignment()));
3812
3813     alignPanel.paintAlignment(true);
3814   }
3815
3816   /**
3817    * DOCUMENT ME!
3818    *
3819    * @param e
3820    *          DOCUMENT ME!
3821    */
3822   @Override
3823   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3824   {
3825     new RedundancyPanel(alignPanel, this);
3826   }
3827
3828   /**
3829    * DOCUMENT ME!
3830    *
3831    * @param e
3832    *          DOCUMENT ME!
3833    */
3834   @Override
3835   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3836   {
3837     if ((viewport.getSelectionGroup() == null)
3838             || (viewport.getSelectionGroup().getSize() < 2))
3839     {
3840       JOptionPane.showInternalMessageDialog(this, MessageManager
3841               .getString("label.you_must_select_least_two_sequences"),
3842               MessageManager.getString("label.invalid_selection"),
3843               JOptionPane.WARNING_MESSAGE);
3844     }
3845     else
3846     {
3847       JInternalFrame frame = new JInternalFrame();
3848       frame.setContentPane(new PairwiseAlignPanel(viewport));
3849       Desktop.addInternalFrame(frame,
3850               MessageManager.getString("action.pairwise_alignment"), 600,
3851               500);
3852     }
3853   }
3854
3855   /**
3856    * DOCUMENT ME!
3857    *
3858    * @param e
3859    *          DOCUMENT ME!
3860    */
3861   @Override
3862   public void PCAMenuItem_actionPerformed(ActionEvent e)
3863   {
3864     if (((viewport.getSelectionGroup() != null)
3865             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3866             .getSelectionGroup().getSize() > 0))
3867             || (viewport.getAlignment().getHeight() < 4))
3868     {
3869       JOptionPane
3870               .showInternalMessageDialog(
3871                       this,
3872                       MessageManager
3873                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3874                       MessageManager
3875                               .getString("label.sequence_selection_insufficient"),
3876                       JOptionPane.WARNING_MESSAGE);
3877
3878       return;
3879     }
3880
3881     new PCAPanel(alignPanel);
3882   }
3883
3884   @Override
3885   public void autoCalculate_actionPerformed(ActionEvent e)
3886   {
3887     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3888     if (viewport.autoCalculateConsensus)
3889     {
3890       viewport.firePropertyChange("alignment", null, viewport
3891               .getAlignment().getSequences());
3892     }
3893   }
3894
3895   @Override
3896   public void sortByTreeOption_actionPerformed(ActionEvent e)
3897   {
3898     viewport.sortByTree = sortByTree.isSelected();
3899   }
3900
3901   @Override
3902   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3903   {
3904     viewport.followSelection = listenToViewSelections.isSelected();
3905   }
3906
3907   /**
3908    * DOCUMENT ME!
3909    *
3910    * @param e
3911    *          DOCUMENT ME!
3912    */
3913   @Override
3914   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3915   {
3916     NewTreePanel("AV", "PID", "Average distance tree using PID");
3917   }
3918
3919   /**
3920    * DOCUMENT ME!
3921    *
3922    * @param e
3923    *          DOCUMENT ME!
3924    */
3925   @Override
3926   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3927   {
3928     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3929   }
3930
3931   /**
3932    * DOCUMENT ME!
3933    *
3934    * @param e
3935    *          DOCUMENT ME!
3936    */
3937   @Override
3938   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3939   {
3940     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3941   }
3942
3943   /**
3944    * DOCUMENT ME!
3945    *
3946    * @param e
3947    *          DOCUMENT ME!
3948    */
3949   @Override
3950   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3951   {
3952     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3953   }
3954
3955   /**
3956    * DOCUMENT ME!
3957    *
3958    * @param type
3959    *          DOCUMENT ME!
3960    * @param pwType
3961    *          DOCUMENT ME!
3962    * @param title
3963    *          DOCUMENT ME!
3964    */
3965   void NewTreePanel(String type, String pwType, String title)
3966   {
3967     TreePanel tp;
3968
3969     if (viewport.getSelectionGroup() != null
3970             && viewport.getSelectionGroup().getSize() > 0)
3971     {
3972       if (viewport.getSelectionGroup().getSize() < 3)
3973       {
3974         JOptionPane
3975                 .showMessageDialog(
3976                         Desktop.desktop,
3977                         MessageManager
3978                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3979                         MessageManager
3980                                 .getString("label.not_enough_sequences"),
3981                         JOptionPane.WARNING_MESSAGE);
3982         return;
3983       }
3984
3985       SequenceGroup sg = viewport.getSelectionGroup();
3986
3987       /* Decide if the selection is a column region */
3988       for (SequenceI _s : sg.getSequences())
3989       {
3990         if (_s.getLength() < sg.getEndRes())
3991         {
3992           JOptionPane
3993                   .showMessageDialog(
3994                           Desktop.desktop,
3995                           MessageManager
3996                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3997                           MessageManager
3998                                   .getString("label.sequences_selection_not_aligned"),
3999                           JOptionPane.WARNING_MESSAGE);
4000
4001           return;
4002         }
4003       }
4004
4005       title = title + " on region";
4006       tp = new TreePanel(alignPanel, type, pwType);
4007     }
4008     else
4009     {
4010       // are the visible sequences aligned?
4011       if (!viewport.getAlignment().isAligned(false))
4012       {
4013         JOptionPane
4014                 .showMessageDialog(
4015                         Desktop.desktop,
4016                         MessageManager
4017                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4018                         MessageManager
4019                                 .getString("label.sequences_not_aligned"),
4020                         JOptionPane.WARNING_MESSAGE);
4021
4022         return;
4023       }
4024
4025       if (viewport.getAlignment().getHeight() < 2)
4026       {
4027         return;
4028       }
4029
4030       tp = new TreePanel(alignPanel, type, pwType);
4031     }
4032
4033     title += " from ";
4034
4035     if (viewport.viewName != null)
4036     {
4037       title += viewport.viewName + " of ";
4038     }
4039
4040     title += this.title;
4041
4042     Desktop.addInternalFrame(tp, title, 600, 500);
4043   }
4044
4045   /**
4046    * DOCUMENT ME!
4047    *
4048    * @param title
4049    *          DOCUMENT ME!
4050    * @param order
4051    *          DOCUMENT ME!
4052    */
4053   public void addSortByOrderMenuItem(String title,
4054           final AlignmentOrder order)
4055   {
4056     final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
4057     sort.add(item);
4058     item.addActionListener(new java.awt.event.ActionListener()
4059     {
4060       @Override
4061       public void actionPerformed(ActionEvent e)
4062       {
4063         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4064
4065         // TODO: JBPNote - have to map order entries to curent SequenceI
4066         // pointers
4067         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4068
4069         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4070                 .getAlignment()));
4071
4072         alignPanel.paintAlignment(true);
4073       }
4074     });
4075   }
4076
4077   /**
4078    * Add a new sort by annotation score menu item
4079    *
4080    * @param sort
4081    *          the menu to add the option to
4082    * @param scoreLabel
4083    *          the label used to retrieve scores for each sequence on the
4084    *          alignment
4085    */
4086   public void addSortByAnnotScoreMenuItem(JMenu sort,
4087           final String scoreLabel)
4088   {
4089     final JMenuItem item = new JMenuItem(scoreLabel);
4090     sort.add(item);
4091     item.addActionListener(new java.awt.event.ActionListener()
4092     {
4093       @Override
4094       public void actionPerformed(ActionEvent e)
4095       {
4096         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4097         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4098                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4099         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4100                 viewport.getAlignment()));
4101         alignPanel.paintAlignment(true);
4102       }
4103     });
4104   }
4105
4106   /**
4107    * last hash for alignment's annotation array - used to minimise cost of
4108    * rebuild.
