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, this);
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.isEmpty())
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", true, seqs,
2577                 column, viewport.getAlignment());
2578         viewport.setStartRes(0);
2579       }
2580       else
2581       {
2582         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2583                 column, viewport.getAlignment());
2584       }
2585
2586       statusBar.setText(MessageManager.formatMessage(
2587               "label.removed_columns",
2588               new String[] { Integer.valueOf(trimRegion.getSize())
2589                       .toString() }));
2590
2591       addHistoryItem(trimRegion);
2592
2593       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2594       {
2595         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2596                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2597         {
2598           viewport.getAlignment().deleteGroup(sg);
2599         }
2600       }
2601
2602       viewport.firePropertyChange("alignment", null, viewport
2603               .getAlignment().getSequences());
2604     }
2605   }
2606
2607   /**
2608    * DOCUMENT ME!
2609    *
2610    * @param e
2611    *          DOCUMENT ME!
2612    */
2613   @Override
2614   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2615   {
2616     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2617
2618     SequenceI[] seqs;
2619     if (viewport.getSelectionGroup() != null)
2620     {
2621       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2622               viewport.getHiddenRepSequences());
2623       start = viewport.getSelectionGroup().getStartRes();
2624       end = viewport.getSelectionGroup().getEndRes();
2625     }
2626     else
2627     {
2628       seqs = viewport.getAlignment().getSequencesArray();
2629     }
2630
2631     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2632             "Remove Gapped Columns", seqs, start, end,
2633             viewport.getAlignment());
2634
2635     addHistoryItem(removeGapCols);
2636
2637     statusBar.setText(MessageManager.formatMessage(
2638             "label.removed_empty_columns",
2639             new Object[] { Integer.valueOf(removeGapCols.getSize())
2640                     .toString() }));
2641
2642     // This is to maintain viewport position on first residue
2643     // of first sequence
2644     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2645     int startRes = seq.findPosition(viewport.startRes);
2646     // ShiftList shifts;
2647     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2648     // edit.alColumnChanges=shifts.getInverse();
2649     // if (viewport.hasHiddenColumns)
2650     // viewport.getColumnSelection().compensateForEdits(shifts);
2651     viewport.setStartRes(seq.findIndex(startRes) - 1);
2652     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2653             .getSequences());
2654
2655   }
2656
2657   /**
2658    * DOCUMENT ME!
2659    *
2660    * @param e
2661    *          DOCUMENT ME!
2662    */
2663   @Override
2664   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2665   {
2666     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2667
2668     SequenceI[] seqs;
2669     if (viewport.getSelectionGroup() != null)
2670     {
2671       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2672               viewport.getHiddenRepSequences());
2673       start = viewport.getSelectionGroup().getStartRes();
2674       end = viewport.getSelectionGroup().getEndRes();
2675     }
2676     else
2677     {
2678       seqs = viewport.getAlignment().getSequencesArray();
2679     }
2680
2681     // This is to maintain viewport position on first residue
2682     // of first sequence
2683     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2684     int startRes = seq.findPosition(viewport.startRes);
2685
2686     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2687             viewport.getAlignment()));
2688
2689     viewport.setStartRes(seq.findIndex(startRes) - 1);
2690
2691     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2692             .getSequences());
2693
2694   }
2695
2696   /**
2697    * DOCUMENT ME!
2698    *
2699    * @param e
2700    *          DOCUMENT ME!
2701    */
2702   @Override
2703   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2704   {
2705     viewport.setPadGaps(padGapsMenuitem.isSelected());
2706     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2707             .getSequences());
2708   }
2709
2710   /**
2711    * DOCUMENT ME!
2712    *
2713    * @param e
2714    *          DOCUMENT ME!
2715    */
2716   @Override
2717   public void findMenuItem_actionPerformed(ActionEvent e)
2718   {
2719     new Finder();
2720   }
2721
2722   /**
2723    * Create a new view of the current alignment.
2724    */
2725   @Override
2726   public void newView_actionPerformed(ActionEvent e)
2727   {
2728     newView(null, true);
2729   }
2730
2731   /**
2732    * Creates and shows a new view of the current alignment.
2733    *
2734    * @param viewTitle
2735    *          title of newly created view; if null, one will be generated
2736    * @param copyAnnotation
2737    *          if true then duplicate all annnotation, groups and settings
2738    * @return new alignment panel, already displayed.
2739    */
2740   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2741   {
2742     /*
2743      * Create a new AlignmentPanel (with its own, new Viewport)
2744      */
2745     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2746             true);
2747     if (!copyAnnotation)
2748     {
2749       /*
2750        * remove all groups and annotation except for the automatic stuff
2751        */
2752       newap.av.getAlignment().deleteAllGroups();
2753       newap.av.getAlignment().deleteAllAnnotations(false);
2754     }
2755
2756     newap.av.setGatherViewsHere(false);
2757
2758     if (viewport.viewName == null)
2759     {
2760       viewport.viewName = MessageManager
2761               .getString("label.view_name_original");
2762     }
2763
2764     /*
2765      * Views share the same edits undo and redo stacks
2766      */
2767     newap.av.setHistoryList(viewport.getHistoryList());
2768     newap.av.setRedoList(viewport.getRedoList());
2769
2770     /*
2771      * Views share the same mappings; need to deregister any new mappings
2772      * created by copyAlignPanel, and register the new reference to the shared
2773      * mappings
2774      */
2775     newap.av.replaceMappings(viewport.getAlignment());
2776
2777     newap.av.viewName = getNewViewName(viewTitle);
2778
2779     addAlignmentPanel(newap, true);
2780     newap.alignmentChanged();
2781
2782     if (alignPanels.size() == 2)
2783     {
2784       viewport.setGatherViewsHere(true);
2785     }
2786     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2787     return newap;
2788   }
2789
2790   /**
2791    * Make a new name for the view, ensuring it is unique within the current
2792    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2793    * these now use viewId. Unique view names are still desirable for usability.)
2794    *
2795    * @param viewTitle
2796    * @return
2797    */
2798   protected String getNewViewName(String viewTitle)
2799   {
2800     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2801     boolean addFirstIndex = false;
2802     if (viewTitle == null || viewTitle.trim().length() == 0)
2803     {
2804       viewTitle = MessageManager.getString("action.view");
2805       addFirstIndex = true;
2806     }
2807     else
2808     {
2809       index = 1;// we count from 1 if given a specific name
2810     }
2811     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2812
2813     List<Component> comps = PaintRefresher.components.get(viewport
2814             .getSequenceSetId());
2815
2816     List<String> existingNames = getExistingViewNames(comps);
2817
2818     while (existingNames.contains(newViewName))
2819     {
2820       newViewName = viewTitle + " " + (++index);
2821     }
2822     return newViewName;
2823   }
2824
2825   /**
2826    * Returns a list of distinct view names found in the given list of
2827    * components. View names are held on the viewport of an AlignmentPanel.
2828    *
2829    * @param comps
2830    * @return
2831    */
2832   protected List<String> getExistingViewNames(List<Component> comps)
2833   {
2834     List<String> existingNames = new ArrayList<String>();
2835     for (Component comp : comps)
2836     {
2837       if (comp instanceof AlignmentPanel)
2838       {
2839         AlignmentPanel ap = (AlignmentPanel) comp;
2840         if (!existingNames.contains(ap.av.viewName))
2841         {
2842           existingNames.add(ap.av.viewName);
2843         }
2844       }
2845     }
2846     return existingNames;
2847   }
2848
2849   /**
2850    * Explode tabbed views into separate windows.
2851    */
2852   @Override
2853   public void expandViews_actionPerformed(ActionEvent e)
2854   {
2855     Desktop.instance.explodeViews(this);
2856   }
2857
2858   /**
2859    * Gather views in separate windows back into a tabbed presentation.
2860    */
2861   @Override
2862   public void gatherViews_actionPerformed(ActionEvent e)
2863   {
2864     Desktop.instance.gatherViews(this);
2865   }
2866
2867   /**
2868    * DOCUMENT ME!
2869    *
2870    * @param e
2871    *          DOCUMENT ME!
2872    */
2873   @Override
2874   public void font_actionPerformed(ActionEvent e)
2875   {
2876     new FontChooser(alignPanel);
2877   }
2878
2879   /**
2880    * DOCUMENT ME!
2881    *
2882    * @param e
2883    *          DOCUMENT ME!
2884    */
2885   @Override
2886   protected void seqLimit_actionPerformed(ActionEvent e)
2887   {
2888     viewport.setShowJVSuffix(seqLimits.isSelected());
2889
2890     alignPanel.getIdPanel().getIdCanvas()
2891             .setPreferredSize(alignPanel.calculateIdWidth());
2892     alignPanel.paintAlignment(true);
2893   }
2894
2895   @Override
2896   public void idRightAlign_actionPerformed(ActionEvent e)
2897   {
2898     viewport.setRightAlignIds(idRightAlign.isSelected());
2899     alignPanel.paintAlignment(true);
2900   }
2901
2902   @Override
2903   public void centreColumnLabels_actionPerformed(ActionEvent e)
2904   {
2905     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2906     alignPanel.paintAlignment(true);
2907   }
2908
2909   /*
2910    * (non-Javadoc)
2911    *
2912    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2913    */
2914   @Override
2915   protected void followHighlight_actionPerformed()
2916   {
2917     /*
2918      * Set the 'follow' flag on the Viewport (and scroll to position if now
2919      * true).
2920      */
2921     final boolean state = this.followHighlightMenuItem.getState();
2922     viewport.setFollowHighlight(state);
2923     if (state)
2924     {
2925       alignPanel.scrollToPosition(
2926               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2927     }
2928   }
2929
2930   /**
2931    * DOCUMENT ME!
2932    *
2933    * @param e
2934    *          DOCUMENT ME!
2935    */
2936   @Override
2937   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2938   {
2939     viewport.setColourText(colourTextMenuItem.isSelected());
2940     alignPanel.paintAlignment(true);
2941   }
2942
2943   /**
2944    * DOCUMENT ME!
2945    *
2946    * @param e
2947    *          DOCUMENT ME!
2948    */
2949   @Override
2950   public void wrapMenuItem_actionPerformed(ActionEvent e)
2951   {
2952     scaleAbove.setVisible(wrapMenuItem.isSelected());
2953     scaleLeft.setVisible(wrapMenuItem.isSelected());
2954     scaleRight.setVisible(wrapMenuItem.isSelected());
2955     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2956     alignPanel.updateLayout();
2957   }
2958
2959   @Override
2960   public void showAllSeqs_actionPerformed(ActionEvent e)
2961   {
2962     viewport.showAllHiddenSeqs();
2963   }
2964
2965   @Override
2966   public void showAllColumns_actionPerformed(ActionEvent e)
2967   {
2968     viewport.showAllHiddenColumns();
2969     repaint();
2970     viewport.sendSelection();
2971   }
2972
2973   @Override
2974   public void hideSelSequences_actionPerformed(ActionEvent e)
2975   {
2976     viewport.hideAllSelectedSeqs();
2977     // alignPanel.paintAlignment(true);
2978   }
2979
2980   /**
2981    * called by key handler and the hide all/show all menu items
2982    *
2983    * @param toggleSeqs
2984    * @param toggleCols
2985    */
2986   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2987   {
2988
2989     boolean hide = false;
2990     SequenceGroup sg = viewport.getSelectionGroup();
2991     if (!toggleSeqs && !toggleCols)
2992     {
2993       // Hide everything by the current selection - this is a hack - we do the
2994       // invert and then hide
2995       // first check that there will be visible columns after the invert.
2996       if ((viewport.getColumnSelection() != null
2997               && viewport.getColumnSelection().getSelected() != null && viewport
2998               .getColumnSelection().getSelected().size() > 0)
2999               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3000                       .getEndRes()))
3001       {
3002         // now invert the sequence set, if required - empty selection implies
3003         // that no hiding is required.
3004         if (sg != null)
3005         {
3006           invertSequenceMenuItem_actionPerformed(null);
3007           sg = viewport.getSelectionGroup();
3008           toggleSeqs = true;
3009
3010         }
3011         viewport.expandColSelection(sg, true);
3012         // finally invert the column selection and get the new sequence
3013         // selection.
