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.AlignmentUtils.MappingResult;
  27 import jalview.analysis.Conservation;
  28 import jalview.analysis.CrossRef;
  29 import jalview.analysis.Dna;
  30 import jalview.analysis.ParseProperties;
  31 import jalview.analysis.SequenceIdMatcher;
  32 import jalview.api.AlignViewControllerGuiI;
  33 import jalview.api.AlignViewControllerI;
  34 import jalview.api.AlignViewportI;
  35 import jalview.api.AlignmentViewPanel;
  36 import jalview.api.analysis.ScoreModelI;
  37 import jalview.bin.Cache;
  38 import jalview.commands.CommandI;
  39 import jalview.commands.EditCommand;
  40 import jalview.commands.EditCommand.Action;
  41 import jalview.commands.OrderCommand;
  42 import jalview.commands.RemoveGapColCommand;
  43 import jalview.commands.RemoveGapsCommand;
  44 import jalview.commands.SlideSequencesCommand;
  45 import jalview.commands.TrimRegionCommand;
  46 import jalview.datamodel.AlignedCodonFrame;
  47 import jalview.datamodel.Alignment;
  48 import jalview.datamodel.AlignmentAnnotation;
  49 import jalview.datamodel.AlignmentI;
  50 import jalview.datamodel.AlignmentOrder;
  51 import jalview.datamodel.AlignmentView;
  52 import jalview.datamodel.ColumnSelection;
  53 import jalview.datamodel.PDBEntry;
  54 import jalview.datamodel.SeqCigar;
  55 import jalview.datamodel.Sequence;
  56 import jalview.datamodel.SequenceGroup;
  57 import jalview.datamodel.SequenceI;
  58 import jalview.io.AlignmentProperties;
  59 import jalview.io.AnnotationFile;
  60 import jalview.io.FeaturesFile;
  61 import jalview.io.FileLoader;
  62 import jalview.io.FormatAdapter;
  63 import jalview.io.HTMLOutput;
  64 import jalview.io.IdentifyFile;
  65 import jalview.io.JalviewFileChooser;
  66 import jalview.io.JalviewFileView;
  67 import jalview.io.JnetAnnotationMaker;
  68 import jalview.io.NewickFile;
  69 import jalview.io.TCoffeeScoreFile;
  70 import jalview.jbgui.GAlignFrame;
  71 import jalview.schemes.Blosum62ColourScheme;
  72 import jalview.schemes.BuriedColourScheme;
  73 import jalview.schemes.ClustalxColourScheme;
  74 import jalview.schemes.ColourSchemeI;
  75 import jalview.schemes.ColourSchemeProperty;
  76 import jalview.schemes.HelixColourScheme;
  77 import jalview.schemes.HydrophobicColourScheme;
  78 import jalview.schemes.NucleotideColourScheme;
  79 import jalview.schemes.PIDColourScheme;
  80 import jalview.schemes.PurinePyrimidineColourScheme;
  81 import jalview.schemes.RNAHelicesColourChooser;
  82 import jalview.schemes.ResidueProperties;
  83 import jalview.schemes.StrandColourScheme;
  84 import jalview.schemes.TCoffeeColourScheme;
  85 import jalview.schemes.TaylorColourScheme;
  86 import jalview.schemes.TurnColourScheme;
  87 import jalview.schemes.UserColourScheme;
  88 import jalview.schemes.ZappoColourScheme;
  89 import jalview.structure.StructureSelectionManager;
  90 import jalview.util.MessageManager;
  91 import jalview.viewmodel.AlignmentViewport;
  92 import jalview.ws.jws1.Discoverer;
  93 import jalview.ws.jws2.Jws2Discoverer;
  94 import jalview.ws.jws2.jabaws2.Jws2Instance;
  95 import jalview.ws.seqfetcher.DbSourceProxy;
  96
  97 import java.awt.BorderLayout;
  98 import java.awt.Component;
  99 import java.awt.GridLayout;
 100 import java.awt.Rectangle;
 101 import java.awt.Toolkit;
 102 import java.awt.datatransfer.Clipboard;
 103 import java.awt.datatransfer.DataFlavor;
 104 import java.awt.datatransfer.StringSelection;
 105 import java.awt.datatransfer.Transferable;
 106 import java.awt.dnd.DnDConstants;
 107 import java.awt.dnd.DropTargetDragEvent;
 108 import java.awt.dnd.DropTargetDropEvent;
 109 import java.awt.dnd.DropTargetEvent;
 110 import java.awt.dnd.DropTargetListener;
 111 import java.awt.event.ActionEvent;
 112 import java.awt.event.ActionListener;
 113 import java.awt.event.KeyAdapter;
 114 import java.awt.event.KeyEvent;
 115 import java.awt.event.MouseAdapter;
 116 import java.awt.event.MouseEvent;
 117 import java.awt.print.PageFormat;
 118 import java.awt.print.PrinterJob;
 119 import java.beans.PropertyChangeEvent;
 120 import java.io.File;
 121 import java.net.URL;
 122 import java.util.ArrayList;
 123 import java.util.Arrays;
 124 import java.util.Enumeration;
 125 import java.util.Hashtable;
 126 import java.util.List;
 127 import java.util.Set;
 128 import java.util.Vector;
 129
 130 import javax.swing.JButton;
 131 import javax.swing.JCheckBoxMenuItem;
 132 import javax.swing.JEditorPane;
 133 import javax.swing.JInternalFrame;
 134 import javax.swing.JLabel;
 135 import javax.swing.JLayeredPane;
 136 import javax.swing.JMenu;
 137 import javax.swing.JMenuItem;
 138 import javax.swing.JOptionPane;
 139 import javax.swing.JPanel;
 140 import javax.swing.JProgressBar;
 141 import javax.swing.JRadioButtonMenuItem;
 142 import javax.swing.JScrollPane;
 143 import javax.swing.SwingUtilities;
 144
 145 /**
 146  * DOCUMENT ME!
 147  *
 148  * @author $author$
 149  * @version $Revision$
 150  */
 151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 152         IProgressIndicator, AlignViewControllerGuiI
 153 {
 154
 155   public static final int DEFAULT_WIDTH = 700;
 156
 157   public static final int DEFAULT_HEIGHT = 500;
 158
 159   /*
 160    * The currently displayed panel (selected tabbed view if more than one)
 161    */
 162   public AlignmentPanel alignPanel;
 163
 164   AlignViewport viewport;
 165
 166   public AlignViewControllerI avc;
 167
 168   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 169
 170   /**
 171    * Last format used to load or save alignments in this window
 172    */
 173   String currentFileFormat = null;
 174
 175   /**
 176    * Current filename for this alignment
 177    */
 178   String fileName = null;
 179
 180   /**
 181    * Creates a new AlignFrame object with specific width and height.
 182    *
 183    * @param al
 184    * @param width
 185    * @param height
 186    */
 187   public AlignFrame(AlignmentI al, int width, int height)
 188   {
 189     this(al, null, width, height);
 190   }
 191
 192   /**
 193    * Creates a new AlignFrame object with specific width, height and
 194    * sequenceSetId
 195    *
 196    * @param al
 197    * @param width
 198    * @param height
 199    * @param sequenceSetId
 200    */
 201   public AlignFrame(AlignmentI al, int width, int height,
 202           String sequenceSetId)
 203   {
 204     this(al, null, width, height, sequenceSetId);
 205   }
 206
 207   /**
 208    * Creates a new AlignFrame object with specific width, height and
 209    * sequenceSetId
 210    *
 211    * @param al
 212    * @param width
 213    * @param height
 214    * @param sequenceSetId
 215    * @param viewId
 216    */
 217   public AlignFrame(AlignmentI al, int width, int height,
 218           String sequenceSetId, String viewId)
 219   {
 220     this(al, null, width, height, sequenceSetId, viewId);
 221   }
 222
 223   /**
 224    * new alignment window with hidden columns
 225    *
 226    * @param al
 227    *          AlignmentI
 228    * @param hiddenColumns
 229    *          ColumnSelection or null
 230    * @param width
 231    *          Width of alignment frame
 232    * @param height
 233    *          height of frame.
 234    */
 235   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 236           int width, int height)
 237   {
 238     this(al, hiddenColumns, width, height, null);
 239   }
 240
 241   /**
 242    * Create alignment frame for al with hiddenColumns, a specific width and
 243    * height, and specific sequenceId
 244    *
 245    * @param al
 246    * @param hiddenColumns
 247    * @param width
 248    * @param height
 249    * @param sequenceSetId
 250    *          (may be null)
 251    */
 252   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 253           int width, int height, String sequenceSetId)
 254   {
 255     this(al, hiddenColumns, width, height, sequenceSetId, null);
 256   }
 257
 258   /**
 259    * Create alignment frame for al with hiddenColumns, a specific width and
 260    * height, and specific sequenceId
 261    *
 262    * @param al
 263    * @param hiddenColumns
 264    * @param width
 265    * @param height
 266    * @param sequenceSetId
 267    *          (may be null)
 268    * @param viewId
 269    *          (may be null)
 270    */
 271   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 272           int width, int height, String sequenceSetId, String viewId)
 273   {
 274     setSize(width, height);
 275
 276     if (al.getDataset() == null)
 277     {
 278       al.setDataset(null);
 279     }
 280
 281     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 282
 283     alignPanel = new AlignmentPanel(this, viewport);
 284
 285
 286     addAlignmentPanel(alignPanel, true);
 287     init();
 288   }
 289
 290   /**
 291    * Make a new AlignFrame from existing alignmentPanels
 292    *
 293    * @param ap
 294    *          AlignmentPanel
 295    * @param av
 296    *          AlignViewport
 297    */
 298   public AlignFrame(AlignmentPanel ap)
 299   {
 300     viewport = ap.av;
 301     alignPanel = ap;
 302     addAlignmentPanel(ap, false);
 303     init();
 304   }
 305
 306   /**
 307    * initalise the alignframe from the underlying viewport data and the
 308    * configurations
 309    */
 310   void init()
 311   {
 312     avc = new jalview.controller.AlignViewController(this, viewport,
 313             alignPanel);
 314     if (viewport.getAlignmentConservationAnnotation() == null)
 315     {
 316       BLOSUM62Colour.setEnabled(false);
 317       conservationMenuItem.setEnabled(false);
 318       modifyConservation.setEnabled(false);
 319       // PIDColour.setEnabled(false);
 320       // abovePIDThreshold.setEnabled(false);
 321       // modifyPID.setEnabled(false);
 322     }
 323
 324     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 325             "No sort");
 326
 327     if (sortby.equals("Id"))
 328     {
 329       sortIDMenuItem_actionPerformed(null);
 330     }
 331     else if (sortby.equals("Pairwise Identity"))
 332     {
 333       sortPairwiseMenuItem_actionPerformed(null);
 334     }
 335
 336     if (Desktop.desktop != null)
 337     {
 338       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 339       addServiceListeners();
 340       setGUINucleotide(viewport.getAlignment().isNucleotide());
 341     }
 342
 343     setMenusFromViewport(viewport);
 344     buildSortByAnnotationScoresMenu();
 345     buildTreeMenu();
 346
 347     if (viewport.wrapAlignment)
 348     {
 349       wrapMenuItem_actionPerformed(null);
 350     }
 351
 352     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 353     {
 354       this.overviewMenuItem_actionPerformed(null);
 355     }
 356
 357     addKeyListener();
 358
 359   }
 360
 361   /**
 362    * Change the filename and format for the alignment, and enable the 'reload'
 363    * button functionality.
 364    *
 365    * @param file
 366    *          valid filename
 367    * @param format
 368    *          format of file
 369    */
 370   public void setFileName(String file, String format)
 371   {
 372     fileName = file;
 373     currentFileFormat = format;
 374     reload.setEnabled(true);
 375   }
 376
 377   /**
 378    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 379    * events
 380    */
 381   void addKeyListener()
 382   {
 383     addKeyListener(new KeyAdapter()
 384     {
 385       @Override
 386       public void keyPressed(KeyEvent evt)
 387       {
 388         if (viewport.cursorMode
 389                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 390                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 391                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 392                 && Character.isDigit(evt.getKeyChar()))
 393         {
 394           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 395         }
 396
 397         switch (evt.getKeyCode())
 398         {
 399
 400         case 27: // escape key
 401           deselectAllSequenceMenuItem_actionPerformed(null);
 402
 403           break;
 404
 405         case KeyEvent.VK_DOWN:
 406           if (evt.isAltDown() || !viewport.cursorMode)
 407           {
 408             moveSelectedSequences(false);
 409           }
 410           if (viewport.cursorMode)
 411           {
 412             alignPanel.seqPanel.moveCursor(0, 1);
 413           }
 414           break;
 415
 416         case KeyEvent.VK_UP:
 417           if (evt.isAltDown() || !viewport.cursorMode)
 418           {
 419             moveSelectedSequences(true);
 420           }
 421           if (viewport.cursorMode)
 422           {
 423             alignPanel.seqPanel.moveCursor(0, -1);
 424           }
 425
 426           break;
 427
 428         case KeyEvent.VK_LEFT:
 429           if (evt.isAltDown() || !viewport.cursorMode)
 430           {
 431             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 432           }
 433           else
 434           {
 435             alignPanel.seqPanel.moveCursor(-1, 0);
 436           }
 437
 438           break;
 439
 440         case KeyEvent.VK_RIGHT:
 441           if (evt.isAltDown() || !viewport.cursorMode)
 442           {
 443             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 444           }
 445           else
 446           {
 447             alignPanel.seqPanel.moveCursor(1, 0);
 448           }
 449           break;
 450
 451         case KeyEvent.VK_SPACE:
 452           if (viewport.cursorMode)
 453           {
 454             alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 455                     || evt.isShiftDown() || evt.isAltDown());
 456           }
 457           break;
 458
 459         // case KeyEvent.VK_A:
 460         // if (viewport.cursorMode)
 461         // {
 462         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 463         // //System.out.println("A");
 464         // }
 465         // break;
 466         /*
 467          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 468          * System.out.println("closing bracket"); } break;
 469          */
 470         case KeyEvent.VK_DELETE:
 471         case KeyEvent.VK_BACK_SPACE:
 472           if (!viewport.cursorMode)
 473           {
 474             cut_actionPerformed(null);
 475           }
 476           else
 477           {
 478             alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 479                     || evt.isShiftDown() || evt.isAltDown());
 480           }
 481
 482           break;
 483
 484         case KeyEvent.VK_S:
 485           if (viewport.cursorMode)
 486           {
 487             alignPanel.seqPanel.setCursorRow();
 488           }
 489           break;
 490         case KeyEvent.VK_C:
 491           if (viewport.cursorMode && !evt.isControlDown())
 492           {
 493             alignPanel.seqPanel.setCursorColumn();
 494           }
 495           break;
 496         case KeyEvent.VK_P:
 497           if (viewport.cursorMode)
 498           {
 499             alignPanel.seqPanel.setCursorPosition();
 500           }
 501           break;
 502
 503         case KeyEvent.VK_ENTER:
 504         case KeyEvent.VK_COMMA:
 505           if (viewport.cursorMode)
 506           {
 507             alignPanel.seqPanel.setCursorRowAndColumn();
 508           }
 509           break;
 510
 511         case KeyEvent.VK_Q:
 512           if (viewport.cursorMode)
 513           {
 514             alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 515           }
 516           break;
 517         case KeyEvent.VK_M:
 518           if (viewport.cursorMode)
 519           {
 520             alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 521           }
 522           break;
 523
 524         case KeyEvent.VK_F2:
 525           viewport.cursorMode = !viewport.cursorMode;
 526           statusBar.setText(MessageManager.formatMessage(
 527                   "label.keyboard_editing_mode", new String[]
 528                   { (viewport.cursorMode ? "on" : "off") }));
 529           if (viewport.cursorMode)
 530           {
 531             alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 532             alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 533           }
 534           alignPanel.seqPanel.seqCanvas.repaint();
 535           break;
 536
 537         case KeyEvent.VK_F1:
 538           try
 539           {
 540             Help.showHelpWindow();
 541           } catch (Exception ex)
 542           {
 543             ex.printStackTrace();
 544           }
 545           break;
 546         case KeyEvent.VK_H:
 547         {
 548           boolean toggleSeqs = !evt.isControlDown();
 549           boolean toggleCols = !evt.isShiftDown();
 550           toggleHiddenRegions(toggleSeqs, toggleCols);
 551           break;
 552         }
 553         case KeyEvent.VK_PAGE_UP:
 554           if (viewport.wrapAlignment)
 555           {
 556             alignPanel.scrollUp(true);
 557           }
 558           else
 559           {
 560             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 561                     - viewport.endSeq + viewport.startSeq);
 562           }
 563           break;
 564         case KeyEvent.VK_PAGE_DOWN:
 565           if (viewport.wrapAlignment)
 566           {
 567             alignPanel.scrollUp(false);
 568           }
 569           else
 570           {
 571             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 572                     + viewport.endSeq - viewport.startSeq);
 573           }
 574           break;
 575         }
 576       }
 577
 578       @Override
 579       public void keyReleased(KeyEvent evt)
 580       {
 581         switch (evt.getKeyCode())
 582         {
 583         case KeyEvent.VK_LEFT:
 584           if (evt.isAltDown() || !viewport.cursorMode)
 585           {
 586             viewport.firePropertyChange("alignment", null, viewport
 587                     .getAlignment().getSequences());
 588           }
 589           break;
 590
 591         case KeyEvent.VK_RIGHT:
 592           if (evt.isAltDown() || !viewport.cursorMode)
 593           {
 594             viewport.firePropertyChange("alignment", null, viewport
 595                     .getAlignment().getSequences());
 596           }
 597           break;
 598         }
 599       }
 600     });
 601   }
 602
 603   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 604   {
 605     ap.alignFrame = this;
 606     avc = new jalview.controller.AlignViewController(this, viewport,
 607             alignPanel);
 608
 609     alignPanels.add(ap);
 610
 611     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 612
 613     int aSize = alignPanels.size();
 614
 615     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 616
 617     if (aSize == 1 && ap.av.viewName == null)
 618     {
 619       this.getContentPane().add(ap, BorderLayout.CENTER);
 620     }
 621     else
 622     {
 623       if (aSize == 2)
 624       {
 625         setInitialTabVisible();
 626       }
 627
 628       expandViews.setEnabled(true);
 629       gatherViews.setEnabled(true);
 630       tabbedPane.addTab(ap.av.viewName, ap);
 631
 632       ap.setVisible(false);
 633     }
 634
 635     if (newPanel)
 636     {
 637       if (ap.av.isPadGaps())
 638       {
 639         ap.av.getAlignment().padGaps();
 640       }
 641       ap.av.updateConservation(ap);
 642       ap.av.updateConsensus(ap);
 643       ap.av.updateStrucConsensus(ap);
 644     }
 645   }
 646
 647   public void setInitialTabVisible()
 648   {
 649     expandViews.setEnabled(true);
 650     gatherViews.setEnabled(true);
 651     tabbedPane.setVisible(true);
 652     AlignmentPanel first = alignPanels.get(0);
 653     tabbedPane.addTab(first.av.viewName, first);
 654     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 655   }
 656
 657   public AlignViewport getViewport()
 658   {
 659     return viewport;
 660   }
 661
 662   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 663   private void addServiceListeners()
 664   {
 665     final java.beans.PropertyChangeListener thisListener;
 666     Desktop.instance.addJalviewPropertyChangeListener("services",
 667             thisListener = new java.beans.PropertyChangeListener()
 668             {
 669               @Override
 670               public void propertyChange(PropertyChangeEvent evt)
 671               {
 672                 // // System.out.println("Discoverer property change.");
 673                 // if (evt.getPropertyName().equals("services"))
 674                 {
 675                   SwingUtilities.invokeLater(new Runnable()
 676                   {
 677
 678                     @Override
 679                     public void run()
 680                     {
 681                       System.err
 682                               .println("Rebuild WS Menu for service change");
 683                       BuildWebServiceMenu();
 684                     }
 685
 686                   });
 687                 }
 688               }
 689             });
 690     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 691     {
 692       @Override
 693       public void internalFrameClosed(
 694               javax.swing.event.InternalFrameEvent evt)
 695       {
 696         System.out.println("deregistering discoverer listener");
 697         Desktop.instance.removeJalviewPropertyChangeListener("services",
 698                 thisListener);
 699         closeMenuItem_actionPerformed(true);
 700       };
 701     });
 702     // Finally, build the menu once to get current service state
 703     new Thread(new Runnable()
 704     {
 705       @Override
 706       public void run()
 707       {
 708         BuildWebServiceMenu();
 709       }
 710     }).start();
 711   }
 712
 713   public void setGUINucleotide(boolean nucleotide)
 714   {
 715     showTranslation.setVisible(nucleotide);
 716     cdna.setVisible(!nucleotide);
 717     conservationMenuItem.setEnabled(!nucleotide);
 718     modifyConservation.setEnabled(!nucleotide);
 719     showGroupConservation.setEnabled(!nucleotide);
 720     rnahelicesColour.setEnabled(nucleotide);
 721     purinePyrimidineColour.setEnabled(nucleotide);
 722   }
 723
 724   /**
 725    * Builds codon mappings from this (protein) alignment to any compatible
 726    * nucleotide alignments. Mappings are built between sequences with the same
 727    * name and compatible lengths. Also makes the cDNA alignment a
 728    * CommandListener for the protein alignment so that edits are mirrored.
