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.FeatureSettingsModelI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.ScoreModelI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.DBRefSource;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.FileLoader;
  69 import jalview.io.FormatAdapter;
  70 import jalview.io.HtmlSvgOutput;
  71 import jalview.io.IdentifyFile;
  72 import jalview.io.JalviewFileChooser;
  73 import jalview.io.JalviewFileView;
  74 import jalview.io.JnetAnnotationMaker;
  75 import jalview.io.NewickFile;
  76 import jalview.io.TCoffeeScoreFile;
  77 import jalview.jbgui.GAlignFrame;
  78 import jalview.schemes.Blosum62ColourScheme;
  79 import jalview.schemes.BuriedColourScheme;
  80 import jalview.schemes.ClustalxColourScheme;
  81 import jalview.schemes.ColourSchemeI;
  82 import jalview.schemes.ColourSchemeProperty;
  83 import jalview.schemes.HelixColourScheme;
  84 import jalview.schemes.HydrophobicColourScheme;
  85 import jalview.schemes.NucleotideColourScheme;
  86 import jalview.schemes.PIDColourScheme;
  87 import jalview.schemes.PurinePyrimidineColourScheme;
  88 import jalview.schemes.RNAHelicesColourChooser;
  89 import jalview.schemes.ResidueProperties;
  90 import jalview.schemes.StrandColourScheme;
  91 import jalview.schemes.TCoffeeColourScheme;
  92 import jalview.schemes.TaylorColourScheme;
  93 import jalview.schemes.TurnColourScheme;
  94 import jalview.schemes.UserColourScheme;
  95 import jalview.schemes.ZappoColourScheme;
  96 import jalview.structure.StructureSelectionManager;
  97 import jalview.util.MessageManager;
  98 import jalview.viewmodel.AlignmentViewport;
  99 import jalview.ws.DBRefFetcher;
 100 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 101 import jalview.ws.SequenceFetcher;
 102 import jalview.ws.jws1.Discoverer;
 103 import jalview.ws.jws2.Jws2Discoverer;
 104 import jalview.ws.jws2.jabaws2.Jws2Instance;
 105 import jalview.ws.seqfetcher.DbSourceProxy;
 106
 107 import java.awt.BorderLayout;
 108 import java.awt.Component;
 109 import java.awt.Rectangle;
 110 import java.awt.Toolkit;
 111 import java.awt.datatransfer.Clipboard;
 112 import java.awt.datatransfer.DataFlavor;
 113 import java.awt.datatransfer.StringSelection;
 114 import java.awt.datatransfer.Transferable;
 115 import java.awt.dnd.DnDConstants;
 116 import java.awt.dnd.DropTargetDragEvent;
 117 import java.awt.dnd.DropTargetDropEvent;
 118 import java.awt.dnd.DropTargetEvent;
 119 import java.awt.dnd.DropTargetListener;
 120 import java.awt.event.ActionEvent;
 121 import java.awt.event.ActionListener;
 122 import java.awt.event.ItemEvent;
 123 import java.awt.event.ItemListener;
 124 import java.awt.event.KeyAdapter;
 125 import java.awt.event.KeyEvent;
 126 import java.awt.event.MouseAdapter;
 127 import java.awt.event.MouseEvent;
 128 import java.awt.print.PageFormat;
 129 import java.awt.print.PrinterJob;
 130 import java.beans.PropertyChangeEvent;
 131 import java.io.File;
 132 import java.net.URL;
 133 import java.util.ArrayList;
 134 import java.util.Arrays;
 135 import java.util.Deque;
 136 import java.util.Enumeration;
 137 import java.util.Hashtable;
 138 import java.util.List;
 139 import java.util.Vector;
 140
 141 import javax.swing.JCheckBoxMenuItem;
 142 import javax.swing.JEditorPane;
 143 import javax.swing.JInternalFrame;
 144 import javax.swing.JLayeredPane;
 145 import javax.swing.JMenu;
 146 import javax.swing.JMenuItem;
 147 import javax.swing.JOptionPane;
 148 import javax.swing.JRadioButtonMenuItem;
 149 import javax.swing.JScrollPane;
 150 import javax.swing.SwingUtilities;
 151
 152 /**
 153  * DOCUMENT ME!
 154  *
 155  * @author $author$
 156  * @version $Revision$
 157  */
 158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 159         IProgressIndicator, AlignViewControllerGuiI
 160 {
 161
 162   public static final int DEFAULT_WIDTH = 700;
 163
 164   public static final int DEFAULT_HEIGHT = 500;
 165
 166   /*
 167    * The currently displayed panel (selected tabbed view if more than one)
 168    */
 169   public AlignmentPanel alignPanel;
 170
 171   AlignViewport viewport;
 172
 173   public AlignViewControllerI avc;
 174
 175   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 176
 177   /**
 178    * Last format used to load or save alignments in this window
 179    */
 180   String currentFileFormat = null;
 181
 182   /**
 183    * Current filename for this alignment
 184    */
 185   String fileName = null;
 186
 187   /**
 188    * Creates a new AlignFrame object with specific width and height.
 189    *
 190    * @param al
 191    * @param width
 192    * @param height
 193    */
 194   public AlignFrame(AlignmentI al, int width, int height)
 195   {
 196     this(al, null, width, height);
 197   }
 198
 199   /**
 200    * Creates a new AlignFrame object with specific width, height and
 201    * sequenceSetId
 202    *
 203    * @param al
 204    * @param width
 205    * @param height
 206    * @param sequenceSetId
 207    */
 208   public AlignFrame(AlignmentI al, int width, int height,
 209           String sequenceSetId)
 210   {
 211     this(al, null, width, height, sequenceSetId);
 212   }
 213
 214   /**
 215    * Creates a new AlignFrame object with specific width, height and
 216    * sequenceSetId
 217    *
 218    * @param al
 219    * @param width
 220    * @param height
 221    * @param sequenceSetId
 222    * @param viewId
 223    */
 224   public AlignFrame(AlignmentI al, int width, int height,
 225           String sequenceSetId, String viewId)
 226   {
 227     this(al, null, width, height, sequenceSetId, viewId);
 228   }
 229
 230   /**
 231    * new alignment window with hidden columns
 232    *
 233    * @param al
 234    *          AlignmentI
 235    * @param hiddenColumns
 236    *          ColumnSelection or null
 237    * @param width
 238    *          Width of alignment frame
 239    * @param height
 240    *          height of frame.
 241    */
 242   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 243           int width, int height)
 244   {
 245     this(al, hiddenColumns, width, height, null);
 246   }
 247
 248   /**
 249    * Create alignment frame for al with hiddenColumns, a specific width and
 250    * height, and specific sequenceId
 251    *
 252    * @param al
 253    * @param hiddenColumns
 254    * @param width
 255    * @param height
 256    * @param sequenceSetId
 257    *          (may be null)
 258    */
 259   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 260           int width, int height, String sequenceSetId)
 261   {
 262     this(al, hiddenColumns, width, height, sequenceSetId, null);
 263   }
 264
 265   /**
 266    * Create alignment frame for al with hiddenColumns, a specific width and
 267    * height, and specific sequenceId
 268    *
 269    * @param al
 270    * @param hiddenColumns
 271    * @param width
 272    * @param height
 273    * @param sequenceSetId
 274    *          (may be null)
 275    * @param viewId
 276    *          (may be null)
 277    */
 278   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 279           int width, int height, String sequenceSetId, String viewId)
 280   {
 281     setSize(width, height);
 282
 283     if (al.getDataset() == null)
 284     {
 285       al.setDataset(null);
 286     }
 287
 288     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 289
 290     alignPanel = new AlignmentPanel(this, viewport);
 291
 292     addAlignmentPanel(alignPanel, true);
 293     init();
 294   }
 295
 296   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 297           ColumnSelection hiddenColumns, int width, int height)
 298   {
 299     setSize(width, height);
 300
 301     if (al.getDataset() == null)
 302     {
 303       al.setDataset(null);
 304     }
 305
 306     viewport = new AlignViewport(al, hiddenColumns);
 307
 308     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 309     {
 310       viewport.hideSequence(hiddenSeqs);
 311     }
 312     alignPanel = new AlignmentPanel(this, viewport);
 313     addAlignmentPanel(alignPanel, true);
 314     init();
 315   }
 316
 317   /**
 318    * Make a new AlignFrame from existing alignmentPanels
 319    *
 320    * @param ap
 321    *          AlignmentPanel
 322    * @param av
 323    *          AlignViewport
 324    */
 325   public AlignFrame(AlignmentPanel ap)
 326   {
 327     viewport = ap.av;
 328     alignPanel = ap;
 329     addAlignmentPanel(ap, false);
 330     init();
 331   }
 332
 333   /**
 334    * initalise the alignframe from the underlying viewport data and the
 335    * configurations
 336    */
 337   void init()
 338   {
 339     if (!Jalview.isHeadlessMode())
 340     {
 341       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 342     }
 343
 344     avc = new jalview.controller.AlignViewController(this, viewport,
 345             alignPanel);
 346     if (viewport.getAlignmentConservationAnnotation() == null)
 347     {
 348       BLOSUM62Colour.setEnabled(false);
 349       conservationMenuItem.setEnabled(false);
 350       modifyConservation.setEnabled(false);
 351       // PIDColour.setEnabled(false);
 352       // abovePIDThreshold.setEnabled(false);
 353       // modifyPID.setEnabled(false);
 354     }
 355
 356     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 357             "No sort");
 358
 359     if (sortby.equals("Id"))
 360     {
 361       sortIDMenuItem_actionPerformed(null);
 362     }
 363     else if (sortby.equals("Pairwise Identity"))
 364     {
 365       sortPairwiseMenuItem_actionPerformed(null);
 366     }
 367
 368     if (Desktop.desktop != null)
 369     {
 370       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 371       addServiceListeners();
 372       setGUINucleotide(viewport.getAlignment().isNucleotide());
 373     }
 374
 375     this.alignPanel.av
 376             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 377
 378     setMenusFromViewport(viewport);
 379     buildSortByAnnotationScoresMenu();
 380     buildTreeMenu();
 381
 382     if (viewport.getWrapAlignment())
 383     {
 384       wrapMenuItem_actionPerformed(null);
 385     }
 386
 387     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 388     {
 389       this.overviewMenuItem_actionPerformed(null);
 390     }
 391
 392     addKeyListener();
 393
 394     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 395     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 396     final String menuLabel = MessageManager
 397             .getString("label.copy_format_from");
 398     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 399             new ViewSetProvider()
 400             {
 401
 402               @Override
 403               public AlignmentPanel[] getAllAlignmentPanels()
 404               {
 405                 origview.clear();
 406                 origview.add(alignPanel);
 407                 // make an array of all alignment panels except for this one
 408                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 409                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 410                 aps.remove(AlignFrame.this.alignPanel);
 411                 return aps.toArray(new AlignmentPanel[aps.size()]);
 412               }
 413             }, selviews, new ItemListener()
 414             {
 415
 416               @Override
 417               public void itemStateChanged(ItemEvent e)
 418               {
 419                 if (origview.size() > 0)
 420                 {
 421                   final AlignmentPanel ap = origview.get(0);
 422
 423                   /*
 424                    * Copy the ViewStyle of the selected panel to 'this one'.
 425                    * Don't change value of 'scaleProteinAsCdna' unless copying
 426                    * from a SplitFrame.
 427                    */
 428                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 429                           .getViewStyle();
 430                   boolean fromSplitFrame = selviews.get(0)
 431                           .getAlignViewport().getCodingComplement() != null;
 432                   if (!fromSplitFrame)
 433                   {
 434                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 435                             .getViewStyle().isScaleProteinAsCdna());
 436                   }
 437                   ap.getAlignViewport().setViewStyle(vs);
 438
 439                   /*
 440                    * Also rescale ViewStyle of SplitFrame complement if there is
 441                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 442                    * the whole ViewStyle (allow cDNA protein to have different
 443                    * fonts)
 444                    */
 445                   AlignViewportI complement = ap.getAlignViewport()
 446                           .getCodingComplement();
 447                   if (complement != null && vs.isScaleProteinAsCdna())
 448                   {
 449                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 450                     ((SplitFrame) af.getSplitViewContainer())
 451                             .adjustLayout();
 452                     af.setMenusForViewport();
 453                   }
 454
 455                   ap.updateLayout();
 456                   ap.setSelected(true);
 457                   ap.alignFrame.setMenusForViewport();
 458
 459                 }
 460               }
 461             });
 462     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 463             .indexOf("devel") > -1
 464             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 465                     .indexOf("test") > -1)
 466     {
 467       formatMenu.add(vsel);
 468     }
 469
 470   }
 471
 472   /**
 473    * Change the filename and format for the alignment, and enable the 'reload'
 474    * button functionality.