3014         invertColSel_actionPerformed(null);
3015         toggleCols = true;
3016       }
3017     }
3018
3019     if (toggleSeqs)
3020     {
3021       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3022       {
3023         hideSelSequences_actionPerformed(null);
3024         hide = true;
3025       }
3026       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3027               .size() > 0))
3028       {
3029         showAllSeqs_actionPerformed(null);
3030       }
3031     }
3032
3033     if (toggleCols)
3034     {
3035       if (viewport.getColumnSelection().getSelected().size() > 0)
3036       {
3037         hideSelColumns_actionPerformed(null);
3038         if (!toggleSeqs)
3039         {
3040           viewport.setSelectionGroup(sg);
3041         }
3042       }
3043       else if (!hide)
3044       {
3045         showAllColumns_actionPerformed(null);
3046       }
3047     }
3048   }
3049
3050   /*
3051    * (non-Javadoc)
3052    *
3053    * @see
3054    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3055    * event.ActionEvent)
3056    */
3057   @Override
3058   public void hideAllButSelection_actionPerformed(ActionEvent e)
3059   {
3060     toggleHiddenRegions(false, false);
3061     viewport.sendSelection();
3062   }
3063
3064   /*
3065    * (non-Javadoc)
3066    *
3067    * @see
3068    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3069    * .ActionEvent)
3070    */
3071   @Override
3072   public void hideAllSelection_actionPerformed(ActionEvent e)
3073   {
3074     SequenceGroup sg = viewport.getSelectionGroup();
3075     viewport.expandColSelection(sg, false);
3076     viewport.hideAllSelectedSeqs();
3077     viewport.hideSelectedColumns();
3078     alignPanel.paintAlignment(true);
3079     viewport.sendSelection();
3080   }
3081
3082   /*
3083    * (non-Javadoc)
3084    *
3085    * @see
3086    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3087    * ActionEvent)
3088    */
3089   @Override
3090   public void showAllhidden_actionPerformed(ActionEvent e)
3091   {
3092     viewport.showAllHiddenColumns();
3093     viewport.showAllHiddenSeqs();
3094     alignPanel.paintAlignment(true);
3095     viewport.sendSelection();
3096   }
3097
3098   @Override
3099   public void hideSelColumns_actionPerformed(ActionEvent e)
3100   {
3101     viewport.hideSelectedColumns();
3102     alignPanel.paintAlignment(true);
3103     viewport.sendSelection();
3104   }
3105
3106   @Override
3107   public void hiddenMarkers_actionPerformed(ActionEvent e)
3108   {
3109     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3110     repaint();
3111   }
3112
3113   /**
3114    * DOCUMENT ME!
3115    *
3116    * @param e
3117    *          DOCUMENT ME!
3118    */
3119   @Override
3120   protected void scaleAbove_actionPerformed(ActionEvent e)
3121   {
3122     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3123     alignPanel.paintAlignment(true);
3124   }
3125
3126   /**
3127    * DOCUMENT ME!
3128    *
3129    * @param e
3130    *          DOCUMENT ME!
3131    */
3132   @Override
3133   protected void scaleLeft_actionPerformed(ActionEvent e)
3134   {
3135     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3136     alignPanel.paintAlignment(true);
3137   }
3138
3139   /**
3140    * DOCUMENT ME!
3141    *
3142    * @param e
3143    *          DOCUMENT ME!
3144    */
3145   @Override
3146   protected void scaleRight_actionPerformed(ActionEvent e)
3147   {
3148     viewport.setScaleRightWrapped(scaleRight.isSelected());
3149     alignPanel.paintAlignment(true);
3150   }
3151
3152   /**
3153    * DOCUMENT ME!
3154    *
3155    * @param e
3156    *          DOCUMENT ME!
3157    */
3158   @Override
3159   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3160   {
3161     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3162     alignPanel.paintAlignment(true);
3163   }
3164
3165   /**
3166    * DOCUMENT ME!
3167    *
3168    * @param e
3169    *          DOCUMENT ME!
3170    */
3171   @Override
3172   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3173   {
3174     viewport.setShowText(viewTextMenuItem.isSelected());
3175     alignPanel.paintAlignment(true);
3176   }
3177
3178   /**
3179    * DOCUMENT ME!
3180    *
3181    * @param e
3182    *          DOCUMENT ME!
3183    */
3184   @Override
3185   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3186   {
3187     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3188     alignPanel.paintAlignment(true);
3189   }
3190
3191   public FeatureSettings featureSettings;
3192
3193   @Override
3194   public FeatureSettingsControllerI getFeatureSettingsUI()
3195   {
3196     return featureSettings;
3197   }
3198
3199   @Override
3200   public void featureSettings_actionPerformed(ActionEvent e)
3201   {
3202     if (featureSettings != null)
3203     {
3204       featureSettings.close();
3205       featureSettings = null;
3206     }
3207     if (!showSeqFeatures.isSelected())
3208     {
3209       // make sure features are actually displayed
3210       showSeqFeatures.setSelected(true);
3211       showSeqFeatures_actionPerformed(null);
3212     }
3213     featureSettings = new FeatureSettings(this);
3214   }
3215
3216   /**
3217    * Set or clear 'Show Sequence Features'
3218    *
3219    * @param evt
3220    *          DOCUMENT ME!
3221    */
3222   @Override
3223   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3224   {
3225     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3226     alignPanel.paintAlignment(true);
3227     if (alignPanel.getOverviewPanel() != null)
3228     {
3229       alignPanel.getOverviewPanel().updateOverviewImage();
3230     }
3231   }
3232
3233   /**
3234    * Set or clear 'Show Sequence Features'
3235    *
3236    * @param evt
3237    *          DOCUMENT ME!
3238    */
3239   @Override
3240   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3241   {
3242     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3243             .isSelected());
3244     if (viewport.isShowSequenceFeaturesHeight())
3245     {
3246       // ensure we're actually displaying features
3247       viewport.setShowSequenceFeatures(true);
3248       showSeqFeatures.setSelected(true);
3249     }
3250     alignPanel.paintAlignment(true);
3251     if (alignPanel.getOverviewPanel() != null)
3252     {
3253       alignPanel.getOverviewPanel().updateOverviewImage();
3254     }
3255   }
3256
3257   /**
3258    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3259    * the annotations panel as a whole.
3260    *
3261    * The options to show/hide all annotations should be enabled when the panel
3262    * is shown, and disabled when the panel is hidden.
3263    *
3264    * @param e
3265    */
3266   @Override
3267   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3268   {
3269     final boolean setVisible = annotationPanelMenuItem.isSelected();
3270     viewport.setShowAnnotation(setVisible);
3271     this.showAllSeqAnnotations.setEnabled(setVisible);
3272     this.hideAllSeqAnnotations.setEnabled(setVisible);
3273     this.showAllAlAnnotations.setEnabled(setVisible);
3274     this.hideAllAlAnnotations.setEnabled(setVisible);
3275     alignPanel.updateLayout();
3276   }
3277
3278   @Override
3279   public void alignmentProperties()
3280   {
3281     JEditorPane editPane = new JEditorPane("text/html", "");
3282     editPane.setEditable(false);
3283     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3284             .formatAsHtml();
3285     editPane.setText(MessageManager.formatMessage("label.html_content",
3286             new Object[] { contents.toString() }));
3287     JInternalFrame frame = new JInternalFrame();
3288     frame.getContentPane().add(new JScrollPane(editPane));
3289
3290     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3291             "label.alignment_properties", new Object[] { getTitle() }),
3292             500, 400);
3293   }
3294
3295   /**
3296    * DOCUMENT ME!
3297    *
3298    * @param e
3299    *          DOCUMENT ME!
3300    */
3301   @Override
3302   public void overviewMenuItem_actionPerformed(ActionEvent e)
3303   {
3304     if (alignPanel.overviewPanel != null)
3305     {
3306       return;
3307     }
3308
3309     JInternalFrame frame = new JInternalFrame();
3310     OverviewPanel overview = new OverviewPanel(alignPanel);
3311     frame.setContentPane(overview);
3312     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3313             "label.overview_params", new Object[] { this.getTitle() }),
3314             frame.getWidth(), frame.getHeight());
3315     frame.pack();
3316     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3317     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3318     {
3319       @Override
3320       public void internalFrameClosed(
3321               javax.swing.event.InternalFrameEvent evt)
3322       {
3323         alignPanel.setOverviewPanel(null);
3324       };
3325     });
3326
3327     alignPanel.setOverviewPanel(overview);
3328   }
3329
3330   @Override
3331   public void textColour_actionPerformed(ActionEvent e)
3332   {
3333     new TextColourChooser().chooseColour(alignPanel, null);
3334   }
3335
3336   /**
3337    * DOCUMENT ME!
3338    *
3339    * @param e
3340    *          DOCUMENT ME!
3341    */
3342   @Override
3343   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3344   {
3345     changeColour(null);
3346   }
3347
3348   /**
3349    * DOCUMENT ME!
3350    *
3351    * @param e
3352    *          DOCUMENT ME!
3353    */
3354   @Override
3355   public void clustalColour_actionPerformed(ActionEvent e)
3356   {
3357     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3358             viewport.getHiddenRepSequences()));
3359   }
3360
3361   /**
3362    * DOCUMENT ME!
3363    *
3364    * @param e
3365    *          DOCUMENT ME!
3366    */
3367   @Override
3368   public void zappoColour_actionPerformed(ActionEvent e)
3369   {
3370     changeColour(new ZappoColourScheme());
3371   }
3372
3373   /**
3374    * DOCUMENT ME!
3375    *
3376    * @param e
3377    *          DOCUMENT ME!
3378    */
3379   @Override
3380   public void taylorColour_actionPerformed(ActionEvent e)
3381   {
3382     changeColour(new TaylorColourScheme());
3383   }
3384
3385   /**
3386    * DOCUMENT ME!
3387    *
3388    * @param e
3389    *          DOCUMENT ME!
3390    */
3391   @Override
3392   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3393   {
3394     changeColour(new HydrophobicColourScheme());
3395   }
3396
3397   /**
3398    * DOCUMENT ME!
3399    *
3400    * @param e
3401    *          DOCUMENT ME!
3402    */
3403   @Override
3404   public void helixColour_actionPerformed(ActionEvent e)
3405   {
3406     changeColour(new HelixColourScheme());
3407   }
3408
3409   /**
3410    * DOCUMENT ME!
3411    *
3412    * @param e
3413    *          DOCUMENT ME!
3414    */
3415   @Override
3416   public void strandColour_actionPerformed(ActionEvent e)
3417   {
3418     changeColour(new StrandColourScheme());
3419   }
3420
3421   /**
3422    * DOCUMENT ME!
3423    *
3424    * @param e
3425    *          DOCUMENT ME!
3426    */
3427   @Override
3428   public void turnColour_actionPerformed(ActionEvent e)
3429   {
3430     changeColour(new TurnColourScheme());
3431   }
3432
3433   /**
3434    * DOCUMENT ME!
3435    *
3436    * @param e
3437    *          DOCUMENT ME!
3438    */
3439   @Override
3440   public void buriedColour_actionPerformed(ActionEvent e)
3441   {
3442     changeColour(new BuriedColourScheme());
3443   }
3444
3445   /**
3446    * DOCUMENT ME!
3447    *
3448    * @param e
3449    *          DOCUMENT ME!
3450    */
3451   @Override
3452   public void nucleotideColour_actionPerformed(ActionEvent e)
3453   {
3454     changeColour(new NucleotideColourScheme());
3455   }
3456
3457   @Override
3458   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3459   {
3460     changeColour(new PurinePyrimidineColourScheme());
3461   }
3462
3463   /*
3464    * public void covariationColour_actionPerformed(ActionEvent e) {
3465    * changeColour(new
3466    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3467    * ()[0])); }
3468    */
3469   @Override
3470   public void annotationColour_actionPerformed(ActionEvent e)
3471   {
3472     new AnnotationColourChooser(viewport, alignPanel);
3473   }
3474
3475   @Override
3476   public void annotationColumn_actionPerformed(ActionEvent e)
3477   {
3478     new AnnotationColumnChooser(viewport, alignPanel);
3479   }
3480
3481   @Override
3482   public void rnahelicesColour_actionPerformed(ActionEvent e)
3483   {
3484     new RNAHelicesColourChooser(viewport, alignPanel);
3485   }
3486
3487   /**
3488    * DOCUMENT ME!