 729    */
 730   @Override
 731   protected void linkCdna_actionPerformed()
 732   {
 733     int linkedCount = 0;
 734     int alreadyLinkedCount = 0;
 735     final AlignmentI thisAlignment = this.alignPanel.getAlignment();
 736
 737     for (AlignFrame af : Desktop.getAlignFrames())
 738     {
 739       if (af.alignPanel != null)
 740       {
 741         final AlignmentI thatAlignment = af.alignPanel.getAlignment();
 742         if (thatAlignment.isNucleotide())
 743         {
 744           MappingResult mapped = AlignmentUtils.mapProteinToCdna(
 745                   thisAlignment, thatAlignment);
 746           if (mapped == MappingResult.AlreadyMapped)
 747           {
 748             alreadyLinkedCount++;
 749           }
 750           else if (mapped == MappingResult.Mapped)
 751           {
 752             final StructureSelectionManager ssm = StructureSelectionManager
 753                     .getStructureSelectionManager(Desktop.instance);
 754             ssm.addMappings(thisAlignment.getCodonFrames());
 755             // enable the next line to enable linked editing
 756             // ssm.addCommandListener(af.getViewport());
 757             linkedCount++;
 758           }
 759         }
 760       }
 761     }
 762     String msg = "";
 763     if (linkedCount == 0 && alreadyLinkedCount == 0)
 764     {
 765       msg = MessageManager.getString("label.no_cdna");
 766     }
 767     else if (linkedCount > 0)
 768     {
 769       msg = MessageManager.formatMessage("label.linked_cdna", linkedCount);
 770     }
 771     else
 772     {
 773       msg = MessageManager.formatMessage("label.cdna_all_linked",
 774               alreadyLinkedCount);
 775     }
 776     setStatus(msg);
 777   }
 778
 779   /**
 780    * Align any linked cDNA to match the alignment of this (protein) alignment.
 781    * Any mapped sequence regions will be realigned, unmapped sequences are not
 782    * affected.
 783    */
 784   @Override
 785   protected void alignCdna_actionPerformed()
 786   {
 787     int seqCount = 0;
 788     int alignCount = 0;
 789     final AlignmentI thisAlignment = this.alignPanel.getAlignment();
 790     for (AlignFrame af : Desktop.getAlignFrames())
 791     {
 792       if (af.alignPanel != null)
 793       {
 794         final AlignmentI thatAlignment = af.alignPanel.getAlignment();
 795         if (thatAlignment.isNucleotide())
 796         {
 797           int seqsAligned = thatAlignment.alignAs(thisAlignment);
 798           seqCount += seqsAligned;
 799           if (seqsAligned > 0)
 800           {
 801             af.alignPanel.alignmentChanged();
 802             alignCount++;
 803           }
 804         }
 805       }
 806     }
 807     setStatus(MessageManager.formatMessage("label.cdna_aligned", seqCount,
 808             alignCount));
 809   }
 810   /**
 811    * set up menus for the current viewport. This may be called after any
 812    * operation that affects the data in the current view (selection changed,
 813    * etc) to update the menus to reflect the new state.
 814    */
 815   public void setMenusForViewport()
 816   {
 817     setMenusFromViewport(viewport);
 818   }
 819
 820   /**
 821    * Need to call this method when tabs are selected for multiple views, or when
 822    * loading from Jalview2XML.java
 823    *
 824    * @param av
 825    *          AlignViewport
 826    */
 827   void setMenusFromViewport(AlignViewport av)
 828   {
 829     padGapsMenuitem.setSelected(av.isPadGaps());
 830     colourTextMenuItem.setSelected(av.showColourText);
 831     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 832     conservationMenuItem.setSelected(av.getConservationSelected());
 833     seqLimits.setSelected(av.getShowJVSuffix());
 834     idRightAlign.setSelected(av.rightAlignIds);
 835     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
 836     renderGapsMenuItem.setSelected(av.renderGaps);
 837     wrapMenuItem.setSelected(av.wrapAlignment);
 838     scaleAbove.setVisible(av.wrapAlignment);
 839     scaleLeft.setVisible(av.wrapAlignment);
 840     scaleRight.setVisible(av.wrapAlignment);
 841     annotationPanelMenuItem.setState(av.showAnnotation);
 842     /*
 843      * Show/hide annotations only enabled if annotation panel is shown
 844      */
 845     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 846     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 847     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 848     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 849     viewBoxesMenuItem.setSelected(av.showBoxes);
 850     viewTextMenuItem.setSelected(av.showText);
 851     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 852     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 853     showGroupConservation.setSelected(av.isShowGroupConservation());
 854     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 855     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 856     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 857
 858     setColourSelected(ColourSchemeProperty.getColourName(av
 859             .getGlobalColourScheme()));
 860
 861     showSeqFeatures.setSelected(av.showSequenceFeatures);
 862     hiddenMarkers.setState(av.showHiddenMarkers);
 863     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 864     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
 865     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
 866     autoCalculate.setSelected(av.autoCalculateConsensus);
 867     sortByTree.setSelected(av.sortByTree);
 868     listenToViewSelections.setSelected(av.followSelection);
 869     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 870     rnahelicesColour
 871             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 872     setShowProductsEnabled();
 873     updateEditMenuBar();
 874   }
 875
 876   // methods for implementing IProgressIndicator
 877   // need to refactor to a reusable stub class
 878   Hashtable progressBars, progressBarHandlers;
 879
 880   /*
 881    * (non-Javadoc)
 882    *
 883    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 884    */
 885   @Override
 886   public void setProgressBar(String message, long id)
 887   {
 888     if (progressBars == null)
 889     {
 890       progressBars = new Hashtable();
 891       progressBarHandlers = new Hashtable();
 892     }
 893
 894     JPanel progressPanel;
 895     Long lId = new Long(id);
 896     GridLayout layout = (GridLayout) statusPanel.getLayout();
 897     if (progressBars.get(lId) != null)
 898     {
 899       progressPanel = (JPanel) progressBars.get(new Long(id));
 900       statusPanel.remove(progressPanel);
 901       progressBars.remove(lId);
 902       progressPanel = null;
 903       if (message != null)
 904       {
 905         statusBar.setText(message);
 906       }
 907       if (progressBarHandlers.contains(lId))
 908       {
 909         progressBarHandlers.remove(lId);
 910       }
 911       layout.setRows(layout.getRows() - 1);
 912     }
 913     else
 914     {
 915       progressPanel = new JPanel(new BorderLayout(10, 5));
 916
 917       JProgressBar progressBar = new JProgressBar();
 918       progressBar.setIndeterminate(true);
 919
 920       progressPanel.add(new JLabel(message), BorderLayout.WEST);
 921       progressPanel.add(progressBar, BorderLayout.CENTER);
 922
 923       layout.setRows(layout.getRows() + 1);
 924       statusPanel.add(progressPanel);
 925
 926       progressBars.put(lId, progressPanel);
 927     }
 928     // update GUI
 929     // setMenusForViewport();
 930     validate();
 931   }
 932
 933   @Override
 934   public void registerHandler(final long id,
 935           final IProgressIndicatorHandler handler)
 936   {
 937     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
 938     {
 939       throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
 940     }
 941     progressBarHandlers.put(new Long(id), handler);
 942     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
 943     if (handler.canCancel())
 944     {
 945       JButton cancel = new JButton(
 946               MessageManager.getString("action.cancel"));
 947       final IProgressIndicator us = this;
 948       cancel.addActionListener(new ActionListener()
 949       {
 950
 951         @Override
 952         public void actionPerformed(ActionEvent e)
 953         {
 954           handler.cancelActivity(id);
 955           us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
 956         }
 957       });
 958       progressPanel.add(cancel, BorderLayout.EAST);
 959     }
 960   }
 961
 962   /**
 963    *
 964    * @return true if any progress bars are still active
 965    */
 966   @Override
 967   public boolean operationInProgress()
 968   {
 969     if (progressBars != null && progressBars.size() > 0)
 970     {
 971       return true;
 972     }
 973     return false;
 974   }
 975
 976   @Override
 977   public void setStatus(String text)
 978   {
 979     statusBar.setText(text);
 980   };
 981
 982   /*
 983    * Added so Castor Mapping file can obtain Jalview Version
 984    */
 985   public String getVersion()
 986   {
 987     return jalview.bin.Cache.getProperty("VERSION");
 988   }
 989
 990   public FeatureRenderer getFeatureRenderer()
 991   {
 992     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
 993   }
 994
 995   @Override
 996   public void fetchSequence_actionPerformed(ActionEvent e)
 997   {
 998     new SequenceFetcher(this);
 999   }
1000
1001   @Override
1002   public void addFromFile_actionPerformed(ActionEvent e)
1003   {
1004     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1005   }
1006
1007   @Override
1008   public void reload_actionPerformed(ActionEvent e)
1009   {
1010     if (fileName != null)
1011     {
1012       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1013       // originating file's format
1014       // TODO: work out how to recover feature settings for correct view(s) when
1015       // file is reloaded.
1016       if (currentFileFormat.equals("Jalview"))
1017       {
1018         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1019         for (int i = 0; i < frames.length; i++)
1020         {
1021           if (frames[i] instanceof AlignFrame && frames[i] != this
1022                   && ((AlignFrame) frames[i]).fileName != null
1023                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1024           {
1025             try
1026             {
1027               frames[i].setSelected(true);
1028               Desktop.instance.closeAssociatedWindows();
1029             } catch (java.beans.PropertyVetoException ex)
1030             {
1031             }
1032           }
1033
1034         }
1035         Desktop.instance.closeAssociatedWindows();
1036
1037         FileLoader loader = new FileLoader();
1038         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1039         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1040       }
1041       else
1042       {
1043         Rectangle bounds = this.getBounds();
1044
1045         FileLoader loader = new FileLoader();
1046         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1047         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1048                 protocol, currentFileFormat);
1049
1050         newframe.setBounds(bounds);
1051         if (featureSettings != null && featureSettings.isShowing())
1052         {
1053           final Rectangle fspos = featureSettings.frame.getBounds();
1054           // TODO: need a 'show feature settings' function that takes bounds -
1055           // need to refactor Desktop.addFrame
1056           newframe.featureSettings_actionPerformed(null);
1057           final FeatureSettings nfs = newframe.featureSettings;
1058           SwingUtilities.invokeLater(new Runnable()
1059           {
1060             @Override
1061             public void run()
1062             {
1063               nfs.frame.setBounds(fspos);
1064             }
1065           });
1066           this.featureSettings.close();
1067           this.featureSettings = null;
1068         }
1069         this.closeMenuItem_actionPerformed(true);
1070       }
1071     }
1072   }
1073
1074   @Override
1075   public void addFromText_actionPerformed(ActionEvent e)
1076   {
1077     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
1078   }
1079
1080   @Override
1081   public void addFromURL_actionPerformed(ActionEvent e)
1082   {
1083     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1084   }
1085
1086   @Override
1087   public void save_actionPerformed(ActionEvent e)
1088   {
1089     if (fileName == null
1090             || (currentFileFormat == null || !jalview.io.FormatAdapter
1091                     .isValidIOFormat(currentFileFormat, true))
1092             || fileName.startsWith("http"))
1093     {
1094       saveAs_actionPerformed(null);
1095     }
1096     else
1097     {
1098       saveAlignment(fileName, currentFileFormat);
1099     }
1100   }
1101
1102   /**
1103    * DOCUMENT ME!
1104    *
1105    * @param e
1106    *          DOCUMENT ME!
1107    */
1108   @Override
1109   public void saveAs_actionPerformed(ActionEvent e)
1110   {
1111     JalviewFileChooser chooser = new JalviewFileChooser(
1112             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1113             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1114             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1115             currentFileFormat, false);
1116
1117     chooser.setFileView(new JalviewFileView());
1118     chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1119     chooser.setToolTipText(MessageManager.getString("action.save"));
1120
1121     int value = chooser.showSaveDialog(this);
1122
1123     if (value == JalviewFileChooser.APPROVE_OPTION)
1124     {
1125       currentFileFormat = chooser.getSelectedFormat();
1126       while (currentFileFormat == null)
1127       {
1128         JOptionPane
1129                 .showInternalMessageDialog(
1130                         Desktop.desktop,
1131                         MessageManager
1132                                 .getString("label.select_file_format_before_saving"),
1133                         MessageManager
1134                                 .getString("label.file_format_not_specified"),
1135                         JOptionPane.WARNING_MESSAGE);
1136         currentFileFormat = chooser.getSelectedFormat();
1137         value = chooser.showSaveDialog(this);
1138         if (value != JalviewFileChooser.APPROVE_OPTION)
1139         {
1140           return;
1141         }
1142       }
1143
1144       fileName = chooser.getSelectedFile().getPath();
1145
1146       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1147               currentFileFormat);
1148
1149       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1150       if (currentFileFormat.indexOf(" ") > -1)
1151       {
1152         currentFileFormat = currentFileFormat.substring(0,
1153                 currentFileFormat.indexOf(" "));
1154       }
1155       saveAlignment(fileName, currentFileFormat);
1156     }
1157   }
1158
1159   public boolean saveAlignment(String file, String format)
1160   {
1161     boolean success = true;
1162
1163     if (format.equalsIgnoreCase("Jalview"))
1164     {
1165       String shortName = title;
1166
1167       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1168       {
1169         shortName = shortName.substring(shortName
1170                 .lastIndexOf(java.io.File.separatorChar) + 1);
1171       }
1172
1173       success = new Jalview2XML().SaveAlignment(this, file, shortName);
1174
1175       statusBar.setText(MessageManager.formatMessage(
1176               "label.successfully_saved_to_file_in_format", new String[]
1177               { fileName, format }));
1178
1179     }
1180     else
1181     {
1182       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1183       {
1184         warningMessage("Cannot save file " + fileName + " using format "
1185                 + format, "Alignment output format not supported");
1186         saveAs_actionPerformed(null);
1187         // JBPNote need to have a raise_gui flag here
1188         return false;
1189       }
1190
1191       String[] omitHidden = null;
1192
1193       if (viewport.hasHiddenColumns())
1194       {
1195         int reply = JOptionPane
1196                 .showInternalConfirmDialog(
1197                         Desktop.desktop,
1198                         MessageManager
1199                                 .getString("label.alignment_contains_hidden_columns"),
1200                         MessageManager
1201                                 .getString("action.save_omit_hidden_columns"),
1202                         JOptionPane.YES_NO_OPTION,
1203                         JOptionPane.QUESTION_MESSAGE);
1204
1205         if (reply == JOptionPane.YES_OPTION)
1206         {
1207           omitHidden = viewport.getViewAsString(false);
1208         }
1209       }
1210       FormatAdapter f = new FormatAdapter();
1211       String output = f.formatSequences(format,
1212               viewport.getAlignment(), // class cast exceptions will
1213               // occur in the distant future
1214               omitHidden, f.getCacheSuffixDefault(format),
1215               viewport.getColumnSelection());
1216
1217       if (output == null)
1218       {
1219         success = false;
1220       }
1221       else
1222       {
1223         try
1224         {
1225           java.io.PrintWriter out = new java.io.PrintWriter(
1226                   new java.io.FileWriter(file));
1227
1228           out.print(output);
1229           out.close();
1230           this.setTitle(file);
1231           statusBar.setText(MessageManager.formatMessage(
1232                   "label.successfully_saved_to_file_in_format",
1233                   new String[]
1234                   { fileName, format }));
1235         } catch (Exception ex)
1236         {
1237           success = false;
1238           ex.printStackTrace();
1239         }
1240       }
1241     }
1242
1243     if (!success)
1244     {
1245       JOptionPane.showInternalMessageDialog(this, MessageManager
1246               .formatMessage("label.couldnt_save_file", new String[]
1247               { fileName }), MessageManager
1248               .getString("label.error_saving_file"),
1249               JOptionPane.WARNING_MESSAGE);
1250     }
1251
1252     return success;
1253   }
1254
1255   private void warningMessage(String warning, String title)
1256   {
1257     if (new jalview.util.Platform().isHeadless())
1258     {
1259       System.err.println("Warning: " + title + "\nWarning: " + warning);
1260
1261     }
1262     else
1263     {
1264       JOptionPane.showInternalMessageDialog(this, warning, title,
1265               JOptionPane.WARNING_MESSAGE);
1266     }
1267     return;
1268   }
1269
1270   /**
1271    * DOCUMENT ME!
1272    *
1273    * @param e
1274    *          DOCUMENT ME!
1275    */
1276   @Override
1277   protected void outputText_actionPerformed(ActionEvent e)
1278   {
1279     String[] omitHidden = null;
1280
1281     if (viewport.hasHiddenColumns())
1282     {
1283       int reply = JOptionPane
1284               .showInternalConfirmDialog(
1285                       Desktop.desktop,
1286                       MessageManager
1287                               .getString("label.alignment_contains_hidden_columns"),
1288                       MessageManager
1289                               .getString("action.save_omit_hidden_columns"),
1290                       JOptionPane.YES_NO_OPTION,
1291                       JOptionPane.QUESTION_MESSAGE);
1292
1293       if (reply == JOptionPane.YES_OPTION)
1294       {
1295         omitHidden = viewport.getViewAsString(false);
1296       }
1297     }
1298
1299     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1300     cap.setForInput(null);
1301
1302     try
1303     {
1304       cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1305               viewport.getAlignment(), omitHidden,
1306               viewport.getColumnSelection()));
1307       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1308               "label.alignment_output_command", new String[]
1309               { e.getActionCommand() }), 600, 500);
1310     } catch (OutOfMemoryError oom)
1311     {
1312       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1313       cap.dispose();
1314     }
1315
1316   }
1317
1318   /**
1319    * DOCUMENT ME!
1320    *
1321    * @param e
1322    *          DOCUMENT ME!
1323    */
1324   @Override
1325   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1326   {
1327     new HTMLOutput(alignPanel,
1328             alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1329             alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1330   }
1331
1332   public void createImageMap(File file, String image)
1333   {
1334     alignPanel.makePNGImageMap(file, image);
1335   }
1336
1337   /**
1338    * DOCUMENT ME!
1339    *
1340    * @param e
1341    *          DOCUMENT ME!
1342    */
1343   @Override
1344   public void createPNG(File f)
1345   {
1346     alignPanel.makePNG(f);
1347   }
1348
1349   /**
1350    * DOCUMENT ME!
1351    *
1352    * @param e
1353    *          DOCUMENT ME!
1354    */
1355   @Override
1356   public void createEPS(File f)
1357   {
1358     alignPanel.makeEPS(f);
1359   }
1360
1361   public void createSVG(File f)
1362   {
1363     alignPanel.makeSVG(f);
1364   }
1365   @Override
1366   public void pageSetup_actionPerformed(ActionEvent e)
1367   {
1368     PrinterJob printJob = PrinterJob.getPrinterJob();
1369     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1370   }
1371
1372   /**
1373    * DOCUMENT ME!
1374    *
1375    * @param e
1376    *          DOCUMENT ME!
1377    */
1378   @Override
1379   public void printMenuItem_actionPerformed(ActionEvent e)
1380   {
1381     // Putting in a thread avoids Swing painting problems
1382     PrintThread thread = new PrintThread(alignPanel);
1383     thread.start();
1384   }
1385
1386   @Override
1387   public void exportFeatures_actionPerformed(ActionEvent e)
1388   {
1389     new AnnotationExporter().exportFeatures(alignPanel);
1390   }
1391
1392   @Override
1393   public void exportAnnotations_actionPerformed(ActionEvent e)
1394   {
1395     new AnnotationExporter().exportAnnotations(alignPanel,
1396             viewport.showAnnotation ? viewport.getAlignment()
1397                     .getAlignmentAnnotation() : null, viewport
1398                     .getAlignment().getGroups(), ((Alignment) viewport
1399                     .getAlignment()).alignmentProperties);
1400   }
1401
1402   @Override
1403   public void associatedData_actionPerformed(ActionEvent e)
1404   {
1405     // Pick the tree file
1406     JalviewFileChooser chooser = new JalviewFileChooser(
1407             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1408     chooser.setFileView(new JalviewFileView());
1409     chooser.setDialogTitle(MessageManager
1410             .getString("label.load_jalview_annotations"));
1411     chooser.setToolTipText(MessageManager
1412             .getString("label.load_jalview_annotations"));
1413
1414     int value = chooser.showOpenDialog(null);
1415
1416     if (value == JalviewFileChooser.APPROVE_OPTION)
1417     {
1418       String choice = chooser.getSelectedFile().getPath();
1419       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1420       loadJalviewDataFile(choice, null, null, null);
1421     }
1422
1423   }
1424
1425   /**
1426    * Close the current view or all views in the alignment frame. If the frame
1427    * only contains one view then the alignment will be removed from memory.