 475    *
 476    * @param file
 477    *          valid filename
 478    * @param format
 479    *          format of file
 480    */
 481   public void setFileName(String file, String format)
 482   {
 483     fileName = file;
 484     setFileFormat(format);
 485     reload.setEnabled(true);
 486   }
 487
 488   /**
 489    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 490    * events
 491    */
 492   void addKeyListener()
 493   {
 494     addKeyListener(new KeyAdapter()
 495     {
 496       @Override
 497       public void keyPressed(KeyEvent evt)
 498       {
 499         if (viewport.cursorMode
 500                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 501                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 502                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 503                 && Character.isDigit(evt.getKeyChar()))
 504         {
 505           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 506         }
 507
 508         switch (evt.getKeyCode())
 509         {
 510
 511         case 27: // escape key
 512           deselectAllSequenceMenuItem_actionPerformed(null);
 513
 514           break;
 515
 516         case KeyEvent.VK_DOWN:
 517           if (evt.isAltDown() || !viewport.cursorMode)
 518           {
 519             moveSelectedSequences(false);
 520           }
 521           if (viewport.cursorMode)
 522           {
 523             alignPanel.getSeqPanel().moveCursor(0, 1);
 524           }
 525           break;
 526
 527         case KeyEvent.VK_UP:
 528           if (evt.isAltDown() || !viewport.cursorMode)
 529           {
 530             moveSelectedSequences(true);
 531           }
 532           if (viewport.cursorMode)
 533           {
 534             alignPanel.getSeqPanel().moveCursor(0, -1);
 535           }
 536
 537           break;
 538
 539         case KeyEvent.VK_LEFT:
 540           if (evt.isAltDown() || !viewport.cursorMode)
 541           {
 542             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 543           }
 544           else
 545           {
 546             alignPanel.getSeqPanel().moveCursor(-1, 0);
 547           }
 548
 549           break;
 550
 551         case KeyEvent.VK_RIGHT:
 552           if (evt.isAltDown() || !viewport.cursorMode)
 553           {
 554             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 555           }
 556           else
 557           {
 558             alignPanel.getSeqPanel().moveCursor(1, 0);
 559           }
 560           break;
 561
 562         case KeyEvent.VK_SPACE:
 563           if (viewport.cursorMode)
 564           {
 565             alignPanel.getSeqPanel().insertGapAtCursor(
 566                     evt.isControlDown() || evt.isShiftDown()
 567                             || evt.isAltDown());
 568           }
 569           break;
 570
 571         // case KeyEvent.VK_A:
 572         // if (viewport.cursorMode)
 573         // {
 574         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 575         // //System.out.println("A");
 576         // }
 577         // break;
 578         /*
 579          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 580          * System.out.println("closing bracket"); } break;
 581          */
 582         case KeyEvent.VK_DELETE:
 583         case KeyEvent.VK_BACK_SPACE:
 584           if (!viewport.cursorMode)
 585           {
 586             cut_actionPerformed(null);
 587           }
 588           else
 589           {
 590             alignPanel.getSeqPanel().deleteGapAtCursor(
 591                     evt.isControlDown() || evt.isShiftDown()
 592                             || evt.isAltDown());
 593           }
 594
 595           break;
 596
 597         case KeyEvent.VK_S:
 598           if (viewport.cursorMode)
 599           {
 600             alignPanel.getSeqPanel().setCursorRow();
 601           }
 602           break;
 603         case KeyEvent.VK_C:
 604           if (viewport.cursorMode && !evt.isControlDown())
 605           {
 606             alignPanel.getSeqPanel().setCursorColumn();
 607           }
 608           break;
 609         case KeyEvent.VK_P:
 610           if (viewport.cursorMode)
 611           {
 612             alignPanel.getSeqPanel().setCursorPosition();
 613           }
 614           break;
 615
 616         case KeyEvent.VK_ENTER:
 617         case KeyEvent.VK_COMMA:
 618           if (viewport.cursorMode)
 619           {
 620             alignPanel.getSeqPanel().setCursorRowAndColumn();
 621           }
 622           break;
 623
 624         case KeyEvent.VK_Q:
 625           if (viewport.cursorMode)
 626           {
 627             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 628           }
 629           break;
 630         case KeyEvent.VK_M:
 631           if (viewport.cursorMode)
 632           {
 633             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 634           }
 635           break;
 636
 637         case KeyEvent.VK_F2:
 638           viewport.cursorMode = !viewport.cursorMode;
 639           statusBar.setText(MessageManager.formatMessage(
 640                   "label.keyboard_editing_mode",
 641                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 642           if (viewport.cursorMode)
 643           {
 644             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 645             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 646           }
 647           alignPanel.getSeqPanel().seqCanvas.repaint();
 648           break;
 649
 650         case KeyEvent.VK_F1:
 651           try
 652           {
 653             Help.showHelpWindow();
 654           } catch (Exception ex)
 655           {
 656             ex.printStackTrace();
 657           }
 658           break;
 659         case KeyEvent.VK_H:
 660         {
 661           boolean toggleSeqs = !evt.isControlDown();
 662           boolean toggleCols = !evt.isShiftDown();
 663           toggleHiddenRegions(toggleSeqs, toggleCols);
 664           break;
 665         }
 666         case KeyEvent.VK_PAGE_UP:
 667           if (viewport.getWrapAlignment())
 668           {
 669             alignPanel.scrollUp(true);
 670           }
 671           else
 672           {
 673             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 674                     - viewport.endSeq + viewport.startSeq);
 675           }
 676           break;
 677         case KeyEvent.VK_PAGE_DOWN:
 678           if (viewport.getWrapAlignment())
 679           {
 680             alignPanel.scrollUp(false);
 681           }
 682           else
 683           {
 684             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 685                     + viewport.endSeq - viewport.startSeq);
 686           }
 687           break;
 688         }
 689       }
 690
 691       @Override
 692       public void keyReleased(KeyEvent evt)
 693       {
 694         switch (evt.getKeyCode())
 695         {
 696         case KeyEvent.VK_LEFT:
 697           if (evt.isAltDown() || !viewport.cursorMode)
 698           {
 699             viewport.firePropertyChange("alignment", null, viewport
 700                     .getAlignment().getSequences());
 701           }
 702           break;
 703
 704         case KeyEvent.VK_RIGHT:
 705           if (evt.isAltDown() || !viewport.cursorMode)
 706           {
 707             viewport.firePropertyChange("alignment", null, viewport
 708                     .getAlignment().getSequences());
 709           }
 710           break;
 711         }
 712       }
 713     });
 714   }
 715
 716   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 717   {
 718     ap.alignFrame = this;
 719     avc = new jalview.controller.AlignViewController(this, viewport,
 720             alignPanel);
 721
 722     alignPanels.add(ap);
 723
 724     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 725
 726     int aSize = alignPanels.size();
 727
 728     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 729
 730     if (aSize == 1 && ap.av.viewName == null)
 731     {
 732       this.getContentPane().add(ap, BorderLayout.CENTER);
 733     }
 734     else
 735     {
 736       if (aSize == 2)
 737       {
 738         setInitialTabVisible();
 739       }
 740
 741       expandViews.setEnabled(true);
 742       gatherViews.setEnabled(true);
 743       tabbedPane.addTab(ap.av.viewName, ap);
 744
 745       ap.setVisible(false);
 746     }
 747
 748     if (newPanel)
 749     {
 750       if (ap.av.isPadGaps())
 751       {
 752         ap.av.getAlignment().padGaps();
 753       }
 754       ap.av.updateConservation(ap);
 755       ap.av.updateConsensus(ap);
 756       ap.av.updateStrucConsensus(ap);
 757     }
 758   }
 759
 760   public void setInitialTabVisible()
 761   {
 762     expandViews.setEnabled(true);
 763     gatherViews.setEnabled(true);
 764     tabbedPane.setVisible(true);
 765     AlignmentPanel first = alignPanels.get(0);
 766     tabbedPane.addTab(first.av.viewName, first);
 767     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 768   }
 769
 770   public AlignViewport getViewport()
 771   {
 772     return viewport;
 773   }
 774
 775   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 776   private void addServiceListeners()
 777   {
 778     final java.beans.PropertyChangeListener thisListener;
 779     Desktop.instance.addJalviewPropertyChangeListener("services",
 780             thisListener = new java.beans.PropertyChangeListener()
 781             {
 782               @Override
 783               public void propertyChange(PropertyChangeEvent evt)
 784               {
 785                 // // System.out.println("Discoverer property change.");
 786                 // if (evt.getPropertyName().equals("services"))
 787                 {
 788                   SwingUtilities.invokeLater(new Runnable()
 789                   {
 790
 791                     @Override
 792                     public void run()
 793                     {
 794                       System.err
 795                               .println("Rebuild WS Menu for service change");
 796                       BuildWebServiceMenu();
 797                     }
 798
 799                   });
 800                 }
 801               }
 802             });
 803     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 804     {
 805       @Override
 806       public void internalFrameClosed(
 807               javax.swing.event.InternalFrameEvent evt)
 808       {
 809         // System.out.println("deregistering discoverer listener");
 810         Desktop.instance.removeJalviewPropertyChangeListener("services",
 811                 thisListener);
 812         closeMenuItem_actionPerformed(true);
 813       };
 814     });
 815     // Finally, build the menu once to get current service state
 816     new Thread(new Runnable()
 817     {
 818       @Override
 819       public void run()
 820       {
 821         BuildWebServiceMenu();
 822       }
 823     }).start();
 824   }
 825
 826   /**
 827    * Configure menu items that vary according to whether the alignment is
 828    * nucleotide or protein
 829    *
 830    * @param nucleotide
 831    */
 832   public void setGUINucleotide(boolean nucleotide)
 833   {
 834     showTranslation.setVisible(nucleotide);
 835     showReverse.setVisible(nucleotide);
 836     showReverseComplement.setVisible(nucleotide);
 837     conservationMenuItem.setEnabled(!nucleotide);
 838     modifyConservation.setEnabled(!nucleotide);
 839     showGroupConservation.setEnabled(!nucleotide);
 840     rnahelicesColour.setEnabled(nucleotide);
 841     purinePyrimidineColour.setEnabled(nucleotide);
 842     showComplementMenuItem.setText(MessageManager
 843             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 844     setColourSelected(jalview.bin.Cache.getDefault(
 845             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 846                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 847   }
 848
 849   /**
 850    * set up menus for the current viewport. This may be called after any
 851    * operation that affects the data in the current view (selection changed,
 852    * etc) to update the menus to reflect the new state.
 853    */
 854   @Override
 855   public void setMenusForViewport()
 856   {
 857     setMenusFromViewport(viewport);
 858   }
 859
 860   /**
 861    * Need to call this method when tabs are selected for multiple views, or when
 862    * loading from Jalview2XML.java
 863    *
 864    * @param av
 865    *          AlignViewport
 866    */
 867   void setMenusFromViewport(AlignViewport av)
 868   {
 869     padGapsMenuitem.setSelected(av.isPadGaps());
 870     colourTextMenuItem.setSelected(av.isShowColourText());
 871     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 872     conservationMenuItem.setSelected(av.getConservationSelected());
 873     seqLimits.setSelected(av.getShowJVSuffix());
 874     idRightAlign.setSelected(av.isRightAlignIds());
 875     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 876     renderGapsMenuItem.setSelected(av.isRenderGaps());
 877     wrapMenuItem.setSelected(av.getWrapAlignment());
 878     scaleAbove.setVisible(av.getWrapAlignment());
 879     scaleLeft.setVisible(av.getWrapAlignment());
 880     scaleRight.setVisible(av.getWrapAlignment());
 881     annotationPanelMenuItem.setState(av.isShowAnnotation());
 882     /*
 883      * Show/hide annotations only enabled if annotation panel is shown
 884      */
 885     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 886     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 887     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 888     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 889     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 890     viewTextMenuItem.setSelected(av.getShowText());
 891     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 892     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 893     showGroupConservation.setSelected(av.isShowGroupConservation());
 894     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 895     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 896     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 897
 898     setColourSelected(ColourSchemeProperty.getColourName(av
 899             .getGlobalColourScheme()));
 900
 901     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 902     hiddenMarkers.setState(av.getShowHiddenMarkers());
 903     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 904     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 905     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 906     autoCalculate.setSelected(av.autoCalculateConsensus);
 907     sortByTree.setSelected(av.sortByTree);
 908     listenToViewSelections.setSelected(av.followSelection);
 909     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 910     rnahelicesColour
 911             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 912
 913     showProducts.setEnabled(canShowProducts());
 914
 915     updateEditMenuBar();
 916   }
 917
 918   private IProgressIndicator progressBar;
 919
 920   /*
 921    * (non-Javadoc)
 922    *
 923    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 924    */
 925   @Override
 926   public void setProgressBar(String message, long id)
 927   {
 928     progressBar.setProgressBar(message, id);
 929   }
 930
 931   @Override
 932   public void registerHandler(final long id,
 933           final IProgressIndicatorHandler handler)
 934   {
 935     progressBar.registerHandler(id, handler);
 936   }
 937
 938   /**
 939    *
 940    * @return true if any progress bars are still active
 941    */
 942   @Override
 943   public boolean operationInProgress()
 944   {
 945     return progressBar.operationInProgress();
 946   }
 947
 948   @Override
 949   public void setStatus(String text)
 950   {
 951     statusBar.setText(text);
 952   }
 953
 954   /*
 955    * Added so Castor Mapping file can obtain Jalview Version
 956    */
 957   public String getVersion()
 958   {
 959     return jalview.bin.Cache.getProperty("VERSION");
 960   }
 961
 962   public FeatureRenderer getFeatureRenderer()
 963   {
 964     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 965   }
 966
 967   @Override
 968   public void fetchSequence_actionPerformed(ActionEvent e)
 969   {
 970     new jalview.gui.SequenceFetcher(this);
 971   }
 972
 973   @Override
 974   public void addFromFile_actionPerformed(ActionEvent e)
 975   {
 976     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 977   }
 978
 979   @Override
 980   public void reload_actionPerformed(ActionEvent e)
 981   {
 982     if (fileName != null)
 983     {
 984       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 985       // originating file's format
 986       // TODO: work out how to recover feature settings for correct view(s) when
 987       // file is reloaded.