3489    *
3490    * @param e
3491    *          DOCUMENT ME!
3492    */
3493   @Override
3494   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3495   {
3496     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3497   }
3498
3499   /**
3500    * DOCUMENT ME!
3501    *
3502    * @param cs
3503    *          DOCUMENT ME!
3504    */
3505   @Override
3506   public void changeColour(ColourSchemeI cs)
3507   {
3508     // TODO: pull up to controller method
3509
3510     if (cs != null)
3511     {
3512       // Make sure viewport is up to date w.r.t. any sliders
3513       if (viewport.getAbovePIDThreshold())
3514       {
3515         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3516                 "Background");
3517         viewport.setThreshold(threshold);
3518       }
3519
3520       if (viewport.getConservationSelected())
3521       {
3522         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3523                 cs, "Background"));
3524       }
3525       if (cs instanceof TCoffeeColourScheme)
3526       {
3527         tcoffeeColour.setEnabled(true);
3528         tcoffeeColour.setSelected(true);
3529       }
3530     }
3531
3532     viewport.setGlobalColourScheme(cs);
3533
3534     alignPanel.paintAlignment(true);
3535   }
3536
3537   /**
3538    * DOCUMENT ME!
3539    *
3540    * @param e
3541    *          DOCUMENT ME!
3542    */
3543   @Override
3544   protected void modifyPID_actionPerformed(ActionEvent e)
3545   {
3546     if (viewport.getAbovePIDThreshold()
3547             && viewport.getGlobalColourScheme() != null)
3548     {
3549       SliderPanel.setPIDSliderSource(alignPanel,
3550               viewport.getGlobalColourScheme(), "Background");
3551       SliderPanel.showPIDSlider();
3552     }
3553   }
3554
3555   /**
3556    * DOCUMENT ME!
3557    *
3558    * @param e
3559    *          DOCUMENT ME!
3560    */
3561   @Override
3562   protected void modifyConservation_actionPerformed(ActionEvent e)
3563   {
3564     if (viewport.getConservationSelected()
3565             && viewport.getGlobalColourScheme() != null)
3566     {
3567       SliderPanel.setConservationSlider(alignPanel,
3568               viewport.getGlobalColourScheme(), "Background");
3569       SliderPanel.showConservationSlider();
3570     }
3571   }
3572
3573   /**
3574    * DOCUMENT ME!
3575    *
3576    * @param e
3577    *          DOCUMENT ME!
3578    */
3579   @Override
3580   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3581   {
3582     viewport.setConservationSelected(conservationMenuItem.isSelected());
3583
3584     viewport.setAbovePIDThreshold(false);
3585     abovePIDThreshold.setSelected(false);
3586
3587     changeColour(viewport.getGlobalColourScheme());
3588
3589     modifyConservation_actionPerformed(null);
3590   }
3591
3592   /**
3593    * DOCUMENT ME!
3594    *
3595    * @param e
3596    *          DOCUMENT ME!
3597    */
3598   @Override
3599   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3600   {
3601     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3602
3603     conservationMenuItem.setSelected(false);
3604     viewport.setConservationSelected(false);
3605
3606     changeColour(viewport.getGlobalColourScheme());
3607
3608     modifyPID_actionPerformed(null);
3609   }
3610
3611   /**
3612    * DOCUMENT ME!
3613    *
3614    * @param e
3615    *          DOCUMENT ME!
3616    */
3617   @Override
3618   public void userDefinedColour_actionPerformed(ActionEvent e)
3619   {
3620     if (e.getActionCommand().equals(
3621             MessageManager.getString("action.user_defined")))
3622     {
3623       new UserDefinedColours(alignPanel, null);
3624     }
3625     else
3626     {
3627       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3628               .getUserColourSchemes().get(e.getActionCommand());
3629
3630       changeColour(udc);
3631     }
3632   }
3633
3634   public void updateUserColourMenu()
3635   {
3636
3637     Component[] menuItems = colourMenu.getMenuComponents();
3638     int iSize = menuItems.length;
3639     for (int i = 0; i < iSize; i++)
3640     {
3641       if (menuItems[i].getName() != null
3642               && menuItems[i].getName().equals("USER_DEFINED"))
3643       {
3644         colourMenu.remove(menuItems[i]);
3645         iSize--;
3646       }
3647     }
3648     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3649     {
3650       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3651               .getUserColourSchemes().keys();
3652
3653       while (userColours.hasMoreElements())
3654       {
3655         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3656                 userColours.nextElement().toString());
3657         radioItem.setName("USER_DEFINED");
3658         radioItem.addMouseListener(new MouseAdapter()
3659         {
3660           @Override
3661           public void mousePressed(MouseEvent evt)
3662           {
3663             if (evt.isControlDown()
3664                     || SwingUtilities.isRightMouseButton(evt))
3665             {
3666               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3667
3668               int option = JOptionPane.showInternalConfirmDialog(
3669                       jalview.gui.Desktop.desktop,
3670                       MessageManager
3671                               .getString("label.remove_from_default_list"),
3672                       MessageManager
3673                               .getString("label.remove_user_defined_colour"),
3674                       JOptionPane.YES_NO_OPTION);
3675               if (option == JOptionPane.YES_OPTION)
3676               {
3677                 jalview.gui.UserDefinedColours
3678                         .removeColourFromDefaults(radioItem.getText());
3679                 colourMenu.remove(radioItem);
3680               }
3681               else
3682               {
3683                 radioItem.addActionListener(new ActionListener()
3684                 {
3685                   @Override
3686                   public void actionPerformed(ActionEvent evt)
3687                   {
3688                     userDefinedColour_actionPerformed(evt);
3689                   }
3690                 });
3691               }
3692             }
3693           }
3694         });
3695         radioItem.addActionListener(new ActionListener()
3696         {
3697           @Override
3698           public void actionPerformed(ActionEvent evt)
3699           {
3700             userDefinedColour_actionPerformed(evt);
3701           }
3702         });
3703
3704         colourMenu.insert(radioItem, 15);
3705         colours.add(radioItem);
3706       }
3707     }
3708   }
3709
3710   /**
3711    * DOCUMENT ME!
3712    *
3713    * @param e
3714    *          DOCUMENT ME!
3715    */
3716   @Override
3717   public void PIDColour_actionPerformed(ActionEvent e)
3718   {
3719     changeColour(new PIDColourScheme());
3720   }
3721
3722   /**
3723    * DOCUMENT ME!
3724    *
3725    * @param e
3726    *          DOCUMENT ME!
3727    */
3728   @Override
3729   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3730   {
3731     changeColour(new Blosum62ColourScheme());
3732   }
3733
3734   /**
3735    * DOCUMENT ME!
3736    *
3737    * @param e
3738    *          DOCUMENT ME!
3739    */
3740   @Override
3741   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3742   {
3743     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3744     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3745             .getAlignment().getSequenceAt(0), null);
3746     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3747             viewport.getAlignment()));
3748     alignPanel.paintAlignment(true);
3749   }
3750
3751   /**
3752    * DOCUMENT ME!
3753    *
3754    * @param e
3755    *          DOCUMENT ME!
3756    */
3757   @Override
3758   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3759   {
3760     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3761     AlignmentSorter.sortByID(viewport.getAlignment());
3762     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3763             viewport.getAlignment()));
3764     alignPanel.paintAlignment(true);
3765   }
3766
3767   /**
3768    * DOCUMENT ME!
3769    *
3770    * @param e
3771    *          DOCUMENT ME!
3772    */
3773   @Override
3774   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3775   {
3776     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3777     AlignmentSorter.sortByLength(viewport.getAlignment());
3778     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3779             viewport.getAlignment()));
3780     alignPanel.paintAlignment(true);
3781   }
3782
3783   /**
3784    * DOCUMENT ME!
3785    *
3786    * @param e
3787    *          DOCUMENT ME!
3788    */
3789   @Override
3790   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3791   {
3792     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3793     AlignmentSorter.sortByGroup(viewport.getAlignment());
3794     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3795             viewport.getAlignment()));
3796
3797     alignPanel.paintAlignment(true);
3798   }
3799
3800   /**
3801    * DOCUMENT ME!
3802    *
3803    * @param e
3804    *          DOCUMENT ME!
3805    */
3806   @Override
3807   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3808   {
3809     new RedundancyPanel(alignPanel, this);
3810   }
3811
3812   /**
3813    * DOCUMENT ME!
3814    *
3815    * @param e
3816    *          DOCUMENT ME!
3817    */
3818   @Override
3819   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3820   {
3821     if ((viewport.getSelectionGroup() == null)
3822             || (viewport.getSelectionGroup().getSize() < 2))
3823     {
3824       JOptionPane.showInternalMessageDialog(this, MessageManager
3825               .getString("label.you_must_select_least_two_sequences"),
3826               MessageManager.getString("label.invalid_selection"),
3827               JOptionPane.WARNING_MESSAGE);
3828     }
3829     else
3830     {
3831       JInternalFrame frame = new JInternalFrame();
3832       frame.setContentPane(new PairwiseAlignPanel(viewport));
3833       Desktop.addInternalFrame(frame,
3834               MessageManager.getString("action.pairwise_alignment"), 600,
3835               500);
3836     }
3837   }
3838
3839   /**
3840    * DOCUMENT ME!
3841    *
3842    * @param e
3843    *          DOCUMENT ME!
3844    */
3845   @Override
3846   public void PCAMenuItem_actionPerformed(ActionEvent e)
3847   {
3848     if (((viewport.getSelectionGroup() != null)
3849             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3850             .getSelectionGroup().getSize() > 0))
3851             || (viewport.getAlignment().getHeight() < 4))
3852     {
3853       JOptionPane
3854               .showInternalMessageDialog(
3855                       this,
3856                       MessageManager
3857                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3858                       MessageManager
3859                               .getString("label.sequence_selection_insufficient"),
3860                       JOptionPane.WARNING_MESSAGE);
3861
3862       return;
3863     }
3864
3865     new PCAPanel(alignPanel);
3866   }
3867
3868   @Override
3869   public void autoCalculate_actionPerformed(ActionEvent e)
3870   {
3871     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3872     if (viewport.autoCalculateConsensus)
3873     {
3874       viewport.firePropertyChange("alignment", null, viewport
3875               .getAlignment().getSequences());
3876     }
3877   }
3878
3879   @Override
3880   public void sortByTreeOption_actionPerformed(ActionEvent e)
3881   {
3882     viewport.sortByTree = sortByTree.isSelected();
3883   }
3884
3885   @Override
3886   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3887   {
3888     viewport.followSelection = listenToViewSelections.isSelected();
3889   }
3890
3891   /**
3892    * DOCUMENT ME!
3893    *
3894    * @param e
3895    *          DOCUMENT ME!
3896    */
3897   @Override
3898   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3899   {
3900     newTreePanel("AV", "PID", "Average distance tree using PID");
3901   }
3902
3903   /**
3904    * DOCUMENT ME!
3905    *
3906    * @param e
3907    *          DOCUMENT ME!
3908    */
3909   @Override
3910   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3911   {
3912     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3913   }
3914
3915   /**
3916    * DOCUMENT ME!
3917    *
3918    * @param e
3919    *          DOCUMENT ME!
3920    */
3921   @Override
3922   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3923   {
3924     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3925   }
3926
3927   /**
3928    * DOCUMENT ME!
3929    *
3930    * @param e
3931    *          DOCUMENT ME!
3932    */
3933   @Override
3934   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3935   {
3936     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3937   }
3938
3939   /**
3940    * DOCUMENT ME!
3941    *
3942    * @param type
3943    *          DOCUMENT ME!
3944    * @param pwType
3945    *          DOCUMENT ME!
3946    * @param title
3947    *          DOCUMENT ME!