1428    *
1429    * @param closeAllTabs
1430    */
1431   @Override
1432   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1433   {
1434     if (alignPanels != null && alignPanels.size() < 2)
1435     {
1436       closeAllTabs = true;
1437     }
1438
1439     try
1440     {
1441       if (alignPanels != null)
1442       {
1443         if (closeAllTabs)
1444         {
1445           if (this.isClosed())
1446           {
1447             // really close all the windows - otherwise wait till
1448             // setClosed(true) is called
1449             for (int i = 0; i < alignPanels.size(); i++)
1450             {
1451               AlignmentPanel ap = alignPanels.get(i);
1452               ap.closePanel();
1453             }
1454           }
1455         }
1456         else
1457         {
1458           closeView(alignPanel);
1459         }
1460       }
1461
1462       if (closeAllTabs)
1463       {
1464         this.setClosed(true);
1465       }
1466     } catch (Exception ex)
1467     {
1468       ex.printStackTrace();
1469     }
1470   }
1471
1472   /**
1473    * close alignPanel2 and shuffle tabs appropriately.
1474    *
1475    * @param alignPanel2
1476    */
1477   public void closeView(AlignmentPanel alignPanel2)
1478   {
1479     int index = tabbedPane.getSelectedIndex();
1480     int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1481     alignPanels.remove(alignPanel2);
1482     // Unnecessary
1483     // if (viewport == alignPanel2.av)
1484     // {
1485     // viewport = null;
1486     // }
1487     alignPanel2.closePanel();
1488     alignPanel2 = null;
1489
1490     tabbedPane.removeTabAt(closedindex);
1491     tabbedPane.validate();
1492
1493     if (index > closedindex || index == tabbedPane.getTabCount())
1494     {
1495       // modify currently selected tab index if necessary.
1496       index--;
1497     }
1498
1499     this.tabSelectionChanged(index);
1500   }
1501
1502   /**
1503    * DOCUMENT ME!
1504    */
1505   void updateEditMenuBar()
1506   {
1507
1508     if (viewport.getHistoryList().size() > 0)
1509     {
1510       undoMenuItem.setEnabled(true);
1511       CommandI command = viewport.getHistoryList().peek();
1512       undoMenuItem.setText(MessageManager.formatMessage(
1513               "label.undo_command", new String[]
1514               { command.getDescription() }));
1515     }
1516     else
1517     {
1518       undoMenuItem.setEnabled(false);
1519       undoMenuItem.setText(MessageManager.getString("action.undo"));
1520     }
1521
1522     if (viewport.getRedoList().size() > 0)
1523     {
1524       redoMenuItem.setEnabled(true);
1525
1526       CommandI command = viewport.getRedoList().peek();
1527       redoMenuItem.setText(MessageManager.formatMessage(
1528               "label.redo_command", new String[]
1529               { command.getDescription() }));
1530     }
1531     else
1532     {
1533       redoMenuItem.setEnabled(false);
1534       redoMenuItem.setText(MessageManager.getString("action.redo"));
1535     }
1536   }
1537
1538   public void addHistoryItem(CommandI command)
1539   {
1540     if (command.getSize() > 0)
1541     {
1542       viewport.addToHistoryList(command);
1543       viewport.clearRedoList();
1544       updateEditMenuBar();
1545       viewport.updateHiddenColumns();
1546       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1547       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1548       // viewport.getColumnSelection()
1549       // .getHiddenColumns().size() > 0);
1550     }
1551   }
1552
1553   /**
1554    *
1555    * @return alignment objects for all views
1556    */
1557   AlignmentI[] getViewAlignments()
1558   {
1559     if (alignPanels != null)
1560     {
1561       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1562       int i = 0;
1563       for (AlignmentPanel ap : alignPanels)
1564       {
1565         als[i++] = ap.av.getAlignment();
1566       }
1567       return als;
1568     }
1569     if (viewport != null)
1570     {
1571       return new AlignmentI[]
1572       { viewport.getAlignment() };
1573     }
1574     return null;
1575   }
1576
1577   /**
1578    * DOCUMENT ME!
1579    *
1580    * @param e
1581    *          DOCUMENT ME!
1582    */
1583   @Override
1584   protected void undoMenuItem_actionPerformed(ActionEvent e)
1585   {
1586     if (viewport.getHistoryList().isEmpty())
1587     {
1588       return;
1589     }
1590     CommandI command = viewport.getHistoryList().pop();
1591     viewport.addToRedoList(command);
1592     // TODO: execute command before adding to redo list / broadcasting?
1593     command.undoCommand(getViewAlignments());
1594
1595     AlignmentViewport originalSource = getOriginatingSource(command);
1596     updateEditMenuBar();
1597
1598     if (originalSource != null)
1599     {
1600       if (originalSource != viewport)
1601       {
1602         Cache.log
1603                 .warn("Implementation worry: mismatch of viewport origin for undo");
1604       }
1605       originalSource.updateHiddenColumns();
1606       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1607       // null
1608       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1609       // viewport.getColumnSelection()
1610       // .getHiddenColumns().size() > 0);
1611       originalSource.firePropertyChange("alignment", null, originalSource
1612               .getAlignment().getSequences());
1613     }
1614   }
1615
1616   /**
1617    * DOCUMENT ME!
1618    *
1619    * @param e
1620    *          DOCUMENT ME!
1621    */
1622   @Override
1623   protected void redoMenuItem_actionPerformed(ActionEvent e)
1624   {
1625     if (viewport.getRedoList().size() < 1)
1626     {
1627       return;
1628     }
1629
1630     CommandI command = viewport.getRedoList().pop();
1631     viewport.addToHistoryList(command);
1632     command.doCommand(getViewAlignments());
1633
1634     AlignmentViewport originalSource = getOriginatingSource(command);
1635     updateEditMenuBar();
1636
1637     if (originalSource != null)
1638     {
1639
1640       if (originalSource != viewport)
1641       {
1642         Cache.log
1643                 .warn("Implementation worry: mismatch of viewport origin for redo");
1644       }
1645       originalSource.updateHiddenColumns();
1646       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1647       // null
1648       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649       // viewport.getColumnSelection()
1650       // .getHiddenColumns().size() > 0);
1651       originalSource.firePropertyChange("alignment", null, originalSource
1652               .getAlignment().getSequences());
1653     }
1654   }
1655
1656   AlignmentViewport getOriginatingSource(CommandI command)
1657   {
1658     AlignmentViewport originalSource = null;
1659     // For sequence removal and addition, we need to fire
1660     // the property change event FROM the viewport where the
1661     // original alignment was altered
1662     AlignmentI al = null;
1663     if (command instanceof EditCommand)
1664     {
1665       EditCommand editCommand = (EditCommand) command;
1666       al = editCommand.getAlignment();
1667       List<Component> comps = PaintRefresher.components.get(viewport
1668               .getSequenceSetId());
1669
1670       for (Component comp : comps)
1671       {
1672         if (comp instanceof AlignmentPanel)
1673         {
1674           if (al == ((AlignmentPanel) comp).av.getAlignment())
1675           {
1676             originalSource = ((AlignmentPanel) comp).av;
1677             break;
1678           }
1679         }
1680       }
1681     }
1682
1683     if (originalSource == null)
1684     {
1685       // The original view is closed, we must validate
1686       // the current view against the closed view first
1687       if (al != null)
1688       {
1689         PaintRefresher.validateSequences(al, viewport.getAlignment());
1690       }
1691
1692       originalSource = viewport;
1693     }
1694
1695     return originalSource;
1696   }
1697
1698   /**
1699    * DOCUMENT ME!
1700    *
1701    * @param up
1702    *          DOCUMENT ME!
1703    */
1704   public void moveSelectedSequences(boolean up)
1705   {
1706     SequenceGroup sg = viewport.getSelectionGroup();
1707
1708     if (sg == null)
1709     {
1710       return;
1711     }
1712     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1713             viewport.getHiddenRepSequences(), up);
1714     alignPanel.paintAlignment(true);
1715
1716     final AlignViewportI peer = viewport.getCodingComplement();
1717     if (peer != null)
1718     {
1719       final SequenceGroup selectionGroup = peer.getSelectionGroup();
1720       if (selectionGroup != null)
1721       {
1722         peer.getAlignment().moveSelectedSequencesByOne(
1723                 peer.getSelectionGroup(), peer.getHiddenRepSequences(), up);
1724         ((AlignViewport) peer).getAlignPanel().paintAlignment(true);
1725       }
1726     }
1727   }
1728
1729   synchronized void slideSequences(boolean right, int size)
1730   {
1731     List<SequenceI> sg = new ArrayList<SequenceI>();
1732     if (viewport.cursorMode)
1733     {
1734       sg.add(viewport.getAlignment().getSequenceAt(
1735               alignPanel.seqPanel.seqCanvas.cursorY));
1736     }
1737     else if (viewport.getSelectionGroup() != null
1738             && viewport.getSelectionGroup().getSize() != viewport
1739                     .getAlignment().getHeight())
1740     {
1741       sg = viewport.getSelectionGroup().getSequences(
1742               viewport.getHiddenRepSequences());
1743     }
1744
1745     if (sg.size() < 1)
1746     {
1747       return;
1748     }
1749
1750     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1751
1752     for (SequenceI seq : viewport.getAlignment().getSequences())
1753     {
1754       if (!sg.contains(seq))
1755       {
1756         invertGroup.add(seq);
1757       }
1758     }
1759
1760     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1761
1762     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1763     for (int i = 0; i < invertGroup.size(); i++)
1764     {
1765       seqs2[i] = invertGroup.get(i);
1766     }
1767
1768     SlideSequencesCommand ssc;
1769     if (right)
1770     {
1771       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1772               size, viewport.getGapCharacter());
1773     }
1774     else
1775     {
1776       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1777               size, viewport.getGapCharacter());
1778     }
1779
1780     int groupAdjustment = 0;
1781     if (ssc.getGapsInsertedBegin() && right)
1782     {
1783       if (viewport.cursorMode)
1784       {
1785         alignPanel.seqPanel.moveCursor(size, 0);
1786       }
1787       else
1788       {
1789         groupAdjustment = size;
1790       }
1791     }
1792     else if (!ssc.getGapsInsertedBegin() && !right)
1793     {
1794       if (viewport.cursorMode)
1795       {
1796         alignPanel.seqPanel.moveCursor(-size, 0);
1797       }
1798       else
1799       {
1800         groupAdjustment = -size;
1801       }
1802     }
1803
1804     if (groupAdjustment != 0)
1805     {
1806       viewport.getSelectionGroup().setStartRes(
1807               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1808       viewport.getSelectionGroup().setEndRes(
1809               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1810     }
1811
1812     boolean appendHistoryItem = false;
1813     if (viewport.getHistoryList() != null
1814             && viewport.getHistoryList().size() > 0
1815             && viewport.getHistoryList().peek() instanceof SlideSequencesCommand)
1816     {
1817       appendHistoryItem = ssc
1818               .appendSlideCommand((SlideSequencesCommand) viewport
1819                       .getHistoryList()
1820                       .peek());
1821     }
1822
1823     if (!appendHistoryItem)
1824     {
1825       addHistoryItem(ssc);
1826     }
1827
1828     repaint();
1829   }
1830
1831   /**
1832    * DOCUMENT ME!
1833    *
1834    * @param e
1835    *          DOCUMENT ME!
1836    */
1837   @Override
1838   protected void copy_actionPerformed(ActionEvent e)
1839   {
1840     System.gc();
1841     if (viewport.getSelectionGroup() == null)
1842     {
1843       return;
1844     }
1845     // TODO: preserve the ordering of displayed alignment annotation in any
1846     // internal paste (particularly sequence associated annotation)
1847     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1848     String[] omitHidden = null;
1849
1850     if (viewport.hasHiddenColumns())
1851     {
1852       omitHidden = viewport.getViewAsString(true);
1853     }
1854
1855     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1856             omitHidden);
1857
1858     StringSelection ss = new StringSelection(output);
1859
1860     try
1861     {
1862       jalview.gui.Desktop.internalCopy = true;
1863       // Its really worth setting the clipboard contents
1864       // to empty before setting the large StringSelection!!
1865       Toolkit.getDefaultToolkit().getSystemClipboard()
1866               .setContents(new StringSelection(""), null);
1867
1868       Toolkit.getDefaultToolkit().getSystemClipboard()
1869               .setContents(ss, Desktop.instance);
1870     } catch (OutOfMemoryError er)
1871     {
1872       new OOMWarning("copying region", er);
1873       return;
1874     }
1875
1876     Vector hiddenColumns = null;
1877     if (viewport.hasHiddenColumns())
1878     {
1879       hiddenColumns = new Vector();
1880       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1881               .getSelectionGroup().getEndRes();
1882       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1883               .size(); i++)
1884       {
1885         int[] region = viewport.getColumnSelection()
1886                 .getHiddenColumns().get(i);
1887         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1888         {
1889           hiddenColumns.addElement(new int[]
1890           { region[0] - hiddenOffset, region[1] - hiddenOffset });
1891         }
1892       }
1893     }
1894
1895     Desktop.jalviewClipboard = new Object[]
1896     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1897     statusBar.setText(MessageManager.formatMessage(
1898             "label.copied_sequences_to_clipboard", new Object[]
1899             { Integer.valueOf(seqs.length).toString() }));
1900   }
1901
1902   /**
1903    * DOCUMENT ME!
1904    *
1905    * @param e
1906    *          DOCUMENT ME!
1907    */
1908   @Override
1909   protected void pasteNew_actionPerformed(ActionEvent e)
1910   {
1911     paste(true);
1912   }
1913
1914   /**
1915    * DOCUMENT ME!
1916    *
1917    * @param e
1918    *          DOCUMENT ME!
1919    */
1920   @Override
1921   protected void pasteThis_actionPerformed(ActionEvent e)
1922   {
1923     paste(false);
1924   }
1925
1926   /**
1927    * Paste contents of Jalview clipboard
1928    *
1929    * @param newAlignment
1930    *          true to paste to a new alignment, otherwise add to this.
1931    */
1932   void paste(boolean newAlignment)
1933   {
1934     boolean externalPaste = true;
1935     try
1936     {
1937       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1938       Transferable contents = c.getContents(this);
1939
1940       if (contents == null)
1941       {
1942         return;
1943       }
1944
1945       String str, format;
1946       try
1947       {
1948         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1949         if (str.length() < 1)
1950         {
1951           return;
1952         }
1953
1954         format = new IdentifyFile().Identify(str, "Paste");
1955
1956       } catch (OutOfMemoryError er)
1957       {
1958         new OOMWarning("Out of memory pasting sequences!!", er);
1959         return;
1960       }
1961
1962       SequenceI[] sequences;
1963       boolean annotationAdded = false;
1964       AlignmentI alignment = null;
1965
1966       if (Desktop.jalviewClipboard != null)
1967       {
1968         // The clipboard was filled from within Jalview, we must use the
1969         // sequences
1970         // And dataset from the copied alignment
1971         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1972         // be doubly sure that we create *new* sequence objects.
1973         sequences = new SequenceI[newseq.length];
1974         for (int i = 0; i < newseq.length; i++)
1975         {
1976           sequences[i] = new Sequence(newseq[i]);
1977         }
1978         alignment = new Alignment(sequences);
1979         externalPaste = false;
1980       }
1981       else
1982       {
1983         // parse the clipboard as an alignment.
1984         alignment = new FormatAdapter().readFile(str, "Paste", format);
1985         sequences = alignment.getSequencesArray();
1986       }
1987
1988       int alwidth = 0;
1989       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1990       int fgroup = -1;
1991
1992       if (newAlignment)
1993       {
1994
1995         if (Desktop.jalviewClipboard != null)
1996         {
1997           // dataset is inherited
1998           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1999         }
2000         else
2001         {
2002           // new dataset is constructed
2003           alignment.setDataset(null);
2004         }
2005         alwidth = alignment.getWidth() + 1;
2006       }
2007       else
2008       {
2009         AlignmentI pastedal = alignment; // preserve pasted alignment object
2010         // Add pasted sequences and dataset into existing alignment.
2011         alignment = viewport.getAlignment();
2012         alwidth = alignment.getWidth() + 1;
2013         // decide if we need to import sequences from an existing dataset
2014         boolean importDs = Desktop.jalviewClipboard != null
2015                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2016         // importDs==true instructs us to copy over new dataset sequences from
2017         // an existing alignment
2018         Vector newDs = (importDs) ? new Vector() : null; // used to create
2019         // minimum dataset set
2020
2021         for (int i = 0; i < sequences.length; i++)
2022         {
2023           if (importDs)
2024           {
2025             newDs.addElement(null);
2026           }
2027           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2028           // paste
2029           if (importDs && ds != null)
2030           {
2031             if (!newDs.contains(ds))
2032             {
2033               newDs.setElementAt(ds, i);
2034               ds = new Sequence(ds);
2035               // update with new dataset sequence
2036               sequences[i].setDatasetSequence(ds);
2037             }
2038             else
2039             {
2040               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2041             }
2042           }
2043           else
2044           {
2045             // copy and derive new dataset sequence
2046             sequences[i] = sequences[i].deriveSequence();
2047             alignment.getDataset().addSequence(
2048                     sequences[i].getDatasetSequence());
2049             // TODO: avoid creation of duplicate dataset sequences with a
2050             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2051           }
2052           alignment.addSequence(sequences[i]); // merges dataset
2053         }
2054         if (newDs != null)
2055         {
2056           newDs.clear(); // tidy up
2057         }
2058         if (alignment.getAlignmentAnnotation() != null)
2059         {
2060           for (AlignmentAnnotation alan : alignment
2061                   .getAlignmentAnnotation())
2062           {
2063             if (alan.graphGroup > fgroup)
2064             {
2065               fgroup = alan.graphGroup;
2066             }
2067           }
2068         }
2069         if (pastedal.getAlignmentAnnotation() != null)
2070         {
2071           // Add any annotation attached to alignment.
2072           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2073           for (int i = 0; i < alann.length; i++)
2074           {
2075             annotationAdded = true;
2076             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2077             {
2078               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2079               if (newann.graphGroup > -1)
2080               {
2081                 if (newGraphGroups.size() <= newann.graphGroup
2082                         || newGraphGroups.get(newann.graphGroup) == null)
2083                 {
2084                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2085                   {
2086                     newGraphGroups.add(q, null);
2087                   }
2088                   newGraphGroups.set(newann.graphGroup, new Integer(
2089                           ++fgroup));
2090                 }
2091                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2092                         .intValue();
2093               }
2094
2095               newann.padAnnotation(alwidth);
2096               alignment.addAnnotation(newann);
2097             }
2098           }
2099         }
2100       }
2101       if (!newAlignment)
2102       {
2103         // /////
2104         // ADD HISTORY ITEM
2105         //
2106         addHistoryItem(new EditCommand(
2107                 MessageManager.getString("label.add_sequences"),
2108                 Action.PASTE,
2109                 sequences, 0, alignment.getWidth(), alignment));
2110       }
2111       // Add any annotations attached to sequences
2112       for (int i = 0; i < sequences.length; i++)
2113       {
2114         if (sequences[i].getAnnotation() != null)
2115         {
2116           AlignmentAnnotation newann;
2117           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2118           {
2119             annotationAdded = true;
2120             newann = sequences[i].getAnnotation()[a];
2121             newann.adjustForAlignment();
2122             newann.padAnnotation(alwidth);
2123             if (newann.graphGroup > -1)
2124             {
2125               if (newann.graphGroup > -1)
2126               {
2127                 if (newGraphGroups.size() <= newann.graphGroup
2128                         || newGraphGroups.get(newann.graphGroup) == null)
2129                 {
2130                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2131                   {
2132                     newGraphGroups.add(q, null);
2133                   }
2134                   newGraphGroups.set(newann.graphGroup, new Integer(
2135                           ++fgroup));
2136                 }
2137                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2138                         .intValue();
2139               }
2140             }
2141             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2142             // was
2143             // duplicated
2144             // earlier
2145             alignment
2146                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2147           }
2148         }
2149       }
2150       if (!newAlignment)
2151       {
2152
2153         // propagate alignment changed.
2154         viewport.setEndSeq(alignment.getHeight());
2155         if (annotationAdded)
2156         {
2157           // Duplicate sequence annotation in all views.