 988       if (currentFileFormat.equals("Jalview"))
 989       {
 990         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 991         for (int i = 0; i < frames.length; i++)
 992         {
 993           if (frames[i] instanceof AlignFrame && frames[i] != this
 994                   && ((AlignFrame) frames[i]).fileName != null
 995                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 996           {
 997             try
 998             {
 999               frames[i].setSelected(true);
1000               Desktop.instance.closeAssociatedWindows();
1001             } catch (java.beans.PropertyVetoException ex)
1002             {
1003             }
1004           }
1005
1006         }
1007         Desktop.instance.closeAssociatedWindows();
1008
1009         FileLoader loader = new FileLoader();
1010         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1011         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1012       }
1013       else
1014       {
1015         Rectangle bounds = this.getBounds();
1016
1017         FileLoader loader = new FileLoader();
1018         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1019         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1020                 protocol, currentFileFormat);
1021
1022         newframe.setBounds(bounds);
1023         if (featureSettings != null && featureSettings.isShowing())
1024         {
1025           final Rectangle fspos = featureSettings.frame.getBounds();
1026           // TODO: need a 'show feature settings' function that takes bounds -
1027           // need to refactor Desktop.addFrame
1028           newframe.featureSettings_actionPerformed(null);
1029           final FeatureSettings nfs = newframe.featureSettings;
1030           SwingUtilities.invokeLater(new Runnable()
1031           {
1032             @Override
1033             public void run()
1034             {
1035               nfs.frame.setBounds(fspos);
1036             }
1037           });
1038           this.featureSettings.close();
1039           this.featureSettings = null;
1040         }
1041         this.closeMenuItem_actionPerformed(true);
1042       }
1043     }
1044   }
1045
1046   @Override
1047   public void addFromText_actionPerformed(ActionEvent e)
1048   {
1049     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1050             .getAlignPanel());
1051   }
1052
1053   @Override
1054   public void addFromURL_actionPerformed(ActionEvent e)
1055   {
1056     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1057   }
1058
1059   @Override
1060   public void save_actionPerformed(ActionEvent e)
1061   {
1062     if (fileName == null
1063             || (currentFileFormat == null || !jalview.io.FormatAdapter
1064                     .isValidIOFormat(currentFileFormat, true))
1065             || fileName.startsWith("http"))
1066     {
1067       saveAs_actionPerformed(null);
1068     }
1069     else
1070     {
1071       saveAlignment(fileName, currentFileFormat);
1072     }
1073   }
1074
1075   /**
1076    * DOCUMENT ME!
1077    *
1078    * @param e
1079    *          DOCUMENT ME!
1080    */
1081   @Override
1082   public void saveAs_actionPerformed(ActionEvent e)
1083   {
1084     JalviewFileChooser chooser = new JalviewFileChooser(
1085             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1086             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1087             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1088             currentFileFormat, false);
1089
1090     chooser.setFileView(new JalviewFileView());
1091     chooser.setDialogTitle(MessageManager
1092             .getString("label.save_alignment_to_file"));
1093     chooser.setToolTipText(MessageManager.getString("action.save"));
1094
1095     int value = chooser.showSaveDialog(this);
1096
1097     if (value == JalviewFileChooser.APPROVE_OPTION)
1098     {
1099       currentFileFormat = chooser.getSelectedFormat();
1100       while (currentFileFormat == null)
1101       {
1102         JOptionPane
1103                 .showInternalMessageDialog(
1104                         Desktop.desktop,
1105                         MessageManager
1106                                 .getString("label.select_file_format_before_saving"),
1107                         MessageManager
1108                                 .getString("label.file_format_not_specified"),
1109                         JOptionPane.WARNING_MESSAGE);
1110         currentFileFormat = chooser.getSelectedFormat();
1111         value = chooser.showSaveDialog(this);
1112         if (value != JalviewFileChooser.APPROVE_OPTION)
1113         {
1114           return;
1115         }
1116       }
1117
1118       fileName = chooser.getSelectedFile().getPath();
1119
1120       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1121               currentFileFormat);
1122
1123       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1124       if (currentFileFormat.indexOf(" ") > -1)
1125       {
1126         currentFileFormat = currentFileFormat.substring(0,
1127                 currentFileFormat.indexOf(" "));
1128       }
1129       saveAlignment(fileName, currentFileFormat);
1130     }
1131   }
1132
1133   public boolean saveAlignment(String file, String format)
1134   {
1135     boolean success = true;
1136
1137     if (format.equalsIgnoreCase("Jalview"))
1138     {
1139       String shortName = title;
1140
1141       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1142       {
1143         shortName = shortName.substring(shortName
1144                 .lastIndexOf(java.io.File.separatorChar) + 1);
1145       }
1146
1147       success = new Jalview2XML().saveAlignment(this, file, shortName);
1148
1149       statusBar.setText(MessageManager.formatMessage(
1150               "label.successfully_saved_to_file_in_format", new Object[] {
1151                   fileName, format }));
1152
1153     }
1154     else
1155     {
1156       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1157       {
1158         warningMessage("Cannot save file " + fileName + " using format "
1159                 + format, "Alignment output format not supported");
1160         if (!Jalview.isHeadlessMode())
1161         {
1162           saveAs_actionPerformed(null);
1163         }
1164         return false;
1165       }
1166
1167       AlignmentExportData exportData = getAlignmentForExport(format,
1168               viewport, null);
1169       if (exportData.getSettings().isCancelled())
1170       {
1171         return false;
1172       }
1173       FormatAdapter f = new FormatAdapter(alignPanel,
1174               exportData.getSettings());
1175       String output = f.formatSequences(
1176               format,
1177               exportData.getAlignment(), // class cast exceptions will
1178               // occur in the distant future
1179               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180               f.getCacheSuffixDefault(format),
1181               viewport.getColumnSelection());
1182
1183       if (output == null)
1184       {
1185         success = false;
1186       }
1187       else
1188       {
1189         try
1190         {
1191           java.io.PrintWriter out = new java.io.PrintWriter(
1192                   new java.io.FileWriter(file));
1193
1194           out.print(output);
1195           out.close();
1196           this.setTitle(file);
1197           statusBar.setText(MessageManager.formatMessage(
1198                   "label.successfully_saved_to_file_in_format",
1199                   new Object[] { fileName, format }));
1200         } catch (Exception ex)
1201         {
1202           success = false;
1203           ex.printStackTrace();
1204         }
1205       }
1206     }
1207
1208     if (!success)
1209     {
1210       JOptionPane.showInternalMessageDialog(this, MessageManager
1211               .formatMessage("label.couldnt_save_file",
1212                       new Object[] { fileName }), MessageManager
1213               .getString("label.error_saving_file"),
1214               JOptionPane.WARNING_MESSAGE);
1215     }
1216
1217     return success;
1218   }
1219
1220   private void warningMessage(String warning, String title)
1221   {
1222     if (new jalview.util.Platform().isHeadless())
1223     {
1224       System.err.println("Warning: " + title + "\nWarning: " + warning);
1225
1226     }
1227     else
1228     {
1229       JOptionPane.showInternalMessageDialog(this, warning, title,
1230               JOptionPane.WARNING_MESSAGE);
1231     }
1232     return;
1233   }
1234
1235   /**
1236    * DOCUMENT ME!
1237    *
1238    * @param e
1239    *          DOCUMENT ME!
1240    */
1241   @Override
1242   protected void outputText_actionPerformed(ActionEvent e)
1243   {
1244
1245     AlignmentExportData exportData = getAlignmentForExport(
1246             e.getActionCommand(), viewport, null);
1247     if (exportData.getSettings().isCancelled())
1248     {
1249       return;
1250     }
1251     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252     cap.setForInput(null);
1253     try
1254     {
1255       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1256               .formatSequences(e.getActionCommand(),
1257                       exportData.getAlignment(),
1258                       exportData.getOmitHidden(),
1259                       exportData.getStartEndPostions(),
1260                       viewport.getColumnSelection()));
1261       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1262               "label.alignment_output_command",
1263               new Object[] { e.getActionCommand() }), 600, 500);
1264     } catch (OutOfMemoryError oom)
1265     {
1266       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1267       cap.dispose();
1268     }
1269
1270   }
1271
1272   public static AlignmentExportData getAlignmentForExport(
1273           String exportFormat, AlignViewportI viewport,
1274           AlignExportSettingI exportSettings)
1275   {
1276     AlignmentI alignmentToExport = null;
1277     AlignExportSettingI settings = exportSettings;
1278     String[] omitHidden = null;
1279     int[] alignmentStartEnd = new int[2];
1280
1281     HiddenSequences hiddenSeqs = viewport.getAlignment()
1282             .getHiddenSequences();
1283
1284     alignmentToExport = viewport.getAlignment();
1285     alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1286
1287     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1288     if (settings == null)
1289     {
1290       settings = new AlignExportSettings(hasHiddenSeqs,
1291               viewport.hasHiddenColumns(), exportFormat);
1292     }
1293     // settings.isExportAnnotations();
1294
1295     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1296     {
1297       omitHidden = viewport.getViewAsString(false);
1298     }
1299
1300     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1301     {
1302       alignmentToExport = hiddenSeqs.getFullAlignment();
1303     }
1304     else
1305     {
1306       alignmentToExport = viewport.getAlignment();
1307       alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1308               .getColumnSelection().getHiddenColumns());
1309     }
1310     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1311             omitHidden, alignmentStartEnd, settings);
1312     return ed;
1313   }
1314
1315   public static int[] getStartEnd(int[] aligmentStartEnd,
1316           List<int[]> hiddenCols)
1317   {
1318     int startPos = aligmentStartEnd[0];
1319     int endPos = aligmentStartEnd[1];
1320
1321     int[] lowestRange = new int[] { -1, -1 };
1322     int[] higestRange = new int[] { -1, -1 };
1323
1324     for (int[] hiddenCol : hiddenCols)
1325     {
1326       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1327       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1328     }
1329
1330     if (lowestRange[0] == -1 && lowestRange[1] == -1)
1331     {
1332       startPos = aligmentStartEnd[0];
1333     }
1334     else
1335     {
1336       startPos = lowestRange[1] + 1;
1337     }
1338
1339     if (higestRange[0] == -1 && higestRange[1] == -1)
1340     {
1341       endPos = aligmentStartEnd[1];
1342     }
1343     else
1344     {
1345       endPos = higestRange[0] - 1;
1346     }
1347
1348     // System.out.println("Export range : " + startPos + " - " + endPos);
1349     return new int[] { startPos, endPos };
1350   }
1351
1352   public static void main(String[] args)
1353   {
1354     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1355     hiddenCols.add(new int[] { 0, 0 });
1356     hiddenCols.add(new int[] { 6, 9 });
1357     hiddenCols.add(new int[] { 11, 12 });
1358     hiddenCols.add(new int[] { 33, 33 });
1359     hiddenCols.add(new int[] { 50, 50 });
1360
1361     int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1362     // System.out.println("Export range : " + x[0] + " - " + x[1]);
1363   }
1364
1365   /**
1366    * DOCUMENT ME!
1367    *
1368    * @param e
1369    *          DOCUMENT ME!
1370    */
1371   @Override
1372   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1373   {
1374     new HtmlSvgOutput(null, alignPanel);
1375   }
1376
1377   @Override
1378   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1379   {
1380     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1381     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1382   }
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   @Override
1414   public void createSVG(File f)
1415   {
1416     alignPanel.makeSVG(f);
1417   }
1418
1419   @Override
1420   public void pageSetup_actionPerformed(ActionEvent e)
1421   {
1422     PrinterJob printJob = PrinterJob.getPrinterJob();
1423     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1424   }
1425
1426   /**
1427    * DOCUMENT ME!
1428    *
1429    * @param e
1430    *          DOCUMENT ME!
1431    */
1432   @Override
1433   public void printMenuItem_actionPerformed(ActionEvent e)
1434   {
1435     // Putting in a thread avoids Swing painting problems
1436     PrintThread thread = new PrintThread(alignPanel);
1437     thread.start();
1438   }
1439
1440   @Override
1441   public void exportFeatures_actionPerformed(ActionEvent e)
1442   {
1443     new AnnotationExporter().exportFeatures(alignPanel);
1444   }
1445
1446   @Override
1447   public void exportAnnotations_actionPerformed(ActionEvent e)
1448   {
1449     new AnnotationExporter().exportAnnotations(alignPanel);
1450   }
1451
1452   @Override
1453   public void associatedData_actionPerformed(ActionEvent e)
1454   {
1455     // Pick the tree file
1456     JalviewFileChooser chooser = new JalviewFileChooser(
1457             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1458     chooser.setFileView(new JalviewFileView());
1459     chooser.setDialogTitle(MessageManager
1460             .getString("label.load_jalview_annotations"));
1461     chooser.setToolTipText(MessageManager
1462             .getString("label.load_jalview_annotations"));
1463
1464     int value = chooser.showOpenDialog(null);
1465
1466     if (value == JalviewFileChooser.APPROVE_OPTION)
1467     {
1468       String choice = chooser.getSelectedFile().getPath();
1469       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1470       loadJalviewDataFile(choice, null, null, null);
1471     }
1472
1473   }
1474
1475   /**
1476    * Close the current view or all views in the alignment frame. If the frame
1477    * only contains one view then the alignment will be removed from memory.
1478    *
1479    * @param closeAllTabs
1480    */
1481   @Override
1482   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1483   {
1484     if (alignPanels != null && alignPanels.size() < 2)
1485     {
1486       closeAllTabs = true;
1487     }
1488
1489     try
1490     {
1491       if (alignPanels != null)
1492       {
1493         if (closeAllTabs)
1494         {
1495           if (this.isClosed())
1496           {
1497             // really close all the windows - otherwise wait till
1498             // setClosed(true) is called
1499             for (int i = 0; i < alignPanels.size(); i++)
1500             {
1501               AlignmentPanel ap = alignPanels.get(i);
1502               ap.closePanel();
1503             }
1504           }
1505         }
1506         else
1507         {
1508           closeView(alignPanel);
1509         }
1510       }
1511
1512       if (closeAllTabs)
1513       {
1514         /*
1515          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1516          * be called recursively, with the frame now in 'closed' state
1517          */
1518         this.setClosed(true);
1519       }
1520     } catch (Exception ex)
1521     {
1522       ex.printStackTrace();
1523     }
1524   }
1525
1526   /**
1527    * Close the specified panel and close up tabs appropriately.
1528    *
1529    * @param panelToClose
1530    */
1531   public void closeView(AlignmentPanel panelToClose)
1532   {
1533     int index = tabbedPane.getSelectedIndex();
1534     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1535     alignPanels.remove(panelToClose);
1536     panelToClose.closePanel();
1537     panelToClose = null;
1538
1539     tabbedPane.removeTabAt(closedindex);
1540     tabbedPane.validate();
1541
1542     if (index > closedindex || index == tabbedPane.getTabCount())
1543     {
1544       // modify currently selected tab index if necessary.
1545       index--;
1546     }
1547
1548     this.tabSelectionChanged(index);
1549   }
1550
1551   /**
1552    * DOCUMENT ME!