3948    */
3949   void newTreePanel(String type, String pwType, String title)
3950   {
3951     TreePanel tp;
3952
3953     if (viewport.getSelectionGroup() != null
3954             && viewport.getSelectionGroup().getSize() > 0)
3955     {
3956       if (viewport.getSelectionGroup().getSize() < 3)
3957       {
3958         JOptionPane
3959                 .showMessageDialog(
3960                         Desktop.desktop,
3961                         MessageManager
3962                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3963                         MessageManager
3964                                 .getString("label.not_enough_sequences"),
3965                         JOptionPane.WARNING_MESSAGE);
3966         return;
3967       }
3968
3969       SequenceGroup sg = viewport.getSelectionGroup();
3970
3971       /* Decide if the selection is a column region */
3972       for (SequenceI _s : sg.getSequences())
3973       {
3974         if (_s.getLength() < sg.getEndRes())
3975         {
3976           JOptionPane
3977                   .showMessageDialog(
3978                           Desktop.desktop,
3979                           MessageManager
3980                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3981                           MessageManager
3982                                   .getString("label.sequences_selection_not_aligned"),
3983                           JOptionPane.WARNING_MESSAGE);
3984
3985           return;
3986         }
3987       }
3988
3989       title = title + " on region";
3990       tp = new TreePanel(alignPanel, type, pwType);
3991     }
3992     else
3993     {
3994       // are the visible sequences aligned?
3995       if (!viewport.getAlignment().isAligned(false))
3996       {
3997         JOptionPane
3998                 .showMessageDialog(
3999                         Desktop.desktop,
4000                         MessageManager
4001                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4002                         MessageManager
4003                                 .getString("label.sequences_not_aligned"),
4004                         JOptionPane.WARNING_MESSAGE);
4005
4006         return;
4007       }
4008
4009       if (viewport.getAlignment().getHeight() < 2)
4010       {
4011         return;
4012       }
4013
4014       tp = new TreePanel(alignPanel, type, pwType);
4015     }
4016
4017     title += " from ";
4018
4019     if (viewport.viewName != null)
4020     {
4021       title += viewport.viewName + " of ";
4022     }
4023
4024     title += this.title;
4025
4026     Desktop.addInternalFrame(tp, title, 600, 500);
4027   }
4028
4029   /**
4030    * DOCUMENT ME!
4031    *
4032    * @param title
4033    *          DOCUMENT ME!
4034    * @param order
4035    *          DOCUMENT ME!
4036    */
4037   public void addSortByOrderMenuItem(String title,
4038           final AlignmentOrder order)
4039   {
4040     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4041             "action.by_title_param", new Object[] { title }));
4042     sort.add(item);
4043     item.addActionListener(new java.awt.event.ActionListener()
4044     {
4045       @Override
4046       public void actionPerformed(ActionEvent e)
4047       {
4048         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4049
4050         // TODO: JBPNote - have to map order entries to curent SequenceI
4051         // pointers
4052         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4053
4054         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4055                 .getAlignment()));
4056
4057         alignPanel.paintAlignment(true);
4058       }
4059     });
4060   }
4061
4062   /**
4063    * Add a new sort by annotation score menu item
4064    *
4065    * @param sort
4066    *          the menu to add the option to
4067    * @param scoreLabel
4068    *          the label used to retrieve scores for each sequence on the
4069    *          alignment
4070    */
4071   public void addSortByAnnotScoreMenuItem(JMenu sort,
4072           final String scoreLabel)
4073   {
4074     final JMenuItem item = new JMenuItem(scoreLabel);
4075     sort.add(item);
4076     item.addActionListener(new java.awt.event.ActionListener()
4077     {
4078       @Override
4079       public void actionPerformed(ActionEvent e)
4080       {
4081         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4082         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4083                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4084         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4085                 viewport.getAlignment()));
4086         alignPanel.paintAlignment(true);
4087       }
4088     });
4089   }
4090
4091   /**
4092    * last hash for alignment's annotation array - used to minimise cost of
4093    * rebuild.
4094    */
4095   protected int _annotationScoreVectorHash;
4096
4097   /**
4098    * search the alignment and rebuild the sort by annotation score submenu the
4099    * last alignment annotation vector hash is stored to minimize cost of
4100    * rebuilding in subsequence calls.
4101    *
4102    */
4103   @Override
4104   public void buildSortByAnnotationScoresMenu()
4105   {
4106     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4107     {
4108       return;
4109     }
4110
4111     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4112     {
4113       sortByAnnotScore.removeAll();
4114       // almost certainly a quicker way to do this - but we keep it simple
4115       Hashtable scoreSorts = new Hashtable();
4116       AlignmentAnnotation aann[];
4117       for (SequenceI sqa : viewport.getAlignment().getSequences())
4118       {
4119         aann = sqa.getAnnotation();
4120         for (int i = 0; aann != null && i < aann.length; i++)
4121         {
4122           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4123           {
4124             scoreSorts.put(aann[i].label, aann[i].label);
4125           }
4126         }
4127       }
4128       Enumeration labels = scoreSorts.keys();
4129       while (labels.hasMoreElements())
4130       {
4131         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4132                 (String) labels.nextElement());
4133       }
4134       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4135       scoreSorts.clear();
4136
4137       _annotationScoreVectorHash = viewport.getAlignment()
4138               .getAlignmentAnnotation().hashCode();
4139     }
4140   }
4141
4142   /**
4143    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4144    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4145    * call. Listeners are added to remove the menu item when the treePanel is
4146    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4147    * modified.
4148    *
4149    * @param treePanel
4150    *          Displayed tree window.
4151    * @param title
4152    *          SortBy menu item title.
4153    */
4154   @Override
4155   public void buildTreeMenu()
4156   {
4157     calculateTree.removeAll();
4158     // build the calculate menu
4159
4160     for (final String type : new String[] { "NJ", "AV" })
4161     {
4162       String treecalcnm = MessageManager.getString("label.tree_calc_"
4163               + type.toLowerCase());
4164       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4165       {
4166         JMenuItem tm = new JMenuItem();
4167         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4168         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4169         {
4170           String smn = MessageManager.getStringOrReturn(
4171                   "label.score_model_", sm.getName());
4172           final String title = MessageManager.formatMessage(
4173                   "label.treecalc_title", treecalcnm, smn);
4174           tm.setText(title);//
4175           tm.addActionListener(new java.awt.event.ActionListener()
4176           {
4177             @Override
4178             public void actionPerformed(ActionEvent e)
4179             {
4180               newTreePanel(type, pwtype, title);
4181             }
4182           });
4183           calculateTree.add(tm);
4184         }
4185
4186       }
4187     }
4188     sortByTreeMenu.removeAll();
4189
4190     List<Component> comps = PaintRefresher.components.get(viewport
4191             .getSequenceSetId());
4192     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4193     for (Component comp : comps)
4194     {
4195       if (comp instanceof TreePanel)
4196       {
4197         treePanels.add((TreePanel) comp);
4198       }
4199     }
4200
4201     if (treePanels.size() < 1)
4202     {
4203       sortByTreeMenu.setVisible(false);
4204       return;
4205     }
4206
4207     sortByTreeMenu.setVisible(true);
4208
4209     for (final TreePanel tp : treePanels)
4210     {
4211       final JMenuItem item = new JMenuItem(tp.getTitle());
4212       item.addActionListener(new java.awt.event.ActionListener()
4213       {
4214         @Override
4215         public void actionPerformed(ActionEvent e)
4216         {
4217           tp.sortByTree_actionPerformed();
4218           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4219
4220         }
4221       });
4222
4223       sortByTreeMenu.add(item);
4224     }
4225   }
4226
4227   public boolean sortBy(AlignmentOrder alorder, String undoname)
4228   {
4229     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4230     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4231     if (undoname != null)
4232     {
4233       addHistoryItem(new OrderCommand(undoname, oldOrder,
4234               viewport.getAlignment()));
4235     }
4236     alignPanel.paintAlignment(true);
4237     return true;
4238   }
4239
4240   /**
4241    * Work out whether the whole set of sequences or just the selected set will
4242    * be submitted for multiple alignment.
4243    *
4244    */
4245   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4246   {
4247     // Now, check we have enough sequences
4248     AlignmentView msa = null;
4249
4250     if ((viewport.getSelectionGroup() != null)
4251             && (viewport.getSelectionGroup().getSize() > 1))
4252     {
4253       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4254       // some common interface!
4255       /*
4256        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4257        * SequenceI[sz = seqs.getSize(false)];
4258        *
4259        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4260        * seqs.getSequenceAt(i); }
4261        */
4262       msa = viewport.getAlignmentView(true);
4263     }
4264     else if (viewport.getSelectionGroup() != null
4265             && viewport.getSelectionGroup().getSize() == 1)
4266     {
4267       int option = JOptionPane.showConfirmDialog(this,
4268               MessageManager.getString("warn.oneseq_msainput_selection"),
4269               MessageManager.getString("label.invalid_selection"),
4270               JOptionPane.OK_CANCEL_OPTION);
4271       if (option == JOptionPane.OK_OPTION)
4272       {
4273         msa = viewport.getAlignmentView(false);
4274       }
4275     }
4276     else
4277     {
4278       msa = viewport.getAlignmentView(false);
4279     }
4280     return msa;
4281   }
4282
4283   /**
4284    * Decides what is submitted to a secondary structure prediction service: the
4285    * first sequence in the alignment, or in the current selection, or, if the
4286    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4287    * region or the whole alignment. (where the first sequence in the set is the
4288    * one that the prediction will be for).
4289    */
4290   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4291   {
4292     AlignmentView seqs = null;
4293
4294     if ((viewport.getSelectionGroup() != null)
4295             && (viewport.getSelectionGroup().getSize() > 0))
4296     {
4297       seqs = viewport.getAlignmentView(true);
4298     }
4299     else
4300     {
4301       seqs = viewport.getAlignmentView(false);
4302     }
4303     // limit sequences - JBPNote in future - could spawn multiple prediction
4304     // jobs
4305     // TODO: viewport.getAlignment().isAligned is a global state - the local
4306     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4307     if (!viewport.getAlignment().isAligned(false))
4308     {
4309       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4310       // TODO: if seqs.getSequences().length>1 then should really have warned
4311       // user!
4312
4313     }
4314     return seqs;
4315   }
4316
4317   /**
4318    * DOCUMENT ME!
4319    *
4320    * @param e
4321    *          DOCUMENT ME!
