src/jalview/gui/AlignFrame.java

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