1553    */
1554   void updateEditMenuBar()
1555   {
1556
1557     if (viewport.getHistoryList().size() > 0)
1558     {
1559       undoMenuItem.setEnabled(true);
1560       CommandI command = viewport.getHistoryList().peek();
1561       undoMenuItem.setText(MessageManager.formatMessage(
1562               "label.undo_command",
1563               new Object[] { command.getDescription() }));
1564     }
1565     else
1566     {
1567       undoMenuItem.setEnabled(false);
1568       undoMenuItem.setText(MessageManager.getString("action.undo"));
1569     }
1570
1571     if (viewport.getRedoList().size() > 0)
1572     {
1573       redoMenuItem.setEnabled(true);
1574
1575       CommandI command = viewport.getRedoList().peek();
1576       redoMenuItem.setText(MessageManager.formatMessage(
1577               "label.redo_command",
1578               new Object[] { command.getDescription() }));
1579     }
1580     else
1581     {
1582       redoMenuItem.setEnabled(false);
1583       redoMenuItem.setText(MessageManager.getString("action.redo"));
1584     }
1585   }
1586
1587   @Override
1588   public void addHistoryItem(CommandI command)
1589   {
1590     if (command.getSize() > 0)
1591     {
1592       viewport.addToHistoryList(command);
1593       viewport.clearRedoList();
1594       updateEditMenuBar();
1595       viewport.updateHiddenColumns();
1596       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1597       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1598       // viewport.getColumnSelection()
1599       // .getHiddenColumns().size() > 0);
1600     }
1601   }
1602
1603   /**
1604    *
1605    * @return alignment objects for all views
1606    */
1607   AlignmentI[] getViewAlignments()
1608   {
1609     if (alignPanels != null)
1610     {
1611       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1612       int i = 0;
1613       for (AlignmentPanel ap : alignPanels)
1614       {
1615         als[i++] = ap.av.getAlignment();
1616       }
1617       return als;
1618     }
1619     if (viewport != null)
1620     {
1621       return new AlignmentI[] { viewport.getAlignment() };
1622     }
1623     return null;
1624   }
1625
1626   /**
1627    * DOCUMENT ME!
1628    *
1629    * @param e
1630    *          DOCUMENT ME!
1631    */
1632   @Override
1633   protected void undoMenuItem_actionPerformed(ActionEvent e)
1634   {
1635     if (viewport.getHistoryList().isEmpty())
1636     {
1637       return;
1638     }
1639     CommandI command = viewport.getHistoryList().pop();
1640     viewport.addToRedoList(command);
1641     command.undoCommand(getViewAlignments());
1642
1643     AlignmentViewport originalSource = getOriginatingSource(command);
1644     updateEditMenuBar();
1645
1646     if (originalSource != null)
1647     {
1648       if (originalSource != viewport)
1649       {
1650         Cache.log
1651                 .warn("Implementation worry: mismatch of viewport origin for undo");
1652       }
1653       originalSource.updateHiddenColumns();
1654       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1655       // null
1656       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1657       // viewport.getColumnSelection()
1658       // .getHiddenColumns().size() > 0);
1659       originalSource.firePropertyChange("alignment", null, originalSource
1660               .getAlignment().getSequences());
1661     }
1662   }
1663
1664   /**
1665    * DOCUMENT ME!
1666    *
1667    * @param e
1668    *          DOCUMENT ME!
1669    */
1670   @Override
1671   protected void redoMenuItem_actionPerformed(ActionEvent e)
1672   {
1673     if (viewport.getRedoList().size() < 1)
1674     {
1675       return;
1676     }
1677
1678     CommandI command = viewport.getRedoList().pop();
1679     viewport.addToHistoryList(command);
1680     command.doCommand(getViewAlignments());
1681
1682     AlignmentViewport originalSource = getOriginatingSource(command);
1683     updateEditMenuBar();
1684
1685     if (originalSource != null)
1686     {
1687
1688       if (originalSource != viewport)
1689       {
1690         Cache.log
1691                 .warn("Implementation worry: mismatch of viewport origin for redo");
1692       }
1693       originalSource.updateHiddenColumns();
1694       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1695       // null
1696       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1697       // viewport.getColumnSelection()
1698       // .getHiddenColumns().size() > 0);
1699       originalSource.firePropertyChange("alignment", null, originalSource
1700               .getAlignment().getSequences());
1701     }
1702   }
1703
1704   AlignmentViewport getOriginatingSource(CommandI command)
1705   {
1706     AlignmentViewport originalSource = null;
1707     // For sequence removal and addition, we need to fire
1708     // the property change event FROM the viewport where the
1709     // original alignment was altered
1710     AlignmentI al = null;
1711     if (command instanceof EditCommand)
1712     {
1713       EditCommand editCommand = (EditCommand) command;
1714       al = editCommand.getAlignment();
1715       List<Component> comps = PaintRefresher.components.get(viewport
1716               .getSequenceSetId());
1717
1718       for (Component comp : comps)
1719       {
1720         if (comp instanceof AlignmentPanel)
1721         {
1722           if (al == ((AlignmentPanel) comp).av.getAlignment())
1723           {
1724             originalSource = ((AlignmentPanel) comp).av;
1725             break;
1726           }
1727         }
1728       }
1729     }
1730
1731     if (originalSource == null)
1732     {
1733       // The original view is closed, we must validate
1734       // the current view against the closed view first
1735       if (al != null)
1736       {
1737         PaintRefresher.validateSequences(al, viewport.getAlignment());
1738       }
1739
1740       originalSource = viewport;
1741     }
1742
1743     return originalSource;
1744   }
1745
1746   /**
1747    * DOCUMENT ME!
1748    *
1749    * @param up
1750    *          DOCUMENT ME!
1751    */
1752   public void moveSelectedSequences(boolean up)
1753   {
1754     SequenceGroup sg = viewport.getSelectionGroup();
1755
1756     if (sg == null)
1757     {
1758       return;
1759     }
1760     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1761             viewport.getHiddenRepSequences(), up);
1762     alignPanel.paintAlignment(true);
1763   }
1764
1765   synchronized void slideSequences(boolean right, int size)
1766   {
1767     List<SequenceI> sg = new ArrayList<SequenceI>();
1768     if (viewport.cursorMode)
1769     {
1770       sg.add(viewport.getAlignment().getSequenceAt(
1771               alignPanel.getSeqPanel().seqCanvas.cursorY));
1772     }
1773     else if (viewport.getSelectionGroup() != null
1774             && viewport.getSelectionGroup().getSize() != viewport
1775                     .getAlignment().getHeight())
1776     {
1777       sg = viewport.getSelectionGroup().getSequences(
1778               viewport.getHiddenRepSequences());
1779     }
1780
1781     if (sg.size() < 1)
1782     {
1783       return;
1784     }
1785
1786     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1787
1788     for (SequenceI seq : viewport.getAlignment().getSequences())
1789     {
1790       if (!sg.contains(seq))
1791       {
1792         invertGroup.add(seq);
1793       }
1794     }
1795
1796     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1797
1798     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1799     for (int i = 0; i < invertGroup.size(); i++)
1800     {
1801       seqs2[i] = invertGroup.get(i);
1802     }
1803
1804     SlideSequencesCommand ssc;
1805     if (right)
1806     {
1807       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1808               size, viewport.getGapCharacter());
1809     }
1810     else
1811     {
1812       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1813               size, viewport.getGapCharacter());
1814     }
1815
1816     int groupAdjustment = 0;
1817     if (ssc.getGapsInsertedBegin() && right)
1818     {
1819       if (viewport.cursorMode)
1820       {
1821         alignPanel.getSeqPanel().moveCursor(size, 0);
1822       }
1823       else
1824       {
1825         groupAdjustment = size;
1826       }
1827     }
1828     else if (!ssc.getGapsInsertedBegin() && !right)
1829     {
1830       if (viewport.cursorMode)
1831       {
1832         alignPanel.getSeqPanel().moveCursor(-size, 0);
1833       }
1834       else
1835       {
1836         groupAdjustment = -size;
1837       }
1838     }
1839
1840     if (groupAdjustment != 0)
1841     {
1842       viewport.getSelectionGroup().setStartRes(
1843               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1844       viewport.getSelectionGroup().setEndRes(
1845               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1846     }
1847
1848     /*
1849      * just extend the last slide command if compatible; but not if in
1850      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1851      */
1852     boolean appendHistoryItem = false;
1853     Deque<CommandI> historyList = viewport.getHistoryList();
1854     boolean inSplitFrame = getSplitViewContainer() != null;
1855     if (!inSplitFrame && historyList != null && historyList.size() > 0
1856             && historyList.peek() instanceof SlideSequencesCommand)
1857     {
1858       appendHistoryItem = ssc
1859               .appendSlideCommand((SlideSequencesCommand) historyList
1860                       .peek());
1861     }
1862
1863     if (!appendHistoryItem)
1864     {
1865       addHistoryItem(ssc);
1866     }
1867
1868     repaint();
1869   }
1870
1871   /**
1872    * DOCUMENT ME!
1873    *
1874    * @param e
1875    *          DOCUMENT ME!
1876    */
1877   @Override
1878   protected void copy_actionPerformed(ActionEvent e)
1879   {
1880     System.gc();
1881     if (viewport.getSelectionGroup() == null)
1882     {
1883       return;
1884     }
1885     // TODO: preserve the ordering of displayed alignment annotation in any
1886     // internal paste (particularly sequence associated annotation)
1887     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1888     String[] omitHidden = null;
1889
1890     if (viewport.hasHiddenColumns())
1891     {
1892       omitHidden = viewport.getViewAsString(true);
1893     }
1894
1895     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1896             omitHidden, null);
1897
1898     StringSelection ss = new StringSelection(output);
1899
1900     try
1901     {
1902       jalview.gui.Desktop.internalCopy = true;
1903       // Its really worth setting the clipboard contents
1904       // to empty before setting the large StringSelection!!
1905       Toolkit.getDefaultToolkit().getSystemClipboard()
1906               .setContents(new StringSelection(""), null);
1907
1908       Toolkit.getDefaultToolkit().getSystemClipboard()
1909               .setContents(ss, Desktop.instance);
1910     } catch (OutOfMemoryError er)
1911     {
1912       new OOMWarning("copying region", er);
1913       return;
1914     }
1915
1916     ArrayList<int[]> hiddenColumns = null;
1917     if (viewport.hasHiddenColumns())
1918     {
1919       hiddenColumns = new ArrayList<int[]>();
1920       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1921               .getSelectionGroup().getEndRes();
1922       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1923       {
1924         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1925         {
1926           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1927               region[1] - hiddenOffset });
1928         }
1929       }
1930     }
1931
1932     Desktop.jalviewClipboard = new Object[] { seqs,
1933         viewport.getAlignment().getDataset(), hiddenColumns };
1934     statusBar.setText(MessageManager.formatMessage(
1935             "label.copied_sequences_to_clipboard", new Object[] { Integer
1936                     .valueOf(seqs.length).toString() }));
1937   }
1938
1939   /**
1940    * DOCUMENT ME!
1941    *
1942    * @param e
1943    *          DOCUMENT ME!
1944    */
1945   @Override
1946   protected void pasteNew_actionPerformed(ActionEvent e)
1947   {
1948     paste(true);
1949   }
1950
1951   /**
1952    * DOCUMENT ME!
1953    *
1954    * @param e
1955    *          DOCUMENT ME!
1956    */
1957   @Override
1958   protected void pasteThis_actionPerformed(ActionEvent e)
1959   {
1960     paste(false);
1961   }
1962
1963   /**
1964    * Paste contents of Jalview clipboard
1965    *
1966    * @param newAlignment
1967    *          true to paste to a new alignment, otherwise add to this.
1968    */
1969   void paste(boolean newAlignment)
1970   {
1971     boolean externalPaste = true;
1972     try
1973     {
1974       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1975       Transferable contents = c.getContents(this);
1976
1977       if (contents == null)
1978       {
1979         return;
1980       }
1981
1982       String str, format;
1983       try
1984       {
1985         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1986         if (str.length() < 1)
1987         {
1988           return;
1989         }
1990
1991         format = new IdentifyFile().identify(str, "Paste");
1992
1993       } catch (OutOfMemoryError er)
1994       {
1995         new OOMWarning("Out of memory pasting sequences!!", er);
1996         return;
1997       }
1998
1999       SequenceI[] sequences;
2000       boolean annotationAdded = false;
2001       AlignmentI alignment = null;
2002
2003       if (Desktop.jalviewClipboard != null)
2004       {
2005         // The clipboard was filled from within Jalview, we must use the
2006         // sequences
2007         // And dataset from the copied alignment
2008         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2009         // be doubly sure that we create *new* sequence objects.
2010         sequences = new SequenceI[newseq.length];
2011         for (int i = 0; i < newseq.length; i++)
2012         {
2013           sequences[i] = new Sequence(newseq[i]);
2014         }
2015         alignment = new Alignment(sequences);
2016         externalPaste = false;
2017       }
2018       else
2019       {
2020         // parse the clipboard as an alignment.
2021         alignment = new FormatAdapter().readFile(str, "Paste", format);
2022         sequences = alignment.getSequencesArray();
2023       }
2024
2025       int alwidth = 0;
2026       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2027       int fgroup = -1;
2028
2029       if (newAlignment)
2030       {
2031
2032         if (Desktop.jalviewClipboard != null)
2033         {
2034           // dataset is inherited
2035           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2036         }
2037         else
2038         {
2039           // new dataset is constructed
2040           alignment.setDataset(null);
2041         }
2042         alwidth = alignment.getWidth() + 1;
2043       }
2044       else
2045       {
2046         AlignmentI pastedal = alignment; // preserve pasted alignment object
2047         // Add pasted sequences and dataset into existing alignment.
