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