4109    */
4110   protected int _annotationScoreVectorHash;
4111
4112   /**
4113    * search the alignment and rebuild the sort by annotation score submenu the
4114    * last alignment annotation vector hash is stored to minimize cost of
4115    * rebuilding in subsequence calls.
4116    *
4117    */
4118   @Override
4119   public void buildSortByAnnotationScoresMenu()
4120   {
4121     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4122     {
4123       return;
4124     }
4125
4126     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4127     {
4128       sortByAnnotScore.removeAll();
4129       // almost certainly a quicker way to do this - but we keep it simple
4130       Hashtable scoreSorts = new Hashtable();
4131       AlignmentAnnotation aann[];
4132       for (SequenceI sqa : viewport.getAlignment().getSequences())
4133       {
4134         aann = sqa.getAnnotation();
4135         for (int i = 0; aann != null && i < aann.length; i++)
4136         {
4137           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4138           {
4139             scoreSorts.put(aann[i].label, aann[i].label);
4140           }
4141         }
4142       }
4143       Enumeration labels = scoreSorts.keys();
4144       while (labels.hasMoreElements())
4145       {
4146         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4147                 (String) labels.nextElement());
4148       }
4149       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4150       scoreSorts.clear();
4151
4152       _annotationScoreVectorHash = viewport.getAlignment()
4153               .getAlignmentAnnotation().hashCode();
4154     }
4155   }
4156
4157   /**
4158    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4159    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4160    * call. Listeners are added to remove the menu item when the treePanel is
4161    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4162    * modified.
4163    *
4164    * @param treePanel
4165    *          Displayed tree window.
4166    * @param title
4167    *          SortBy menu item title.
4168    */
4169   @Override
4170   public void buildTreeMenu()
4171   {
4172     calculateTree.removeAll();
4173     // build the calculate menu
4174
4175     for (final String type : new String[]
4176     { "NJ", "AV" })
4177     {
4178       String treecalcnm = MessageManager.getString("label.tree_calc_"
4179               + type.toLowerCase());
4180       for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4181       {
4182         JMenuItem tm = new JMenuItem();
4183         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4184         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4185         {
4186           String smn = MessageManager.getStringOrReturn(
4187                   "label.score_model_", sm.getName());
4188           final String title = MessageManager.formatMessage(
4189                   "label.treecalc_title", treecalcnm, smn);
4190           tm.setText(title);//
4191           tm.addActionListener(new java.awt.event.ActionListener()
4192           {
4193             @Override
4194             public void actionPerformed(ActionEvent e)
4195             {
4196               NewTreePanel(type, (String) pwtype, title);
4197             }
4198           });
4199           calculateTree.add(tm);
4200         }
4201
4202       }
4203     }
4204     sortByTreeMenu.removeAll();
4205
4206     Vector comps = (Vector) PaintRefresher.components.get(viewport
4207             .getSequenceSetId());
4208     Vector treePanels = new Vector();
4209     int i, iSize = comps.size();
4210     for (i = 0; i < iSize; i++)
4211     {
4212       if (comps.elementAt(i) instanceof TreePanel)
4213       {
4214         treePanels.add(comps.elementAt(i));
4215       }
4216     }
4217
4218     iSize = treePanels.size();
4219
4220     if (iSize < 1)
4221     {
4222       sortByTreeMenu.setVisible(false);
4223       return;
4224     }
4225
4226     sortByTreeMenu.setVisible(true);
4227
4228     for (i = 0; i < treePanels.size(); i++)
4229     {
4230       final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4231       final JMenuItem item = new JMenuItem(tp.getTitle());
4232       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4233       item.addActionListener(new java.awt.event.ActionListener()
4234       {
4235         @Override
4236         public void actionPerformed(ActionEvent e)
4237         {
4238           tp.sortByTree_actionPerformed(null);
4239           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4240
4241         }
4242       });
4243
4244       sortByTreeMenu.add(item);
4245     }
4246   }
4247
4248   public boolean sortBy(AlignmentOrder alorder, String undoname)
4249   {
4250     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4251     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4252     if (undoname != null)
4253     {
4254       addHistoryItem(new OrderCommand(undoname, oldOrder,
4255               viewport.getAlignment()));
4256     }
4257     alignPanel.paintAlignment(true);
4258     return true;
4259   }
4260
4261   /**
4262    * Work out whether the whole set of sequences or just the selected set will
4263    * be submitted for multiple alignment.
4264    *
4265    */
4266   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4267   {
4268     // Now, check we have enough sequences
4269     AlignmentView msa = null;
4270
4271     if ((viewport.getSelectionGroup() != null)
4272             && (viewport.getSelectionGroup().getSize() > 1))
4273     {
4274       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4275       // some common interface!
4276       /*
4277        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4278        * SequenceI[sz = seqs.getSize(false)];
4279        *
4280        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4281        * seqs.getSequenceAt(i); }
4282        */
4283       msa = viewport.getAlignmentView(true);
4284     }
4285     else if (viewport.getSelectionGroup() != null
4286             && viewport.getSelectionGroup().getSize() == 1)
4287     {
4288       int option = JOptionPane.showConfirmDialog(this,
4289               MessageManager.getString("warn.oneseq_msainput_selection"),
4290               MessageManager.getString("label.invalid_selection"),
4291               JOptionPane.OK_CANCEL_OPTION);
4292       if (option == JOptionPane.OK_OPTION)
4293       {
4294         msa = viewport.getAlignmentView(false);
4295       }
4296     }
4297     else
4298     {
4299       msa = viewport.getAlignmentView(false);
4300     }
4301     return msa;
4302   }
4303
4304   /**
4305    * Decides what is submitted to a secondary structure prediction service: the
4306    * first sequence in the alignment, or in the current selection, or, if the
4307    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4308    * region or the whole alignment. (where the first sequence in the set is the
4309    * one that the prediction will be for).
4310    */
4311   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4312   {
4313     AlignmentView seqs = null;
4314
4315     if ((viewport.getSelectionGroup() != null)
4316             && (viewport.getSelectionGroup().getSize() > 0))
4317     {
4318       seqs = viewport.getAlignmentView(true);
4319     }
4320     else
4321     {
4322       seqs = viewport.getAlignmentView(false);
4323     }
4324     // limit sequences - JBPNote in future - could spawn multiple prediction
4325     // jobs
4326     // TODO: viewport.getAlignment().isAligned is a global state - the local
4327     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4328     if (!viewport.getAlignment().isAligned(false))
4329     {
4330       seqs.setSequences(new SeqCigar[]
4331       { seqs.getSequences()[0] });
4332       // TODO: if seqs.getSequences().length>1 then should really have warned
4333       // user!
4334
4335     }
4336     return seqs;
4337   }
4338
4339   /**
4340    * DOCUMENT ME!
4341    *
4342    * @param e
4343    *          DOCUMENT ME!