2048         alignment = viewport.getAlignment();
2049         alwidth = alignment.getWidth() + 1;
2050         // decide if we need to import sequences from an existing dataset
2051         boolean importDs = Desktop.jalviewClipboard != null
2052                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2053         // importDs==true instructs us to copy over new dataset sequences from
2054         // an existing alignment
2055         Vector newDs = (importDs) ? new Vector() : null; // used to create
2056         // minimum dataset set
2057
2058         for (int i = 0; i < sequences.length; i++)
2059         {
2060           if (importDs)
2061           {
2062             newDs.addElement(null);
2063           }
2064           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2065           // paste
2066           if (importDs && ds != null)
2067           {
2068             if (!newDs.contains(ds))
2069             {
2070               newDs.setElementAt(ds, i);
2071               ds = new Sequence(ds);
2072               // update with new dataset sequence
2073               sequences[i].setDatasetSequence(ds);
2074             }
2075             else
2076             {
2077               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2078             }
2079           }
2080           else
2081           {
2082             // copy and derive new dataset sequence
2083             sequences[i] = sequences[i].deriveSequence();
2084             alignment.getDataset().addSequence(
2085                     sequences[i].getDatasetSequence());
2086             // TODO: avoid creation of duplicate dataset sequences with a
2087             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2088           }
2089           alignment.addSequence(sequences[i]); // merges dataset
2090         }
2091         if (newDs != null)
2092         {
2093           newDs.clear(); // tidy up
2094         }
2095         if (alignment.getAlignmentAnnotation() != null)
2096         {
2097           for (AlignmentAnnotation alan : alignment
2098                   .getAlignmentAnnotation())
2099           {
2100             if (alan.graphGroup > fgroup)
2101             {
2102               fgroup = alan.graphGroup;
2103             }
2104           }
2105         }
2106         if (pastedal.getAlignmentAnnotation() != null)
2107         {
2108           // Add any annotation attached to alignment.
2109           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2110           for (int i = 0; i < alann.length; i++)
2111           {
2112             annotationAdded = true;
2113             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2114             {
2115               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2116               if (newann.graphGroup > -1)
2117               {
2118                 if (newGraphGroups.size() <= newann.graphGroup
2119                         || newGraphGroups.get(newann.graphGroup) == null)
2120                 {
2121                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2122                   {
2123                     newGraphGroups.add(q, null);
2124                   }
2125                   newGraphGroups.set(newann.graphGroup, new Integer(
2126                           ++fgroup));
2127                 }
2128                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2129                         .intValue();
2130               }
2131
2132               newann.padAnnotation(alwidth);
2133               alignment.addAnnotation(newann);
2134             }
2135           }
2136         }
2137       }
2138       if (!newAlignment)
2139       {
2140         // /////
2141         // ADD HISTORY ITEM
2142         //
2143         addHistoryItem(new EditCommand(
2144                 MessageManager.getString("label.add_sequences"),
2145                 Action.PASTE, 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
2264                                 .getFeatureRenderer());
2265
2266         // TODO: maintain provenance of an alignment, rather than just make the
2267         // title a concatenation of operations.
2268         if (!externalPaste)
2269         {
2270           if (title.startsWith("Copied sequences"))
2271           {
2272             newtitle = title;
2273           }
2274           else
2275           {
2276             newtitle = newtitle.concat("- from " + title);
2277           }
2278         }
2279         else
2280         {
2281           newtitle = new String("Pasted sequences");
2282         }
2283
2284         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2285                 DEFAULT_HEIGHT);
2286
2287       }
2288
2289     } catch (Exception ex)
2290     {
2291       ex.printStackTrace();
2292       System.out.println("Exception whilst pasting: " + ex);
2293       // could be anything being pasted in here
2294     }
2295
2296   }
2297
2298   @Override
2299   protected void expand_newalign(ActionEvent e)
2300   {
2301     try
2302     {
2303       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2304               .getAlignment(), -1);
2305       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2306               DEFAULT_HEIGHT);
2307       String newtitle = new String("Flanking alignment");
2308
2309       if (Desktop.jalviewClipboard != null
2310               && Desktop.jalviewClipboard[2] != null)
2311       {
2312         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2313         for (int region[] : hc)
2314         {
2315           af.viewport.hideColumns(region[0], region[1]);
2316         }
2317       }
2318
2319       // >>>This is a fix for the moment, until a better solution is
2320       // found!!<<<
2321       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2322               .transferSettings(
2323                       alignPanel.getSeqPanel().seqCanvas
2324                               .getFeatureRenderer());
2325
2326       // TODO: maintain provenance of an alignment, rather than just make the
2327       // title a concatenation of operations.
2328       {
2329         if (title.startsWith("Copied sequences"))
2330         {
2331           newtitle = title;
2332         }
2333         else
2334         {
2335           newtitle = newtitle.concat("- from " + title);
2336         }
2337       }
2338
2339       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2340
2341     } catch (Exception ex)
2342     {
2343       ex.printStackTrace();
2344       System.out.println("Exception whilst pasting: " + ex);
2345       // could be anything being pasted in here
2346     } catch (OutOfMemoryError oom)
2347     {
2348       new OOMWarning("Viewing flanking region of alignment", oom);
2349     }
2350   }
2351
2352   /**
2353    * DOCUMENT ME!
2354    *
2355    * @param e
2356    *          DOCUMENT ME!
2357    */
2358   @Override
2359   protected void cut_actionPerformed(ActionEvent e)
2360   {
2361     copy_actionPerformed(null);
2362     delete_actionPerformed(null);
2363   }
2364
2365   /**
2366    * DOCUMENT ME!
2367    *
2368    * @param e
2369    *          DOCUMENT ME!
2370    */
2371   @Override
2372   protected void delete_actionPerformed(ActionEvent evt)
2373   {
2374
2375     SequenceGroup sg = viewport.getSelectionGroup();
2376     if (sg == null)
2377     {
2378       return;
2379     }
2380
2381     /*
2382      * If the cut affects all sequences, warn, remove highlighted columns
2383      */
2384     if (sg.getSize() == viewport.getAlignment().getHeight())
2385     {
2386       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2387               .getAlignment().getWidth()) ? true : false;
2388       if (isEntireAlignWidth)
2389       {
2390         int confirm = JOptionPane.showConfirmDialog(this,
2391                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2392                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2393                 JOptionPane.OK_CANCEL_OPTION);
2394
2395         if (confirm == JOptionPane.CANCEL_OPTION
2396                 || confirm == JOptionPane.CLOSED_OPTION)
2397         {
2398           return;
2399         }
2400       }
2401       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2402               sg.getEndRes() + 1);
2403     }
2404     SequenceI[] cut = sg.getSequences()
2405             .toArray(new SequenceI[sg.getSize()]);
2406
2407     addHistoryItem(new EditCommand(
2408             MessageManager.getString("label.cut_sequences"), Action.CUT,
2409             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2410             viewport.getAlignment()));
2411
2412     viewport.setSelectionGroup(null);
2413     viewport.sendSelection();
2414     viewport.getAlignment().deleteGroup(sg);
2415
2416     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2417             .getSequences());
2418     if (viewport.getAlignment().getHeight() < 1)
2419     {
2420       try
2421       {
2422         this.setClosed(true);
2423       } catch (Exception ex)
2424       {
2425       }
2426     }
2427   }
2428
2429   /**
2430    * DOCUMENT ME!
2431    *
2432    * @param e
2433    *          DOCUMENT ME!
2434    */
2435   @Override
2436   protected void deleteGroups_actionPerformed(ActionEvent e)
2437   {
2438     if (avc.deleteGroups())
2439     {
2440       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2441       alignPanel.updateAnnotation();
2442       alignPanel.paintAlignment(true);
2443     }
2444   }
2445
2446   /**
2447    * DOCUMENT ME!
2448    *
2449    * @param e
2450    *          DOCUMENT ME!
2451    */
2452   @Override
2453   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2454   {
2455     SequenceGroup sg = new SequenceGroup();
2456
2457     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2458     {
2459       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2460     }
2461
2462     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2463     viewport.setSelectionGroup(sg);
2464     viewport.sendSelection();
2465     // JAL-2034 - should delegate to
2466     // alignPanel to decide if overview needs
2467     // updating.
2468     alignPanel.paintAlignment(false);
2469     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2470   }
2471
2472   /**
2473    * DOCUMENT ME!
2474    *
2475    * @param e
2476    *          DOCUMENT ME!
2477    */
2478   @Override
2479   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2480   {
2481     if (viewport.cursorMode)
2482     {
2483       alignPanel.getSeqPanel().keyboardNo1 = null;
2484       alignPanel.getSeqPanel().keyboardNo2 = null;
2485     }
2486     viewport.setSelectionGroup(null);
2487     viewport.getColumnSelection().clear();
2488     viewport.setSelectionGroup(null);
2489     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2490     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2491     // JAL-2034 - should delegate to
2492     // alignPanel to decide if overview needs
2493     // updating.
2494     alignPanel.paintAlignment(false);
2495     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2496     viewport.sendSelection();
2497   }
2498
2499   /**
2500    * DOCUMENT ME!
2501    *
2502    * @param e
2503    *          DOCUMENT ME!
2504    */
2505   @Override
2506   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2507   {
2508     SequenceGroup sg = viewport.getSelectionGroup();
2509
2510     if (sg == null)
2511     {
2512       selectAllSequenceMenuItem_actionPerformed(null);
2513
2514       return;
2515     }
2516
2517     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2518     {
2519       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2520     }
2521     // JAL-2034 - should delegate to
2522     // alignPanel to decide if overview needs
2523     // updating.
2524
2525     alignPanel.paintAlignment(true);
2526     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2527     viewport.sendSelection();
2528   }
2529
2530   @Override
2531   public void invertColSel_actionPerformed(ActionEvent e)
2532   {
2533     viewport.invertColumnSelection();
2534     alignPanel.paintAlignment(true);
2535     viewport.sendSelection();
2536   }
2537
2538   /**
2539    * DOCUMENT ME!
2540    *
2541    * @param e
2542    *          DOCUMENT ME!
2543    */
2544   @Override
2545   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2546   {
2547     trimAlignment(true);
2548   }
2549
2550   /**
2551    * DOCUMENT ME!
2552    *
2553    * @param e
2554    *          DOCUMENT ME!
2555    */
2556   @Override
2557   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2558   {
2559     trimAlignment(false);
2560   }
2561
2562   void trimAlignment(boolean trimLeft)
2563   {
2564     ColumnSelection colSel = viewport.getColumnSelection();
2565     int column;
2566
2567     if (!colSel.isEmpty())
2568     {
2569       if (trimLeft)
2570       {
2571         column = colSel.getMin();
2572       }
2573       else
2574       {
2575         column = colSel.getMax();
2576       }
2577
2578       SequenceI[] seqs;
2579       if (viewport.getSelectionGroup() != null)
2580       {
2581         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2582                 viewport.getHiddenRepSequences());
2583       }
2584       else
2585       {
2586         seqs = viewport.getAlignment().getSequencesArray();
2587       }
2588
2589       TrimRegionCommand trimRegion;
2590       if (trimLeft)
2591       {
2592         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2593                 column, viewport.getAlignment());
2594         viewport.setStartRes(0);
2595       }
2596       else
2597       {
2598         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2599                 column, viewport.getAlignment());
2600       }
2601
2602       statusBar.setText(MessageManager.formatMessage(
2603               "label.removed_columns",
2604               new String[] { Integer.valueOf(trimRegion.getSize())
2605                       .toString() }));
2606
2607       addHistoryItem(trimRegion);
2608
2609       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2610       {
2611         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2612                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2613         {
2614           viewport.getAlignment().deleteGroup(sg);
2615         }
2616       }
2617
2618       viewport.firePropertyChange("alignment", null, viewport
2619               .getAlignment().getSequences());
2620     }
2621   }
2622
2623   /**
2624    * DOCUMENT ME!
2625    *
2626    * @param e
2627    *          DOCUMENT ME!
2628    */
2629   @Override
2630   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2631   {
2632     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2633
2634     SequenceI[] seqs;
2635     if (viewport.getSelectionGroup() != null)
2636     {
2637       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2638               viewport.getHiddenRepSequences());
2639       start = viewport.getSelectionGroup().getStartRes();
2640       end = viewport.getSelectionGroup().getEndRes();
2641     }
2642     else
2643     {
2644       seqs = viewport.getAlignment().getSequencesArray();
2645     }
2646
2647     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2648             "Remove Gapped Columns", seqs, start, end,
2649             viewport.getAlignment());
2650
2651     addHistoryItem(removeGapCols);
2652
2653     statusBar.setText(MessageManager.formatMessage(
2654             "label.removed_empty_columns",
2655             new Object[] { Integer.valueOf(removeGapCols.getSize())
2656                     .toString() }));
2657
2658     // This is to maintain viewport position on first residue
2659     // of first sequence
2660     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2661     int startRes = seq.findPosition(viewport.startRes);
2662     // ShiftList shifts;
2663     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2664     // edit.alColumnChanges=shifts.getInverse();
2665     // if (viewport.hasHiddenColumns)
2666     // viewport.getColumnSelection().compensateForEdits(shifts);
2667     viewport.setStartRes(seq.findIndex(startRes) - 1);
2668     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2669             .getSequences());
2670
2671   }
2672
2673   /**
2674    * DOCUMENT ME!
2675    *
2676    * @param e
2677    *          DOCUMENT ME!
2678    */
2679   @Override
2680   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2681   {
2682     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2683
2684     SequenceI[] seqs;
2685     if (viewport.getSelectionGroup() != null)
2686     {
2687       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2688               viewport.getHiddenRepSequences());
2689       start = viewport.getSelectionGroup().getStartRes();
2690       end = viewport.getSelectionGroup().getEndRes();
2691     }
2692     else
2693     {
2694       seqs = viewport.getAlignment().getSequencesArray();
2695     }
2696
2697     // This is to maintain viewport position on first residue
2698     // of first sequence
2699     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2700     int startRes = seq.findPosition(viewport.startRes);
2701
2702     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2703             viewport.getAlignment()));
2704
2705     viewport.setStartRes(seq.findIndex(startRes) - 1);
2706
2707     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2708             .getSequences());
2709
2710   }
2711
2712   /**
2713    * DOCUMENT ME!
2714    *
2715    * @param e
2716    *          DOCUMENT ME!