4322    */
4323   @Override
4324   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4325   {
4326     // Pick the tree file
4327     JalviewFileChooser chooser = new JalviewFileChooser(
4328             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4329     chooser.setFileView(new JalviewFileView());
4330     chooser.setDialogTitle(MessageManager
4331             .getString("label.select_newick_like_tree_file"));
4332     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4333
4334     int value = chooser.showOpenDialog(null);
4335
4336     if (value == JalviewFileChooser.APPROVE_OPTION)
4337     {
4338       String choice = chooser.getSelectedFile().getPath();
4339       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4340       jalview.io.NewickFile fin = null;
4341       try
4342       {
4343         fin = new jalview.io.NewickFile(choice, "File");
4344         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4345       } catch (Exception ex)
4346       {
4347         JOptionPane
4348                 .showMessageDialog(
4349                         Desktop.desktop,
4350                         ex.getMessage(),
4351                         MessageManager
4352                                 .getString("label.problem_reading_tree_file"),
4353                         JOptionPane.WARNING_MESSAGE);
4354         ex.printStackTrace();
4355       }
4356       if (fin != null && fin.hasWarningMessage())
4357       {
4358         JOptionPane.showMessageDialog(Desktop.desktop, fin
4359                 .getWarningMessage(), MessageManager
4360                 .getString("label.possible_problem_with_tree_file"),
4361                 JOptionPane.WARNING_MESSAGE);
4362       }
4363     }
4364   }
4365
4366   @Override
4367   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4368   {
4369     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4370   }
4371
4372   public TreePanel ShowNewickTree(NewickFile nf, String title)
4373   {
4374     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4375   }
4376
4377   public TreePanel ShowNewickTree(NewickFile nf, String title,
4378           AlignmentView input)
4379   {
4380     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4381   }
4382
4383   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4384           int h, int x, int y)
4385   {
4386     return ShowNewickTree(nf, title, null, w, h, x, y);
4387   }
4388
4389   /**
4390    * Add a treeviewer for the tree extracted from a newick file object to the
4391    * current alignment view
4392    *
4393    * @param nf
4394    *          the tree
4395    * @param title
4396    *          tree viewer title
4397    * @param input
4398    *          Associated alignment input data (or null)
4399    * @param w
4400    *          width
4401    * @param h
4402    *          height
4403    * @param x
4404    *          position
4405    * @param y
4406    *          position
4407    * @return TreePanel handle
4408    */
4409   public TreePanel ShowNewickTree(NewickFile nf, String title,
4410           AlignmentView input, int w, int h, int x, int y)
4411   {
4412     TreePanel tp = null;
4413
4414     try
4415     {
4416       nf.parse();
4417
4418       if (nf.getTree() != null)
4419       {
4420         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4421
4422         tp.setSize(w, h);
4423
4424         if (x > 0 && y > 0)
4425         {
4426           tp.setLocation(x, y);
4427         }
4428
4429         Desktop.addInternalFrame(tp, title, w, h);
4430       }
4431     } catch (Exception ex)
4432     {
4433       ex.printStackTrace();
4434     }
4435
4436     return tp;
4437   }
4438
4439   private boolean buildingMenu = false;
4440
4441   /**
4442    * Generates menu items and listener event actions for web service clients
4443    *
4444    */
4445   public void BuildWebServiceMenu()
4446   {
4447     while (buildingMenu)
4448     {
4449       try
4450       {
4451         System.err.println("Waiting for building menu to finish.");
4452         Thread.sleep(10);
4453       } catch (Exception e)
4454       {
4455       }
4456     }
4457     final AlignFrame me = this;
4458     buildingMenu = true;
4459     new Thread(new Runnable()
4460     {
4461       @Override
4462       public void run()
4463       {
4464         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4465         try
4466         {
4467           // System.err.println("Building ws menu again "
4468           // + Thread.currentThread());
4469           // TODO: add support for context dependent disabling of services based
4470           // on
4471           // alignment and current selection
4472           // TODO: add additional serviceHandle parameter to specify abstract
4473           // handler
4474           // class independently of AbstractName
4475           // TODO: add in rediscovery GUI function to restart discoverer
4476           // TODO: group services by location as well as function and/or
4477           // introduce
4478           // object broker mechanism.
4479           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4480           final IProgressIndicator af = me;
4481           final JMenu msawsmenu = new JMenu("Alignment");
4482           final JMenu secstrmenu = new JMenu(
4483                   "Secondary Structure Prediction");
4484           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4485           final JMenu analymenu = new JMenu("Analysis");
4486           final JMenu dismenu = new JMenu("Protein Disorder");
4487           // final JMenu msawsmenu = new
4488           // JMenu(MessageManager.getString("label.alignment"));
4489           // final JMenu secstrmenu = new
4490           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4491           // final JMenu seqsrchmenu = new
4492           // JMenu(MessageManager.getString("label.sequence_database_search"));
4493           // final JMenu analymenu = new
4494           // JMenu(MessageManager.getString("label.analysis"));
4495           // final JMenu dismenu = new
4496           // JMenu(MessageManager.getString("label.protein_disorder"));
4497           // JAL-940 - only show secondary structure prediction services from
4498           // the legacy server
4499           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4500               // &&
4501           Discoverer.services != null && (Discoverer.services.size() > 0))
4502           {
4503             // TODO: refactor to allow list of AbstractName/Handler bindings to
4504             // be
4505             // stored or retrieved from elsewhere
4506             // No MSAWS used any more:
4507             // Vector msaws = null; // (Vector)
4508             // Discoverer.services.get("MsaWS");
4509             Vector secstrpr = (Vector) Discoverer.services
4510                     .get("SecStrPred");
4511             if (secstrpr != null)
4512             {
4513               // Add any secondary structure prediction services
4514               for (int i = 0, j = secstrpr.size(); i < j; i++)
4515               {
4516                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4517                         .get(i);
4518                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4519                         .getServiceClient(sh);
4520                 int p = secstrmenu.getItemCount();
4521                 impl.attachWSMenuEntry(secstrmenu, me);
4522                 int q = secstrmenu.getItemCount();
4523                 for (int litm = p; litm < q; litm++)
4524                 {
4525                   legacyItems.add(secstrmenu.getItem(litm));
4526                 }
4527               }
4528             }
4529           }
4530
4531           // Add all submenus in the order they should appear on the web
4532           // services menu
4533           wsmenu.add(msawsmenu);
4534           wsmenu.add(secstrmenu);
4535           wsmenu.add(dismenu);
4536           wsmenu.add(analymenu);
4537           // No search services yet
4538           // wsmenu.add(seqsrchmenu);
4539
4540           javax.swing.SwingUtilities.invokeLater(new Runnable()
4541           {
4542             @Override
4543             public void run()
4544             {
4545               try
4546               {
4547                 webService.removeAll();
4548                 // first, add discovered services onto the webservices menu
4549                 if (wsmenu.size() > 0)
4550                 {
4551                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4552                   {
4553                     webService.add(wsmenu.get(i));
4554                   }
4555                 }
4556                 else
4557                 {
4558                   webService.add(me.webServiceNoServices);
4559                 }
4560                 // TODO: move into separate menu builder class.
4561                 boolean new_sspred = false;
4562                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4563                 {
4564                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4565                   if (jws2servs != null)
4566                   {
4567                     if (jws2servs.hasServices())
4568                     {
4569                       jws2servs.attachWSMenuEntry(webService, me);
4570                       for (Jws2Instance sv : jws2servs.getServices())
4571                       {
4572                         if (sv.description.toLowerCase().contains("jpred"))
4573                         {
4574                           for (JMenuItem jmi : legacyItems)
4575                           {
4576                             jmi.setVisible(false);
4577                           }
4578                         }
4579                       }
4580
4581                     }
4582                     if (jws2servs.isRunning())
4583                     {
4584                       JMenuItem tm = new JMenuItem(
4585                               "Still discovering JABA Services");
4586                       tm.setEnabled(false);
4587                       webService.add(tm);
4588                     }
4589                   }
4590                 }
4591                 build_urlServiceMenu(me.webService);
4592                 build_fetchdbmenu(webService);
4593                 for (JMenu item : wsmenu)
4594                 {
4595                   if (item.getItemCount() == 0)
4596                   {
4597                     item.setEnabled(false);
4598                   }
4599                   else
4600                   {
4601                     item.setEnabled(true);
4602                   }
4603                 }
4604               } catch (Exception e)
4605               {
4606                 Cache.log
4607                         .debug("Exception during web service menu building process.",
4608                                 e);
4609               }
4610             }
4611           });
4612         } catch (Exception e)
4613         {
4614         }
4615         buildingMenu = false;
4616       }
4617     }).start();
4618
4619   }
4620
4621   /**
4622    * construct any groupURL type service menu entries.
4623    *
4624    * @param webService
4625    */
4626   private void build_urlServiceMenu(JMenu webService)
4627   {
4628     // TODO: remove this code when 2.7 is released
4629     // DEBUG - alignmentView
4630     /*
4631      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4632      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4633      *
4634      * @Override public void actionPerformed(ActionEvent e) {
4635      * jalview.datamodel.AlignmentView
4636      * .testSelectionViews(af.viewport.getAlignment(),
4637      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4638      *
4639      * }); webService.add(testAlView);
4640      */
4641     // TODO: refactor to RestClient discoverer and merge menu entries for
4642     // rest-style services with other types of analysis/calculation service
4643     // SHmmr test client - still being implemented.
4644     // DEBUG - alignmentView
4645
4646     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4647             .getRestClients())
4648     {
4649       client.attachWSMenuEntry(
4650               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4651               this);
4652     }
4653   }
4654
4655   /*
4656    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4657    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4658    * getProperty("LAST_DIRECTORY"));
4659    *
4660    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4661    * to Vamsas file"); chooser.setToolTipText("Export");
4662    *
4663    * int value = chooser.showSaveDialog(this);
4664    *
4665    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4666    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4667    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4668    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4669    */
4670   /**
4671    * prototype of an automatically enabled/disabled analysis function
4672    *
4673    */
4674   protected void setShowProductsEnabled()
4675   {
4676     SequenceI[] selection = viewport.getSequenceSelection();
4677     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4678             viewport.getAlignment().getDataset()))
4679     {
4680       showProducts.setEnabled(true);
4681
4682     }
4683     else
4684     {
4685       showProducts.setEnabled(false);
4686     }
4687   }
4688
4689   /**
4690    * search selection for sequence xRef products and build the show products
4691    * menu.
4692    *
4693    * @param selection
4694    * @param dataset
4695    * @return true if showProducts menu should be enabled.
4696    */
4697   public boolean canShowProducts(SequenceI[] selection,
4698           boolean isRegionSelection, Alignment dataset)
4699   {
4700     boolean showp = false;
4701     try
4702     {
4703       showProducts.removeAll();
4704       final boolean dna = viewport.getAlignment().isNucleotide();
4705       final Alignment ds = dataset;
4706       String[] ptypes = (selection == null || selection.length == 0) ? null
4707               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4708       // Object[] prods =
4709       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4710       // selection, dataset, true);
4711       final SequenceI[] sel = selection;
4712       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4713       {
4714         showp = true;
4715         final boolean isRegSel = isRegionSelection;
4716         final AlignFrame af = this;
4717         final String source = ptypes[t];
4718         JMenuItem xtype = new JMenuItem(ptypes[t]);
4719         xtype.addActionListener(new ActionListener()
4720         {
4721
4722           @Override
4723           public void actionPerformed(ActionEvent e)
4724           {
4725             // TODO: new thread for this call with vis-delay
4726             af.showProductsFor(af.viewport.getSequenceSelection(),
4727                     isRegSel, dna, source);
4728           }
4729
4730         });
4731         showProducts.add(xtype);
4732       }
4733       showProducts.setVisible(showp);
4734       showProducts.setEnabled(showp);
4735     } catch (Exception e)
4736     {
4737       jalview.bin.Cache.log
4738               .warn("canTranslate threw an exception - please report to help@jalview.org",
4739                       e);
4740       return false;
4741     }
4742     return showp;
4743   }
4744
4745   protected void showProductsFor(final SequenceI[] sel,
4746           final boolean isRegSel, final boolean dna, final String source)
4747   {
4748     Runnable foo = new Runnable()
4749     {
4750
4751       @Override
4752       public void run()
4753       {
4754         final long sttime = System.currentTimeMillis();
4755         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4756                 "status.searching_for_sequences_from",
4757                 new Object[] { source }), sttime);
4758         try
4759         {
4760           // update our local dataset reference
4761           Alignment ds = AlignFrame.this.getViewport().getAlignment()
4762                   .getDataset();
4763           Alignment prods = CrossRef
4764                   .findXrefSequences(sel, dna, source, ds);
4765           if (prods != null)
4766           {
4767             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4768             for (int s = 0; s < sprods.length; s++)
4769             {
4770               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4771               if (ds.getSequences() == null
4772                       || !ds.getSequences().contains(
4773                               sprods[s].getDatasetSequence()))
4774               {
4775                 ds.addSequence(sprods[s].getDatasetSequence());