2158           AlignmentI[] alview = this.getViewAlignments();
2159           for (int i = 0; i < sequences.length; i++)
2160           {
2161             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2162             if (sann == null)
2163             {
2164               continue;
2165             }
2166             for (int avnum = 0; avnum < alview.length; avnum++)
2167             {
2168               if (alview[avnum] != alignment)
2169               {
2170                 // duplicate in a view other than the one with input focus
2171                 int avwidth = alview[avnum].getWidth() + 1;
2172                 // this relies on sann being preserved after we
2173                 // modify the sequence's annotation array for each duplication
2174                 for (int a = 0; a < sann.length; a++)
2175                 {
2176                   AlignmentAnnotation newann = new AlignmentAnnotation(
2177                           sann[a]);
2178                   sequences[i].addAlignmentAnnotation(newann);
2179                   newann.padAnnotation(avwidth);
2180                   alview[avnum].addAnnotation(newann); // annotation was
2181                   // duplicated earlier
2182                   // TODO JAL-1145 graphGroups are not updated for sequence
2183                   // annotation added to several views. This may cause
2184                   // strangeness
2185                   alview[avnum].setAnnotationIndex(newann, a);
2186                 }
2187               }
2188             }
2189           }
2190           buildSortByAnnotationScoresMenu();
2191         }
2192         viewport.firePropertyChange("alignment", null,
2193                 alignment.getSequences());
2194         if (alignPanels != null)
2195         {
2196           for (AlignmentPanel ap : alignPanels)
2197           {
2198             ap.validateAnnotationDimensions(false);
2199           }
2200         }
2201         else
2202         {
2203           alignPanel.validateAnnotationDimensions(false);
2204         }
2205
2206       }
2207       else
2208       {
2209         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2210                 DEFAULT_HEIGHT);
2211         String newtitle = new String("Copied sequences");
2212
2213         if (Desktop.jalviewClipboard != null
2214                 && Desktop.jalviewClipboard[2] != null)
2215         {
2216           Vector hc = (Vector) Desktop.jalviewClipboard[2];
2217           for (int i = 0; i < hc.size(); i++)
2218           {
2219             int[] region = (int[]) hc.elementAt(i);
2220             af.viewport.hideColumns(region[0], region[1]);
2221           }
2222         }
2223
2224         // >>>This is a fix for the moment, until a better solution is
2225         // found!!<<<
2226         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2227                 .transferSettings(
2228                         alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2229
2230         // TODO: maintain provenance of an alignment, rather than just make the
2231         // title a concatenation of operations.
2232         if (!externalPaste)
2233         {
2234           if (title.startsWith("Copied sequences"))
2235           {
2236             newtitle = title;
2237           }
2238           else
2239           {
2240             newtitle = newtitle.concat("- from " + title);
2241           }
2242         }
2243         else
2244         {
2245           newtitle = new String("Pasted sequences");
2246         }
2247
2248         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2249                 DEFAULT_HEIGHT);
2250
2251       }
2252
2253     } catch (Exception ex)
2254     {
2255       ex.printStackTrace();
2256       System.out.println("Exception whilst pasting: " + ex);
2257       // could be anything being pasted in here
2258     }
2259
2260   }
2261
2262   @Override
2263   protected void expand_newalign(ActionEvent e)
2264   {
2265     try
2266     {
2267       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2268               .getAlignment(), -1);
2269       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2270               DEFAULT_HEIGHT);
2271       String newtitle = new String("Flanking alignment");
2272
2273       if (Desktop.jalviewClipboard != null
2274               && Desktop.jalviewClipboard[2] != null)
2275       {
2276         Vector hc = (Vector) Desktop.jalviewClipboard[2];
2277         for (int i = 0; i < hc.size(); i++)
2278         {
2279           int[] region = (int[]) hc.elementAt(i);
2280           af.viewport.hideColumns(region[0], region[1]);
2281         }
2282       }
2283
2284       // >>>This is a fix for the moment, until a better solution is
2285       // found!!<<<
2286       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2287               .transferSettings(
2288                       alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2289
2290       // TODO: maintain provenance of an alignment, rather than just make the
2291       // title a concatenation of operations.
2292       {
2293         if (title.startsWith("Copied sequences"))
2294         {
2295           newtitle = title;
2296         }
2297         else
2298         {
2299           newtitle = newtitle.concat("- from " + title);
2300         }
2301       }
2302
2303       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2304
2305     } catch (Exception ex)
2306     {
2307       ex.printStackTrace();
2308       System.out.println("Exception whilst pasting: " + ex);
2309       // could be anything being pasted in here
2310     } catch (OutOfMemoryError oom)
2311     {
2312       new OOMWarning("Viewing flanking region of alignment", oom);
2313     }
2314   }
2315
2316   /**
2317    * DOCUMENT ME!
2318    *
2319    * @param e
2320    *          DOCUMENT ME!
2321    */
2322   @Override
2323   protected void cut_actionPerformed(ActionEvent e)
2324   {
2325     copy_actionPerformed(null);
2326     delete_actionPerformed(null);
2327   }
2328
2329   /**
2330    * DOCUMENT ME!
2331    *
2332    * @param e
2333    *          DOCUMENT ME!
2334    */
2335   @Override
2336   protected void delete_actionPerformed(ActionEvent evt)
2337   {
2338
2339     SequenceGroup sg = viewport.getSelectionGroup();
2340     if (sg == null)
2341     {
2342       return;
2343     }
2344
2345     List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2346     SequenceI seq;
2347     for (int i = 0; i < sg.getSize(); i++)
2348     {
2349       seq = sg.getSequenceAt(i);
2350       seqs.add(seq);
2351     }
2352
2353     // If the cut affects all sequences, warn, remove highlighted columns
2354     if (sg.getSize() == viewport.getAlignment().getHeight())
2355     {
2356       int confirm = JOptionPane.showConfirmDialog(this,
2357               MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2358               MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2359               JOptionPane.OK_CANCEL_OPTION);
2360
2361       if (confirm == JOptionPane.CANCEL_OPTION
2362               || confirm == JOptionPane.CLOSED_OPTION)
2363       {
2364         return;
2365       }
2366       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2367               sg.getEndRes() + 1);
2368     }
2369
2370     SequenceI[] cut = new SequenceI[seqs.size()];
2371     for (int i = 0; i < seqs.size(); i++)
2372     {
2373       cut[i] = seqs.get(i);
2374     }
2375
2376     /*
2377      * //ADD HISTORY ITEM
2378      */
2379     addHistoryItem(new EditCommand(
2380             MessageManager.getString("label.cut_sequences"), Action.CUT,
2381             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2382             viewport.getAlignment()));
2383
2384     viewport.setSelectionGroup(null);
2385     viewport.sendSelection();
2386     viewport.getAlignment().deleteGroup(sg);
2387
2388     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2389             .getSequences());
2390     if (viewport.getAlignment().getHeight() < 1)
2391     {
2392       try
2393       {
2394         this.setClosed(true);
2395       } catch (Exception ex)
2396       {
2397       }
2398     }
2399   }
2400
2401   /**
2402    * DOCUMENT ME!
2403    *
2404    * @param e
2405    *          DOCUMENT ME!
2406    */
2407   @Override
2408   protected void deleteGroups_actionPerformed(ActionEvent e)
2409   {
2410     if (avc.deleteGroups())
2411     {
2412       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2413       alignPanel.updateAnnotation();
2414       alignPanel.paintAlignment(true);
2415     }
2416   }
2417
2418   /**
2419    * DOCUMENT ME!
2420    *
2421    * @param e
2422    *          DOCUMENT ME!
2423    */
2424   @Override
2425   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2426   {
2427     SequenceGroup sg = new SequenceGroup();
2428
2429     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2430     {
2431       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2432     }
2433
2434     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2435     viewport.setSelectionGroup(sg);
2436     viewport.sendSelection();
2437     alignPanel.paintAlignment(true);
2438     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2439   }
2440
2441   /**
2442    * DOCUMENT ME!
2443    *
2444    * @param e
2445    *          DOCUMENT ME!
2446    */
2447   @Override
2448   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2449   {
2450     if (viewport.cursorMode)
2451     {
2452       alignPanel.seqPanel.keyboardNo1 = null;
2453       alignPanel.seqPanel.keyboardNo2 = null;
2454     }
2455     viewport.setSelectionGroup(null);
2456     viewport.getColumnSelection().clear();
2457     viewport.setSelectionGroup(null);
2458     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2459     alignPanel.idPanel.idCanvas.searchResults = null;
2460     alignPanel.paintAlignment(true);
2461     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2462     viewport.sendSelection();
2463   }
2464
2465   /**
2466    * DOCUMENT ME!
2467    *
2468    * @param e
2469    *          DOCUMENT ME!
2470    */
2471   @Override
2472   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2473   {
2474     SequenceGroup sg = viewport.getSelectionGroup();
2475
2476     if (sg == null)
2477     {
2478       selectAllSequenceMenuItem_actionPerformed(null);
2479
2480       return;
2481     }
2482
2483     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2484     {
2485       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2486     }
2487
2488     alignPanel.paintAlignment(true);
2489     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2490     viewport.sendSelection();
2491   }
2492
2493   @Override
2494   public void invertColSel_actionPerformed(ActionEvent e)
2495   {
2496     viewport.invertColumnSelection();
2497     alignPanel.paintAlignment(true);
2498     viewport.sendSelection();
2499   }
2500
2501   /**
2502    * DOCUMENT ME!
2503    *
2504    * @param e
2505    *          DOCUMENT ME!
2506    */
2507   @Override
2508   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2509   {
2510     trimAlignment(true);
2511   }
2512
2513   /**
2514    * DOCUMENT ME!
2515    *
2516    * @param e
2517    *          DOCUMENT ME!
2518    */
2519   @Override
2520   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2521   {
2522     trimAlignment(false);
2523   }
2524
2525   void trimAlignment(boolean trimLeft)
2526   {
2527     ColumnSelection colSel = viewport.getColumnSelection();
2528     int column;
2529
2530     if (colSel.size() > 0)
2531     {
2532       if (trimLeft)
2533       {
2534         column = colSel.getMin();
2535       }
2536       else
2537       {
2538         column = colSel.getMax();
2539       }
2540
2541       SequenceI[] seqs;
2542       if (viewport.getSelectionGroup() != null)
2543       {
2544         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2545                 viewport.getHiddenRepSequences());
2546       }
2547       else
2548       {
2549         seqs = viewport.getAlignment().getSequencesArray();
2550       }
2551
2552       TrimRegionCommand trimRegion;
2553       if (trimLeft)
2554       {
2555         trimRegion = new TrimRegionCommand("Remove Left",
2556                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2557                 viewport.getAlignment(), viewport.getColumnSelection(),
2558                 viewport.getSelectionGroup());
2559         viewport.setStartRes(0);
2560       }
2561       else
2562       {
2563         trimRegion = new TrimRegionCommand("Remove Right",
2564                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2565                 viewport.getAlignment(), viewport.getColumnSelection(),
2566                 viewport.getSelectionGroup());
2567       }
2568
2569       statusBar.setText(MessageManager.formatMessage(
2570               "label.removed_columns", new String[]
2571               { Integer.valueOf(trimRegion.getSize()).toString() }));
2572
2573       addHistoryItem(trimRegion);
2574
2575       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2576       {
2577         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2578                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2579         {
2580           viewport.getAlignment().deleteGroup(sg);
2581         }
2582       }
2583
2584       viewport.firePropertyChange("alignment", null, viewport
2585               .getAlignment().getSequences());
2586     }
2587   }
2588
2589   /**
2590    * DOCUMENT ME!
2591    *
2592    * @param e
2593    *          DOCUMENT ME!
2594    */
2595   @Override
2596   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2597   {
2598     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2599
2600     SequenceI[] seqs;
2601     if (viewport.getSelectionGroup() != null)
2602     {
2603       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2604               viewport.getHiddenRepSequences());
2605       start = viewport.getSelectionGroup().getStartRes();
2606       end = viewport.getSelectionGroup().getEndRes();
2607     }
2608     else
2609     {
2610       seqs = viewport.getAlignment().getSequencesArray();
2611     }
2612
2613     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2614             "Remove Gapped Columns", seqs, start, end,
2615             viewport.getAlignment());
2616
2617     addHistoryItem(removeGapCols);
2618
2619     statusBar.setText(MessageManager.formatMessage(
2620             "label.removed_empty_columns", new String[]
2621             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2622
2623     // This is to maintain viewport position on first residue
2624     // of first sequence
2625     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2626     int startRes = seq.findPosition(viewport.startRes);
2627     // ShiftList shifts;
2628     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2629     // edit.alColumnChanges=shifts.getInverse();
2630     // if (viewport.hasHiddenColumns)
2631     // viewport.getColumnSelection().compensateForEdits(shifts);
2632     viewport.setStartRes(seq.findIndex(startRes) - 1);
2633     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2634             .getSequences());
2635
2636   }
2637
2638   /**
2639    * DOCUMENT ME!
2640    *
2641    * @param e
2642    *          DOCUMENT ME!
2643    */
2644   @Override
2645   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2646   {
2647     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2648
2649     SequenceI[] seqs;
2650     if (viewport.getSelectionGroup() != null)
2651     {
2652       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2653               viewport.getHiddenRepSequences());
2654       start = viewport.getSelectionGroup().getStartRes();
2655       end = viewport.getSelectionGroup().getEndRes();
2656     }
2657     else
2658     {
2659       seqs = viewport.getAlignment().getSequencesArray();
2660     }
2661
2662     // This is to maintain viewport position on first residue
2663     // of first sequence
2664     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2665     int startRes = seq.findPosition(viewport.startRes);
2666
2667     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2668             viewport.getAlignment()));
2669
2670     viewport.setStartRes(seq.findIndex(startRes) - 1);
2671
2672     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2673             .getSequences());
2674
2675   }
2676
2677   /**
2678    * DOCUMENT ME!
2679    *
2680    * @param e
2681    *          DOCUMENT ME!
2682    */
2683   @Override
2684   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2685   {
2686     viewport.setPadGaps(padGapsMenuitem.isSelected());
2687     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2688             .getSequences());
2689   }
2690
2691   /**
2692    * DOCUMENT ME!
2693    *
2694    * @param e
2695    *          DOCUMENT ME!
2696    */
2697   @Override
2698   public void findMenuItem_actionPerformed(ActionEvent e)
2699   {
2700     new Finder();
2701   }
2702
2703   /**
2704    * Create a new view of the current alignment.
2705    */
2706   @Override
2707   public void newView_actionPerformed(ActionEvent e)
2708   {
2709     /*
2710      * Note if the current view has a protein/cdna complementary view
2711      */
2712     AlignViewportI linkedView = this.viewport.getCodingComplement();
2713
2714     AlignmentPanel newPanel = newView(null, true);
2715
2716     /*
2717      * If the original view has a protein/cdna linked view, make and link a new
2718      * view there also.
2719      */
2720     // TODO refactor the hell out of this - move to a controller, lose the casts
2721     // and direct member access, etc
2722     if (linkedView != null)
2723     {
2724       AlignFrame linkedAlignFrame = ((AlignViewport) linkedView)
2725               .getAlignPanel().alignFrame;
2726       AlignmentPanel newLinkedPanel = linkedAlignFrame.newView(null, true);
2727       newLinkedPanel.av.viewName = newPanel.av.viewName;
2728       newPanel.av.setCodingComplement(newLinkedPanel.av);
2729       final StructureSelectionManager ssm = StructureSelectionManager
2730               .getStructureSelectionManager(Desktop.instance);
2731       ssm.addCommandListener(newPanel.av);
2732       ssm.addCommandListener(newLinkedPanel.av);
2733
2734     }
2735   }
2736
2737   /**
2738    * Creates and shows a new view of the current alignment.
2739    *
2740    * @param viewTitle
2741    *          title of newly created view; if null, one will be generated
2742    * @param copyAnnotation
2743    *          if true then duplicate all annnotation, groups and settings
2744    * @return new alignment panel, already displayed.
2745    */
2746   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2747   {
2748     /*
2749      * Create a new AlignmentPanel (with its own, new Viewport)
2750      */
2751     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2752             true);
2753     if (!copyAnnotation)
2754     {
2755       /*
2756        * remove all groups and annotation except for the automatic stuff
2757        */
2758       newap.av.getAlignment().deleteAllGroups();
2759       newap.av.getAlignment().deleteAllAnnotations(false);
2760     }
2761
2762     newap.av.gatherViewsHere = false;
2763
2764     if (viewport.viewName == null)
2765     {
2766       viewport.viewName = MessageManager
2767               .getString("label.view_name_original");
2768     }
2769
2770     /*
2771      * Views share the same edits, undo and redo stacks, mappings.
2772      */
2773     newap.av.setHistoryList(viewport.getHistoryList());
2774     newap.av.setRedoList(viewport.getRedoList());
2775     newap.av.getAlignment().setCodonFrames(
2776             viewport.getAlignment().getCodonFrames());
2777
2778     newap.av.viewName = getNewViewName(viewTitle);
2779
2780     addAlignmentPanel(newap, true);
2781     newap.alignmentChanged();
2782
2783     if (alignPanels.size() == 2)
2784     {
2785       viewport.gatherViewsHere = true;
2786     }
2787     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2788     return newap;
2789   }
2790
2791   /**
2792    * Make a new name for the view, ensuring it is unique within the current
2793    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2794    * these now use viewId. Unique view names are still desirable for usability.)
2795    *
2796    * @param viewTitle
2797    * @return
2798    */
2799   protected String getNewViewName(String viewTitle)
2800   {
2801     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2802     boolean addFirstIndex = false;
2803     if (viewTitle == null || viewTitle.trim().length() == 0)
2804     {
2805       viewTitle = MessageManager.getString("action.view");
2806       addFirstIndex = true;
2807     }
2808     else
2809     {
2810       index = 1;// we count from 1 if given a specific name
2811     }
2812     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2813
2814     List<Component> comps = PaintRefresher.components.get(viewport
2815             .getSequenceSetId());
2816
2817     List<String> existingNames = getExistingViewNames(comps);
2818
2819     while (existingNames.contains(newViewName))
2820     {
2821       newViewName = viewTitle + " " + (++index);
2822     }
2823     return newViewName;
2824   }
2825
2826   /**
2827    * Returns a list of distinct view names found in the given list of
2828    * components. View names are held on the viewport of an AlignmentPanel.
2829    *
2830    * @param comps
2831    * @return
2832    */
2833   protected List<String> getExistingViewNames(List<Component> comps)
2834   {
2835     List<String> existingNames = new ArrayList<String>();
2836     for (Component comp : comps)
2837     {
2838       if (comp instanceof AlignmentPanel)
2839       {
2840         AlignmentPanel ap = (AlignmentPanel) comp;
2841         if (!existingNames.contains(ap.av.viewName))
2842         {
2843           existingNames.add(ap.av.viewName);
2844         }
2845       }
2846     }
2847     return existingNames;
2848   }
2849
2850   /**
2851    * Explode tabbed views into separate windows.
2852    */
2853   @Override
2854   public void expandViews_actionPerformed(ActionEvent e)
2855   {
2856     Desktop.instance.explodeViews(this);
2857   }
2858
2859   /**
2860    * Gather views in separate windows back into a tabbed presentation.
2861    */
2862   @Override
2863   public void gatherViews_actionPerformed(ActionEvent e)
2864   {
2865     Desktop.instance.gatherViews(this);
2866   }
2867
2868   /**
2869    * DOCUMENT ME!
2870    *
2871    * @param e
2872    *          DOCUMENT ME!
2873    */
2874   @Override
2875   public void font_actionPerformed(ActionEvent e)
2876   {
2877     new FontChooser(alignPanel);
2878   }
2879
2880   /**
2881    * DOCUMENT ME!
2882    *
2883    * @param e
2884    *          DOCUMENT ME!
2885    */
2886   @Override
2887   protected void seqLimit_actionPerformed(ActionEvent e)
2888   {
2889     viewport.setShowJVSuffix(seqLimits.isSelected());
2890
2891     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2892             .calculateIdWidth());
2893     alignPanel.paintAlignment(true);
2894   }
2895
2896   @Override
2897   public void idRightAlign_actionPerformed(ActionEvent e)
2898   {
2899     viewport.rightAlignIds = idRightAlign.isSelected();
2900     alignPanel.paintAlignment(true);
2901   }
2902
2903   @Override
2904   public void centreColumnLabels_actionPerformed(ActionEvent e)
2905   {
2906     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2907     alignPanel.paintAlignment(true);
2908   }
2909
2910   /*
2911    * (non-Javadoc)
2912    *
2913    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2914    */
2915   @Override
2916   protected void followHighlight_actionPerformed()
2917   {
2918     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2919     {
2920       alignPanel.scrollToPosition(
2921               alignPanel.seqPanel.seqCanvas.searchResults, false);
2922     }
2923   }
2924
2925   /**
2926    * DOCUMENT ME!
2927    *
2928    * @param e
2929    *          DOCUMENT ME!
2930    */
2931   @Override
2932   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2933   {
2934     viewport.setColourText(colourTextMenuItem.isSelected());
2935     alignPanel.paintAlignment(true);
2936   }
2937
2938   /**
2939    * DOCUMENT ME!
2940    *
2941    * @param e
2942    *          DOCUMENT ME!