4344    */
4345   @Override
4346   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4347   {
4348     // Pick the tree file
4349     JalviewFileChooser chooser = new JalviewFileChooser(
4350             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4351     chooser.setFileView(new JalviewFileView());
4352     chooser.setDialogTitle(MessageManager
4353             .getString("label.select_newick_like_tree_file"));
4354     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4355
4356     int value = chooser.showOpenDialog(null);
4357
4358     if (value == JalviewFileChooser.APPROVE_OPTION)
4359     {
4360       String choice = chooser.getSelectedFile().getPath();
4361       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4362       jalview.io.NewickFile fin = null;
4363       try
4364       {
4365         fin = new jalview.io.NewickFile(choice, "File");
4366         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4367       } catch (Exception ex)
4368       {
4369         JOptionPane
4370                 .showMessageDialog(
4371                         Desktop.desktop,
4372                         ex.getMessage(),
4373                         MessageManager
4374                                 .getString("label.problem_reading_tree_file"),
4375                         JOptionPane.WARNING_MESSAGE);
4376         ex.printStackTrace();
4377       }
4378       if (fin != null && fin.hasWarningMessage())
4379       {
4380         JOptionPane.showMessageDialog(Desktop.desktop, fin
4381                 .getWarningMessage(), MessageManager
4382                 .getString("label.possible_problem_with_tree_file"),
4383                 JOptionPane.WARNING_MESSAGE);
4384       }
4385     }
4386   }
4387
4388   @Override
4389   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4390   {
4391     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4392   }
4393
4394   public TreePanel ShowNewickTree(NewickFile nf, String title)
4395   {
4396     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4397   }
4398
4399   public TreePanel ShowNewickTree(NewickFile nf, String title,
4400           AlignmentView input)
4401   {
4402     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4403   }
4404
4405   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4406           int h, int x, int y)
4407   {
4408     return ShowNewickTree(nf, title, null, w, h, x, y);
4409   }
4410
4411   /**
4412    * Add a treeviewer for the tree extracted from a newick file object to the
4413    * current alignment view
4414    *
4415    * @param nf
4416    *          the tree
4417    * @param title
4418    *          tree viewer title
4419    * @param input
4420    *          Associated alignment input data (or null)
4421    * @param w
4422    *          width
4423    * @param h
4424    *          height
4425    * @param x
4426    *          position
4427    * @param y
4428    *          position
4429    * @return TreePanel handle
4430    */
4431   public TreePanel ShowNewickTree(NewickFile nf, String title,
4432           AlignmentView input, int w, int h, int x, int y)
4433   {
4434     TreePanel tp = null;
4435
4436     try
4437     {
4438       nf.parse();
4439
4440       if (nf.getTree() != null)
4441       {
4442         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4443
4444         tp.setSize(w, h);
4445
4446         if (x > 0 && y > 0)
4447         {
4448           tp.setLocation(x, y);
4449         }
4450
4451         Desktop.addInternalFrame(tp, title, w, h);
4452       }
4453     } catch (Exception ex)
4454     {
4455       ex.printStackTrace();
4456     }
4457
4458     return tp;
4459   }
4460
4461   private boolean buildingMenu = false;
4462
4463   /**
4464    * Generates menu items and listener event actions for web service clients
4465    *
4466    */
4467   public void BuildWebServiceMenu()
4468   {
4469     while (buildingMenu)
4470     {
4471       try
4472       {
4473         System.err.println("Waiting for building menu to finish.");
4474         Thread.sleep(10);
4475       } catch (Exception e)
4476       {
4477       }
4478       ;
4479     }
4480     final AlignFrame me = this;
4481     buildingMenu = true;
4482     new Thread(new Runnable()
4483     {
4484       @Override
4485       public void run()
4486       {
4487         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4488         try
4489         {
4490           System.err.println("Building ws menu again "
4491                   + Thread.currentThread());
4492           // TODO: add support for context dependent disabling of services based
4493           // on
4494           // alignment and current selection
4495           // TODO: add additional serviceHandle parameter to specify abstract
4496           // handler
4497           // class independently of AbstractName
4498           // TODO: add in rediscovery GUI function to restart discoverer
4499           // TODO: group services by location as well as function and/or
4500           // introduce
4501           // object broker mechanism.
4502           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4503           final IProgressIndicator af = me;
4504           final JMenu msawsmenu = new JMenu("Alignment");
4505           final JMenu secstrmenu = new JMenu(
4506                   "Secondary Structure Prediction");
4507           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4508           final JMenu analymenu = new JMenu("Analysis");
4509           final JMenu dismenu = new JMenu("Protein Disorder");
4510           // final JMenu msawsmenu = new
4511           // JMenu(MessageManager.getString("label.alignment"));
4512           // final JMenu secstrmenu = new
4513           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4514           // final JMenu seqsrchmenu = new
4515           // JMenu(MessageManager.getString("label.sequence_database_search"));
4516           // final JMenu analymenu = new
4517           // JMenu(MessageManager.getString("label.analysis"));
4518           // final JMenu dismenu = new
4519           // JMenu(MessageManager.getString("label.protein_disorder"));
4520           // JAL-940 - only show secondary structure prediction services from
4521           // the legacy server
4522           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4523               // &&
4524           Discoverer.services != null && (Discoverer.services.size() > 0))
4525           {
4526             // TODO: refactor to allow list of AbstractName/Handler bindings to
4527             // be
4528             // stored or retrieved from elsewhere
4529             // No MSAWS used any more:
4530             // Vector msaws = null; // (Vector)
4531             // Discoverer.services.get("MsaWS");
4532             Vector secstrpr = (Vector) Discoverer.services
4533                     .get("SecStrPred");
4534             if (secstrpr != null)
4535             {
4536               // Add any secondary structure prediction services
4537               for (int i = 0, j = secstrpr.size(); i < j; i++)
4538               {
4539                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4540                         .get(i);
4541                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4542                         .getServiceClient(sh);
4543                 int p = secstrmenu.getItemCount();
4544                 impl.attachWSMenuEntry(secstrmenu, me);
4545                 int q = secstrmenu.getItemCount();
4546                 for (int litm = p; litm < q; litm++)
4547                 {
4548                   legacyItems.add(secstrmenu.getItem(litm));
4549                 }
4550               }
4551             }
4552           }
4553
4554           // Add all submenus in the order they should appear on the web
4555           // services menu
4556           wsmenu.add(msawsmenu);
4557           wsmenu.add(secstrmenu);
4558           wsmenu.add(dismenu);
4559           wsmenu.add(analymenu);
4560           // No search services yet
4561           // wsmenu.add(seqsrchmenu);
4562
4563           javax.swing.SwingUtilities.invokeLater(new Runnable()
4564           {
4565             @Override
4566             public void run()
4567             {
4568               try
4569               {
4570                 webService.removeAll();
4571                 // first, add discovered services onto the webservices menu
4572                 if (wsmenu.size() > 0)
4573                 {
4574                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4575                   {
4576                     webService.add(wsmenu.get(i));
4577                   }
4578                 }
4579                 else
4580                 {
4581                   webService.add(me.webServiceNoServices);
4582                 }
4583                 // TODO: move into separate menu builder class.
4584                 boolean new_sspred = false;
4585                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4586                 {
4587                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4588                   if (jws2servs != null)
4589                   {
4590                     if (jws2servs.hasServices())
4591                     {
4592                       jws2servs.attachWSMenuEntry(webService, me);
4593                       for (Jws2Instance sv : jws2servs.getServices())
4594                       {
4595                         if (sv.description.toLowerCase().contains("jpred"))
4596                         {
4597                           for (JMenuItem jmi : legacyItems)
4598                           {
4599                             jmi.setVisible(false);
4600                           }
4601                         }
4602                       }
4603
4604                     }
4605                     if (jws2servs.isRunning())
4606                     {
4607                       JMenuItem tm = new JMenuItem(
4608                               "Still discovering JABA Services");
4609                       tm.setEnabled(false);
4610                       webService.add(tm);
4611                     }
4612                   }
4613                 }
4614                 build_urlServiceMenu(me.webService);
4615                 build_fetchdbmenu(webService);
4616                 for (JMenu item : wsmenu)
4617                 {
4618                   if (item.getItemCount() == 0)
4619                   {
4620                     item.setEnabled(false);
4621                   }
4622                   else
4623                   {
4624                     item.setEnabled(true);
4625                   }
4626                 }
4627               } catch (Exception e)
4628               {
4629                 Cache.log
4630                         .debug("Exception during web service menu building process.",
4631                                 e);
4632               }
4633               ;
4634             }
4635           });
4636         } catch (Exception e)
4637         {
4638         }
4639         ;
4640
4641         buildingMenu = false;
4642       }
4643     }).start();
4644
4645   }
4646
4647   /**
4648    * construct any groupURL type service menu entries.