2717    */
2718   @Override
2719   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2720   {
2721     viewport.setPadGaps(padGapsMenuitem.isSelected());
2722     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2723             .getSequences());
2724   }
2725
2726   /**
2727    * DOCUMENT ME!
2728    *
2729    * @param e
2730    *          DOCUMENT ME!
2731    */
2732   @Override
2733   public void findMenuItem_actionPerformed(ActionEvent e)
2734   {
2735     new Finder();
2736   }
2737
2738   /**
2739    * Create a new view of the current alignment.
2740    */
2741   @Override
2742   public void newView_actionPerformed(ActionEvent e)
2743   {
2744     newView(null, true);
2745   }
2746
2747   /**
2748    * Creates and shows a new view of the current alignment.
2749    *
2750    * @param viewTitle
2751    *          title of newly created view; if null, one will be generated
2752    * @param copyAnnotation
2753    *          if true then duplicate all annnotation, groups and settings
2754    * @return new alignment panel, already displayed.
2755    */
2756   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2757   {
2758     /*
2759      * Create a new AlignmentPanel (with its own, new Viewport)
2760      */
2761     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2762             true);
2763     if (!copyAnnotation)
2764     {
2765       /*
2766        * remove all groups and annotation except for the automatic stuff
2767        */
2768       newap.av.getAlignment().deleteAllGroups();
2769       newap.av.getAlignment().deleteAllAnnotations(false);
2770     }
2771
2772     newap.av.setGatherViewsHere(false);
2773
2774     if (viewport.viewName == null)
2775     {
2776       viewport.viewName = MessageManager
2777               .getString("label.view_name_original");
2778     }
2779
2780     /*
2781      * Views share the same edits undo and redo stacks
2782      */
2783     newap.av.setHistoryList(viewport.getHistoryList());
2784     newap.av.setRedoList(viewport.getRedoList());
2785
2786     /*
2787      * Views share the same mappings; need to deregister any new mappings
2788      * created by copyAlignPanel, and register the new reference to the shared
2789      * mappings
2790      */
2791     newap.av.replaceMappings(viewport.getAlignment());
2792
2793     newap.av.viewName = getNewViewName(viewTitle);
2794
2795     addAlignmentPanel(newap, true);
2796     newap.alignmentChanged();
2797
2798     if (alignPanels.size() == 2)
2799     {
2800       viewport.setGatherViewsHere(true);
2801     }
2802     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2803     return newap;
2804   }
2805
2806   /**
2807    * Make a new name for the view, ensuring it is unique within the current
2808    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2809    * these now use viewId. Unique view names are still desirable for usability.)
2810    *
2811    * @param viewTitle
2812    * @return
2813    */
2814   protected String getNewViewName(String viewTitle)
2815   {
2816     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2817     boolean addFirstIndex = false;
2818     if (viewTitle == null || viewTitle.trim().length() == 0)
2819     {
2820       viewTitle = MessageManager.getString("action.view");
2821       addFirstIndex = true;
2822     }
2823     else
2824     {
2825       index = 1;// we count from 1 if given a specific name
2826     }
2827     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2828
2829     List<Component> comps = PaintRefresher.components.get(viewport
2830             .getSequenceSetId());
2831
2832     List<String> existingNames = getExistingViewNames(comps);
2833
2834     while (existingNames.contains(newViewName))
2835     {
2836       newViewName = viewTitle + " " + (++index);
2837     }
2838     return newViewName;
2839   }
2840
2841   /**
2842    * Returns a list of distinct view names found in the given list of
2843    * components. View names are held on the viewport of an AlignmentPanel.
2844    *
2845    * @param comps
2846    * @return
2847    */
2848   protected List<String> getExistingViewNames(List<Component> comps)
2849   {
2850     List<String> existingNames = new ArrayList<String>();
2851     for (Component comp : comps)
2852     {
2853       if (comp instanceof AlignmentPanel)
2854       {
2855         AlignmentPanel ap = (AlignmentPanel) comp;
2856         if (!existingNames.contains(ap.av.viewName))
2857         {
2858           existingNames.add(ap.av.viewName);
2859         }
2860       }
2861     }
2862     return existingNames;
2863   }
2864
2865   /**
2866    * Explode tabbed views into separate windows.
2867    */
2868   @Override
2869   public void expandViews_actionPerformed(ActionEvent e)
2870   {
2871     Desktop.instance.explodeViews(this);
2872   }
2873
2874   /**
2875    * Gather views in separate windows back into a tabbed presentation.
2876    */
2877   @Override
2878   public void gatherViews_actionPerformed(ActionEvent e)
2879   {
2880     Desktop.instance.gatherViews(this);
2881   }
2882
2883   /**
2884    * DOCUMENT ME!
2885    *
2886    * @param e
2887    *          DOCUMENT ME!
2888    */
2889   @Override
2890   public void font_actionPerformed(ActionEvent e)
2891   {
2892     new FontChooser(alignPanel);
2893   }
2894
2895   /**
2896    * DOCUMENT ME!
2897    *
2898    * @param e
2899    *          DOCUMENT ME!
2900    */
2901   @Override
2902   protected void seqLimit_actionPerformed(ActionEvent e)
2903   {
2904     viewport.setShowJVSuffix(seqLimits.isSelected());
2905
2906     alignPanel.getIdPanel().getIdCanvas()
2907             .setPreferredSize(alignPanel.calculateIdWidth());
2908     alignPanel.paintAlignment(true);
2909   }
2910
2911   @Override
2912   public void idRightAlign_actionPerformed(ActionEvent e)
2913   {
2914     viewport.setRightAlignIds(idRightAlign.isSelected());
2915     alignPanel.paintAlignment(true);
2916   }
2917
2918   @Override
2919   public void centreColumnLabels_actionPerformed(ActionEvent e)
2920   {
2921     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2922     alignPanel.paintAlignment(true);
2923   }
2924
2925   /*
2926    * (non-Javadoc)
2927    *
2928    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2929    */
2930   @Override
2931   protected void followHighlight_actionPerformed()
2932   {
2933     /*
2934      * Set the 'follow' flag on the Viewport (and scroll to position if now
2935      * true).
2936      */
2937     final boolean state = this.followHighlightMenuItem.getState();
2938     viewport.setFollowHighlight(state);
2939     if (state)
2940     {
2941       alignPanel.scrollToPosition(
2942               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2943     }
2944   }
2945
2946   /**
2947    * DOCUMENT ME!
2948    *
2949    * @param e
2950    *          DOCUMENT ME!
2951    */
2952   @Override
2953   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2954   {
2955     viewport.setColourText(colourTextMenuItem.isSelected());
2956     alignPanel.paintAlignment(true);
2957   }
2958
2959   /**
2960    * DOCUMENT ME!
2961    *
2962    * @param e
2963    *          DOCUMENT ME!
2964    */
2965   @Override
2966   public void wrapMenuItem_actionPerformed(ActionEvent e)
2967   {
2968     scaleAbove.setVisible(wrapMenuItem.isSelected());
2969     scaleLeft.setVisible(wrapMenuItem.isSelected());
2970     scaleRight.setVisible(wrapMenuItem.isSelected());
2971     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2972     alignPanel.updateLayout();
2973   }
2974
2975   @Override
2976   public void showAllSeqs_actionPerformed(ActionEvent e)
2977   {
2978     viewport.showAllHiddenSeqs();
2979   }
2980
2981   @Override
2982   public void showAllColumns_actionPerformed(ActionEvent e)
2983   {
2984     viewport.showAllHiddenColumns();
2985     repaint();
2986     viewport.sendSelection();
2987   }
2988
2989   @Override
2990   public void hideSelSequences_actionPerformed(ActionEvent e)
2991   {
2992     viewport.hideAllSelectedSeqs();
2993     // alignPanel.paintAlignment(true);
2994   }
2995
2996   /**
2997    * called by key handler and the hide all/show all menu items
2998    *
2999    * @param toggleSeqs
3000    * @param toggleCols
3001    */
3002   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3003   {
3004
3005     boolean hide = false;
3006     SequenceGroup sg = viewport.getSelectionGroup();
3007     if (!toggleSeqs && !toggleCols)
3008     {
3009       // Hide everything by the current selection - this is a hack - we do the
3010       // invert and then hide
3011       // first check that there will be visible columns after the invert.
3012       if ((viewport.getColumnSelection() != null
3013               && viewport.getColumnSelection().getSelected() != null && viewport
3014               .getColumnSelection().getSelected().size() > 0)
3015               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3016                       .getEndRes()))
3017       {
3018         // now invert the sequence set, if required - empty selection implies
3019         // that no hiding is required.
3020         if (sg != null)
3021         {
3022           invertSequenceMenuItem_actionPerformed(null);
3023           sg = viewport.getSelectionGroup();
3024           toggleSeqs = true;
3025
3026         }
3027         viewport.expandColSelection(sg, true);
3028         // finally invert the column selection and get the new sequence
3029         // selection.
3030         invertColSel_actionPerformed(null);
3031         toggleCols = true;
3032       }
3033     }
3034
3035     if (toggleSeqs)
3036     {
3037       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3038       {
3039         hideSelSequences_actionPerformed(null);
3040         hide = true;
3041       }
3042       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3043               .size() > 0))
3044       {
3045         showAllSeqs_actionPerformed(null);
3046       }
3047     }
3048
3049     if (toggleCols)
3050     {
3051       if (viewport.getColumnSelection().getSelected().size() > 0)
3052       {
3053         hideSelColumns_actionPerformed(null);
3054         if (!toggleSeqs)
3055         {
3056           viewport.setSelectionGroup(sg);
3057         }
3058       }
3059       else if (!hide)
3060       {
3061         showAllColumns_actionPerformed(null);
3062       }
3063     }
3064   }
3065
3066   /*
3067    * (non-Javadoc)
3068    *
3069    * @see
3070    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3071    * event.ActionEvent)
3072    */
3073   @Override
3074   public void hideAllButSelection_actionPerformed(ActionEvent e)
3075   {
3076     toggleHiddenRegions(false, false);
3077     viewport.sendSelection();
3078   }
3079
3080   /*
3081    * (non-Javadoc)
3082    *
3083    * @see
3084    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3085    * .ActionEvent)
3086    */
3087   @Override
3088   public void hideAllSelection_actionPerformed(ActionEvent e)
3089   {
3090     SequenceGroup sg = viewport.getSelectionGroup();
3091     viewport.expandColSelection(sg, false);
3092     viewport.hideAllSelectedSeqs();
3093     viewport.hideSelectedColumns();
3094     alignPanel.paintAlignment(true);
3095     viewport.sendSelection();
3096   }
3097
3098   /*
3099    * (non-Javadoc)
3100    *
3101    * @see
3102    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3103    * ActionEvent)
3104    */
3105   @Override
3106   public void showAllhidden_actionPerformed(ActionEvent e)
3107   {
3108     viewport.showAllHiddenColumns();
3109     viewport.showAllHiddenSeqs();
3110     alignPanel.paintAlignment(true);
3111     viewport.sendSelection();
3112   }
3113
3114   @Override
3115   public void hideSelColumns_actionPerformed(ActionEvent e)
3116   {
3117     viewport.hideSelectedColumns();
3118     alignPanel.paintAlignment(true);
3119     viewport.sendSelection();
3120   }
3121
3122   @Override
3123   public void hiddenMarkers_actionPerformed(ActionEvent e)
3124   {
3125     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3126     repaint();
3127   }
3128
3129   /**
3130    * DOCUMENT ME!
3131    *
3132    * @param e
3133    *          DOCUMENT ME!
3134    */
3135   @Override
3136   protected void scaleAbove_actionPerformed(ActionEvent e)
3137   {
3138     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3139     alignPanel.paintAlignment(true);
3140   }
3141
3142   /**
3143    * DOCUMENT ME!
3144    *
3145    * @param e
3146    *          DOCUMENT ME!
3147    */
3148   @Override
3149   protected void scaleLeft_actionPerformed(ActionEvent e)
3150   {
3151     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3152     alignPanel.paintAlignment(true);
3153   }
3154
3155   /**
3156    * DOCUMENT ME!
3157    *
3158    * @param e
3159    *          DOCUMENT ME!
3160    */
3161   @Override
3162   protected void scaleRight_actionPerformed(ActionEvent e)
3163   {
3164     viewport.setScaleRightWrapped(scaleRight.isSelected());
3165     alignPanel.paintAlignment(true);
3166   }
3167
3168   /**
3169    * DOCUMENT ME!
3170    *
3171    * @param e
3172    *          DOCUMENT ME!
3173    */
3174   @Override
3175   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3176   {
3177     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3178     alignPanel.paintAlignment(true);
3179   }
3180
3181   /**
3182    * DOCUMENT ME!
3183    *
3184    * @param e
3185    *          DOCUMENT ME!
3186    */
3187   @Override
3188   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3189   {
3190     viewport.setShowText(viewTextMenuItem.isSelected());
3191     alignPanel.paintAlignment(true);
3192   }
3193
3194   /**
3195    * DOCUMENT ME!
3196    *
3197    * @param e
3198    *          DOCUMENT ME!
3199    */
3200   @Override
3201   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3202   {
3203     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3204     alignPanel.paintAlignment(true);
3205   }
3206
3207   public FeatureSettings featureSettings;
3208
3209   @Override
3210   public FeatureSettingsControllerI getFeatureSettingsUI()
3211   {
3212     return featureSettings;
3213   }
3214
3215   @Override
3216   public void featureSettings_actionPerformed(ActionEvent e)
3217   {
3218     if (featureSettings != null)
3219     {
3220       featureSettings.close();
3221       featureSettings = null;
3222     }
3223     if (!showSeqFeatures.isSelected())
3224     {
3225       // make sure features are actually displayed
3226       showSeqFeatures.setSelected(true);
3227       showSeqFeatures_actionPerformed(null);
3228     }
3229     featureSettings = new FeatureSettings(this);
3230   }
3231
3232   /**
3233    * Set or clear 'Show Sequence Features'
3234    *
3235    * @param evt
3236    *          DOCUMENT ME!