2943    */
2944   @Override
2945   public void wrapMenuItem_actionPerformed(ActionEvent e)
2946   {
2947     scaleAbove.setVisible(wrapMenuItem.isSelected());
2948     scaleLeft.setVisible(wrapMenuItem.isSelected());
2949     scaleRight.setVisible(wrapMenuItem.isSelected());
2950     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2951     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2952   }
2953
2954   @Override
2955   public void showAllSeqs_actionPerformed(ActionEvent e)
2956   {
2957     viewport.showAllHiddenSeqs();
2958   }
2959
2960   @Override
2961   public void showAllColumns_actionPerformed(ActionEvent e)
2962   {
2963     viewport.showAllHiddenColumns();
2964     repaint();
2965   }
2966
2967   @Override
2968   public void hideSelSequences_actionPerformed(ActionEvent e)
2969   {
2970     viewport.hideAllSelectedSeqs();
2971     alignPanel.paintAlignment(true);
2972   }
2973
2974   /**
2975    * called by key handler and the hide all/show all menu items
2976    *
2977    * @param toggleSeqs
2978    * @param toggleCols
2979    */
2980   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2981   {
2982
2983     boolean hide = false;
2984     SequenceGroup sg = viewport.getSelectionGroup();
2985     if (!toggleSeqs && !toggleCols)
2986     {
2987       // Hide everything by the current selection - this is a hack - we do the
2988       // invert and then hide
2989       // first check that there will be visible columns after the invert.
2990       if ((viewport.getColumnSelection() != null
2991               && viewport.getColumnSelection().getSelected() != null && viewport
2992               .getColumnSelection().getSelected().size() > 0)
2993               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2994                       .getEndRes()))
2995       {
2996         // now invert the sequence set, if required - empty selection implies
2997         // that no hiding is required.
2998         if (sg != null)
2999         {
3000           invertSequenceMenuItem_actionPerformed(null);
3001           sg = viewport.getSelectionGroup();
3002           toggleSeqs = true;
3003
3004         }
3005         viewport.expandColSelection(sg, true);
3006         // finally invert the column selection and get the new sequence
3007         // selection.
3008         invertColSel_actionPerformed(null);
3009         toggleCols = true;
3010       }
3011     }
3012
3013     if (toggleSeqs)
3014     {
3015       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3016       {
3017         hideSelSequences_actionPerformed(null);
3018         hide = true;
3019       }
3020       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3021               .size() > 0))
3022       {
3023         showAllSeqs_actionPerformed(null);
3024       }
3025     }
3026
3027     if (toggleCols)
3028     {
3029       if (viewport.getColumnSelection().getSelected().size() > 0)
3030       {
3031         hideSelColumns_actionPerformed(null);
3032         if (!toggleSeqs)
3033         {
3034           viewport.setSelectionGroup(sg);
3035         }
3036       }
3037       else if (!hide)
3038       {
3039         showAllColumns_actionPerformed(null);
3040       }
3041     }
3042   }
3043
3044   /*
3045    * (non-Javadoc)
3046    *
3047    * @see
3048    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3049    * event.ActionEvent)
3050    */
3051   @Override
3052   public void hideAllButSelection_actionPerformed(ActionEvent e)
3053   {
3054     toggleHiddenRegions(false, false);
3055   }
3056
3057   /*
3058    * (non-Javadoc)
3059    *
3060    * @see
3061    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3062    * .ActionEvent)
3063    */
3064   @Override
3065   public void hideAllSelection_actionPerformed(ActionEvent e)
3066   {
3067     SequenceGroup sg = viewport.getSelectionGroup();
3068     viewport.expandColSelection(sg, false);
3069     viewport.hideAllSelectedSeqs();
3070     viewport.hideSelectedColumns();
3071     alignPanel.paintAlignment(true);
3072   }
3073
3074   /*
3075    * (non-Javadoc)
3076    *
3077    * @see
3078    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3079    * ActionEvent)
3080    */
3081   @Override
3082   public void showAllhidden_actionPerformed(ActionEvent e)
3083   {
3084     viewport.showAllHiddenColumns();
3085     viewport.showAllHiddenSeqs();
3086     alignPanel.paintAlignment(true);
3087   }
3088
3089   @Override
3090   public void hideSelColumns_actionPerformed(ActionEvent e)
3091   {
3092     viewport.hideSelectedColumns();
3093     alignPanel.paintAlignment(true);
3094   }
3095
3096   @Override
3097   public void hiddenMarkers_actionPerformed(ActionEvent e)
3098   {
3099     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3100     repaint();
3101   }
3102
3103   /**
3104    * DOCUMENT ME!
3105    *
3106    * @param e
3107    *          DOCUMENT ME!
3108    */
3109   @Override
3110   protected void scaleAbove_actionPerformed(ActionEvent e)
3111   {
3112     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3113     alignPanel.paintAlignment(true);
3114   }
3115
3116   /**
3117    * DOCUMENT ME!
3118    *
3119    * @param e
3120    *          DOCUMENT ME!
3121    */
3122   @Override
3123   protected void scaleLeft_actionPerformed(ActionEvent e)
3124   {
3125     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3126     alignPanel.paintAlignment(true);
3127   }
3128
3129   /**
3130    * DOCUMENT ME!
3131    *
3132    * @param e
3133    *          DOCUMENT ME!
3134    */
3135   @Override
3136   protected void scaleRight_actionPerformed(ActionEvent e)
3137   {
3138     viewport.setScaleRightWrapped(scaleRight.isSelected());
3139     alignPanel.paintAlignment(true);
3140   }
3141
3142   /**
3143    * DOCUMENT ME!
3144    *
3145    * @param e
3146    *          DOCUMENT ME!
3147    */
3148   @Override
3149   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3150   {
3151     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3152     alignPanel.paintAlignment(true);
3153   }
3154
3155   /**
3156    * DOCUMENT ME!
3157    *
3158    * @param e
3159    *          DOCUMENT ME!
3160    */
3161   @Override
3162   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3163   {
3164     viewport.setShowText(viewTextMenuItem.isSelected());
3165     alignPanel.paintAlignment(true);
3166   }
3167
3168   /**
3169    * DOCUMENT ME!
3170    *
3171    * @param e
3172    *          DOCUMENT ME!
3173    */
3174   @Override
3175   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3176   {
3177     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3178     alignPanel.paintAlignment(true);
3179   }
3180
3181   public FeatureSettings featureSettings;
3182
3183   @Override
3184   public void featureSettings_actionPerformed(ActionEvent e)
3185   {
3186     if (featureSettings != null)
3187     {
3188       featureSettings.close();
3189       featureSettings = null;
3190     }
3191     if (!showSeqFeatures.isSelected())
3192     {
3193       // make sure features are actually displayed
3194       showSeqFeatures.setSelected(true);
3195       showSeqFeatures_actionPerformed(null);
3196     }
3197     featureSettings = new FeatureSettings(this);
3198   }
3199
3200   /**
3201    * Set or clear 'Show Sequence Features'
3202    *
3203    * @param evt
3204    *          DOCUMENT ME!
3205    */
3206   @Override
3207   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3208   {
3209     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3210     alignPanel.paintAlignment(true);
3211     if (alignPanel.getOverviewPanel() != null)
3212     {
3213       alignPanel.getOverviewPanel().updateOverviewImage();
3214     }
3215   }
3216
3217   /**
3218    * Set or clear 'Show Sequence Features'
3219    *
3220    * @param evt
3221    *          DOCUMENT ME!
3222    */
3223   @Override
3224   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3225   {
3226     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3227             .isSelected());
3228     if (viewport.getShowSequenceFeaturesHeight())
3229     {
3230       // ensure we're actually displaying features
3231       viewport.setShowSequenceFeatures(true);
3232       showSeqFeatures.setSelected(true);
3233     }
3234     alignPanel.paintAlignment(true);
3235     if (alignPanel.getOverviewPanel() != null)
3236     {
3237       alignPanel.getOverviewPanel().updateOverviewImage();
3238     }
3239   }
3240
3241   /**
3242    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3243    * the annotations panel as a whole.
3244    *
3245    * The options to show/hide all annotations should be enabled when the panel
3246    * is shown, and disabled when the panel is hidden.
3247    *
3248    * @param e
3249    */
3250   @Override
3251   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3252   {
3253     final boolean setVisible = annotationPanelMenuItem.isSelected();
3254     viewport.setShowAnnotation(setVisible);
3255     alignPanel.setAnnotationVisible(setVisible);
3256     this.showAllSeqAnnotations.setEnabled(setVisible);
3257     this.hideAllSeqAnnotations.setEnabled(setVisible);
3258     this.showAllAlAnnotations.setEnabled(setVisible);
3259     this.hideAllAlAnnotations.setEnabled(setVisible);
3260   }
3261
3262   @Override
3263   public void alignmentProperties()
3264   {
3265     JEditorPane editPane = new JEditorPane("text/html", "");
3266     editPane.setEditable(false);
3267     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3268             .formatAsHtml();
3269     editPane.setText(MessageManager.formatMessage("label.html_content",
3270             new String[]
3271             { contents.toString() }));
3272     JInternalFrame frame = new JInternalFrame();
3273     frame.getContentPane().add(new JScrollPane(editPane));
3274
3275     Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3276             "label.alignment_properties", new String[]
3277             { getTitle() }), 500, 400);
3278   }
3279
3280   /**
3281    * DOCUMENT ME!
3282    *
3283    * @param e
3284    *          DOCUMENT ME!
3285    */
3286   @Override
3287   public void overviewMenuItem_actionPerformed(ActionEvent e)
3288   {
3289     if (alignPanel.overviewPanel != null)
3290     {
3291       return;
3292     }
3293
3294     JInternalFrame frame = new JInternalFrame();
3295     OverviewPanel overview = new OverviewPanel(alignPanel);
3296     frame.setContentPane(overview);
3297     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3298             "label.overview_params", new String[]
3299             { this.getTitle() }), frame.getWidth(), frame.getHeight());
3300     frame.pack();
3301     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3302     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3303     {
3304       @Override
3305       public void internalFrameClosed(
3306               javax.swing.event.InternalFrameEvent evt)
3307       {
3308         alignPanel.setOverviewPanel(null);
3309       };
3310     });
3311
3312     alignPanel.setOverviewPanel(overview);
3313   }
3314
3315   @Override
3316   public void textColour_actionPerformed(ActionEvent e)
3317   {
3318     new TextColourChooser().chooseColour(alignPanel, null);
3319   }
3320
3321   /**
3322    * DOCUMENT ME!
3323    *
3324    * @param e
3325    *          DOCUMENT ME!
3326    */
3327   @Override
3328   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3329   {
3330     changeColour(null);
3331   }
3332
3333   /**
3334    * DOCUMENT ME!
3335    *
3336    * @param e
3337    *          DOCUMENT ME!
3338    */
3339   @Override
3340   public void clustalColour_actionPerformed(ActionEvent e)
3341   {
3342     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3343             viewport.getHiddenRepSequences()));
3344   }
3345
3346   /**
3347    * DOCUMENT ME!
3348    *
3349    * @param e
3350    *          DOCUMENT ME!
3351    */
3352   @Override
3353   public void zappoColour_actionPerformed(ActionEvent e)
3354   {
3355     changeColour(new ZappoColourScheme());
3356   }
3357
3358   /**
3359    * DOCUMENT ME!
3360    *
3361    * @param e
3362    *          DOCUMENT ME!
3363    */
3364   @Override
3365   public void taylorColour_actionPerformed(ActionEvent e)
3366   {
3367     changeColour(new TaylorColourScheme());
3368   }
3369
3370   /**
3371    * DOCUMENT ME!
3372    *
3373    * @param e
3374    *          DOCUMENT ME!
3375    */
3376   @Override
3377   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3378   {
3379     changeColour(new HydrophobicColourScheme());
3380   }
3381
3382   /**
3383    * DOCUMENT ME!
3384    *
3385    * @param e
3386    *          DOCUMENT ME!
3387    */
3388   @Override
3389   public void helixColour_actionPerformed(ActionEvent e)
3390   {
3391     changeColour(new HelixColourScheme());
3392   }
3393
3394   /**
3395    * DOCUMENT ME!
3396    *
3397    * @param e
3398    *          DOCUMENT ME!
3399    */
3400   @Override
3401   public void strandColour_actionPerformed(ActionEvent e)
3402   {
3403     changeColour(new StrandColourScheme());
3404   }
3405
3406   /**
3407    * DOCUMENT ME!
3408    *
3409    * @param e
3410    *          DOCUMENT ME!
3411    */
3412   @Override
3413   public void turnColour_actionPerformed(ActionEvent e)
3414   {
3415     changeColour(new TurnColourScheme());
3416   }
3417
3418   /**
3419    * DOCUMENT ME!
3420    *
3421    * @param e
3422    *          DOCUMENT ME!
3423    */
3424   @Override
3425   public void buriedColour_actionPerformed(ActionEvent e)
3426   {
3427     changeColour(new BuriedColourScheme());
3428   }
3429
3430   /**
3431    * DOCUMENT ME!
3432    *
3433    * @param e
3434    *          DOCUMENT ME!
3435    */
3436   @Override
3437   public void nucleotideColour_actionPerformed(ActionEvent e)
3438   {
3439     changeColour(new NucleotideColourScheme());
3440   }
3441
3442   @Override
3443   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3444   {
3445     changeColour(new PurinePyrimidineColourScheme());
3446   }
3447
3448   /*
3449    * public void covariationColour_actionPerformed(ActionEvent e) {
3450    * changeColour(new
3451    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3452    * ()[0])); }
3453    */
3454   @Override
3455   public void annotationColour_actionPerformed(ActionEvent e)
3456   {
3457     new AnnotationColourChooser(viewport, alignPanel);
3458   }
3459
3460   @Override
3461   public void rnahelicesColour_actionPerformed(ActionEvent e)
3462   {
3463     new RNAHelicesColourChooser(viewport, alignPanel);
3464   }
3465
3466   /**
3467    * DOCUMENT ME!
3468    *
3469    * @param e
3470    *          DOCUMENT ME!
3471    */
3472   @Override
3473   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3474   {
3475     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3476   }
3477
3478   /**
3479    * DOCUMENT ME!
3480    *
3481    * @param cs
3482    *          DOCUMENT ME!
3483    */
3484   public void changeColour(ColourSchemeI cs)
3485   {
3486     // TODO: compare with applet and pull up to model method
3487     int threshold = 0;
3488
3489     if (cs != null)
3490     {
3491       if (viewport.getAbovePIDThreshold())
3492       {
3493         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3494                 "Background");
3495         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3496       }
3497       else
3498       {
3499         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3500       }
3501
3502       if (viewport.getConservationSelected())
3503       {
3504
3505         Alignment al = (Alignment) viewport.getAlignment();
3506         Conservation c = new Conservation("All",
3507                 ResidueProperties.propHash, 3, al.getSequences(), 0,
3508                 al.getWidth() - 1);
3509
3510         c.calculate();
3511         c.verdict(false, viewport.getConsPercGaps());
3512
3513         cs.setConservation(c);
3514
3515         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3516                 cs, "Background"));
3517       }
3518       else
3519       {
3520         cs.setConservation(null);
3521       }
3522
3523       cs.setConsensus(viewport.getSequenceConsensusHash());
3524     }
3525
3526     viewport.setGlobalColourScheme(cs);
3527
3528     if (viewport.getColourAppliesToAllGroups())
3529     {
3530
3531       for (SequenceGroup sg : viewport.getAlignment().getGroups())
3532       {
3533         if (cs == null)
3534         {
3535           sg.cs = null;
3536           continue;
3537         }
3538
3539         if (cs instanceof ClustalxColourScheme)
3540         {
3541           sg.cs = new ClustalxColourScheme(sg,
3542                   viewport.getHiddenRepSequences());
3543         }
3544         else if (cs instanceof UserColourScheme)
3545         {
3546           sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3547         }
3548         else
3549         {
3550           try
3551           {
3552             sg.cs = cs.getClass().newInstance();
3553           } catch (Exception ex)
3554           {
3555           }
3556         }
3557
3558         if (viewport.getAbovePIDThreshold()
3559                 || cs instanceof PIDColourScheme
3560                 || cs instanceof Blosum62ColourScheme)
3561         {
3562           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3563
3564           sg.cs.setConsensus(AAFrequency.calculate(
3565                   sg.getSequences(viewport.getHiddenRepSequences()),
3566                   sg.getStartRes(), sg.getEndRes() + 1));
3567         }
3568         else
3569         {
3570           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3571         }
3572
3573         if (viewport.getConservationSelected())
3574         {
3575           Conservation c = new Conservation("Group",
3576                   ResidueProperties.propHash, 3, sg.getSequences(viewport
3577                           .getHiddenRepSequences()), sg.getStartRes(),
3578                   sg.getEndRes() + 1);
3579           c.calculate();
3580           c.verdict(false, viewport.getConsPercGaps());
3581           sg.cs.setConservation(c);
3582         }
3583         else
3584         {
3585           sg.cs.setConservation(null);
3586         }
3587       }
3588     }
3589
3590     if (alignPanel.getOverviewPanel() != null)
3591     {
3592       alignPanel.getOverviewPanel().updateOverviewImage();
3593     }
3594
3595     alignPanel.paintAlignment(true);
3596   }
3597
3598   /**
3599    * DOCUMENT ME!
3600    *
3601    * @param e
3602    *          DOCUMENT ME!
3603    */
3604   @Override
3605   protected void modifyPID_actionPerformed(ActionEvent e)
3606   {
3607     if (viewport.getAbovePIDThreshold()
3608             && viewport.getGlobalColourScheme() != null)
3609     {
3610       SliderPanel.setPIDSliderSource(alignPanel,
3611               viewport.getGlobalColourScheme(), "Background");
3612       SliderPanel.showPIDSlider();
3613     }
3614   }
3615
3616   /**
3617    * DOCUMENT ME!
3618    *
3619    * @param e
3620    *          DOCUMENT ME!
3621    */
3622   @Override
3623   protected void modifyConservation_actionPerformed(ActionEvent e)
3624   {
3625     if (viewport.getConservationSelected()
3626             && viewport.getGlobalColourScheme() != null)
3627     {
3628       SliderPanel.setConservationSlider(alignPanel,
3629               viewport.getGlobalColourScheme(), "Background");
3630       SliderPanel.showConservationSlider();
3631     }
3632   }
3633
3634   /**
3635    * DOCUMENT ME!
3636    *
3637    * @param e
3638    *          DOCUMENT ME!
3639    */
3640   @Override
3641   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3642   {
3643     viewport.setConservationSelected(conservationMenuItem.isSelected());
3644
3645     viewport.setAbovePIDThreshold(false);
3646     abovePIDThreshold.setSelected(false);
3647
3648     changeColour(viewport.getGlobalColourScheme());
3649
3650     modifyConservation_actionPerformed(null);
3651   }
3652
3653   /**
3654    * DOCUMENT ME!
3655    *
3656    * @param e
3657    *          DOCUMENT ME!
3658    */
3659   @Override
3660   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3661   {
3662     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3663
3664     conservationMenuItem.setSelected(false);
3665     viewport.setConservationSelected(false);
3666
3667     changeColour(viewport.getGlobalColourScheme());
3668
3669     modifyPID_actionPerformed(null);
3670   }
3671
3672   /**
3673    * DOCUMENT ME!
3674    *
3675    * @param e
3676    *          DOCUMENT ME!
3677    */
3678   @Override
3679   public void userDefinedColour_actionPerformed(ActionEvent e)
3680   {
3681     if (e.getActionCommand().equals(
3682             MessageManager.getString("action.user_defined")))
3683     {
3684       new UserDefinedColours(alignPanel, null);
3685     }
3686     else
3687     {
3688       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3689               .getUserColourSchemes().get(e.getActionCommand());
3690
3691       changeColour(udc);
3692     }
3693   }
3694
3695   public void updateUserColourMenu()
3696   {
3697
3698     Component[] menuItems = colourMenu.getMenuComponents();
3699     int iSize = menuItems.length;
3700     for (int i = 0; i < iSize; i++)
3701     {
3702       if (menuItems[i].getName() != null
3703               && menuItems[i].getName().equals("USER_DEFINED"))
3704       {
3705         colourMenu.remove(menuItems[i]);
3706         iSize--;
3707       }
3708     }
3709     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3710     {
3711       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3712               .getUserColourSchemes().keys();
3713
3714       while (userColours.hasMoreElements())
3715       {
3716         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3717                 userColours.nextElement().toString());
3718         radioItem.setName("USER_DEFINED");
3719         radioItem.addMouseListener(new MouseAdapter()
3720         {
3721           @Override
3722           public void mousePressed(MouseEvent evt)
3723           {
3724             if (evt.isControlDown()
3725                     || SwingUtilities.isRightMouseButton(evt))
3726             {
3727               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3728
3729               int option = JOptionPane.showInternalConfirmDialog(
3730                       jalview.gui.Desktop.desktop,
3731                       MessageManager
3732                               .getString("label.remove_from_default_list"),
3733                       MessageManager
3734                               .getString("label.remove_user_defined_colour"),
3735                       JOptionPane.YES_NO_OPTION);
3736               if (option == JOptionPane.YES_OPTION)
3737               {
3738                 jalview.gui.UserDefinedColours
3739                         .removeColourFromDefaults(radioItem.getText());
3740                 colourMenu.remove(radioItem);
3741               }
3742               else
3743               {
3744                 radioItem.addActionListener(new ActionListener()
3745                 {
3746                   @Override
3747                   public void actionPerformed(ActionEvent evt)
3748                   {
3749                     userDefinedColour_actionPerformed(evt);
3750                   }
3751                 });
3752               }
3753             }
3754           }
3755         });
3756         radioItem.addActionListener(new ActionListener()
3757         {
3758           @Override
3759           public void actionPerformed(ActionEvent evt)
3760           {
3761             userDefinedColour_actionPerformed(evt);
3762           }
3763         });
3764
3765         colourMenu.insert(radioItem, 15);
3766         colours.add(radioItem);
3767       }
3768     }
3769   }
3770
3771   /**
3772    * DOCUMENT ME!