4649    *
4650    * @param webService
4651    */
4652   private void build_urlServiceMenu(JMenu webService)
4653   {
4654     // TODO: remove this code when 2.7 is released
4655     // DEBUG - alignmentView
4656     /*
4657      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4658      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4659      *
4660      * @Override public void actionPerformed(ActionEvent e) {
4661      * jalview.datamodel.AlignmentView
4662      * .testSelectionViews(af.viewport.getAlignment(),
4663      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4664      *
4665      * }); webService.add(testAlView);
4666      */
4667     // TODO: refactor to RestClient discoverer and merge menu entries for
4668     // rest-style services with other types of analysis/calculation service
4669     // SHmmr test client - still being implemented.
4670     // DEBUG - alignmentView
4671
4672     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4673             .getRestClients())
4674     {
4675       client.attachWSMenuEntry(
4676               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4677               this);
4678     }
4679   }
4680
4681   /*
4682    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4683    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4684    * getProperty("LAST_DIRECTORY"));
4685    *
4686    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4687    * to Vamsas file"); chooser.setToolTipText("Export");
4688    *
4689    * int value = chooser.showSaveDialog(this);
4690    *
4691    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4692    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4693    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4694    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4695    */
4696   /**
4697    * prototype of an automatically enabled/disabled analysis function
4698    *
4699    */
4700   protected void setShowProductsEnabled()
4701   {
4702     SequenceI[] selection = viewport.getSequenceSelection();
4703     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4704             viewport.getAlignment().getDataset()))
4705     {
4706       showProducts.setEnabled(true);
4707
4708     }
4709     else
4710     {
4711       showProducts.setEnabled(false);
4712     }
4713   }
4714
4715   /**
4716    * search selection for sequence xRef products and build the show products
4717    * menu.
4718    *
4719    * @param selection
4720    * @param dataset
4721    * @return true if showProducts menu should be enabled.
4722    */
4723   public boolean canShowProducts(SequenceI[] selection,
4724           boolean isRegionSelection, Alignment dataset)
4725   {
4726     boolean showp = false;
4727     try
4728     {
4729       showProducts.removeAll();
4730       final boolean dna = viewport.getAlignment().isNucleotide();
4731       final Alignment ds = dataset;
4732       String[] ptypes = (selection == null || selection.length == 0) ? null
4733               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4734       // Object[] prods =
4735       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4736       // selection, dataset, true);
4737       final SequenceI[] sel = selection;
4738       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4739       {
4740         showp = true;
4741         final boolean isRegSel = isRegionSelection;
4742         final AlignFrame af = this;
4743         final String source = ptypes[t];
4744         JMenuItem xtype = new JMenuItem(ptypes[t]);
4745         xtype.addActionListener(new ActionListener()
4746         {
4747
4748           @Override
4749           public void actionPerformed(ActionEvent e)
4750           {
4751             // TODO: new thread for this call with vis-delay
4752             af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4753                     isRegSel, dna, source);
4754           }
4755
4756         });
4757         showProducts.add(xtype);
4758       }
4759       showProducts.setVisible(showp);
4760       showProducts.setEnabled(showp);
4761     } catch (Exception e)
4762     {
4763       jalview.bin.Cache.log
4764               .warn("canTranslate threw an exception - please report to help@jalview.org",
4765                       e);
4766       return false;
4767     }
4768     return showp;
4769   }
4770
4771   protected void showProductsFor(SequenceI[] sel, Alignment ds,
4772           boolean isRegSel, boolean dna, String source)
4773   {
4774     final boolean fisRegSel = isRegSel;
4775     final boolean fdna = dna;
4776     final String fsrc = source;
4777     final AlignFrame ths = this;
4778     final SequenceI[] fsel = sel;
4779     Runnable foo = new Runnable()
4780     {
4781
4782       @Override
4783       public void run()
4784       {
4785         final long sttime = System.currentTimeMillis();
4786         ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4787         try
4788         {
4789           Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4790           // our local
4791           // dataset
4792           // reference
4793           Alignment prods = CrossRef
4794                   .findXrefSequences(fsel, fdna, fsrc, ds);
4795           if (prods != null)
4796           {
4797             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4798             for (int s = 0; s < sprods.length; s++)
4799             {
4800               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4801               if (ds.getSequences() == null
4802                       || !ds.getSequences().contains(
4803                               sprods[s].getDatasetSequence()))
4804               {
4805                 ds.addSequence(sprods[s].getDatasetSequence());
4806               }
4807               sprods[s].updatePDBIds();
4808             }
4809             Alignment al = new Alignment(sprods);
4810             AlignedCodonFrame[] cf = prods.getCodonFrames();
4811             al.setDataset(ds);
4812             for (int s = 0; cf != null && s < cf.length; s++)
4813             {
4814               al.addCodonFrame(cf[s]);
4815               cf[s] = null;
4816             }
4817             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4818                     DEFAULT_HEIGHT);
4819             String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4820                     + " for " + ((fisRegSel) ? "selected region of " : "")
4821                     + getTitle();
4822             Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4823                     DEFAULT_HEIGHT);
4824           }
4825           else
4826           {
4827             System.err.println("No Sequences generated for xRef type "
4828                     + fsrc);
4829           }
4830         } catch (Exception e)
4831         {
4832           jalview.bin.Cache.log.error(
4833                   "Exception when finding crossreferences", e);
4834         } catch (OutOfMemoryError e)
4835         {
4836           new OOMWarning("whilst fetching crossreferences", e);
4837         } catch (Error e)
4838         {
4839           jalview.bin.Cache.log.error("Error when finding crossreferences",
4840                   e);
4841         }
4842         ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4843                 sttime);
4844       }
4845
4846     };
4847     Thread frunner = new Thread(foo);
4848     frunner.start();
4849   }
4850
4851   public boolean canShowTranslationProducts(SequenceI[] selection,
4852           AlignmentI alignment)
4853   {
4854     // old way
4855     try
4856     {
4857       return (jalview.analysis.Dna.canTranslate(selection,
4858               viewport.getViewAsVisibleContigs(true)));
4859     } catch (Exception e)
4860     {
4861       jalview.bin.Cache.log
4862               .warn("canTranslate threw an exception - please report to help@jalview.org",
4863                       e);
4864       return false;
4865     }
4866   }
4867
4868   @Override
4869   public void showProducts_actionPerformed(ActionEvent e)
4870   {
4871     // /////////////////////////////
4872     // Collect Data to be translated/transferred
4873
4874     SequenceI[] selection = viewport.getSequenceSelection();
4875     AlignmentI al = null;
4876     try
4877     {
4878       al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4879               .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4880               viewport.getAlignment().getDataset());
4881     } catch (Exception ex)
4882     {
4883       al = null;
4884       jalview.bin.Cache.log.debug("Exception during translation.", ex);
4885     }
4886     if (al == null)
4887     {
4888       JOptionPane
4889               .showMessageDialog(
4890                       Desktop.desktop,
4891                       MessageManager
4892                               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4893                       MessageManager.getString("label.translation_failed"),
4894                       JOptionPane.WARNING_MESSAGE);
4895     }
4896     else
4897     {
4898       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4899       Desktop.addInternalFrame(af, MessageManager.formatMessage(
4900               "label.translation_of_params", new String[]
4901               { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4902     }
4903   }
4904
4905   /**
4906    * Construct and display a new frame containing the translation of this
4907    * frame's cDNA sequences to their protein (amino acid) equivalents.