4776               }
4777               sprods[s].updatePDBIds();
4778             }
4779             Alignment al = new Alignment(sprods);
4780             al.setDataset(ds);
4781
4782             /*
4783              * Copy dna-to-protein mappings to new alignment
4784              */
4785             // TODO 1: no mappings are set up for EMBL product
4786             // TODO 2: if they were, should add them to protein alignment, not
4787             // dna
4788             List<AlignedCodonFrame> cf = prods.getCodonFrames();
4789             for (AlignedCodonFrame acf : cf)
4790             {
4791               al.addCodonFrame(acf);
4792             }
4793             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4794                     DEFAULT_HEIGHT);
4795             String newtitle = "" + (dna ? "Proteins" : "Nucleotides")
4796                     + " for " + (isRegSel ? "selected region of " : "")
4797                     + getTitle();
4798             newFrame.setTitle(newtitle);
4799
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               boolean showSequenceFeatures = viewport
4831                       .isShowSequenceFeatures();
4832               newFrame.setShowSeqFeatures(showSequenceFeatures);
4833               copyThis.setShowSeqFeatures(showSequenceFeatures);
4834               FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4835                       .getFeatureRenderer();
4836               /*
4837                * copy feature rendering settings to split frame
4838                */
4839               newFrame.alignPanel.getSeqPanel().seqCanvas
4840                       .getFeatureRenderer().transferSettings(
4841                               myFeatureStyling);
4842               copyThis.alignPanel.getSeqPanel().seqCanvas
4843                       .getFeatureRenderer().transferSettings(
4844                               myFeatureStyling);
4845               SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4846                       dna ? newFrame : copyThis);
4847               newFrame.setVisible(true);
4848               copyThis.setVisible(true);
4849               String linkedTitle = MessageManager
4850                       .getString("label.linked_view_title");
4851               Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4852             }
4853             else
4854             {
4855               Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4856                       DEFAULT_HEIGHT);
4857             }
4858           }
4859           else
4860           {
4861             System.err.println("No Sequences generated for xRef type "
4862                     + source);
4863           }
4864         } catch (Exception e)
4865         {
4866           jalview.bin.Cache.log.error(
4867                   "Exception when finding crossreferences", e);
4868         } catch (OutOfMemoryError e)
4869         {
4870           new OOMWarning("whilst fetching crossreferences", e);
4871         } catch (Error e)
4872         {
4873           jalview.bin.Cache.log.error("Error when finding crossreferences",
4874                   e);
4875         }
4876         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4877                 "status.finished_searching_for_sequences_from",
4878                 new Object[] { source }), sttime);
4879       }
4880
4881     };
4882     Thread frunner = new Thread(foo);
4883     frunner.start();
4884   }
4885
4886   public boolean canShowTranslationProducts(SequenceI[] selection,
4887           AlignmentI alignment)
4888   {
4889     // old way
4890     try
4891     {
4892       return (jalview.analysis.Dna.canTranslate(selection,
4893               viewport.getViewAsVisibleContigs(true)));
4894     } catch (Exception e)
4895     {
4896       jalview.bin.Cache.log
4897               .warn("canTranslate threw an exception - please report to help@jalview.org",
4898                       e);
4899       return false;
4900     }
4901   }
4902
4903   /**
4904    * Construct and display a new frame containing the translation of this
4905    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4906    */
4907   @Override
4908   public void showTranslation_actionPerformed(ActionEvent e)
4909   {
4910     AlignmentI al = null;
4911     try
4912     {
4913       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4914
4915       al = dna.translateCdna();
4916     } catch (Exception ex)
4917     {
4918       jalview.bin.Cache.log.error(
4919               "Exception during translation. Please report this !", ex);
4920       final String msg = MessageManager
4921               .getString("label.error_when_translating_sequences_submit_bug_report");
4922       final String errorTitle = MessageManager
4923               .getString("label.implementation_error")
4924               + MessageManager.getString("translation_failed");
4925       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4926               JOptionPane.ERROR_MESSAGE);
4927       return;
4928     }
4929     if (al == null || al.getHeight() == 0)
4930     {
4931       final String msg = MessageManager
4932               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4933       final String errorTitle = MessageManager
4934               .getString("label.translation_failed");
4935       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4936               JOptionPane.WARNING_MESSAGE);
4937     }
4938     else
4939     {
4940       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4941       af.setFileFormat(this.currentFileFormat);
4942       final String newTitle = MessageManager.formatMessage(
4943               "label.translation_of_params",
4944               new Object[] { this.getTitle() });
4945       af.setTitle(newTitle);
4946       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4947       {
4948         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4949         viewport.openSplitFrame(af, new Alignment(seqs));
4950       }
4951       else
4952       {
4953         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4954                 DEFAULT_HEIGHT);
4955       }
4956     }
4957   }
4958
4959   /**
4960    * Set the file format
4961    *
4962    * @param fileFormat
4963    */
4964   public void setFileFormat(String fileFormat)
4965   {
4966     this.currentFileFormat = fileFormat;
4967   }
4968
4969   /**
4970    * Try to load a features file onto the alignment.
4971    *
4972    * @param file
4973    *          contents or path to retrieve file
4974    * @param type
4975    *          access mode of file (see jalview.io.AlignFile)
4976    * @return true if features file was parsed correctly.
4977    */
4978   public boolean parseFeaturesFile(String file, String type)
4979   {
4980     return avc.parseFeaturesFile(file, type,
4981             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4982
4983   }
4984
4985   @Override
4986   public void refreshFeatureUI(boolean enableIfNecessary)
4987   {
4988     // note - currently this is only still here rather than in the controller
4989     // because of the featureSettings hard reference that is yet to be
4990     // abstracted
4991     if (enableIfNecessary)
4992     {
4993       viewport.setShowSequenceFeatures(true);
4994       showSeqFeatures.setSelected(true);
4995     }
4996
4997   }
4998
4999   @Override
5000   public void dragEnter(DropTargetDragEvent evt)
5001   {
5002   }
5003
5004   @Override
5005   public void dragExit(DropTargetEvent evt)
5006   {
5007   }
5008
5009   @Override
5010   public void dragOver(DropTargetDragEvent evt)
5011   {
5012   }
5013
5014   @Override
5015   public void dropActionChanged(DropTargetDragEvent evt)
5016   {
5017   }
5018
5019   @Override
5020   public void drop(DropTargetDropEvent evt)
5021   {
5022     Transferable t = evt.getTransferable();
5023     java.util.List files = null;
5024
5025     try
5026     {
5027       DataFlavor uriListFlavor = new DataFlavor(
5028               "text/uri-list;class=java.lang.String");
5029       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5030       {
5031         // Works on Windows and MacOSX
5032         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5033         files = (java.util.List) t
5034                 .getTransferData(DataFlavor.javaFileListFlavor);
5035       }
5036       else if (t.isDataFlavorSupported(uriListFlavor))
5037       {
5038         // This is used by Unix drag system
5039         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5040         String data = (String) t.getTransferData(uriListFlavor);
5041         files = new java.util.ArrayList(1);
5042         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5043                 data, "\r\n"); st.hasMoreTokens();)
5044         {
5045           String s = st.nextToken();
5046           if (s.startsWith("#"))
5047           {
5048             // the line is a comment (as per the RFC 2483)
5049             continue;
5050           }
5051
5052           java.net.URI uri = new java.net.URI(s);
5053           // check to see if we can handle this kind of URI
5054           if (uri.getScheme().toLowerCase().startsWith("http"))
5055           {
5056             files.add(uri.toString());
5057           }
5058           else
5059           {
5060             // otherwise preserve old behaviour: catch all for file objects
5061             java.io.File file = new java.io.File(uri);
5062             files.add(file.toString());
5063           }
5064         }
5065       }
5066     } catch (Exception e)
5067     {
5068       e.printStackTrace();
5069     }
5070     if (files != null)
5071     {
5072       try
5073       {
5074         // check to see if any of these files have names matching sequences in
5075         // the alignment
5076         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5077                 .getAlignment().getSequencesArray());
5078         /**
5079          * Object[] { String,SequenceI}
5080          */
5081         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5082         ArrayList<String> filesnotmatched = new ArrayList<String>();
5083         for (int i = 0; i < files.size(); i++)
5084         {
5085           String file = files.get(i).toString();
5086           String pdbfn = "";
5087           String protocol = FormatAdapter.checkProtocol(file);
5088           if (protocol == jalview.io.FormatAdapter.FILE)
5089           {
5090             File fl = new File(file);
5091             pdbfn = fl.getName();
5092           }
5093           else if (protocol == jalview.io.FormatAdapter.URL)
5094           {
5095             URL url = new URL(file);
5096             pdbfn = url.getFile();
5097           }
5098           if (pdbfn.length() > 0)
5099           {
5100             // attempt to find a match in the alignment
5101             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5102             int l = 0, c = pdbfn.indexOf(".");
5103             while (mtch == null && c != -1)
5104             {
5105               do
5106               {
5107                 l = c;
5108               } while ((c = pdbfn.indexOf(".", l)) > l);
5109               if (l > -1)
5110               {
5111                 pdbfn = pdbfn.substring(0, l);
5112               }
5113               mtch = idm.findAllIdMatches(pdbfn);
5114             }
5115             if (mtch != null)
5116             {
5117               String type = null;
5118               try
5119               {
5120                 type = new IdentifyFile().identify(file, protocol);
5121               } catch (Exception ex)
5122               {
5123                 type = null;
5124               }
5125               if (type != null)
5126               {
5127                 if (type.equalsIgnoreCase("PDB"))
5128                 {
5129                   filesmatched.add(new Object[] { file, protocol, mtch });
5130                   continue;
5131                 }
5132               }
5133             }
5134             // File wasn't named like one of the sequences or wasn't a PDB file.
5135             filesnotmatched.add(file);
5136           }
5137         }
5138         int assocfiles = 0;
5139         if (filesmatched.size() > 0)
5140         {
5141           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5142                   || JOptionPane
5143                           .showConfirmDialog(
5144                                   this,
5145                                   MessageManager
5146                                           .formatMessage(
5147                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5148                                                   new Object[] { Integer
5149                                                           .valueOf(
5150                                                                   filesmatched
5151                                                                           .size())
5152                                                           .toString() }),
5153                                   MessageManager
5154                                           .getString("label.automatically_associate_pdb_files_by_name"),
5155                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5156
5157           {
5158             for (Object[] fm : filesmatched)
5159             {
5160               // try and associate
5161               // TODO: may want to set a standard ID naming formalism for
5162               // associating PDB files which have no IDs.
5163               for (SequenceI toassoc : (SequenceI[]) fm[2])
5164               {
5165                 PDBEntry pe = new AssociatePdbFileWithSeq()
5166                         .associatePdbWithSeq((String) fm[0],
5167                                 (String) fm[1], toassoc, false,
5168                                 Desktop.instance);
5169                 if (pe != null)
5170                 {
5171                   System.err.println("Associated file : "
5172                           + ((String) fm[0]) + " with "
5173                           + toassoc.getDisplayId(true));
5174                   assocfiles++;
5175                 }
5176               }
5177               alignPanel.paintAlignment(true);
5178             }
5179           }
5180         }
5181         if (filesnotmatched.size() > 0)
5182         {
5183           if (assocfiles > 0
5184                   && (Cache.getDefault(
5185                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5186                           .showConfirmDialog(
5187                                   this,
5188                                   "<html>"
5189                                           + MessageManager
5190                                                   .formatMessage(
5191                                                           "label.ignore_unmatched_dropped_files_info",
5192                                                           new Object[] { Integer
5193                                                                   .valueOf(
5194                                                                           filesnotmatched
5195                                                                                   .size())
5196                                                                   .toString() })
5197                                           + "</html>",
5198                                   MessageManager
5199                                           .getString("label.ignore_unmatched_dropped_files"),
5200                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5201           {
5202             return;
5203           }
5204           for (String fn : filesnotmatched)
5205           {
5206             loadJalviewDataFile(fn, null, null, null);
5207           }
5208
5209         }
5210       } catch (Exception ex)
5211       {
5212         ex.printStackTrace();
5213       }
5214     }
5215   }
5216
5217   /**
5218    * Attempt to load a "dropped" file or URL string: First by testing whether
5219    * it's an Annotation file, then a JNet file, and finally a features file. If
5220    * all are false then the user may have dropped an alignment file onto this
5221    * AlignFrame.
5222    *
5223    * @param file
5224    *          either a filename or a URL string.
5225    */
5226   public void loadJalviewDataFile(String file, String protocol,
5227           String format, SequenceI assocSeq)
5228   {
5229     try
5230     {
5231       if (protocol == null)
5232       {
5233         protocol = FormatAdapter.checkProtocol(file);
5234       }
5235       // if the file isn't identified, or not positively identified as some
5236       // other filetype (PFAM is default unidentified alignment file type) then
5237       // try to parse as annotation.