3237    */
3238   @Override
3239   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3240   {
3241     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3242     alignPanel.paintAlignment(true);
3243     if (alignPanel.getOverviewPanel() != null)
3244     {
3245       alignPanel.getOverviewPanel().updateOverviewImage();
3246     }
3247   }
3248
3249   /**
3250    * Set or clear 'Show Sequence Features'
3251    *
3252    * @param evt
3253    *          DOCUMENT ME!
3254    */
3255   @Override
3256   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3257   {
3258     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3259             .isSelected());
3260     if (viewport.isShowSequenceFeaturesHeight())
3261     {
3262       // ensure we're actually displaying features
3263       viewport.setShowSequenceFeatures(true);
3264       showSeqFeatures.setSelected(true);
3265     }
3266     alignPanel.paintAlignment(true);
3267     if (alignPanel.getOverviewPanel() != null)
3268     {
3269       alignPanel.getOverviewPanel().updateOverviewImage();
3270     }
3271   }
3272
3273   /**
3274    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3275    * the annotations panel as a whole.
3276    *
3277    * The options to show/hide all annotations should be enabled when the panel
3278    * is shown, and disabled when the panel is hidden.
3279    *
3280    * @param e
3281    */
3282   @Override
3283   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3284   {
3285     final boolean setVisible = annotationPanelMenuItem.isSelected();
3286     viewport.setShowAnnotation(setVisible);
3287     this.showAllSeqAnnotations.setEnabled(setVisible);
3288     this.hideAllSeqAnnotations.setEnabled(setVisible);
3289     this.showAllAlAnnotations.setEnabled(setVisible);
3290     this.hideAllAlAnnotations.setEnabled(setVisible);
3291     alignPanel.updateLayout();
3292   }
3293
3294   @Override
3295   public void alignmentProperties()
3296   {
3297     JEditorPane editPane = new JEditorPane("text/html", "");
3298     editPane.setEditable(false);
3299     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3300             .formatAsHtml();
3301     editPane.setText(MessageManager.formatMessage("label.html_content",
3302             new Object[] { contents.toString() }));
3303     JInternalFrame frame = new JInternalFrame();
3304     frame.getContentPane().add(new JScrollPane(editPane));
3305
3306     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3307             "label.alignment_properties", new Object[] { getTitle() }),
3308             500, 400);
3309   }
3310
3311   /**
3312    * DOCUMENT ME!
3313    *
3314    * @param e
3315    *          DOCUMENT ME!
3316    */
3317   @Override
3318   public void overviewMenuItem_actionPerformed(ActionEvent e)
3319   {
3320     if (alignPanel.overviewPanel != null)
3321     {
3322       return;
3323     }
3324
3325     JInternalFrame frame = new JInternalFrame();
3326     OverviewPanel overview = new OverviewPanel(alignPanel);
3327     frame.setContentPane(overview);
3328     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3329             "label.overview_params", new Object[] { this.getTitle() }),
3330             frame.getWidth(), frame.getHeight());
3331     frame.pack();
3332     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3333     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3334     {
3335       @Override
3336       public void internalFrameClosed(
3337               javax.swing.event.InternalFrameEvent evt)
3338       {
3339         alignPanel.setOverviewPanel(null);
3340       };
3341     });
3342
3343     alignPanel.setOverviewPanel(overview);
3344   }
3345
3346   @Override
3347   public void textColour_actionPerformed(ActionEvent e)
3348   {
3349     new TextColourChooser().chooseColour(alignPanel, null);
3350   }
3351
3352   /**
3353    * DOCUMENT ME!
3354    *
3355    * @param e
3356    *          DOCUMENT ME!
3357    */
3358   @Override
3359   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3360   {
3361     changeColour(null);
3362   }
3363
3364   /**
3365    * DOCUMENT ME!
3366    *
3367    * @param e
3368    *          DOCUMENT ME!
3369    */
3370   @Override
3371   public void clustalColour_actionPerformed(ActionEvent e)
3372   {
3373     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3374             viewport.getHiddenRepSequences()));
3375   }
3376
3377   /**
3378    * DOCUMENT ME!
3379    *
3380    * @param e
3381    *          DOCUMENT ME!
3382    */
3383   @Override
3384   public void zappoColour_actionPerformed(ActionEvent e)
3385   {
3386     changeColour(new ZappoColourScheme());
3387   }
3388
3389   /**
3390    * DOCUMENT ME!
3391    *
3392    * @param e
3393    *          DOCUMENT ME!
3394    */
3395   @Override
3396   public void taylorColour_actionPerformed(ActionEvent e)
3397   {
3398     changeColour(new TaylorColourScheme());
3399   }
3400
3401   /**
3402    * DOCUMENT ME!
3403    *
3404    * @param e
3405    *          DOCUMENT ME!
3406    */
3407   @Override
3408   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3409   {
3410     changeColour(new HydrophobicColourScheme());
3411   }
3412
3413   /**
3414    * DOCUMENT ME!
3415    *
3416    * @param e
3417    *          DOCUMENT ME!
3418    */
3419   @Override
3420   public void helixColour_actionPerformed(ActionEvent e)
3421   {
3422     changeColour(new HelixColourScheme());
3423   }
3424
3425   /**
3426    * DOCUMENT ME!
3427    *
3428    * @param e
3429    *          DOCUMENT ME!
3430    */
3431   @Override
3432   public void strandColour_actionPerformed(ActionEvent e)
3433   {
3434     changeColour(new StrandColourScheme());
3435   }
3436
3437   /**
3438    * DOCUMENT ME!
3439    *
3440    * @param e
3441    *          DOCUMENT ME!
3442    */
3443   @Override
3444   public void turnColour_actionPerformed(ActionEvent e)
3445   {
3446     changeColour(new TurnColourScheme());
3447   }
3448
3449   /**
3450    * DOCUMENT ME!
3451    *
3452    * @param e
3453    *          DOCUMENT ME!
3454    */
3455   @Override
3456   public void buriedColour_actionPerformed(ActionEvent e)
3457   {
3458     changeColour(new BuriedColourScheme());
3459   }
3460
3461   /**
3462    * DOCUMENT ME!
3463    *
3464    * @param e
3465    *          DOCUMENT ME!
3466    */
3467   @Override
3468   public void nucleotideColour_actionPerformed(ActionEvent e)
3469   {
3470     changeColour(new NucleotideColourScheme());
3471   }
3472
3473   @Override
3474   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3475   {
3476     changeColour(new PurinePyrimidineColourScheme());
3477   }
3478
3479   /*
3480    * public void covariationColour_actionPerformed(ActionEvent e) {
3481    * changeColour(new
3482    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3483    * ()[0])); }
3484    */
3485   @Override
3486   public void annotationColour_actionPerformed(ActionEvent e)
3487   {
3488     new AnnotationColourChooser(viewport, alignPanel);
3489   }
3490
3491   @Override
3492   public void annotationColumn_actionPerformed(ActionEvent e)
3493   {
3494     new AnnotationColumnChooser(viewport, alignPanel);
3495   }
3496
3497   @Override
3498   public void rnahelicesColour_actionPerformed(ActionEvent e)
3499   {
3500     new RNAHelicesColourChooser(viewport, alignPanel);
3501   }
3502
3503   /**
3504    * DOCUMENT ME!
3505    *
3506    * @param e
3507    *          DOCUMENT ME!
3508    */
3509   @Override
3510   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3511   {
3512     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3513   }
3514
3515   /**
3516    * DOCUMENT ME!
3517    *
3518    * @param cs
3519    *          DOCUMENT ME!
3520    */
3521   @Override
3522   public void changeColour(ColourSchemeI cs)
3523   {
3524     // TODO: pull up to controller method
3525
3526     if (cs != null)
3527     {
3528       // Make sure viewport is up to date w.r.t. any sliders
3529       if (viewport.getAbovePIDThreshold())
3530       {
3531         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3532                 "Background");
3533         viewport.setThreshold(threshold);
3534       }
3535
3536       if (viewport.getConservationSelected())
3537       {
3538         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3539                 cs, "Background"));
3540       }
3541       if (cs instanceof TCoffeeColourScheme)
3542       {
3543         tcoffeeColour.setEnabled(true);
3544         tcoffeeColour.setSelected(true);
3545       }
3546     }
3547
3548     viewport.setGlobalColourScheme(cs);
3549
3550     alignPanel.paintAlignment(true);
3551   }
3552
3553   /**
3554    * DOCUMENT ME!
3555    *
3556    * @param e
3557    *          DOCUMENT ME!
3558    */
3559   @Override
3560   protected void modifyPID_actionPerformed(ActionEvent e)
3561   {
3562     if (viewport.getAbovePIDThreshold()
3563             && viewport.getGlobalColourScheme() != null)
3564     {
3565       SliderPanel.setPIDSliderSource(alignPanel,
3566               viewport.getGlobalColourScheme(), "Background");
3567       SliderPanel.showPIDSlider();
3568     }
3569   }
3570
3571   /**
3572    * DOCUMENT ME!
3573    *
3574    * @param e
3575    *          DOCUMENT ME!
3576    */
3577   @Override
3578   protected void modifyConservation_actionPerformed(ActionEvent e)
3579   {
3580     if (viewport.getConservationSelected()
3581             && viewport.getGlobalColourScheme() != null)
3582     {
3583       SliderPanel.setConservationSlider(alignPanel,
3584               viewport.getGlobalColourScheme(), "Background");
3585       SliderPanel.showConservationSlider();
3586     }
3587   }
3588
3589   /**
3590    * DOCUMENT ME!
3591    *
3592    * @param e
3593    *          DOCUMENT ME!
3594    */
3595   @Override
3596   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3597   {
3598     viewport.setConservationSelected(conservationMenuItem.isSelected());
3599
3600     viewport.setAbovePIDThreshold(false);
3601     abovePIDThreshold.setSelected(false);
3602
3603     changeColour(viewport.getGlobalColourScheme());
3604
3605     modifyConservation_actionPerformed(null);
3606   }
3607
3608   /**
3609    * DOCUMENT ME!
3610    *
3611    * @param e
3612    *          DOCUMENT ME!
3613    */
3614   @Override
3615   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3616   {
3617     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3618
3619     conservationMenuItem.setSelected(false);
3620     viewport.setConservationSelected(false);
3621
3622     changeColour(viewport.getGlobalColourScheme());
3623
3624     modifyPID_actionPerformed(null);
3625   }
3626
3627   /**
3628    * DOCUMENT ME!
3629    *
3630    * @param e
3631    *          DOCUMENT ME!
3632    */
3633   @Override
3634   public void userDefinedColour_actionPerformed(ActionEvent e)
3635   {
3636     if (e.getActionCommand().equals(
3637             MessageManager.getString("action.user_defined")))
3638     {
3639       new UserDefinedColours(alignPanel, null);
3640     }
3641     else
3642     {
3643       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3644               .getUserColourSchemes().get(e.getActionCommand());
3645
3646       changeColour(udc);
3647     }
3648   }
3649
3650   public void updateUserColourMenu()
3651   {
3652
3653     Component[] menuItems = colourMenu.getMenuComponents();
3654     int iSize = menuItems.length;
3655     for (int i = 0; i < iSize; i++)
3656     {
3657       if (menuItems[i].getName() != null
3658               && menuItems[i].getName().equals("USER_DEFINED"))
3659       {
3660         colourMenu.remove(menuItems[i]);
3661         iSize--;
3662       }
3663     }
3664     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3665     {
3666       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3667               .getUserColourSchemes().keys();
3668
3669       while (userColours.hasMoreElements())
3670       {
3671         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3672                 userColours.nextElement().toString());
3673         radioItem.setName("USER_DEFINED");
3674         radioItem.addMouseListener(new MouseAdapter()
3675         {
3676           @Override
3677           public void mousePressed(MouseEvent evt)
3678           {
3679             if (evt.isControlDown()
3680                     || SwingUtilities.isRightMouseButton(evt))
3681             {
3682               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3683
3684               int option = JOptionPane.showInternalConfirmDialog(
3685                       jalview.gui.Desktop.desktop,
3686                       MessageManager
3687                               .getString("label.remove_from_default_list"),
3688                       MessageManager
3689                               .getString("label.remove_user_defined_colour"),
3690                       JOptionPane.YES_NO_OPTION);
3691               if (option == JOptionPane.YES_OPTION)
3692               {
3693                 jalview.gui.UserDefinedColours
3694                         .removeColourFromDefaults(radioItem.getText());
3695                 colourMenu.remove(radioItem);
3696               }
3697               else
3698               {
3699                 radioItem.addActionListener(new ActionListener()
3700                 {
3701                   @Override
3702                   public void actionPerformed(ActionEvent evt)
3703                   {
3704                     userDefinedColour_actionPerformed(evt);
3705                   }
3706                 });
3707               }
3708             }
3709           }
3710         });
3711         radioItem.addActionListener(new ActionListener()
3712         {
3713           @Override
3714           public void actionPerformed(ActionEvent evt)
3715           {
3716             userDefinedColour_actionPerformed(evt);
3717           }
3718         });
3719
3720         colourMenu.insert(radioItem, 15);
3721         colours.add(radioItem);
3722       }
3723     }
3724   }
3725
3726   /**
3727    * DOCUMENT ME!
3728    *
3729    * @param e
3730    *          DOCUMENT ME!
3731    */
3732   @Override
3733   public void PIDColour_actionPerformed(ActionEvent e)
3734   {
3735     changeColour(new PIDColourScheme());
3736   }
3737
3738   /**
3739    * DOCUMENT ME!
3740    *
3741    * @param e
3742    *          DOCUMENT ME!
3743    */
3744   @Override
3745   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3746   {
3747     changeColour(new Blosum62ColourScheme());
3748   }
3749
3750   /**
3751    * DOCUMENT ME!
3752    *
3753    * @param e
3754    *          DOCUMENT ME!
3755    */
3756   @Override
3757   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3758   {
3759     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3760     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3761             .getAlignment().getSequenceAt(0), null);
3762     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3763             viewport.getAlignment()));
3764     alignPanel.paintAlignment(true);
3765   }
3766
3767   /**
3768    * DOCUMENT ME!