4908    */
4909   @Override
4910   public void showTranslation_actionPerformed(ActionEvent e)
4911   {
4912     // /////////////////////////////
4913     // Collect Data to be translated/transferred
4914
4915     SequenceI[] selection = viewport.getSequenceSelection();
4916     String[] seqstring = viewport.getViewAsString(true);
4917     AlignmentI al = null;
4918     try
4919     {
4920       al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4921               viewport.getViewAsVisibleContigs(true), viewport
4922                       .getGapCharacter(), viewport.getAlignment()
4923                       .getAlignmentAnnotation(), viewport.getAlignment()
4924                       .getWidth(), viewport.getAlignment().getDataset());
4925     } catch (Exception ex)
4926     {
4927       al = null;
4928       jalview.bin.Cache.log.error(
4929               "Exception during translation. Please report this !", ex);
4930       JOptionPane
4931               .showMessageDialog(
4932                       Desktop.desktop,
4933                       MessageManager
4934                               .getString("label.error_when_translating_sequences_submit_bug_report"),
4935                       MessageManager
4936                               .getString("label.implementation_error")
4937                               + MessageManager
4938                                       .getString("translation_failed"),
4939                       JOptionPane.ERROR_MESSAGE);
4940       return;
4941     }
4942     if (al == null)
4943     {
4944       JOptionPane
4945               .showMessageDialog(
4946                       Desktop.desktop,
4947                       MessageManager
4948                               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4949                       MessageManager.getString("label.translation_failed"),
4950                       JOptionPane.WARNING_MESSAGE);
4951     }
4952     else
4953     {
4954       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4955       Desktop.addInternalFrame(af, MessageManager.formatMessage(
4956               "label.translation_of_params", new String[]
4957               { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4958       viewport.getStructureSelectionManager().addCommandListener(viewport);
4959     }
4960   }
4961
4962   /**
4963    * Try to load a features file onto the alignment.
4964    *
4965    * @param file
4966    *          contents or path to retrieve file
4967    * @param type
4968    *          access mode of file (see jalview.io.AlignFile)
4969    * @return true if features file was parsed corectly.
4970    */
4971   public boolean parseFeaturesFile(String file, String type)
4972   {
4973     boolean featuresFile = false;
4974     try
4975     {
4976       featuresFile = new FeaturesFile(file, type).parse(viewport
4977               .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4978               .getFeatureRenderer().featureColours, false,
4979               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4980     } catch (Exception ex)
4981     {
4982       ex.printStackTrace();
4983     }
4984
4985     if (featuresFile)
4986     {
4987       viewport.showSequenceFeatures = true;
4988       showSeqFeatures.setSelected(true);
4989       if (alignPanel.seqPanel.seqCanvas.fr != null)
4990       {
4991         // update the min/max ranges where necessary
4992         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4993       }
4994       if (featureSettings != null)
4995       {
4996         featureSettings.setTableData();
4997       }
4998       alignPanel.paintAlignment(true);
4999     }
5000
5001     return featuresFile;
5002   }
5003
5004   @Override
5005   public void dragEnter(DropTargetDragEvent evt)
5006   {
5007   }
5008
5009   @Override
5010   public void dragExit(DropTargetEvent evt)
5011   {
5012   }
5013
5014   @Override
5015   public void dragOver(DropTargetDragEvent evt)
5016   {
5017   }
5018
5019   @Override
5020   public void dropActionChanged(DropTargetDragEvent evt)
5021   {
5022   }
5023
5024   @Override
5025   public void drop(DropTargetDropEvent evt)
5026   {
5027     Transferable t = evt.getTransferable();
5028     java.util.List files = null;
5029
5030     try
5031     {
5032       DataFlavor uriListFlavor = new DataFlavor(
5033               "text/uri-list;class=java.lang.String");
5034       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5035       {
5036         // Works on Windows and MacOSX
5037         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5038         files = (java.util.List) t
5039                 .getTransferData(DataFlavor.javaFileListFlavor);
5040       }
5041       else if (t.isDataFlavorSupported(uriListFlavor))
5042       {
5043         // This is used by Unix drag system
5044         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5045         String data = (String) t.getTransferData(uriListFlavor);
5046         files = new java.util.ArrayList(1);
5047         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5048                 data, "\r\n"); st.hasMoreTokens();)
5049         {
5050           String s = st.nextToken();
5051           if (s.startsWith("#"))
5052           {
5053             // the line is a comment (as per the RFC 2483)
5054             continue;
5055           }
5056
5057           java.net.URI uri = new java.net.URI(s);
5058           // check to see if we can handle this kind of URI
5059           if (uri.getScheme().toLowerCase().startsWith("http"))
5060           {
5061             files.add(uri.toString());
5062           }
5063           else
5064           {
5065             // otherwise preserve old behaviour: catch all for file objects
5066             java.io.File file = new java.io.File(uri);
5067             files.add(file.toString());
5068           }
5069         }
5070       }
5071     } catch (Exception e)
5072     {
5073       e.printStackTrace();
5074     }
5075     if (files != null)
5076     {
5077       try
5078       {
5079         // check to see if any of these files have names matching sequences in
5080         // the alignment
5081         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5082                 .getAlignment().getSequencesArray());
5083         /**
5084          * Object[] { String,SequenceI}
5085          */
5086         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5087         ArrayList<String> filesnotmatched = new ArrayList<String>();
5088         for (int i = 0; i < files.size(); i++)
5089         {
5090           String file = files.get(i).toString();
5091           String pdbfn = "";
5092           String protocol = FormatAdapter.checkProtocol(file);
5093           if (protocol == jalview.io.FormatAdapter.FILE)
5094           {
5095             File fl = new File(file);
5096             pdbfn = fl.getName();
5097           }
5098           else if (protocol == jalview.io.FormatAdapter.URL)
5099           {
5100             URL url = new URL(file);
5101             pdbfn = url.getFile();
5102           }
5103           if (pdbfn.length() > 0)
5104           {
5105             // attempt to find a match in the alignment
5106             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5107             int l = 0, c = pdbfn.indexOf(".");
5108             while (mtch == null && c != -1)
5109             {
5110               do
5111               {
5112                 l = c;
5113               } while ((c = pdbfn.indexOf(".", l)) > l);
5114               if (l > -1)
5115               {
5116                 pdbfn = pdbfn.substring(0, l);
5117               }
5118               mtch = idm.findAllIdMatches(pdbfn);
5119             }
5120             if (mtch != null)
5121             {
5122               String type = null;
5123               try
5124               {
5125                 type = new IdentifyFile().Identify(file, protocol);
5126               } catch (Exception ex)
5127               {
5128                 type = null;
5129               }
5130               if (type != null)
5131               {
5132                 if (type.equalsIgnoreCase("PDB"))
5133                 {
5134                   filesmatched.add(new Object[]
5135                   { file, protocol, mtch });
5136                   continue;
5137                 }
5138               }
5139             }
5140             // File wasn't named like one of the sequences or wasn't a PDB file.