3773    *
3774    * @param e
3775    *          DOCUMENT ME!
3776    */
3777   @Override
3778   public void PIDColour_actionPerformed(ActionEvent e)
3779   {
3780     changeColour(new PIDColourScheme());
3781   }
3782
3783   /**
3784    * DOCUMENT ME!
3785    *
3786    * @param e
3787    *          DOCUMENT ME!
3788    */
3789   @Override
3790   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3791   {
3792     changeColour(new Blosum62ColourScheme());
3793   }
3794
3795   /**
3796    * DOCUMENT ME!
3797    *
3798    * @param e
3799    *          DOCUMENT ME!
3800    */
3801   @Override
3802   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3803   {
3804     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3805     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3806             .getAlignment().getSequenceAt(0), null);
3807     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3808             viewport.getAlignment()));
3809     alignPanel.paintAlignment(true);
3810   }
3811
3812   /**
3813    * DOCUMENT ME!
3814    *
3815    * @param e
3816    *          DOCUMENT ME!
3817    */
3818   @Override
3819   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3820   {
3821     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3822     AlignmentSorter.sortByID(viewport.getAlignment());
3823     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3824             viewport.getAlignment()));
3825     alignPanel.paintAlignment(true);
3826   }
3827
3828   /**
3829    * DOCUMENT ME!
3830    *
3831    * @param e
3832    *          DOCUMENT ME!
3833    */
3834   @Override
3835   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3836   {
3837     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3838     AlignmentSorter.sortByLength(viewport.getAlignment());
3839     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3840             viewport.getAlignment()));
3841     alignPanel.paintAlignment(true);
3842   }
3843
3844   /**
3845    * DOCUMENT ME!
3846    *
3847    * @param e
3848    *          DOCUMENT ME!
3849    */
3850   @Override
3851   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3852   {
3853     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3854     AlignmentSorter.sortByGroup(viewport.getAlignment());
3855     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3856             viewport.getAlignment()));
3857
3858     alignPanel.paintAlignment(true);
3859   }
3860
3861   /**
3862    * DOCUMENT ME!
3863    *
3864    * @param e
3865    *          DOCUMENT ME!
3866    */
3867   @Override
3868   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3869   {
3870     new RedundancyPanel(alignPanel, this);
3871   }
3872
3873   /**
3874    * DOCUMENT ME!
3875    *
3876    * @param e
3877    *          DOCUMENT ME!
3878    */
3879   @Override
3880   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3881   {
3882     if ((viewport.getSelectionGroup() == null)
3883             || (viewport.getSelectionGroup().getSize() < 2))
3884     {
3885       JOptionPane.showInternalMessageDialog(this, MessageManager
3886               .getString("label.you_must_select_least_two_sequences"),
3887               MessageManager.getString("label.invalid_selection"),
3888               JOptionPane.WARNING_MESSAGE);
3889     }
3890     else
3891     {
3892       JInternalFrame frame = new JInternalFrame();
3893       frame.setContentPane(new PairwiseAlignPanel(viewport));
3894       Desktop.addInternalFrame(frame,
3895               MessageManager.getString("action.pairwise_alignment"), 600,
3896               500);
3897     }
3898   }
3899
3900   /**
3901    * DOCUMENT ME!
3902    *
3903    * @param e
3904    *          DOCUMENT ME!
3905    */
3906   @Override
3907   public void PCAMenuItem_actionPerformed(ActionEvent e)
3908   {
3909     if (((viewport.getSelectionGroup() != null)
3910             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3911             .getSelectionGroup().getSize() > 0))
3912             || (viewport.getAlignment().getHeight() < 4))
3913     {
3914       JOptionPane
3915               .showInternalMessageDialog(
3916                       this,
3917                       MessageManager
3918                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3919                       MessageManager
3920                               .getString("label.sequence_selection_insufficient"),
3921                       JOptionPane.WARNING_MESSAGE);
3922
3923       return;
3924     }
3925
3926     new PCAPanel(alignPanel);
3927   }
3928
3929   @Override
3930   public void autoCalculate_actionPerformed(ActionEvent e)
3931   {
3932     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3933     if (viewport.autoCalculateConsensus)
3934     {
3935       viewport.firePropertyChange("alignment", null, viewport
3936               .getAlignment().getSequences());
3937     }
3938   }
3939
3940   @Override
3941   public void sortByTreeOption_actionPerformed(ActionEvent e)
3942   {
3943     viewport.sortByTree = sortByTree.isSelected();
3944   }
3945
3946   @Override
3947   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3948   {
3949     viewport.followSelection = listenToViewSelections.isSelected();
3950   }
3951
3952   /**
3953    * DOCUMENT ME!
3954    *
3955    * @param e
3956    *          DOCUMENT ME!
3957    */
3958   @Override
3959   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3960   {
3961     newTreePanel("AV", "PID", "Average distance tree using PID");
3962   }
3963
3964   /**
3965    * DOCUMENT ME!
3966    *
3967    * @param e
3968    *          DOCUMENT ME!
3969    */
3970   @Override
3971   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3972   {
3973     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3974   }
3975
3976   /**
3977    * DOCUMENT ME!
3978    *
3979    * @param e
3980    *          DOCUMENT ME!
3981    */
3982   @Override
3983   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3984   {
3985     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3986   }
3987
3988   /**
3989    * DOCUMENT ME!
3990    *
3991    * @param e
3992    *          DOCUMENT ME!
3993    */
3994   @Override
3995   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3996   {
3997     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3998   }
3999
4000   /**
4001    * DOCUMENT ME!
4002    *
4003    * @param type
4004    *          DOCUMENT ME!
4005    * @param pwType
4006    *          DOCUMENT ME!
4007    * @param title
4008    *          DOCUMENT ME!
4009    */
4010   void newTreePanel(String type, String pwType, String title)
4011   {
4012     TreePanel tp;
4013
4014     if (viewport.getSelectionGroup() != null
4015             && viewport.getSelectionGroup().getSize() > 0)
4016     {
4017       if (viewport.getSelectionGroup().getSize() < 3)
4018       {
4019         JOptionPane
4020                 .showMessageDialog(
4021                         Desktop.desktop,
4022                         MessageManager
4023                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
4024                         MessageManager
4025                                 .getString("label.not_enough_sequences"),
4026                         JOptionPane.WARNING_MESSAGE);
4027         return;
4028       }
4029
4030       SequenceGroup sg = viewport.getSelectionGroup();
4031
4032       /* Decide if the selection is a column region */
4033       for (SequenceI _s : sg.getSequences())
4034       {
4035         if (_s.getLength() < sg.getEndRes())
4036         {
4037           JOptionPane
4038                   .showMessageDialog(
4039                           Desktop.desktop,
4040                           MessageManager
4041                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
4042                           MessageManager
4043                                   .getString("label.sequences_selection_not_aligned"),
4044                           JOptionPane.WARNING_MESSAGE);
4045
4046           return;
4047         }
4048       }
4049
4050       title = title + " on region";
4051       tp = new TreePanel(alignPanel, type, pwType);
4052     }
4053     else
4054     {
4055       // are the visible sequences aligned?
4056       if (!viewport.getAlignment().isAligned(false))
4057       {
4058         JOptionPane
4059                 .showMessageDialog(
4060                         Desktop.desktop,
4061                         MessageManager
4062                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4063                         MessageManager
4064                                 .getString("label.sequences_not_aligned"),
4065                         JOptionPane.WARNING_MESSAGE);
4066
4067         return;
4068       }
4069
4070       if (viewport.getAlignment().getHeight() < 2)
4071       {
4072         return;
4073       }
4074
4075       tp = new TreePanel(alignPanel, type, pwType);
4076     }
4077
4078     title += " from ";
4079
4080     if (viewport.viewName != null)
4081     {
4082       title += viewport.viewName + " of ";
4083     }
4084
4085     title += this.title;
4086
4087     Desktop.addInternalFrame(tp, title, 600, 500);
4088   }
4089
4090   /**
4091    * DOCUMENT ME!
4092    *
4093    * @param title
4094    *          DOCUMENT ME!
4095    * @param order
4096    *          DOCUMENT ME!
4097    */
4098   public void addSortByOrderMenuItem(String title,
4099           final AlignmentOrder order)
4100   {
4101     final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
4102     sort.add(item);
4103     item.addActionListener(new java.awt.event.ActionListener()
4104     {
4105       @Override
4106       public void actionPerformed(ActionEvent e)
4107       {
4108         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4109
4110         // TODO: JBPNote - have to map order entries to curent SequenceI
4111         // pointers
4112         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4113
4114         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4115                 .getAlignment()));
4116
4117         alignPanel.paintAlignment(true);
4118       }
4119     });
4120   }
4121
4122   /**
4123    * Add a new sort by annotation score menu item
4124    *
4125    * @param sort
4126    *          the menu to add the option to
4127    * @param scoreLabel
4128    *          the label used to retrieve scores for each sequence on the
4129    *          alignment
4130    */
4131   public void addSortByAnnotScoreMenuItem(JMenu sort,
4132           final String scoreLabel)
4133   {
4134     final JMenuItem item = new JMenuItem(scoreLabel);
4135     sort.add(item);
4136     item.addActionListener(new java.awt.event.ActionListener()
4137     {
4138       @Override
4139       public void actionPerformed(ActionEvent e)
4140       {
4141         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4142         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4143                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4144         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4145                 viewport.getAlignment()));
4146         alignPanel.paintAlignment(true);
4147       }
4148     });
4149   }
4150
4151   /**
4152    * last hash for alignment's annotation array - used to minimise cost of
4153    * rebuild.
4154    */
4155   protected int _annotationScoreVectorHash;
4156
4157   /**
4158    * search the alignment and rebuild the sort by annotation score submenu the
4159    * last alignment annotation vector hash is stored to minimize cost of
4160    * rebuilding in subsequence calls.
4161    *
4162    */
4163   @Override
4164   public void buildSortByAnnotationScoresMenu()
4165   {
4166     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4167     {
4168       return;
4169     }
4170
4171     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4172     {
4173       sortByAnnotScore.removeAll();
4174       // almost certainly a quicker way to do this - but we keep it simple
4175       Hashtable scoreSorts = new Hashtable();
4176       AlignmentAnnotation aann[];
4177       for (SequenceI sqa : viewport.getAlignment().getSequences())
4178       {
4179         aann = sqa.getAnnotation();
4180         for (int i = 0; aann != null && i < aann.length; i++)
4181         {
4182           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4183           {
4184             scoreSorts.put(aann[i].label, aann[i].label);
4185           }
4186         }
4187       }
4188       Enumeration labels = scoreSorts.keys();
4189       while (labels.hasMoreElements())
4190       {
4191         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4192                 (String) labels.nextElement());
4193       }
4194       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4195       scoreSorts.clear();
4196
4197       _annotationScoreVectorHash = viewport.getAlignment()
4198               .getAlignmentAnnotation().hashCode();
4199     }
4200   }
4201
4202   /**
4203    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4204    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4205    * call. Listeners are added to remove the menu item when the treePanel is
4206    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4207    * modified.
4208    *
4209    * @param treePanel
4210    *          Displayed tree window.
4211    * @param title
4212    *          SortBy menu item title.
4213    */
4214   @Override
4215   public void buildTreeMenu()
4216   {
4217     calculateTree.removeAll();
4218     // build the calculate menu
4219
4220     for (final String type : new String[]
4221     { "NJ", "AV" })
4222     {
4223       String treecalcnm = MessageManager.getString("label.tree_calc_"
4224               + type.toLowerCase());
4225       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4226       {
4227         JMenuItem tm = new JMenuItem();
4228         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4229         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4230         {
4231           String smn = MessageManager.getStringOrReturn(
4232                   "label.score_model_", sm.getName());
4233           final String title = MessageManager.formatMessage(
4234                   "label.treecalc_title", treecalcnm, smn);
4235           tm.setText(title);//
4236           tm.addActionListener(new java.awt.event.ActionListener()
4237           {
4238             @Override
4239             public void actionPerformed(ActionEvent e)
4240             {
4241               newTreePanel(type, pwtype, title);
4242             }
4243           });
4244           calculateTree.add(tm);
4245         }
4246
4247       }
4248     }
4249     sortByTreeMenu.removeAll();
4250
4251     List<Component> comps = PaintRefresher.components.get(viewport
4252             .getSequenceSetId());
4253     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4254     for (Component comp : comps)
4255     {
4256       if (comp instanceof TreePanel)
4257       {
4258         treePanels.add((TreePanel) comp);
4259       }
4260     }
4261
4262     if (treePanels.size() < 1)
4263     {
4264       sortByTreeMenu.setVisible(false);
4265       return;
4266     }
4267
4268     sortByTreeMenu.setVisible(true);
4269
4270     for (final TreePanel tp : treePanels)
4271     {
4272       final JMenuItem item = new JMenuItem(tp.getTitle());
4273       item.addActionListener(new java.awt.event.ActionListener()
4274       {
4275         @Override
4276         public void actionPerformed(ActionEvent e)
4277         {
4278           tp.sortByTree_actionPerformed();
4279           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4280
4281         }
4282       });
4283
4284       sortByTreeMenu.add(item);
4285     }
4286   }
4287
4288   public boolean sortBy(AlignmentOrder alorder, String undoname)
4289   {
4290     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4291     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4292     if (undoname != null)
4293     {
4294       addHistoryItem(new OrderCommand(undoname, oldOrder,
4295               viewport.getAlignment()));
4296     }
4297     alignPanel.paintAlignment(true);
4298     return true;
4299   }
4300
4301   /**
4302    * Work out whether the whole set of sequences or just the selected set will
4303    * be submitted for multiple alignment.
4304    *
4305    */
4306   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4307   {
4308     // Now, check we have enough sequences
4309     AlignmentView msa = null;
4310
4311     if ((viewport.getSelectionGroup() != null)
4312             && (viewport.getSelectionGroup().getSize() > 1))
4313     {
4314       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4315       // some common interface!
4316       /*
4317        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4318        * SequenceI[sz = seqs.getSize(false)];
4319        *
4320        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4321        * seqs.getSequenceAt(i); }
4322        */
4323       msa = viewport.getAlignmentView(true);
4324     }
4325     else if (viewport.getSelectionGroup() != null
4326             && viewport.getSelectionGroup().getSize() == 1)
4327     {
4328       int option = JOptionPane.showConfirmDialog(this,
4329               MessageManager.getString("warn.oneseq_msainput_selection"),
4330               MessageManager.getString("label.invalid_selection"),
4331               JOptionPane.OK_CANCEL_OPTION);
4332       if (option == JOptionPane.OK_OPTION)
4333       {
4334         msa = viewport.getAlignmentView(false);
4335       }
4336     }
4337     else
4338     {
4339       msa = viewport.getAlignmentView(false);
4340     }
4341     return msa;
4342   }
4343
4344   /**
4345    * Decides what is submitted to a secondary structure prediction service: the
4346    * first sequence in the alignment, or in the current selection, or, if the
4347    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4348    * region or the whole alignment. (where the first sequence in the set is the
4349    * one that the prediction will be for).
4350    */
4351   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4352   {
4353     AlignmentView seqs = null;
4354
4355     if ((viewport.getSelectionGroup() != null)
4356             && (viewport.getSelectionGroup().getSize() > 0))
4357     {
4358       seqs = viewport.getAlignmentView(true);
4359     }
4360     else
4361     {
4362       seqs = viewport.getAlignmentView(false);
4363     }
4364     // limit sequences - JBPNote in future - could spawn multiple prediction
4365     // jobs
4366     // TODO: viewport.getAlignment().isAligned is a global state - the local
4367     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4368     if (!viewport.getAlignment().isAligned(false))
4369     {
4370       seqs.setSequences(new SeqCigar[]
4371       { seqs.getSequences()[0] });
4372       // TODO: if seqs.getSequences().length>1 then should really have warned
4373       // user!
4374
4375     }
4376     return seqs;
4377   }
4378
4379   /**
4380    * DOCUMENT ME!
4381    *
4382    * @param e
4383    *          DOCUMENT ME!
4384    */
4385   @Override
4386   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4387   {
4388     // Pick the tree file
4389     JalviewFileChooser chooser = new JalviewFileChooser(
4390             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4391     chooser.setFileView(new JalviewFileView());
4392     chooser.setDialogTitle(MessageManager
4393             .getString("label.select_newick_like_tree_file"));
4394     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4395
4396     int value = chooser.showOpenDialog(null);
4397
4398     if (value == JalviewFileChooser.APPROVE_OPTION)
4399     {
4400       String choice = chooser.getSelectedFile().getPath();
4401       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4402       jalview.io.NewickFile fin = null;
4403       try
4404       {
4405         fin = new jalview.io.NewickFile(choice, "File");
4406         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4407       } catch (Exception ex)
4408       {
4409         JOptionPane
4410                 .showMessageDialog(
4411                         Desktop.desktop,
4412                         ex.getMessage(),
4413                         MessageManager
4414                                 .getString("label.problem_reading_tree_file"),
4415                         JOptionPane.WARNING_MESSAGE);
4416         ex.printStackTrace();
4417       }
4418       if (fin != null && fin.hasWarningMessage())
4419       {
4420         JOptionPane.showMessageDialog(Desktop.desktop, fin
4421                 .getWarningMessage(), MessageManager
4422                 .getString("label.possible_problem_with_tree_file"),
4423                 JOptionPane.WARNING_MESSAGE);
4424       }
4425     }
4426   }
4427
4428   @Override
4429   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4430   {
4431     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4432   }
4433
4434   public TreePanel ShowNewickTree(NewickFile nf, String title)
4435   {
4436     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4437   }
4438
4439   public TreePanel ShowNewickTree(NewickFile nf, String title,
4440           AlignmentView input)
4441   {
4442     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4443   }
4444
4445   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4446           int h, int x, int y)
4447   {
4448     return ShowNewickTree(nf, title, null, w, h, x, y);
4449   }
4450
4451   /**
4452    * Add a treeviewer for the tree extracted from a newick file object to the
4453    * current alignment view
4454    *
4455    * @param nf
4456    *          the tree
4457    * @param title
4458    *          tree viewer title
4459    * @param input
4460    *          Associated alignment input data (or null)
4461    * @param w
4462    *          width
4463    * @param h
4464    *          height
4465    * @param x
4466    *          position
4467    * @param y
4468    *          position
4469    * @return TreePanel handle
4470    */
4471   public TreePanel ShowNewickTree(NewickFile nf, String title,
4472           AlignmentView input, int w, int h, int x, int y)
4473   {
4474     TreePanel tp = null;
4475
4476     try
4477     {
4478       nf.parse();
4479
4480       if (nf.getTree() != null)
4481       {
4482         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4483
4484         tp.setSize(w, h);
4485
4486         if (x > 0 && y > 0)
4487         {
4488           tp.setLocation(x, y);
4489         }
4490
4491         Desktop.addInternalFrame(tp, title, w, h);
4492       }
4493     } catch (Exception ex)
4494     {
4495       ex.printStackTrace();
4496     }
4497
4498     return tp;
4499   }
4500
4501   private boolean buildingMenu = false;
4502
4503   /**
4504    * Generates menu items and listener event actions for web service clients
4505    *
4506    */
4507   public void BuildWebServiceMenu()
4508   {
4509     while (buildingMenu)
4510     {
4511       try
4512       {
4513         System.err.println("Waiting for building menu to finish.");
4514         Thread.sleep(10);
4515       } catch (Exception e)
4516       {
4517       }
4518       ;
4519     }
4520     final AlignFrame me = this;
4521     buildingMenu = true;
4522     new Thread(new Runnable()
4523     {
4524       @Override
4525       public void run()
4526       {
4527         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4528         try
4529         {
4530           System.err.println("Building ws menu again "
4531                   + Thread.currentThread());
4532           // TODO: add support for context dependent disabling of services based
4533           // on
4534           // alignment and current selection
4535           // TODO: add additional serviceHandle parameter to specify abstract
4536           // handler
4537           // class independently of AbstractName
4538           // TODO: add in rediscovery GUI function to restart discoverer
4539           // TODO: group services by location as well as function and/or
4540           // introduce
4541           // object broker mechanism.