5238       boolean isAnnotation = (format == null || format
5239               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5240               .annotateAlignmentView(viewport, file, protocol) : false;
5241
5242       if (!isAnnotation)
5243       {
5244         // first see if its a T-COFFEE score file
5245         TCoffeeScoreFile tcf = null;
5246         try
5247         {
5248           tcf = new TCoffeeScoreFile(file, protocol);
5249           if (tcf.isValid())
5250           {
5251             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5252             {
5253               tcoffeeColour.setEnabled(true);
5254               tcoffeeColour.setSelected(true);
5255               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5256               isAnnotation = true;
5257               statusBar
5258                       .setText(MessageManager
5259                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5260             }
5261             else
5262             {
5263               // some problem - if no warning its probable that the ID matching
5264               // process didn't work
5265               JOptionPane
5266                       .showMessageDialog(
5267                               Desktop.desktop,
5268                               tcf.getWarningMessage() == null ? MessageManager
5269                                       .getString("label.check_file_matches_sequence_ids_alignment")
5270                                       : tcf.getWarningMessage(),
5271                               MessageManager
5272                                       .getString("label.problem_reading_tcoffee_score_file"),
5273                               JOptionPane.WARNING_MESSAGE);
5274             }
5275           }
5276           else
5277           {
5278             tcf = null;
5279           }
5280         } catch (Exception x)
5281         {
5282           Cache.log
5283                   .debug("Exception when processing data source as T-COFFEE score file",
5284                           x);
5285           tcf = null;
5286         }
5287         if (tcf == null)
5288         {
5289           // try to see if its a JNet 'concise' style annotation file *before*
5290           // we
5291           // try to parse it as a features file
5292           if (format == null)
5293           {
5294             format = new IdentifyFile().identify(file, protocol);
5295           }
5296           if (format.equalsIgnoreCase("JnetFile"))
5297           {
5298             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5299                     file, protocol);
5300             new JnetAnnotationMaker();
5301             JnetAnnotationMaker.add_annotation(predictions,
5302                     viewport.getAlignment(), 0, false);
5303             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5304             viewport.getAlignment().setSeqrep(repseq);
5305             ColumnSelection cs = new ColumnSelection();
5306             cs.hideInsertionsFor(repseq);
5307             viewport.setColumnSelection(cs);
5308             isAnnotation = true;
5309           }
5310           else if (IdentifyFile.FeaturesFile.equals(format))
5311           {
5312             if (parseFeaturesFile(file, protocol))
5313             {
5314               alignPanel.paintAlignment(true);
5315             }
5316           }
5317             else
5318             {
5319               new FileLoader().LoadFile(viewport, file, protocol, format);
5320             }
5321         }
5322       }
5323       if (isAnnotation)
5324       {
5325
5326         alignPanel.adjustAnnotationHeight();
5327         viewport.updateSequenceIdColours();
5328         buildSortByAnnotationScoresMenu();
5329         alignPanel.paintAlignment(true);
5330       }
5331     } catch (Exception ex)
5332     {
5333       ex.printStackTrace();
5334     } catch (OutOfMemoryError oom)
5335     {
5336       try
5337       {
5338         System.gc();
5339       } catch (Exception x)
5340       {
5341       }
5342       new OOMWarning(
5343               "loading data "
5344                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5345                               : "using " + protocol + " from " + file)
5346                               : ".")
5347                       + (format != null ? "(parsing as '" + format
5348                               + "' file)" : ""), oom, Desktop.desktop);
5349     }
5350   }
5351
5352   /**
5353    * Method invoked by the ChangeListener on the tabbed pane, in other words
5354    * when a different tabbed pane is selected by the user or programmatically.
5355    */
5356   @Override
5357   public void tabSelectionChanged(int index)
5358   {
5359     if (index > -1)
5360     {
5361       alignPanel = alignPanels.get(index);
5362       viewport = alignPanel.av;
5363       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5364       setMenusFromViewport(viewport);
5365     }
5366
5367     /*
5368      * If there is a frame linked to this one in a SplitPane, switch it to the
5369      * same view tab index. No infinite recursion of calls should happen, since
5370      * tabSelectionChanged() should not get invoked on setting the selected
5371      * index to an unchanged value. Guard against setting an invalid index
5372      * before the new view peer tab has been created.
5373      */
5374     final AlignViewportI peer = viewport.getCodingComplement();
5375     if (peer != null)
5376     {
5377       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5378       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5379       {
5380         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5381       }
5382     }
5383   }
5384
5385   /**
5386    * On right mouse click on view tab, prompt for and set new view name.
5387    */
5388   @Override
5389   public void tabbedPane_mousePressed(MouseEvent e)
5390   {
5391     if (SwingUtilities.isRightMouseButton(e))
5392     {
5393       String msg = MessageManager.getString("label.enter_view_name");
5394       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5395               JOptionPane.QUESTION_MESSAGE);
5396
5397       if (reply != null)
5398       {
5399         viewport.viewName = reply;
5400         // TODO warn if reply is in getExistingViewNames()?
5401         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5402       }
5403     }
5404   }
5405
5406   public AlignViewport getCurrentView()
5407   {
5408     return viewport;
5409   }
5410
5411   /**
5412    * Open the dialog for regex description parsing.
5413    */
5414   @Override
5415   protected void extractScores_actionPerformed(ActionEvent e)
5416   {
5417     ParseProperties pp = new jalview.analysis.ParseProperties(
5418             viewport.getAlignment());
5419     // TODO: verify regex and introduce GUI dialog for version 2.5
5420     // if (pp.getScoresFromDescription("col", "score column ",
5421     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5422     // true)>0)
5423     if (pp.getScoresFromDescription("description column",
5424             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5425     {
5426       buildSortByAnnotationScoresMenu();
5427     }
5428   }
5429
5430   /*
5431    * (non-Javadoc)
5432    *
5433    * @see
5434    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5435    * )
5436    */
5437   @Override
5438   protected void showDbRefs_actionPerformed(ActionEvent e)
5439   {
5440     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5441   }
5442
5443   /*
5444    * (non-Javadoc)
5445    *
5446    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5447    * ActionEvent)
5448    */
5449   @Override
5450   protected void showNpFeats_actionPerformed(ActionEvent e)
5451   {
5452     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5453   }
5454
5455   /**
5456    * find the viewport amongst the tabs in this alignment frame and close that
5457    * tab
5458    *
5459    * @param av
5460    */
5461   public boolean closeView(AlignViewportI av)
5462   {
5463     if (viewport == av)
5464     {
5465       this.closeMenuItem_actionPerformed(false);
5466       return true;
5467     }
5468     Component[] comp = tabbedPane.getComponents();
5469     for (int i = 0; comp != null && i < comp.length; i++)
5470     {
5471       if (comp[i] instanceof AlignmentPanel)
5472       {
5473         if (((AlignmentPanel) comp[i]).av == av)
5474         {
5475           // close the view.
5476           closeView((AlignmentPanel) comp[i]);
5477           return true;
5478         }
5479       }
5480     }
5481     return false;
5482   }
5483
5484   protected void build_fetchdbmenu(JMenu webService)
5485   {
5486     // Temporary hack - DBRef Fetcher always top level ws entry.
5487     // TODO We probably want to store a sequence database checklist in
5488     // preferences and have checkboxes.. rather than individual sources selected
5489     // here
5490     final JMenu rfetch = new JMenu(
5491             MessageManager.getString("action.fetch_db_references"));
5492     rfetch.setToolTipText(MessageManager
5493             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5494     webService.add(rfetch);
5495
5496     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5497             MessageManager.getString("option.trim_retrieved_seqs"));
5498     trimrs.setToolTipText(MessageManager
5499             .getString("label.trim_retrieved_sequences"));
5500     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5501     trimrs.addActionListener(new ActionListener()
5502     {
5503       @Override
5504       public void actionPerformed(ActionEvent e)
5505       {
5506         trimrs.setSelected(trimrs.isSelected());
5507         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5508                 Boolean.valueOf(trimrs.isSelected()).toString());
5509       };
5510     });
5511     rfetch.add(trimrs);
5512     JMenuItem fetchr = new JMenuItem(
5513             MessageManager.getString("label.standard_databases"));
5514     fetchr.setToolTipText(MessageManager
5515             .getString("label.fetch_embl_uniprot"));
5516     fetchr.addActionListener(new ActionListener()
5517     {
5518
5519       @Override
5520       public void actionPerformed(ActionEvent e)
5521       {
5522         new Thread(new Runnable()
5523         {
5524
5525           @Override
5526           public void run()
5527           {
5528             boolean isNuclueotide = alignPanel.alignFrame
5529                     .getViewport().getAlignment()
5530                     .isNucleotide();
5531             new jalview.ws.DBRefFetcher(alignPanel.av
5532                     .getSequenceSelection(),
5533                     alignPanel.alignFrame, null,
5534                     alignPanel.alignFrame.featureSettings,
5535                     isNuclueotide)
5536                     .fetchDBRefs(false);
5537           }
5538         }).start();
5539
5540       }
5541
5542     });
5543     rfetch.add(fetchr);
5544     final AlignFrame me = this;
5545     new Thread(new Runnable()
5546     {
5547       @Override
5548       public void run()
5549       {
5550         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5551                 .getSequenceFetcherSingleton(me);
5552         javax.swing.SwingUtilities.invokeLater(new Runnable()
5553         {
5554           @Override
5555           public void run()
5556           {
5557             String[] dbclasses = sf.getOrderedSupportedSources();
5558             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5559             // jalview.util.QuickSort.sort(otherdb, otherdb);
5560             List<DbSourceProxy> otherdb;
5561             JMenu dfetch = new JMenu();
5562             JMenu ifetch = new JMenu();
5563             JMenuItem fetchr = null;
5564             int comp = 0, icomp = 0, mcomp = 15;
5565             String mname = null;
5566             int dbi = 0;
5567             for (String dbclass : dbclasses)
5568             {
5569               otherdb = sf.getSourceProxy(dbclass);
5570               // add a single entry for this class, or submenu allowing 'fetch
5571               // all' or pick one
5572               if (otherdb == null || otherdb.size() < 1)
5573               {
5574                 continue;
5575               }
5576               // List<DbSourceProxy> dbs=otherdb;
5577               // otherdb=new ArrayList<DbSourceProxy>();
5578               // for (DbSourceProxy db:dbs)
5579               // {
5580               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5581               // }
5582               if (mname == null)
5583               {
5584                 mname = "From " + dbclass;
5585               }
5586               if (otherdb.size() == 1)
5587               {
5588                 final DbSourceProxy[] dassource = otherdb
5589                         .toArray(new DbSourceProxy[0]);
5590                 DbSourceProxy src = otherdb.get(0);
5591                 fetchr = new JMenuItem(src.getDbSource());
5592                 fetchr.addActionListener(new ActionListener()
5593                 {
5594
5595                   @Override
5596                   public void actionPerformed(ActionEvent e)
5597                   {
5598                     new Thread(new Runnable()
5599                     {
5600
5601                       @Override
5602                       public void run()
5603                       {
5604                         boolean isNuclueotide = alignPanel.alignFrame
5605                                 .getViewport().getAlignment()
5606                                 .isNucleotide();
5607                         new jalview.ws.DBRefFetcher(alignPanel.av
5608                                 .getSequenceSelection(),
5609                                 alignPanel.alignFrame, dassource,
5610                                 alignPanel.alignFrame.featureSettings,
5611                                 isNuclueotide)
5612                                 .fetchDBRefs(false);
5613                       }
5614                     }).start();
5615                   }
5616
5617                 });
5618                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5619                         MessageManager.formatMessage(
5620                                 "label.fetch_retrieve_from",
5621                                 new Object[] { src.getDbName() })));
5622                 dfetch.add(fetchr);
5623                 comp++;
5624               }
5625               else
5626               {
5627                 final DbSourceProxy[] dassource = otherdb
5628                         .toArray(new DbSourceProxy[0]);
5629                 // fetch all entry
5630                 DbSourceProxy src = otherdb.get(0);
5631                 fetchr = new JMenuItem(MessageManager.formatMessage(
5632                         "label.fetch_all_param",
5633                         new Object[] { src.getDbSource() }));
5634                 fetchr.addActionListener(new ActionListener()
5635                 {
5636                   @Override
5637                   public void actionPerformed(ActionEvent e)
5638                   {
5639                     new Thread(new Runnable()
5640                     {
5641
5642                       @Override
5643                       public void run()
5644                       {
5645                         boolean isNuclueotide = alignPanel.alignFrame
5646                                 .getViewport().getAlignment()
5647                                 .isNucleotide();
5648                         new jalview.ws.DBRefFetcher(alignPanel.av
5649                                 .getSequenceSelection(),
5650                                 alignPanel.alignFrame, dassource,
5651                                 alignPanel.alignFrame.featureSettings,
5652                                 isNuclueotide)
5653                                 .fetchDBRefs(false);
5654                       }
5655                     }).start();
5656                   }
5657                 });
5658
5659                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5660                         MessageManager.formatMessage(
5661                                 "label.fetch_retrieve_from_all_sources",
5662                                 new Object[] {
5663                                     Integer.valueOf(otherdb.size())
5664                                             .toString(), src.getDbSource(),
5665                                     src.getDbName() })));
5666                 dfetch.add(fetchr);
5667                 comp++;
5668                 // and then build the rest of the individual menus
5669                 ifetch = new JMenu(MessageManager.formatMessage(
5670                         "label.source_from_db_source",
5671                         new Object[] { src.getDbSource() }));
5672                 icomp = 0;
5673                 String imname = null;
5674                 int i = 0;
5675                 for (DbSourceProxy sproxy : otherdb)
5676                 {
5677                   String dbname = sproxy.getDbName();
5678                   String sname = dbname.length() > 5 ? dbname.substring(0,
5679                           5) + "..." : dbname;
5680                   String msname = dbname.length() > 10 ? dbname.substring(
5681                           0, 10) + "..." : dbname;
5682                   if (imname == null)
5683                   {
5684                     imname = MessageManager.formatMessage(
5685                             "label.from_msname", new Object[] { sname });
5686                   }
5687                   fetchr = new JMenuItem(msname);
5688                   final DbSourceProxy[] dassrc = { sproxy };
5689                   fetchr.addActionListener(new ActionListener()
5690                   {
5691
5692                     @Override
5693                     public void actionPerformed(ActionEvent e)
5694                     {
5695                       new Thread(new Runnable()
5696                       {
5697
5698                         @Override
5699                         public void run()
5700                         {
5701                           boolean isNuclueotide = alignPanel.alignFrame
5702                                   .getViewport().getAlignment()
5703                                   .isNucleotide();
5704                           new jalview.ws.DBRefFetcher(alignPanel.av
5705                                   .getSequenceSelection(),
5706                                   alignPanel.alignFrame, dassrc,
5707                                   alignPanel.alignFrame.featureSettings,
5708                                   isNuclueotide)
5709                                   .fetchDBRefs(false);
5710                         }
5711                       }).start();
5712                     }
5713
5714                   });
5715                   fetchr.setToolTipText("<html>"
5716                           + MessageManager.formatMessage(
5717                                   "label.fetch_retrieve_from", new Object[]
5718                                   { dbname }));
5719                   ifetch.add(fetchr);
5720                   ++i;
5721                   if (++icomp >= mcomp || i == (otherdb.size()))
5722                   {
5723                     ifetch.setText(MessageManager.formatMessage(
5724                             "label.source_to_target", imname, sname));
5725                     dfetch.add(ifetch);
5726                     ifetch = new JMenu();
5727                     imname = null;
5728                     icomp = 0;
5729                     comp++;
5730                   }
5731                 }
5732               }
5733               ++dbi;
5734               if (comp >= mcomp || dbi >= (dbclasses.length))
5735               {
5736                 dfetch.setText(MessageManager.formatMessage(
5737                         "label.source_to_target", mname, dbclass));
5738                 rfetch.add(dfetch);
5739                 dfetch = new JMenu();
5740                 mname = null;
5741                 comp = 0;
5742               }
5743             }
5744           }
5745         });
5746       }
5747     }).start();
5748
5749   }
5750
5751   /**
5752    * Left justify the whole alignment.