5141             filesnotmatched.add(file);
5142           }
5143         }
5144         int assocfiles = 0;
5145         if (filesmatched.size() > 0)
5146         {
5147           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5148                   || JOptionPane
5149                           .showConfirmDialog(
5150                                   this,
5151                                   MessageManager
5152                                           .formatMessage(
5153                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5154                                                   new String[]
5155                                                   { Integer.valueOf(
5156                                                           filesmatched
5157                                                                   .size())
5158                                                           .toString() }),
5159                                   MessageManager
5160                                           .getString("label.automatically_associate_pdb_files_by_name"),
5161                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5162
5163           {
5164             for (Object[] fm : filesmatched)
5165             {
5166               // try and associate
5167               // TODO: may want to set a standard ID naming formalism for
5168               // associating PDB files which have no IDs.
5169               for (SequenceI toassoc : (SequenceI[]) fm[2])
5170               {
5171                 PDBEntry pe = new AssociatePdbFileWithSeq()
5172                         .associatePdbWithSeq((String) fm[0],
5173                                 (String) fm[1], toassoc, false,
5174                                 Desktop.instance);
5175                 if (pe != null)
5176                 {
5177                   System.err.println("Associated file : "
5178                           + ((String) fm[0]) + " with "
5179                           + toassoc.getDisplayId(true));
5180                   assocfiles++;
5181                 }
5182               }
5183               alignPanel.paintAlignment(true);
5184             }
5185           }
5186         }
5187         if (filesnotmatched.size() > 0)
5188         {
5189           if (assocfiles > 0
5190                   && (Cache.getDefault(
5191                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5192                           .showConfirmDialog(
5193                                   this,
5194                                   "<html>"+MessageManager
5195                                           .formatMessage(
5196                                                   "label.ignore_unmatched_dropped_files_info",
5197                                                   new String[]
5198                                                   { Integer.valueOf(
5199                                                           filesnotmatched
5200                                                                   .size())
5201                                                           .toString() })+"</html>",
5202                                   MessageManager
5203                                           .getString("label.ignore_unmatched_dropped_files"),
5204                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5205           {
5206             return;
5207           }
5208           for (String fn : filesnotmatched)
5209           {
5210             loadJalviewDataFile(fn, null, null, null);
5211           }
5212
5213         }
5214       } catch (Exception ex)
5215       {
5216         ex.printStackTrace();
5217       }
5218     }
5219   }
5220
5221   /**
5222    * Attempt to load a "dropped" file or URL string: First by testing whether
5223    * it's and Annotation file, then a JNet file, and finally a features file. If
5224    * all are false then the user may have dropped an alignment file onto this
5225    * AlignFrame.
5226    *
5227    * @param file
5228    *          either a filename or a URL string.
5229    */
5230   public void loadJalviewDataFile(String file, String protocol,
5231           String format, SequenceI assocSeq)
5232   {
5233     try
5234     {
5235       if (protocol == null)
5236       {
5237         protocol = jalview.io.FormatAdapter.checkProtocol(file);
5238       }
5239       // if the file isn't identified, or not positively identified as some
5240       // other filetype (PFAM is default unidentified alignment file type) then
5241       // try to parse as annotation.
5242       boolean isAnnotation = (format == null || format
5243               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5244               .readAnnotationFile(viewport.getAlignment(), file, protocol)
5245               : false;
5246
5247       if (!isAnnotation)
5248       {
5249         // first see if its a T-COFFEE score file
5250         TCoffeeScoreFile tcf = null;
5251         try
5252         {
5253           tcf = new TCoffeeScoreFile(file, protocol);
5254           if (tcf.isValid())
5255           {
5256             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5257             {
5258               tcoffeeColour.setEnabled(true);
5259               tcoffeeColour.setSelected(true);
5260               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5261               isAnnotation = true;
5262               statusBar
5263                       .setText(MessageManager
5264                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5265             }
5266             else
5267             {
5268               // some problem - if no warning its probable that the ID matching
5269               // process didn't work
5270               JOptionPane
5271                       .showMessageDialog(
5272                               Desktop.desktop,
5273                               tcf.getWarningMessage() == null ? MessageManager
5274                                       .getString("label.check_file_matches_sequence_ids_alignment")
5275                                       : tcf.getWarningMessage(),
5276                               MessageManager
5277                                       .getString("label.problem_reading_tcoffee_score_file"),
5278                               JOptionPane.WARNING_MESSAGE);
5279             }
5280           }
5281           else
5282           {
5283             tcf = null;
5284           }
5285         } catch (Exception x)
5286         {
5287           Cache.log
5288                   .debug("Exception when processing data source as T-COFFEE score file",
5289                           x);
5290           tcf = null;
5291         }
5292         if (tcf == null)
5293         {
5294           // try to see if its a JNet 'concise' style annotation file *before*
5295           // we
5296           // try to parse it as a features file
5297           if (format == null)
5298           {
5299             format = new IdentifyFile().Identify(file, protocol);
5300           }
5301           if (format.equalsIgnoreCase("JnetFile"))
5302           {
5303             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5304                     file, protocol);
5305             new JnetAnnotationMaker().add_annotation(predictions,
5306                     viewport.getAlignment(), 0, false);
5307             isAnnotation = true;
5308           }
5309           else
5310           {
5311             /*
5312              * if (format.equalsIgnoreCase("PDB")) {
5313              *
5314              * String pdbfn = ""; // try to match up filename with sequence id
5315              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5316              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5317              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5318              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5319              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5320              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5321              * // attempt to find a match in the alignment SequenceI mtch =
5322              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5323              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5324              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5325              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5326              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5327              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5328              * { System.err.println("Associated file : " + file + " with " +
5329              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5330              * TODO: maybe need to load as normal otherwise return; } }
5331              */
5332             // try to parse it as a features file
5333             boolean isGroupsFile = parseFeaturesFile(file, protocol);
5334             // if it wasn't a features file then we just treat it as a general
5335             // alignment file to load into the current view.
5336             if (!isGroupsFile)
5337             {
5338               new FileLoader().LoadFile(viewport, file, protocol, format);
5339             }
5340             else
5341             {
5342               alignPanel.paintAlignment(true);
5343             }
5344           }
5345         }
5346       }
5347       if (isAnnotation)
5348       {
5349
5350         alignPanel.adjustAnnotationHeight();
5351         viewport.updateSequenceIdColours();
5352         buildSortByAnnotationScoresMenu();
5353         alignPanel.paintAlignment(true);
5354       }
5355     } catch (Exception ex)
5356     {
5357       ex.printStackTrace();
5358     } catch (OutOfMemoryError oom)
5359     {
5360       try
5361       {
5362         System.gc();
5363       } catch (Exception x)
5364       {
5365       }
5366       ;
5367       new OOMWarning(
5368               "loading data "
5369                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5370                               : "using " + protocol + " from " + file)
5371                               : ".")
5372                       + (format != null ? "(parsing as '" + format
5373                               + "' file)" : ""), oom, Desktop.desktop);
5374     }
5375   }
5376
5377   @Override
5378   public void tabSelectionChanged(int index)
5379   {
5380     if (index > -1)
5381     {
5382       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5383       viewport = alignPanel.av;
5384       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5385       setMenusFromViewport(viewport);
5386     }
5387   }
5388
5389   @Override
5390   public void tabbedPane_mousePressed(MouseEvent e)
5391   {
5392     if (SwingUtilities.isRightMouseButton(e))
5393     {
5394       String reply = JOptionPane.showInternalInputDialog(this,
5395               MessageManager.getString("label.enter_view_name"),
5396               MessageManager.getString("label.enter_view_name"),
5397               JOptionPane.QUESTION_MESSAGE);
5398
5399       if (reply != null)
5400       {
5401         viewport.viewName = reply;
5402         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5403       }
5404     }
5405   }
5406
5407   public AlignViewport getCurrentView()
5408   {
5409     return viewport;
5410   }
5411
5412   /**
5413    * Open the dialog for regex description parsing.