4542           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4543           final IProgressIndicator af = me;
4544           final JMenu msawsmenu = new JMenu("Alignment");
4545           final JMenu secstrmenu = new JMenu(
4546                   "Secondary Structure Prediction");
4547           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4548           final JMenu analymenu = new JMenu("Analysis");
4549           final JMenu dismenu = new JMenu("Protein Disorder");
4550           // final JMenu msawsmenu = new
4551           // JMenu(MessageManager.getString("label.alignment"));
4552           // final JMenu secstrmenu = new
4553           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4554           // final JMenu seqsrchmenu = new
4555           // JMenu(MessageManager.getString("label.sequence_database_search"));
4556           // final JMenu analymenu = new
4557           // JMenu(MessageManager.getString("label.analysis"));
4558           // final JMenu dismenu = new
4559           // JMenu(MessageManager.getString("label.protein_disorder"));
4560           // JAL-940 - only show secondary structure prediction services from
4561           // the legacy server
4562           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4563               // &&
4564           Discoverer.services != null && (Discoverer.services.size() > 0))
4565           {
4566             // TODO: refactor to allow list of AbstractName/Handler bindings to
4567             // be
4568             // stored or retrieved from elsewhere
4569             // No MSAWS used any more:
4570             // Vector msaws = null; // (Vector)
4571             // Discoverer.services.get("MsaWS");
4572             Vector secstrpr = (Vector) Discoverer.services
4573                     .get("SecStrPred");
4574             if (secstrpr != null)
4575             {
4576               // Add any secondary structure prediction services
4577               for (int i = 0, j = secstrpr.size(); i < j; i++)
4578               {
4579                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4580                         .get(i);
4581                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4582                         .getServiceClient(sh);
4583                 int p = secstrmenu.getItemCount();
4584                 impl.attachWSMenuEntry(secstrmenu, me);
4585                 int q = secstrmenu.getItemCount();
4586                 for (int litm = p; litm < q; litm++)
4587                 {
4588                   legacyItems.add(secstrmenu.getItem(litm));
4589                 }
4590               }
4591             }
4592           }
4593
4594           // Add all submenus in the order they should appear on the web
4595           // services menu
4596           wsmenu.add(msawsmenu);
4597           wsmenu.add(secstrmenu);
4598           wsmenu.add(dismenu);
4599           wsmenu.add(analymenu);
4600           // No search services yet
4601           // wsmenu.add(seqsrchmenu);
4602
4603           javax.swing.SwingUtilities.invokeLater(new Runnable()
4604           {
4605             @Override
4606             public void run()
4607             {
4608               try
4609               {
4610                 webService.removeAll();
4611                 // first, add discovered services onto the webservices menu
4612                 if (wsmenu.size() > 0)
4613                 {
4614                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4615                   {
4616                     webService.add(wsmenu.get(i));
4617                   }
4618                 }
4619                 else
4620                 {
4621                   webService.add(me.webServiceNoServices);
4622                 }
4623                 // TODO: move into separate menu builder class.
4624                 boolean new_sspred = false;
4625                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4626                 {
4627                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4628                   if (jws2servs != null)
4629                   {
4630                     if (jws2servs.hasServices())
4631                     {
4632                       jws2servs.attachWSMenuEntry(webService, me);
4633                       for (Jws2Instance sv : jws2servs.getServices())
4634                       {
4635                         if (sv.description.toLowerCase().contains("jpred"))
4636                         {
4637                           for (JMenuItem jmi : legacyItems)
4638                           {
4639                             jmi.setVisible(false);
4640                           }
4641                         }
4642                       }
4643
4644                     }
4645                     if (jws2servs.isRunning())
4646                     {
4647                       JMenuItem tm = new JMenuItem(
4648                               "Still discovering JABA Services");
4649                       tm.setEnabled(false);
4650                       webService.add(tm);
4651                     }
4652                   }
4653                 }
4654                 build_urlServiceMenu(me.webService);
4655                 build_fetchdbmenu(webService);
4656                 for (JMenu item : wsmenu)
4657                 {
4658                   if (item.getItemCount() == 0)
4659                   {
4660                     item.setEnabled(false);
4661                   }
4662                   else
4663                   {
4664                     item.setEnabled(true);
4665                   }
4666                 }
4667               } catch (Exception e)
4668               {
4669                 Cache.log
4670                         .debug("Exception during web service menu building process.",
4671                                 e);
4672               }
4673               ;
4674             }
4675           });
4676         } catch (Exception e)
4677         {
4678         }
4679         ;
4680
4681         buildingMenu = false;
4682       }
4683     }).start();
4684
4685   }
4686
4687   /**
4688    * construct any groupURL type service menu entries.
4689    *
4690    * @param webService
4691    */
4692   private void build_urlServiceMenu(JMenu webService)
4693   {
4694     // TODO: remove this code when 2.7 is released
4695     // DEBUG - alignmentView
4696     /*
4697      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4698      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4699      *
4700      * @Override public void actionPerformed(ActionEvent e) {
4701      * jalview.datamodel.AlignmentView
4702      * .testSelectionViews(af.viewport.getAlignment(),
4703      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4704      *
4705      * }); webService.add(testAlView);
4706      */
4707     // TODO: refactor to RestClient discoverer and merge menu entries for
4708     // rest-style services with other types of analysis/calculation service
4709     // SHmmr test client - still being implemented.
4710     // DEBUG - alignmentView
4711
4712     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4713             .getRestClients())
4714     {
4715       client.attachWSMenuEntry(
4716               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4717               this);
4718     }
4719   }
4720
4721   /*
4722    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4723    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4724    * getProperty("LAST_DIRECTORY"));
4725    *
4726    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4727    * to Vamsas file"); chooser.setToolTipText("Export");
4728    *
4729    * int value = chooser.showSaveDialog(this);
4730    *
4731    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4732    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4733    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4734    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4735    */
4736   /**
4737    * prototype of an automatically enabled/disabled analysis function
4738    *
4739    */
4740   protected void setShowProductsEnabled()
4741   {
4742     SequenceI[] selection = viewport.getSequenceSelection();
4743     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4744             viewport.getAlignment().getDataset()))
4745     {
4746       showProducts.setEnabled(true);
4747
4748     }
4749     else
4750     {
4751       showProducts.setEnabled(false);
4752     }
4753   }
4754
4755   /**
4756    * search selection for sequence xRef products and build the show products
4757    * menu.
4758    *
4759    * @param selection
4760    * @param dataset
4761    * @return true if showProducts menu should be enabled.
4762    */
4763   public boolean canShowProducts(SequenceI[] selection,
4764           boolean isRegionSelection, Alignment dataset)
4765   {
4766     boolean showp = false;
4767     try
4768     {
4769       showProducts.removeAll();
4770       final boolean dna = viewport.getAlignment().isNucleotide();
4771       final Alignment ds = dataset;
4772       String[] ptypes = (selection == null || selection.length == 0) ? null
4773               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4774       // Object[] prods =
4775       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4776       // selection, dataset, true);
4777       final SequenceI[] sel = selection;
4778       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4779       {
4780         showp = true;
4781         final boolean isRegSel = isRegionSelection;
4782         final AlignFrame af = this;
4783         final String source = ptypes[t];
4784         JMenuItem xtype = new JMenuItem(ptypes[t]);
4785         xtype.addActionListener(new ActionListener()
4786         {
4787
4788           @Override
4789           public void actionPerformed(ActionEvent e)
4790           {
4791             // TODO: new thread for this call with vis-delay
4792             af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4793                     isRegSel, dna, source);
4794           }
4795
4796         });
4797         showProducts.add(xtype);
4798       }
4799       showProducts.setVisible(showp);
4800       showProducts.setEnabled(showp);
4801     } catch (Exception e)
4802     {
4803       jalview.bin.Cache.log
4804               .warn("canTranslate threw an exception - please report to help@jalview.org",
4805                       e);
4806       return false;
4807     }
4808     return showp;
4809   }
4810
4811   protected void showProductsFor(SequenceI[] sel, Alignment ds,
4812           boolean isRegSel, boolean dna, String source)
4813   {
4814     final boolean fisRegSel = isRegSel;
4815     final boolean fdna = dna;
4816     final String fsrc = source;
4817     final AlignFrame ths = this;
4818     final SequenceI[] fsel = sel;
4819     Runnable foo = new Runnable()
4820     {
4821
4822       @Override
4823       public void run()
4824       {
4825         final long sttime = System.currentTimeMillis();
4826         ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4827         try
4828         {
4829           Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4830           // our local
4831           // dataset
4832           // reference
4833           Alignment prods = CrossRef
4834                   .findXrefSequences(fsel, fdna, fsrc, ds);
4835           if (prods != null)
4836           {
4837             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4838             for (int s = 0; s < sprods.length; s++)
4839             {
4840               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4841               if (ds.getSequences() == null
4842                       || !ds.getSequences().contains(
4843                               sprods[s].getDatasetSequence()))
4844               {
4845                 ds.addSequence(sprods[s].getDatasetSequence());
4846               }
4847               sprods[s].updatePDBIds();
4848             }
4849             Alignment al = new Alignment(sprods);
4850             Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4851             al.setDataset(ds);
4852             for (AlignedCodonFrame acf : cf)
4853             {
4854               al.addCodonFrame(acf);
4855             }
4856             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4857                     DEFAULT_HEIGHT);
4858             String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4859                     + " for " + ((fisRegSel) ? "selected region of " : "")
4860                     + getTitle();
4861             Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4862                     DEFAULT_HEIGHT);
4863           }
4864           else
4865           {
4866             System.err.println("No Sequences generated for xRef type "
4867                     + fsrc);
4868           }
4869         } catch (Exception e)
4870         {
4871           jalview.bin.Cache.log.error(
4872                   "Exception when finding crossreferences", e);
4873         } catch (OutOfMemoryError e)
4874         {
4875           new OOMWarning("whilst fetching crossreferences", e);
4876         } catch (Error e)
4877         {
4878           jalview.bin.Cache.log.error("Error when finding crossreferences",
4879                   e);
4880         }
4881         ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4882                 sttime);
4883       }
4884
4885     };
4886     Thread frunner = new Thread(foo);
4887     frunner.start();
4888   }
4889
4890   public boolean canShowTranslationProducts(SequenceI[] selection,
4891           AlignmentI alignment)
4892   {
4893     // old way
4894     try
4895     {
4896       return (jalview.analysis.Dna.canTranslate(selection,
4897               viewport.getViewAsVisibleContigs(true)));
4898     } catch (Exception e)
4899     {
4900       jalview.bin.Cache.log
4901               .warn("canTranslate threw an exception - please report to help@jalview.org",
4902                       e);
4903       return false;
4904     }
4905   }
4906
4907   /**
4908    * Construct and display a new frame containing the translation of this
4909    * frame's cDNA sequences to their aligned protein (amino acid) equivalents.
4910    */
4911   @Override
4912   public void showTranslation_actionPerformed(ActionEvent e)
4913   {
4914     AlignmentI al = null;
4915     try
4916     {
4917       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4918
4919       al = dna.translateCdna();
4920     } catch (Exception ex)
4921     {
4922       jalview.bin.Cache.log.error(
4923               "Exception during translation. Please report this !", ex);
4924       final String msg = MessageManager
4925               .getString("label.error_when_translating_sequences_submit_bug_report");
4926       final String title = MessageManager
4927               .getString("label.implementation_error")
4928               + MessageManager.getString("translation_failed");
4929       JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4930               JOptionPane.ERROR_MESSAGE);
4931       return;
4932     }
4933     if (al == null || al.getHeight() == 0)
4934     {
4935       final String msg = MessageManager
4936               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4937       final String title = MessageManager
4938               .getString("label.translation_failed");
4939       JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4940               JOptionPane.WARNING_MESSAGE);
4941     }
4942     else
4943     {
4944       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4945       Desktop.addInternalFrame(af, MessageManager.formatMessage(
4946               "label.translation_of_params", new String[]
4947               { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4948       // enable next line for linked editing
4949       // viewport.getStructureSelectionManager().addCommandListener(viewport);
4950     }
4951   }
4952
4953   /**
4954    * Try to load a features file onto the alignment.
4955    *
4956    * @param file
4957    *          contents or path to retrieve file
4958    * @param type
4959    *          access mode of file (see jalview.io.AlignFile)
4960    * @return true if features file was parsed corectly.
4961    */
4962   public boolean parseFeaturesFile(String file, String type)
4963   {
4964     boolean featuresFile = false;
4965     try
4966     {
4967       featuresFile = new FeaturesFile(file, type).parse(viewport
4968               .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4969               .getFeatureRenderer().featureColours, false,
4970               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4971     } catch (Exception ex)
4972     {
4973       ex.printStackTrace();
4974     }
4975
4976     if (featuresFile)
4977     {
4978       viewport.showSequenceFeatures = true;
4979       showSeqFeatures.setSelected(true);
4980       if (alignPanel.seqPanel.seqCanvas.fr != null)
4981       {
4982         // update the min/max ranges where necessary
4983         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4984       }
4985       if (featureSettings != null)
4986       {
4987         featureSettings.setTableData();
4988       }
4989       alignPanel.paintAlignment(true);
4990     }
4991
4992     return featuresFile;
4993   }
4994
4995   @Override
4996   public void dragEnter(DropTargetDragEvent evt)
4997   {
4998   }
4999
5000   @Override
5001   public void dragExit(DropTargetEvent evt)
5002   {
5003   }
5004
5005   @Override
5006   public void dragOver(DropTargetDragEvent evt)
5007   {
5008   }
5009
5010   @Override
5011   public void dropActionChanged(DropTargetDragEvent evt)
5012   {
5013   }
5014
5015   @Override
5016   public void drop(DropTargetDropEvent evt)
5017   {
5018     Transferable t = evt.getTransferable();
5019     java.util.List files = null;
5020
5021     try
5022     {
5023       DataFlavor uriListFlavor = new DataFlavor(
5024               "text/uri-list;class=java.lang.String");
5025       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5026       {
5027         // Works on Windows and MacOSX
5028         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5029         files = (java.util.List) t
5030                 .getTransferData(DataFlavor.javaFileListFlavor);
5031       }
5032       else if (t.isDataFlavorSupported(uriListFlavor))
5033       {
5034         // This is used by Unix drag system
5035         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5036         String data = (String) t.getTransferData(uriListFlavor);
5037         files = new java.util.ArrayList(1);
5038         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5039                 data, "\r\n"); st.hasMoreTokens();)
5040         {
5041           String s = st.nextToken();
5042           if (s.startsWith("#"))
5043           {
5044             // the line is a comment (as per the RFC 2483)
5045             continue;
5046           }
5047
5048           java.net.URI uri = new java.net.URI(s);
5049           // check to see if we can handle this kind of URI
5050           if (uri.getScheme().toLowerCase().startsWith("http"))
5051           {
5052             files.add(uri.toString());
5053           }
5054           else
5055           {
5056             // otherwise preserve old behaviour: catch all for file objects
5057             java.io.File file = new java.io.File(uri);
5058             files.add(file.toString());
5059           }
5060         }
5061       }
5062     } catch (Exception e)
5063     {
5064       e.printStackTrace();
5065     }
5066     if (files != null)
5067     {
5068       try
5069       {
5070         // check to see if any of these files have names matching sequences in
5071         // the alignment
5072         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5073                 .getAlignment().getSequencesArray());
5074         /**
5075          * Object[] { String,SequenceI}
5076          */
5077         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5078         ArrayList<String> filesnotmatched = new ArrayList<String>();
5079         for (int i = 0; i < files.size(); i++)
5080         {
5081           String file = files.get(i).toString();
5082           String pdbfn = "";
5083           String protocol = FormatAdapter.checkProtocol(file);
5084           if (protocol == jalview.io.FormatAdapter.FILE)
5085           {
5086             File fl = new File(file);
5087             pdbfn = fl.getName();
5088           }
5089           else if (protocol == jalview.io.FormatAdapter.URL)
5090           {
5091             URL url = new URL(file);
5092             pdbfn = url.getFile();
5093           }
5094           if (pdbfn.length() > 0)
5095           {
5096             // attempt to find a match in the alignment
5097             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5098             int l = 0, c = pdbfn.indexOf(".");
5099             while (mtch == null && c != -1)
5100             {
5101               do
5102               {
5103                 l = c;
5104               } while ((c = pdbfn.indexOf(".", l)) > l);
5105               if (l > -1)
5106               {
5107                 pdbfn = pdbfn.substring(0, l);
5108               }
5109               mtch = idm.findAllIdMatches(pdbfn);
5110             }
5111             if (mtch != null)
5112             {
5113               String type = null;
5114               try
5115               {
5116                 type = new IdentifyFile().Identify(file, protocol);
5117               } catch (Exception ex)
5118               {
5119                 type = null;
5120               }
5121               if (type != null)
5122               {
5123                 if (type.equalsIgnoreCase("PDB"))
5124                 {
5125                   filesmatched.add(new Object[]
5126                   { file, protocol, mtch });
5127                   continue;
5128                 }
5129               }
5130             }
5131             // File wasn't named like one of the sequences or wasn't a PDB file.
5132             filesnotmatched.add(file);
5133           }
5134         }
5135         int assocfiles = 0;
5136         if (filesmatched.size() > 0)
5137         {
5138           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5139                   || JOptionPane
5140                           .showConfirmDialog(
5141                                   this,
5142                                   MessageManager
5143                                           .formatMessage(
5144                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5145                                                   new String[]
5146                                                   { Integer.valueOf(
5147                                                           filesmatched
5148                                                                   .size())
5149                                                           .toString() }),
5150                                   MessageManager
5151                                           .getString("label.automatically_associate_pdb_files_by_name"),
5152                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5153
5154           {
5155             for (Object[] fm : filesmatched)
5156             {
5157               // try and associate
5158               // TODO: may want to set a standard ID naming formalism for
5159               // associating PDB files which have no IDs.
5160               for (SequenceI toassoc : (SequenceI[]) fm[2])
5161               {
5162                 PDBEntry pe = new AssociatePdbFileWithSeq()
5163                         .associatePdbWithSeq((String) fm[0],
5164                                 (String) fm[1], toassoc, false,
5165                                 Desktop.instance);
5166                 if (pe != null)
5167                 {
5168                   System.err.println("Associated file : "
5169                           + ((String) fm[0]) + " with "
5170                           + toassoc.getDisplayId(true));
5171                   assocfiles++;
5172                 }
5173               }
5174               alignPanel.paintAlignment(true);
5175             }
5176           }
5177         }
5178         if (filesnotmatched.size() > 0)
5179         {
5180           if (assocfiles > 0
5181                   && (Cache.getDefault(
5182                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5183                           .showConfirmDialog(
5184                                   this,
5185                                   "<html>"+MessageManager
5186                                           .formatMessage(
5187                                                   "label.ignore_unmatched_dropped_files_info",
5188                                                   new String[]
5189                                                   { Integer.valueOf(
5190                                                           filesnotmatched
5191                                                                   .size())
5192                                                           .toString() })+"</html>",
5193                                   MessageManager
5194                                           .getString("label.ignore_unmatched_dropped_files"),
5195                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5196           {
5197             return;
5198           }
5199           for (String fn : filesnotmatched)
5200           {
5201             loadJalviewDataFile(fn, null, null, null);
5202           }
5203
5204         }
5205       } catch (Exception ex)
5206       {
5207         ex.printStackTrace();
5208       }
5209     }
5210   }
5211
5212   /**
5213    * Attempt to load a "dropped" file or URL string: First by testing whether
5214    * it's and Annotation file, then a JNet file, and finally a features file. If
5215    * all are false then the user may have dropped an alignment file onto this
5216    * AlignFrame.
5217    *
5218    * @param file
5219    *          either a filename or a URL string.
5220    */
5221   public void loadJalviewDataFile(String file, String protocol,
5222           String format, SequenceI assocSeq)
5223   {
5224     try
5225     {
5226       if (protocol == null)
5227       {
5228         protocol = jalview.io.FormatAdapter.checkProtocol(file);
5229       }
5230       // if the file isn't identified, or not positively identified as some
5231       // other filetype (PFAM is default unidentified alignment file type) then
5232       // try to parse as annotation.