5753    */
5754   @Override
5755   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5756   {
5757     AlignmentI al = viewport.getAlignment();
5758     al.justify(false);
5759     viewport.firePropertyChange("alignment", null, al);
5760   }
5761
5762   /**
5763    * Right justify the whole alignment.
5764    */
5765   @Override
5766   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5767   {
5768     AlignmentI al = viewport.getAlignment();
5769     al.justify(true);
5770     viewport.firePropertyChange("alignment", null, al);
5771   }
5772
5773   @Override
5774   public void setShowSeqFeatures(boolean b)
5775   {
5776     showSeqFeatures.setSelected(b);
5777     viewport.setShowSequenceFeatures(b);
5778   }
5779
5780   /*
5781    * (non-Javadoc)
5782    *
5783    * @see
5784    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5785    * awt.event.ActionEvent)
5786    */
5787   @Override
5788   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5789   {
5790     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5791     alignPanel.paintAlignment(true);
5792   }
5793
5794   /*
5795    * (non-Javadoc)
5796    *
5797    * @see
5798    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5799    * .ActionEvent)
5800    */
5801   @Override
5802   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5803   {
5804     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5805     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5806
5807   }
5808
5809   /*
5810    * (non-Javadoc)
5811    *
5812    * @see
5813    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5814    * .event.ActionEvent)
5815    */
5816   @Override
5817   protected void showGroupConservation_actionPerformed(ActionEvent e)
5818   {
5819     viewport.setShowGroupConservation(showGroupConservation.getState());
5820     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5821   }
5822
5823   /*
5824    * (non-Javadoc)
5825    *
5826    * @see
5827    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5828    * .event.ActionEvent)
5829    */
5830   @Override
5831   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5832   {
5833     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5834     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5835   }
5836
5837   /*
5838    * (non-Javadoc)
5839    *
5840    * @see
5841    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5842    * .event.ActionEvent)
5843    */
5844   @Override
5845   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5846   {
5847     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5848     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5849   }
5850
5851   @Override
5852   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5853   {
5854     showSequenceLogo.setState(true);
5855     viewport.setShowSequenceLogo(true);
5856     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5857     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5858   }
5859
5860   @Override
5861   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5862   {
5863     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5864   }
5865
5866   /*
5867    * (non-Javadoc)
5868    *
5869    * @see
5870    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5871    * .event.ActionEvent)
5872    */
5873   @Override
5874   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5875   {
5876     if (avc.makeGroupsFromSelection())
5877     {
5878       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5879       alignPanel.updateAnnotation();
5880       alignPanel.paintAlignment(true);
5881     }
5882   }
5883
5884   public void clearAlignmentSeqRep()
5885   {
5886     // TODO refactor alignmentseqrep to controller
5887     if (viewport.getAlignment().hasSeqrep())
5888     {
5889       viewport.getAlignment().setSeqrep(null);
5890       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5891       alignPanel.updateAnnotation();
5892       alignPanel.paintAlignment(true);
5893     }
5894   }
5895
5896   @Override
5897   protected void createGroup_actionPerformed(ActionEvent e)
5898   {
5899     if (avc.createGroup())
5900     {
5901       alignPanel.alignmentChanged();
5902     }
5903   }
5904
5905   @Override
5906   protected void unGroup_actionPerformed(ActionEvent e)
5907   {
5908     if (avc.unGroup())
5909     {
5910       alignPanel.alignmentChanged();
5911     }
5912   }
5913
5914   /**
5915    * make the given alignmentPanel the currently selected tab
5916    *
5917    * @param alignmentPanel
5918    */
5919   public void setDisplayedView(AlignmentPanel alignmentPanel)
5920   {
5921     if (!viewport.getSequenceSetId().equals(
5922             alignmentPanel.av.getSequenceSetId()))
5923     {
5924       throw new Error(
5925               MessageManager
5926                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5927     }
5928     if (tabbedPane != null
5929             && tabbedPane.getTabCount() > 0
5930             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5931                     .getSelectedIndex())
5932     {
5933       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5934     }
5935   }
5936
5937   /**
5938    * Action on selection of menu options to Show or Hide annotations.
5939    *
5940    * @param visible
5941    * @param forSequences
5942    *          update sequence-related annotations
5943    * @param forAlignment
5944    *          update non-sequence-related annotations
5945    */
5946   @Override
5947   protected void setAnnotationsVisibility(boolean visible,
5948           boolean forSequences, boolean forAlignment)
5949   {
5950     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5951             .getAlignmentAnnotation())
5952     {
5953       /*
5954        * don't display non-positional annotations on an alignment
5955        */
5956       if (aa.annotations == null)
5957       {
5958         continue;
5959       }
5960       boolean apply = (aa.sequenceRef == null && forAlignment)
5961               || (aa.sequenceRef != null && forSequences);
5962       if (apply)
5963       {
5964         aa.visible = visible;
5965       }
5966     }
5967     alignPanel.validateAnnotationDimensions(true);
5968     alignPanel.alignmentChanged();
5969   }
5970
5971   /**
5972    * Store selected annotation sort order for the view and repaint.
5973    */
5974   @Override
5975   protected void sortAnnotations_actionPerformed()
5976   {
5977     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5978     this.alignPanel.av
5979             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5980     alignPanel.paintAlignment(true);
5981   }
5982
5983   /**
5984    *
5985    * @return alignment panels in this alignment frame
5986    */
5987   public List<? extends AlignmentViewPanel> getAlignPanels()
5988   {
5989     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5990   }
5991
5992   /**
5993    * Open a new alignment window, with the cDNA associated with this (protein)
5994    * alignment, aligned as is the protein.
5995    */
5996   protected void viewAsCdna_actionPerformed()
5997   {
5998     // TODO no longer a menu action - refactor as required
5999     final AlignmentI alignment = getViewport().getAlignment();
6000     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6001     if (mappings == null)
6002     {
6003       return;
6004     }
6005     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6006     for (SequenceI aaSeq : alignment.getSequences())
6007     {
6008       for (AlignedCodonFrame acf : mappings)
6009       {
6010         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6011         if (dnaSeq != null)
6012         {
6013           /*
6014            * There is a cDNA mapping for this protein sequence - add to new
6015            * alignment. It will share the same dataset sequence as other mapped
6016            * cDNA (no new mappings need to be created).
6017            */
6018           final Sequence newSeq = new Sequence(dnaSeq);
6019           newSeq.setDatasetSequence(dnaSeq);
6020           cdnaSeqs.add(newSeq);
6021         }
6022       }
6023     }
6024     if (cdnaSeqs.size() == 0)
6025     {
6026       // show a warning dialog no mapped cDNA
6027       return;
6028     }
6029     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6030             .size()]));
6031     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6032             AlignFrame.DEFAULT_HEIGHT);
6033     cdna.alignAs(alignment);
6034     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6035             + this.title;
6036     Desktop.addInternalFrame(alignFrame, newtitle,
6037             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6038   }
6039
6040   /**
6041    * Set visibility of dna/protein complement view (available when shown in a
6042    * split frame).
6043    *
6044    * @param show
6045    */
6046   @Override
6047   protected void showComplement_actionPerformed(boolean show)
6048   {
6049     SplitContainerI sf = getSplitViewContainer();
6050     if (sf != null)
6051     {
6052       sf.setComplementVisible(this, show);
6053     }
6054   }
6055
6056   /**
6057    * Generate the reverse (optionally complemented) of the selected sequences,
6058    * and add them to the alignment
6059    */
6060   @Override
6061   protected void showReverse_actionPerformed(boolean complement)
6062   {
6063     AlignmentI al = null;
6064     try
6065     {
6066       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6067
6068       al = dna.reverseCdna(complement);
6069       viewport.addAlignment(al, "");
6070     } catch (Exception ex)
6071     {
6072       System.err.println(ex.getMessage());
6073       return;
6074     }
6075   }
6076 }
6077
6078 class PrintThread extends Thread
6079 {
6080   AlignmentPanel ap;
6081
6082   public PrintThread(AlignmentPanel ap)
6083   {
6084     this.ap = ap;
6085   }
6086
6087   static PageFormat pf;
6088
6089   @Override
6090   public void run()
6091   {
6092     PrinterJob printJob = PrinterJob.getPrinterJob();
6093
6094     if (pf != null)
6095     {
6096       printJob.setPrintable(ap, pf);
6097     }
6098     else
6099     {
6100       printJob.setPrintable(ap);
6101     }
6102
6103     if (printJob.printDialog())
6104     {
6105       try
6106       {
6107         printJob.print();
6108       } catch (Exception PrintException)
6109       {
6110         PrintException.printStackTrace();
6111       }
6112     }
6113   }
6114 }