5414    */
5415   @Override
5416   protected void extractScores_actionPerformed(ActionEvent e)
5417   {
5418     ParseProperties pp = new jalview.analysis.ParseProperties(
5419             viewport.getAlignment());
5420     // TODO: verify regex and introduce GUI dialog for version 2.5
5421     // if (pp.getScoresFromDescription("col", "score column ",
5422     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5423     // true)>0)
5424     if (pp.getScoresFromDescription("description column",
5425             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5426     {
5427       buildSortByAnnotationScoresMenu();
5428     }
5429   }
5430
5431   /*
5432    * (non-Javadoc)
5433    *
5434    * @see
5435    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5436    * )
5437    */
5438   @Override
5439   protected void showDbRefs_actionPerformed(ActionEvent e)
5440   {
5441     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5442   }
5443
5444   /*
5445    * (non-Javadoc)
5446    *
5447    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5448    * ActionEvent)
5449    */
5450   @Override
5451   protected void showNpFeats_actionPerformed(ActionEvent e)
5452   {
5453     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5454   }
5455
5456   /**
5457    * find the viewport amongst the tabs in this alignment frame and close that
5458    * tab
5459    *
5460    * @param av
5461    */
5462   public boolean closeView(AlignViewport av)
5463   {
5464     if (viewport == av)
5465     {
5466       this.closeMenuItem_actionPerformed(false);
5467       return true;
5468     }
5469     Component[] comp = tabbedPane.getComponents();
5470     for (int i = 0; comp != null && i < comp.length; i++)
5471     {
5472       if (comp[i] instanceof AlignmentPanel)
5473       {
5474         if (((AlignmentPanel) comp[i]).av == av)
5475         {
5476           // close the view.
5477           closeView((AlignmentPanel) comp[i]);
5478           return true;
5479         }
5480       }
5481     }
5482     return false;
5483   }
5484
5485   protected void build_fetchdbmenu(JMenu webService)
5486   {
5487     // Temporary hack - DBRef Fetcher always top level ws entry.
5488     // TODO We probably want to store a sequence database checklist in
5489     // preferences and have checkboxes.. rather than individual sources selected
5490     // here
5491     final JMenu rfetch = new JMenu(
5492             MessageManager.getString("action.fetch_db_references"));
5493     rfetch.setToolTipText(MessageManager
5494             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5495     webService.add(rfetch);
5496
5497     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5498             MessageManager.getString("option.trim_retrieved_seqs"));
5499     trimrs.setToolTipText(MessageManager
5500             .getString("label.trim_retrieved_sequences"));
5501     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5502     trimrs.addActionListener(new ActionListener()
5503     {
5504       @Override
5505       public void actionPerformed(ActionEvent e)
5506       {
5507         trimrs.setSelected(trimrs.isSelected());
5508         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5509                 Boolean.valueOf(trimrs.isSelected()).toString());
5510       };
5511     });
5512     rfetch.add(trimrs);
5513     JMenuItem fetchr = new JMenuItem(
5514             MessageManager.getString("label.standard_databases"));
5515     fetchr.setToolTipText(MessageManager
5516             .getString("label.fetch_embl_uniprot"));
5517     fetchr.addActionListener(new ActionListener()
5518     {
5519
5520       @Override
5521       public void actionPerformed(ActionEvent e)
5522       {
5523         new Thread(new Runnable()
5524         {
5525
5526           @Override
5527           public void run()
5528           {
5529             new jalview.ws.DBRefFetcher(alignPanel.av
5530                     .getSequenceSelection(), alignPanel.alignFrame)
5531                     .fetchDBRefs(false);
5532           }
5533         }).start();
5534
5535       }
5536
5537     });
5538     rfetch.add(fetchr);
5539     final AlignFrame me = this;
5540     new Thread(new Runnable()
5541     {
5542       @Override
5543       public void run()
5544       {
5545         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5546                 .getSequenceFetcherSingleton(me);
5547         javax.swing.SwingUtilities.invokeLater(new Runnable()
5548         {
5549           @Override
5550           public void run()
5551           {
5552             String[] dbclasses = sf.getOrderedSupportedSources();
5553             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5554             // jalview.util.QuickSort.sort(otherdb, otherdb);
5555             List<DbSourceProxy> otherdb;
5556             JMenu dfetch = new JMenu();
5557             JMenu ifetch = new JMenu();
5558             JMenuItem fetchr = null;
5559             int comp = 0, icomp = 0, mcomp = 15;
5560             String mname = null;
5561             int dbi = 0;
5562             for (String dbclass : dbclasses)
5563             {
5564               otherdb = sf.getSourceProxy(dbclass);
5565               // add a single entry for this class, or submenu allowing 'fetch
5566               // all' or pick one
5567               if (otherdb == null || otherdb.size() < 1)
5568               {
5569                 continue;
5570               }
5571               // List<DbSourceProxy> dbs=otherdb;
5572               // otherdb=new ArrayList<DbSourceProxy>();
5573               // for (DbSourceProxy db:dbs)
5574               // {
5575               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5576               // }
5577               if (mname == null)
5578               {
5579                 mname = "From " + dbclass;
5580               }
5581               if (otherdb.size() == 1)
5582               {
5583                 final DbSourceProxy[] dassource = otherdb
5584                         .toArray(new DbSourceProxy[0]);
5585                 DbSourceProxy src = otherdb.get(0);
5586                 fetchr = new JMenuItem(src.getDbSource());
5587                 fetchr.addActionListener(new ActionListener()
5588                 {
5589
5590                   @Override
5591                   public void actionPerformed(ActionEvent e)
5592                   {
5593                     new Thread(new Runnable()
5594                     {
5595
5596                       @Override
5597                       public void run()
5598                       {
5599                         new jalview.ws.DBRefFetcher(alignPanel.av
5600                                 .getSequenceSelection(),
5601                                 alignPanel.alignFrame, dassource)
5602                                 .fetchDBRefs(false);
5603                       }
5604                     }).start();
5605                   }
5606
5607                 });
5608                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5609                 dfetch.add(fetchr);
5610                 comp++;
5611               }
5612               else
5613               {
5614                 final DbSourceProxy[] dassource = otherdb
5615                         .toArray(new DbSourceProxy[0]);
5616                 // fetch all entry
5617                 DbSourceProxy src = otherdb.get(0);
5618                 fetchr = new JMenuItem(MessageManager.formatMessage(
5619                         "label.fetch_all_param", new String[]
5620                         { src.getDbSource() }));
5621                 fetchr.addActionListener(new ActionListener()
5622                 {
5623                   @Override
5624                   public void actionPerformed(ActionEvent e)
5625                   {
5626                     new Thread(new Runnable()
5627                     {
5628
5629                       @Override
5630                       public void run()
5631                       {
5632                         new jalview.ws.DBRefFetcher(alignPanel.av
5633                                 .getSequenceSelection(),
5634                                 alignPanel.alignFrame, dassource)
5635                                 .fetchDBRefs(false);
5636                       }
5637                     }).start();
5638                   }
5639                 });
5640
5641                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5642                 dfetch.add(fetchr);
5643                 comp++;
5644                 // and then build the rest of the individual menus
5645                 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5646                 icomp = 0;
5647                 String imname = null;
5648                 int i = 0;
5649                 for (DbSourceProxy sproxy : otherdb)
5650                 {
5651                   String dbname = sproxy.getDbName();
5652                   String sname = dbname.length() > 5 ? dbname.substring(0,
5653                           5) + "..." : dbname;
5654                   String msname = dbname.length() > 10 ? dbname.substring(
5655                           0, 10) + "..." : dbname;
5656                   if (imname == null)
5657                   {
5658                     imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5659                   }
5660                   fetchr = new JMenuItem(msname);
5661                   final DbSourceProxy[] dassrc =
5662                   { sproxy };
5663                   fetchr.addActionListener(new ActionListener()
5664                   {
5665
5666                     @Override
5667                     public void actionPerformed(ActionEvent e)
5668                     {
5669                       new Thread(new Runnable()
5670                       {
5671
5672                         @Override
5673                         public void run()
5674                         {
5675                           new jalview.ws.DBRefFetcher(alignPanel.av
5676                                   .getSequenceSelection(),
5677                                   alignPanel.alignFrame, dassrc)
5678                                   .fetchDBRefs(false);
5679                         }
5680                       }).start();
5681                     }
5682
5683                   });
5684                   fetchr.setToolTipText("<html>"
5685                           + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5686                   ifetch.add(fetchr);
5687                   ++i;
5688                   if (++icomp >= mcomp || i == (otherdb.size()))
5689                   {
5690                     ifetch.setText(MessageManager.formatMessage(
5691                             "label.source_to_target", imname, sname));
5692                     dfetch.add(ifetch);
5693                     ifetch = new JMenu();
5694                     imname = null;
5695                     icomp = 0;
5696                     comp++;
5697                   }
5698                 }
5699               }
5700               ++dbi;
5701               if (comp >= mcomp || dbi >= (dbclasses.length))
5702               {
5703                 dfetch.setText(MessageManager.formatMessage(
5704                         "label.source_to_target", mname, dbclass));
5705                 rfetch.add(dfetch);
5706                 dfetch = new JMenu();
5707                 mname = null;
5708                 comp = 0;
5709               }
5710             }
5711           }
5712         });
5713       }
5714     }).start();
5715
5716   }
5717
5718   /**
5719    * Left justify the whole alignment.