5233       boolean isAnnotation = (format == null || format
5234               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5235               .readAnnotationFile(viewport.getAlignment(), file, protocol)
5236               : false;
5237
5238       if (!isAnnotation)
5239       {
5240         // first see if its a T-COFFEE score file
5241         TCoffeeScoreFile tcf = null;
5242         try
5243         {
5244           tcf = new TCoffeeScoreFile(file, protocol);
5245           if (tcf.isValid())
5246           {
5247             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5248             {
5249               tcoffeeColour.setEnabled(true);
5250               tcoffeeColour.setSelected(true);
5251               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5252               isAnnotation = true;
5253               statusBar
5254                       .setText(MessageManager
5255                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5256             }
5257             else
5258             {
5259               // some problem - if no warning its probable that the ID matching
5260               // process didn't work
5261               JOptionPane
5262                       .showMessageDialog(
5263                               Desktop.desktop,
5264                               tcf.getWarningMessage() == null ? MessageManager
5265                                       .getString("label.check_file_matches_sequence_ids_alignment")
5266                                       : tcf.getWarningMessage(),
5267                               MessageManager
5268                                       .getString("label.problem_reading_tcoffee_score_file"),
5269                               JOptionPane.WARNING_MESSAGE);
5270             }
5271           }
5272           else
5273           {
5274             tcf = null;
5275           }
5276         } catch (Exception x)
5277         {
5278           Cache.log
5279                   .debug("Exception when processing data source as T-COFFEE score file",
5280                           x);
5281           tcf = null;
5282         }
5283         if (tcf == null)
5284         {
5285           // try to see if its a JNet 'concise' style annotation file *before*
5286           // we
5287           // try to parse it as a features file
5288           if (format == null)
5289           {
5290             format = new IdentifyFile().Identify(file, protocol);
5291           }
5292           if (format.equalsIgnoreCase("JnetFile"))
5293           {
5294             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5295                     file, protocol);
5296             new JnetAnnotationMaker().add_annotation(predictions,
5297                     viewport.getAlignment(), 0, false);
5298             isAnnotation = true;
5299           }
5300           else
5301           {
5302             /*
5303              * if (format.equalsIgnoreCase("PDB")) {
5304              *
5305              * String pdbfn = ""; // try to match up filename with sequence id
5306              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5307              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5308              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5309              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5310              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5311              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5312              * // attempt to find a match in the alignment SequenceI mtch =
5313              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5314              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5315              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5316              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5317              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5318              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5319              * { System.err.println("Associated file : " + file + " with " +
5320              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5321              * TODO: maybe need to load as normal otherwise return; } }
5322              */
5323             // try to parse it as a features file
5324             boolean isGroupsFile = parseFeaturesFile(file, protocol);
5325             // if it wasn't a features file then we just treat it as a general
5326             // alignment file to load into the current view.
5327             if (!isGroupsFile)
5328             {
5329               new FileLoader().LoadFile(viewport, file, protocol, format);
5330             }
5331             else
5332             {
5333               alignPanel.paintAlignment(true);
5334             }
5335           }
5336         }
5337       }
5338       if (isAnnotation)
5339       {
5340
5341         alignPanel.adjustAnnotationHeight();
5342         viewport.updateSequenceIdColours();
5343         buildSortByAnnotationScoresMenu();
5344         alignPanel.paintAlignment(true);
5345       }
5346     } catch (Exception ex)
5347     {
5348       ex.printStackTrace();
5349     } catch (OutOfMemoryError oom)
5350     {
5351       try
5352       {
5353         System.gc();
5354       } catch (Exception x)
5355       {
5356       }
5357       ;
5358       new OOMWarning(
5359               "loading data "
5360                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5361                               : "using " + protocol + " from " + file)
5362                               : ".")
5363                       + (format != null ? "(parsing as '" + format
5364                               + "' file)" : ""), oom, Desktop.desktop);
5365     }
5366   }
5367
5368   /**
5369    * Method invoked by the ChangeListener on the tabbed pane, in other words
5370    * when a different tabbed pane is selected by the user or programmatically.
5371    */
5372   @Override
5373   public void tabSelectionChanged(int index)
5374   {
5375     if (index > -1)
5376     {
5377       alignPanel = alignPanels.get(index);
5378       viewport = alignPanel.av;
5379       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5380       setMenusFromViewport(viewport);
5381     }
5382   }
5383
5384   /**
5385    * On right mouse click on view tab, prompt for and set new view name.
5386    */
5387   @Override
5388   public void tabbedPane_mousePressed(MouseEvent e)
5389   {
5390     if (SwingUtilities.isRightMouseButton(e))
5391     {
5392       String msg = MessageManager.getString("label.enter_view_name");
5393       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5394               JOptionPane.QUESTION_MESSAGE);
5395
5396       if (reply != null)
5397       {
5398         viewport.viewName = reply;
5399         // TODO warn if reply is in getExistingViewNames()?
5400         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5401       }
5402     }
5403   }
5404
5405   public AlignViewport getCurrentView()
5406   {
5407     return viewport;
5408   }
5409
5410   /**
5411    * Open the dialog for regex description parsing.
5412    */
5413   @Override
5414   protected void extractScores_actionPerformed(ActionEvent e)
5415   {
5416     ParseProperties pp = new jalview.analysis.ParseProperties(
5417             viewport.getAlignment());
5418     // TODO: verify regex and introduce GUI dialog for version 2.5
5419     // if (pp.getScoresFromDescription("col", "score column ",
5420     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5421     // true)>0)
5422     if (pp.getScoresFromDescription("description column",
5423             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5424     {
5425       buildSortByAnnotationScoresMenu();
5426     }
5427   }
5428
5429   /*
5430    * (non-Javadoc)
5431    *
5432    * @see
5433    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5434    * )
5435    */
5436   @Override
5437   protected void showDbRefs_actionPerformed(ActionEvent e)
5438   {
5439     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5440   }
5441
5442   /*
5443    * (non-Javadoc)
5444    *
5445    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5446    * ActionEvent)
5447    */
5448   @Override
5449   protected void showNpFeats_actionPerformed(ActionEvent e)
5450   {
5451     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5452   }
5453
5454   /**
5455    * find the viewport amongst the tabs in this alignment frame and close that
5456    * tab
5457    *
5458    * @param av
5459    */
5460   public boolean closeView(AlignmentViewport av)
5461   {
5462     if (viewport == av)
5463     {
5464       this.closeMenuItem_actionPerformed(false);
5465       return true;
5466     }
5467     Component[] comp = tabbedPane.getComponents();
5468     for (int i = 0; comp != null && i < comp.length; i++)
5469     {
5470       if (comp[i] instanceof AlignmentPanel)
5471       {
5472         if (((AlignmentPanel) comp[i]).av == av)
5473         {
5474           // close the view.
5475           closeView((AlignmentPanel) comp[i]);
5476           return true;
5477         }
5478       }
5479     }
5480     return false;
5481   }
5482
5483   protected void build_fetchdbmenu(JMenu webService)
5484   {
5485     // Temporary hack - DBRef Fetcher always top level ws entry.
5486     // TODO We probably want to store a sequence database checklist in
5487     // preferences and have checkboxes.. rather than individual sources selected
5488     // here
5489     final JMenu rfetch = new JMenu(
5490             MessageManager.getString("action.fetch_db_references"));
5491     rfetch.setToolTipText(MessageManager
5492             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5493     webService.add(rfetch);
5494
5495     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5496             MessageManager.getString("option.trim_retrieved_seqs"));
5497     trimrs.setToolTipText(MessageManager
5498             .getString("label.trim_retrieved_sequences"));
5499     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5500     trimrs.addActionListener(new ActionListener()
5501     {
5502       @Override
5503       public void actionPerformed(ActionEvent e)
5504       {
5505         trimrs.setSelected(trimrs.isSelected());
5506         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5507                 Boolean.valueOf(trimrs.isSelected()).toString());
5508       };
5509     });
5510     rfetch.add(trimrs);
5511     JMenuItem fetchr = new JMenuItem(
5512             MessageManager.getString("label.standard_databases"));
5513     fetchr.setToolTipText(MessageManager
5514             .getString("label.fetch_embl_uniprot"));
5515     fetchr.addActionListener(new ActionListener()
5516     {
5517
5518       @Override
5519       public void actionPerformed(ActionEvent e)
5520       {
5521         new Thread(new Runnable()
5522         {
5523
5524           @Override
5525           public void run()
5526           {
5527             new jalview.ws.DBRefFetcher(alignPanel.av
5528                     .getSequenceSelection(), alignPanel.alignFrame)
5529                     .fetchDBRefs(false);
5530           }
5531         }).start();
5532
5533       }
5534
5535     });
5536     rfetch.add(fetchr);
5537     final AlignFrame me = this;
5538     new Thread(new Runnable()
5539     {
5540       @Override
5541       public void run()
5542       {
5543         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5544                 .getSequenceFetcherSingleton(me);
5545         javax.swing.SwingUtilities.invokeLater(new Runnable()
5546         {
5547           @Override
5548           public void run()
5549           {
5550             String[] dbclasses = sf.getOrderedSupportedSources();
5551             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5552             // jalview.util.QuickSort.sort(otherdb, otherdb);
5553             List<DbSourceProxy> otherdb;
5554             JMenu dfetch = new JMenu();
5555             JMenu ifetch = new JMenu();
5556             JMenuItem fetchr = null;
5557             int comp = 0, icomp = 0, mcomp = 15;
5558             String mname = null;
5559             int dbi = 0;
5560             for (String dbclass : dbclasses)
5561             {
5562               otherdb = sf.getSourceProxy(dbclass);
5563               // add a single entry for this class, or submenu allowing 'fetch
5564               // all' or pick one
5565               if (otherdb == null || otherdb.size() < 1)
5566               {
5567                 continue;
5568               }
5569               // List<DbSourceProxy> dbs=otherdb;
5570               // otherdb=new ArrayList<DbSourceProxy>();
5571               // for (DbSourceProxy db:dbs)
5572               // {
5573               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5574               // }
5575               if (mname == null)
5576               {
5577                 mname = "From " + dbclass;
5578               }
5579               if (otherdb.size() == 1)
5580               {
5581                 final DbSourceProxy[] dassource = otherdb
5582                         .toArray(new DbSourceProxy[0]);
5583                 DbSourceProxy src = otherdb.get(0);
5584                 fetchr = new JMenuItem(src.getDbSource());
5585                 fetchr.addActionListener(new ActionListener()
5586                 {
5587
5588                   @Override
5589                   public void actionPerformed(ActionEvent e)
5590                   {
5591                     new Thread(new Runnable()
5592                     {
5593
5594                       @Override
5595                       public void run()
5596                       {
5597                         new jalview.ws.DBRefFetcher(alignPanel.av
5598                                 .getSequenceSelection(),
5599                                 alignPanel.alignFrame, dassource)
5600                                 .fetchDBRefs(false);
5601                       }
5602                     }).start();
5603                   }
5604
5605                 });
5606                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5607                 dfetch.add(fetchr);
5608                 comp++;
5609               }
5610               else
5611               {
5612                 final DbSourceProxy[] dassource = otherdb
5613                         .toArray(new DbSourceProxy[0]);
5614                 // fetch all entry
5615                 DbSourceProxy src = otherdb.get(0);
5616                 fetchr = new JMenuItem(MessageManager.formatMessage(
5617                         "label.fetch_all_param", new String[]
5618                         { src.getDbSource() }));
5619                 fetchr.addActionListener(new ActionListener()
5620                 {
5621                   @Override
5622                   public void actionPerformed(ActionEvent e)
5623                   {
5624                     new Thread(new Runnable()
5625                     {
5626
5627                       @Override
5628                       public void run()
5629                       {
5630                         new jalview.ws.DBRefFetcher(alignPanel.av
5631                                 .getSequenceSelection(),
5632                                 alignPanel.alignFrame, dassource)
5633                                 .fetchDBRefs(false);
5634                       }
5635                     }).start();
5636                   }
5637                 });
5638
5639                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5640                 dfetch.add(fetchr);
5641                 comp++;
5642                 // and then build the rest of the individual menus
5643                 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5644                 icomp = 0;
5645                 String imname = null;
5646                 int i = 0;
5647                 for (DbSourceProxy sproxy : otherdb)
5648                 {
5649                   String dbname = sproxy.getDbName();
5650                   String sname = dbname.length() > 5 ? dbname.substring(0,
5651                           5) + "..." : dbname;
5652                   String msname = dbname.length() > 10 ? dbname.substring(
5653                           0, 10) + "..." : dbname;
5654                   if (imname == null)
5655                   {
5656                     imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5657                   }
5658                   fetchr = new JMenuItem(msname);
5659                   final DbSourceProxy[] dassrc =
5660                   { sproxy };
5661                   fetchr.addActionListener(new ActionListener()
5662                   {
5663
5664                     @Override
5665                     public void actionPerformed(ActionEvent e)
5666                     {
5667                       new Thread(new Runnable()
5668                       {
5669
5670                         @Override
5671                         public void run()
5672                         {
5673                           new jalview.ws.DBRefFetcher(alignPanel.av
5674                                   .getSequenceSelection(),
5675                                   alignPanel.alignFrame, dassrc)
5676                                   .fetchDBRefs(false);
5677                         }
5678                       }).start();
5679                     }
5680
5681                   });
5682                   fetchr.setToolTipText("<html>"
5683                           + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5684                   ifetch.add(fetchr);
5685                   ++i;
5686                   if (++icomp >= mcomp || i == (otherdb.size()))
5687                   {
5688                     ifetch.setText(MessageManager.formatMessage(
5689                             "label.source_to_target", imname, sname));
5690                     dfetch.add(ifetch);
5691                     ifetch = new JMenu();
5692                     imname = null;
5693                     icomp = 0;
5694                     comp++;
5695                   }
5696                 }
5697               }
5698               ++dbi;
5699               if (comp >= mcomp || dbi >= (dbclasses.length))
5700               {
5701                 dfetch.setText(MessageManager.formatMessage(
5702                         "label.source_to_target", mname, dbclass));
5703                 rfetch.add(dfetch);
5704                 dfetch = new JMenu();
5705                 mname = null;
5706                 comp = 0;
5707               }
5708             }
5709           }
5710         });
5711       }
5712     }).start();
5713
5714   }
5715
5716   /**
5717    * Left justify the whole alignment.
5718    */
5719   @Override
5720   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5721   {
5722     AlignmentI al = viewport.getAlignment();
5723     al.justify(false);
5724     viewport.firePropertyChange("alignment", null, al);
5725   }
5726
5727   /**
5728    * Right justify the whole alignment.
5729    */
5730   @Override
5731   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5732   {
5733     AlignmentI al = viewport.getAlignment();
5734     al.justify(true);
5735     viewport.firePropertyChange("alignment", null, al);
5736   }
5737
5738   public void setShowSeqFeatures(boolean b)
5739   {
5740     showSeqFeatures.setSelected(true);
5741     viewport.setShowSequenceFeatures(true);
5742   }
5743
5744   /*
5745    * (non-Javadoc)
5746    *
5747    * @see
5748    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5749    * awt.event.ActionEvent)
5750    */
5751   @Override
5752   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5753   {
5754     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5755     alignPanel.paintAlignment(true);
5756   }
5757
5758   /*
5759    * (non-Javadoc)
5760    *
5761    * @see
5762    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5763    * .ActionEvent)
5764    */
5765   @Override
5766   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5767   {
5768     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5769     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5770
5771   }
5772
5773   /*
5774    * (non-Javadoc)
5775    *
5776    * @see
5777    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5778    * .event.ActionEvent)
5779    */
5780   @Override
5781   protected void showGroupConservation_actionPerformed(ActionEvent e)
5782   {
5783     viewport.setShowGroupConservation(showGroupConservation.getState());
5784     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5785   }
5786
5787   /*
5788    * (non-Javadoc)
5789    *
5790    * @see
5791    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5792    * .event.ActionEvent)
5793    */
5794   @Override
5795   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5796   {
5797     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5798     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5799   }
5800
5801   /*
5802    * (non-Javadoc)
5803    *
5804    * @see
5805    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5806    * .event.ActionEvent)
5807    */
5808   @Override
5809   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5810   {
5811     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5812     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5813   }
5814
5815   @Override
5816   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5817   {
5818     showSequenceLogo.setState(true);
5819     viewport.setShowSequenceLogo(true);
5820     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5821     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5822   }
5823
5824   @Override
5825   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5826   {
5827     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5828   }
5829
5830   /*
5831    * (non-Javadoc)
5832    *
5833    * @see
5834    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5835    * .event.ActionEvent)
5836    */
5837   @Override
5838   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5839   {
5840     if (avc.makeGroupsFromSelection())
5841     {
5842       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5843       alignPanel.updateAnnotation();
5844       alignPanel.paintAlignment(true);
5845     }
5846   }
5847
5848   @Override
5849   protected void createGroup_actionPerformed(ActionEvent e)
5850   {
5851     if (avc.createGroup())
5852     {
5853       alignPanel.alignmentChanged();
5854     }
5855   }
5856
5857   @Override
5858   protected void unGroup_actionPerformed(ActionEvent e)
5859   {
5860     if (avc.unGroup())
5861     {
5862       alignPanel.alignmentChanged();
5863     }
5864   }
5865
5866   /**
5867    * make the given alignmentPanel the currently selected tab
5868    *
5869    * @param alignmentPanel
5870    */
5871   public void setDisplayedView(AlignmentPanel alignmentPanel)
5872   {
5873     if (!viewport.getSequenceSetId().equals(
5874             alignmentPanel.av.getSequenceSetId()))
5875     {
5876       throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5877     }
5878     if (tabbedPane != null
5879             & alignPanels.indexOf(alignmentPanel) != tabbedPane
5880                     .getSelectedIndex())
5881     {
5882       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5883     }
5884   }
5885
5886   /**
5887    * Action on selection of menu options to Show or Hide annotations.
5888    *
5889    * @param visible
5890    * @param forSequences
5891    *          update sequence-related annotations
5892    * @param forAlignment
5893    *          update non-sequence-related annotations
5894    */
5895   @Override
5896   protected void setAnnotationsVisibility(boolean visible,
5897           boolean forSequences, boolean forAlignment)
5898   {
5899     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5900             .getAlignmentAnnotation())
5901     {
5902       boolean apply = (aa.sequenceRef == null && forAlignment)
5903               || (aa.sequenceRef != null && forSequences);
5904       if (apply)
5905       {
5906         aa.visible = visible;
5907       }
5908     }
5909     alignPanel.validateAnnotationDimensions(false);
5910     alignPanel.alignmentChanged();
5911   }
5912
5913   /**
5914    * Store selected annotation sort order for the view and repaint.
5915    */
5916   @Override
5917   protected void sortAnnotations_actionPerformed()
5918   {
5919     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5920     this.alignPanel.av
5921             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5922     alignPanel.paintAlignment(true);
5923   }
5924
5925   /**
5926    *
5927    * @return alignment panels in this alignment frame
5928    */
5929   public List<? extends AlignmentViewPanel> getAlignPanels()
5930   {
5931     return alignPanels == null ? Arrays.asList(alignPanel)
5932             : alignPanels;
5933   }
5934
5935   /**
5936    * Open a new alignment window, with the cDNA associated with this (protein)
5937    * alignment, aligned as is the protein.
5938    */
5939   @Override
5940   protected void viewAsCdna_actionPerformed()
5941   {
5942     final AlignmentI alignment = getViewport().getAlignment();
5943     Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5944     if (mappings == null)
5945     {
5946       return;
5947     }
5948     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5949     for (SequenceI aaSeq : alignment.getSequences()) {
5950       for (AlignedCodonFrame acf : mappings) {
5951         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5952         if (dnaSeq != null)
5953         {
5954           /*
5955            * There is a cDNA mapping for this protein sequence - add to new
5956            * alignment. It will share the same dataset sequence as other mapped
5957            * cDNA (no new mappings need to be created).
5958            */
5959           final Sequence newSeq = new Sequence(dnaSeq);
5960           newSeq.setDatasetSequence(dnaSeq);
5961           cdnaSeqs.add(newSeq);
5962         }
5963       }
5964     }
5965     if (cdnaSeqs.size() == 0)
5966     {
5967       // show a warning dialog no mapped cDNA
5968       return;
5969     }
5970     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5971             .size()]));
5972     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5973             AlignFrame.DEFAULT_HEIGHT);
5974     cdna.alignAs(alignment);
5975     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5976             + this.title;
5977     Desktop.addInternalFrame(alignFrame, newtitle,
5978             AlignFrame.DEFAULT_WIDTH,
5979             AlignFrame.DEFAULT_HEIGHT);
5980
5981   }
5982 }
5983
5984 class PrintThread extends Thread
5985 {
5986   AlignmentPanel ap;
5987
5988   public PrintThread(AlignmentPanel ap)
5989   {
5990     this.ap = ap;
5991   }
5992
5993   static PageFormat pf;
5994
5995   @Override
5996   public void run()
5997   {
5998     PrinterJob printJob = PrinterJob.getPrinterJob();
5999
6000     if (pf != null)
6001     {
6002       printJob.setPrintable(ap, pf);
6003     }
6004     else
6005     {
6006       printJob.setPrintable(ap);
6007     }
6008
6009     if (printJob.printDialog())
6010     {
6011       try
6012       {
6013         printJob.print();
6014       } catch (Exception PrintException)
6015       {
6016         PrintException.printStackTrace();
6017       }
6018     }
6019   }
6020 }