5720    */
5721   @Override
5722   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5723   {
5724     AlignmentI al = viewport.getAlignment();
5725     al.justify(false);
5726     viewport.firePropertyChange("alignment", null, al);
5727   }
5728
5729   /**
5730    * Right justify the whole alignment.
5731    */
5732   @Override
5733   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5734   {
5735     AlignmentI al = viewport.getAlignment();
5736     al.justify(true);
5737     viewport.firePropertyChange("alignment", null, al);
5738   }
5739
5740   public void setShowSeqFeatures(boolean b)
5741   {
5742     showSeqFeatures.setSelected(true);
5743     viewport.setShowSequenceFeatures(true);
5744   }
5745
5746   /*
5747    * (non-Javadoc)
5748    *
5749    * @see
5750    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5751    * awt.event.ActionEvent)
5752    */
5753   @Override
5754   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5755   {
5756     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5757     alignPanel.paintAlignment(true);
5758   }
5759
5760   /*
5761    * (non-Javadoc)
5762    *
5763    * @see
5764    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5765    * .ActionEvent)
5766    */
5767   @Override
5768   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5769   {
5770     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5771     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5772
5773   }
5774
5775   /*
5776    * (non-Javadoc)
5777    *
5778    * @see
5779    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5780    * .event.ActionEvent)
5781    */
5782   @Override
5783   protected void showGroupConservation_actionPerformed(ActionEvent e)
5784   {
5785     viewport.setShowGroupConservation(showGroupConservation.getState());
5786     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5787   }
5788
5789   /*
5790    * (non-Javadoc)
5791    *
5792    * @see
5793    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5794    * .event.ActionEvent)
5795    */
5796   @Override
5797   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5798   {
5799     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5800     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5801   }
5802
5803   /*
5804    * (non-Javadoc)
5805    *
5806    * @see
5807    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5808    * .event.ActionEvent)
5809    */
5810   @Override
5811   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5812   {
5813     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5814     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5815   }
5816
5817   @Override
5818   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5819   {
5820     showSequenceLogo.setState(true);
5821     viewport.setShowSequenceLogo(true);
5822     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5823     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5824   }
5825
5826   @Override
5827   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5828   {
5829     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5830   }
5831
5832   /*
5833    * (non-Javadoc)
5834    *
5835    * @see
5836    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5837    * .event.ActionEvent)
5838    */
5839   @Override
5840   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5841   {
5842     if (avc.makeGroupsFromSelection())
5843     {
5844       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5845       alignPanel.updateAnnotation();
5846       alignPanel.paintAlignment(true);
5847     }
5848   }
5849
5850   @Override
5851   protected void createGroup_actionPerformed(ActionEvent e)
5852   {
5853     if (avc.createGroup())
5854     {
5855       alignPanel.alignmentChanged();
5856     }
5857   }
5858
5859   @Override
5860   protected void unGroup_actionPerformed(ActionEvent e)
5861   {
5862     if (avc.unGroup())
5863     {
5864       alignPanel.alignmentChanged();
5865     }
5866   }
5867
5868   /**
5869    * make the given alignmentPanel the currently selected tab
5870    *
5871    * @param alignmentPanel
5872    */
5873   public void setDisplayedView(AlignmentPanel alignmentPanel)
5874   {
5875     if (!viewport.getSequenceSetId().equals(
5876             alignmentPanel.av.getSequenceSetId()))
5877     {
5878       throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5879     }
5880     if (tabbedPane != null
5881             & alignPanels.indexOf(alignmentPanel) != tabbedPane
5882                     .getSelectedIndex())
5883     {
5884       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5885     }
5886   }
5887
5888   /**
5889    * Action on selection of menu options to Show or Hide annotations.
5890    *
5891    * @param visible
5892    * @param forSequences
5893    *          update sequence-related annotations
5894    * @param forAlignment
5895    *          update non-sequence-related annotations
5896    */
5897   @Override
5898   protected void setAnnotationsVisibility(boolean visible,
5899           boolean forSequences, boolean forAlignment)
5900   {
5901     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5902             .getAlignmentAnnotation())
5903     {
5904       boolean apply = (aa.sequenceRef == null && forAlignment)
5905               || (aa.sequenceRef != null && forSequences);
5906       if (apply)
5907       {
5908         aa.visible = visible;
5909       }
5910     }
5911     alignPanel.validateAnnotationDimensions(false);
5912     alignPanel.alignmentChanged();
5913   }
5914
5915   /**
5916    * Store selected annotation sort order for the view and repaint.
5917    */
5918   @Override
5919   protected void sortAnnotations_actionPerformed()
5920   {
5921     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5922     this.alignPanel.av
5923             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5924     alignPanel.paintAlignment(true);
5925   }
5926
5927   /**
5928    *
5929    * @return alignment panels in this alignemnt frame
5930    */
5931   public List<AlignmentViewPanel> getAlignPanels()
5932   {
5933     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5934   }
5935 }
5936
5937 class PrintThread extends Thread
5938 {
5939   AlignmentPanel ap;
5940
5941   public PrintThread(AlignmentPanel ap)
5942   {
5943     this.ap = ap;
5944   }
5945
5946   static PageFormat pf;
5947
5948   @Override
5949   public void run()
5950   {
5951     PrinterJob printJob = PrinterJob.getPrinterJob();
5952
5953     if (pf != null)
5954     {
5955       printJob.setPrintable(ap, pf);
5956     }
5957     else
5958     {
5959       printJob.setPrintable(ap);
5960     }
5961
5962     if (printJob.printDialog())
5963     {
5964       try
5965       {
5966         printJob.print();
5967       } catch (Exception PrintException)
5968       {
5969         PrintException.printStackTrace();
5970       }
5971     }
5972   }
5973 }