3769    *
3770    * @param e
3771    *          DOCUMENT ME!
3772    */
3773   @Override
3774   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3775   {
3776     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3777     AlignmentSorter.sortByID(viewport.getAlignment());
3778     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3779             viewport.getAlignment()));
3780     alignPanel.paintAlignment(true);
3781   }
3782
3783   /**
3784    * DOCUMENT ME!
3785    *
3786    * @param e
3787    *          DOCUMENT ME!
3788    */
3789   @Override
3790   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3791   {
3792     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3793     AlignmentSorter.sortByLength(viewport.getAlignment());
3794     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3795             viewport.getAlignment()));
3796     alignPanel.paintAlignment(true);
3797   }
3798
3799   /**
3800    * DOCUMENT ME!
3801    *
3802    * @param e
3803    *          DOCUMENT ME!
3804    */
3805   @Override
3806   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3807   {
3808     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3809     AlignmentSorter.sortByGroup(viewport.getAlignment());
3810     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3811             viewport.getAlignment()));
3812
3813     alignPanel.paintAlignment(true);
3814   }
3815
3816   /**
3817    * DOCUMENT ME!
3818    *
3819    * @param e
3820    *          DOCUMENT ME!
3821    */
3822   @Override
3823   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3824   {
3825     new RedundancyPanel(alignPanel, this);
3826   }
3827
3828   /**
3829    * DOCUMENT ME!
3830    *
3831    * @param e
3832    *          DOCUMENT ME!
3833    */
3834   @Override
3835   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3836   {
3837     if ((viewport.getSelectionGroup() == null)
3838             || (viewport.getSelectionGroup().getSize() < 2))
3839     {
3840       JOptionPane.showInternalMessageDialog(this, MessageManager
3841               .getString("label.you_must_select_least_two_sequences"),
3842               MessageManager.getString("label.invalid_selection"),
3843               JOptionPane.WARNING_MESSAGE);
3844     }
3845     else
3846     {
3847       JInternalFrame frame = new JInternalFrame();
3848       frame.setContentPane(new PairwiseAlignPanel(viewport));
3849       Desktop.addInternalFrame(frame,
3850               MessageManager.getString("action.pairwise_alignment"), 600,
3851               500);
3852     }
3853   }
3854
3855   /**
3856    * DOCUMENT ME!
3857    *
3858    * @param e
3859    *          DOCUMENT ME!
3860    */
3861   @Override
3862   public void PCAMenuItem_actionPerformed(ActionEvent e)
3863   {
3864     if (((viewport.getSelectionGroup() != null)
3865             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3866             .getSelectionGroup().getSize() > 0))
3867             || (viewport.getAlignment().getHeight() < 4))
3868     {
3869       JOptionPane
3870               .showInternalMessageDialog(
3871                       this,
3872                       MessageManager
3873                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3874                       MessageManager
3875                               .getString("label.sequence_selection_insufficient"),
3876                       JOptionPane.WARNING_MESSAGE);
3877
3878       return;
3879     }
3880
3881     new PCAPanel(alignPanel);
3882   }
3883
3884   @Override
3885   public void autoCalculate_actionPerformed(ActionEvent e)
3886   {
3887     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3888     if (viewport.autoCalculateConsensus)
3889     {
3890       viewport.firePropertyChange("alignment", null, viewport
3891               .getAlignment().getSequences());
3892     }
3893   }
3894
3895   @Override
3896   public void sortByTreeOption_actionPerformed(ActionEvent e)
3897   {
3898     viewport.sortByTree = sortByTree.isSelected();
3899   }
3900
3901   @Override
3902   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3903   {
3904     viewport.followSelection = listenToViewSelections.isSelected();
3905   }
3906
3907   /**
3908    * DOCUMENT ME!
3909    *
3910    * @param e
3911    *          DOCUMENT ME!
3912    */
3913   @Override
3914   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3915   {
3916     newTreePanel("AV", "PID", "Average distance tree using PID");
3917   }
3918
3919   /**
3920    * DOCUMENT ME!
3921    *
3922    * @param e
3923    *          DOCUMENT ME!
3924    */
3925   @Override
3926   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3927   {
3928     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3929   }
3930
3931   /**
3932    * DOCUMENT ME!
3933    *
3934    * @param e
3935    *          DOCUMENT ME!
3936    */
3937   @Override
3938   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3939   {
3940     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3941   }
3942
3943   /**
3944    * DOCUMENT ME!
3945    *
3946    * @param e
3947    *          DOCUMENT ME!
3948    */
3949   @Override
3950   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3951   {
3952     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3953   }
3954
3955   /**
3956    * DOCUMENT ME!
3957    *
3958    * @param type
3959    *          DOCUMENT ME!
3960    * @param pwType
3961    *          DOCUMENT ME!
3962    * @param title
3963    *          DOCUMENT ME!
3964    */
3965   void newTreePanel(String type, String pwType, String title)
3966   {
3967     TreePanel tp;
3968
3969     if (viewport.getSelectionGroup() != null
3970             && viewport.getSelectionGroup().getSize() > 0)
3971     {
3972       if (viewport.getSelectionGroup().getSize() < 3)
3973       {
3974         JOptionPane
3975                 .showMessageDialog(
3976                         Desktop.desktop,
3977                         MessageManager
3978                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3979                         MessageManager
3980                                 .getString("label.not_enough_sequences"),
3981                         JOptionPane.WARNING_MESSAGE);
3982         return;
3983       }
3984
3985       SequenceGroup sg = viewport.getSelectionGroup();
3986
3987       /* Decide if the selection is a column region */
3988       for (SequenceI _s : sg.getSequences())
3989       {
3990         if (_s.getLength() < sg.getEndRes())
3991         {
3992           JOptionPane
3993                   .showMessageDialog(
3994                           Desktop.desktop,
3995                           MessageManager
3996                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3997                           MessageManager
3998                                   .getString("label.sequences_selection_not_aligned"),
3999                           JOptionPane.WARNING_MESSAGE);
4000
4001           return;
4002         }
4003       }
4004
4005       title = title + " on region";
4006       tp = new TreePanel(alignPanel, type, pwType);
4007     }
4008     else
4009     {
4010       // are the visible sequences aligned?
4011       if (!viewport.getAlignment().isAligned(false))
4012       {
4013         JOptionPane
4014                 .showMessageDialog(
4015                         Desktop.desktop,
4016                         MessageManager
4017                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4018                         MessageManager
4019                                 .getString("label.sequences_not_aligned"),
4020                         JOptionPane.WARNING_MESSAGE);
4021
4022         return;
4023       }
4024
4025       if (viewport.getAlignment().getHeight() < 2)
4026       {
4027         return;
4028       }
4029
4030       tp = new TreePanel(alignPanel, type, pwType);
4031     }
4032
4033     title += " from ";
4034
4035     if (viewport.viewName != null)
4036     {
4037       title += viewport.viewName + " of ";
4038     }
4039
4040     title += this.title;
4041
4042     Desktop.addInternalFrame(tp, title, 600, 500);
4043   }
4044
4045   /**
4046    * DOCUMENT ME!
4047    *
4048    * @param title
4049    *          DOCUMENT ME!
4050    * @param order
4051    *          DOCUMENT ME!
4052    */
4053   public void addSortByOrderMenuItem(String title,
4054           final AlignmentOrder order)
4055   {
4056     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4057             "action.by_title_param", new Object[] { title }));
4058     sort.add(item);
4059     item.addActionListener(new java.awt.event.ActionListener()
4060     {
4061       @Override
4062       public void actionPerformed(ActionEvent e)
4063       {
4064         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4065
4066         // TODO: JBPNote - have to map order entries to curent SequenceI
4067         // pointers
4068         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4069
4070         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4071                 .getAlignment()));
4072
4073         alignPanel.paintAlignment(true);
4074       }
4075     });
4076   }
4077
4078   /**
4079    * Add a new sort by annotation score menu item
4080    *
4081    * @param sort
4082    *          the menu to add the option to
4083    * @param scoreLabel
4084    *          the label used to retrieve scores for each sequence on the
4085    *          alignment
4086    */
4087   public void addSortByAnnotScoreMenuItem(JMenu sort,
4088           final String scoreLabel)
4089   {
4090     final JMenuItem item = new JMenuItem(scoreLabel);
4091     sort.add(item);
4092     item.addActionListener(new java.awt.event.ActionListener()
4093     {
4094       @Override
4095       public void actionPerformed(ActionEvent e)
4096       {
4097         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4098         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4099                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4100         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4101                 viewport.getAlignment()));
4102         alignPanel.paintAlignment(true);
4103       }
4104     });
4105   }
4106
4107   /**
4108    * last hash for alignment's annotation array - used to minimise cost of
4109    * rebuild.
4110    */
4111   protected int _annotationScoreVectorHash;
4112
4113   /**
4114    * search the alignment and rebuild the sort by annotation score submenu the
4115    * last alignment annotation vector hash is stored to minimize cost of
4116    * rebuilding in subsequence calls.
4117    *
4118    */
4119   @Override
4120   public void buildSortByAnnotationScoresMenu()
4121   {
4122     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4123     {
4124       return;
4125     }
4126
4127     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4128     {
4129       sortByAnnotScore.removeAll();
4130       // almost certainly a quicker way to do this - but we keep it simple
4131       Hashtable scoreSorts = new Hashtable();
4132       AlignmentAnnotation aann[];
4133       for (SequenceI sqa : viewport.getAlignment().getSequences())
4134       {
4135         aann = sqa.getAnnotation();
4136         for (int i = 0; aann != null && i < aann.length; i++)
4137         {
4138           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4139           {
4140             scoreSorts.put(aann[i].label, aann[i].label);
4141           }
4142         }
4143       }
4144       Enumeration labels = scoreSorts.keys();
4145       while (labels.hasMoreElements())
4146       {
4147         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4148                 (String) labels.nextElement());
4149       }
4150       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4151       scoreSorts.clear();
4152
4153       _annotationScoreVectorHash = viewport.getAlignment()
4154               .getAlignmentAnnotation().hashCode();
4155     }
4156   }
4157
4158   /**
4159    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4160    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4161    * call. Listeners are added to remove the menu item when the treePanel is
4162    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4163    * modified.
4164    *
4165    * @param treePanel
4166    *          Displayed tree window.
4167    * @param title
4168    *          SortBy menu item title.
4169    */
4170   @Override
4171   public void buildTreeMenu()
4172   {
4173     calculateTree.removeAll();
4174     // build the calculate menu
4175
4176     for (final String type : new String[] { "NJ", "AV" })
4177     {
4178       String treecalcnm = MessageManager.getString("label.tree_calc_"
4179               + type.toLowerCase());
4180       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4181       {
4182         JMenuItem tm = new JMenuItem();
4183         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4184         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4185         {
4186           String smn = MessageManager.getStringOrReturn(
4187                   "label.score_model_", sm.getName());
4188           final String title = MessageManager.formatMessage(
4189                   "label.treecalc_title", treecalcnm, smn);
4190           tm.setText(title);//
4191           tm.addActionListener(new java.awt.event.ActionListener()
4192           {
4193             @Override
4194             public void actionPerformed(ActionEvent e)
4195             {
4196               newTreePanel(type, pwtype, title);
4197             }
4198           });
4199           calculateTree.add(tm);
4200         }
4201
4202       }
4203     }
4204     sortByTreeMenu.removeAll();
4205
4206     List<Component> comps = PaintRefresher.components.get(viewport
4207             .getSequenceSetId());
4208     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4209     for (Component comp : comps)
4210     {
4211       if (comp instanceof TreePanel)
4212       {
4213         treePanels.add((TreePanel) comp);
4214       }
4215     }
4216
4217     if (treePanels.size() < 1)
4218     {
4219       sortByTreeMenu.setVisible(false);
4220       return;
4221     }
4222
4223     sortByTreeMenu.setVisible(true);
4224
4225     for (final TreePanel tp : treePanels)
4226     {
4227       final JMenuItem item = new JMenuItem(tp.getTitle());
4228       item.addActionListener(new java.awt.event.ActionListener()
4229       {
4230         @Override
4231         public void actionPerformed(ActionEvent e)
4232         {
4233           tp.sortByTree_actionPerformed();
4234           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4235
4236         }
4237       });
4238
4239       sortByTreeMenu.add(item);
4240     }
4241   }
4242
4243   public boolean sortBy(AlignmentOrder alorder, String undoname)
4244   {
4245     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4246     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4247     if (undoname != null)
4248     {
4249       addHistoryItem(new OrderCommand(undoname, oldOrder,
4250               viewport.getAlignment()));
4251     }
4252     alignPanel.paintAlignment(true);
4253     return true;
4254   }
4255
4256   /**
4257    * Work out whether the whole set of sequences or just the selected set will
4258    * be submitted for multiple alignment.
4259    *
4260    */
4261   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4262   {
4263     // Now, check we have enough sequences
4264     AlignmentView msa = null;
4265
4266     if ((viewport.getSelectionGroup() != null)
4267             && (viewport.getSelectionGroup().getSize() > 1))
4268     {
4269       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4270       // some common interface!
4271       /*
4272        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4273        * SequenceI[sz = seqs.getSize(false)];
4274        *
4275        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4276        * seqs.getSequenceAt(i); }
4277        */
4278       msa = viewport.getAlignmentView(true);
4279     }
4280     else if (viewport.getSelectionGroup() != null
4281             && viewport.getSelectionGroup().getSize() == 1)
4282     {
4283       int option = JOptionPane.showConfirmDialog(this,
4284               MessageManager.getString("warn.oneseq_msainput_selection"),
4285               MessageManager.getString("label.invalid_selection"),
4286               JOptionPane.OK_CANCEL_OPTION);
4287       if (option == JOptionPane.OK_OPTION)
4288       {
4289         msa = viewport.getAlignmentView(false);
4290       }
4291     }
4292     else
4293     {
4294       msa = viewport.getAlignmentView(false);
4295     }
4296     return msa;
4297   }
4298
4299   /**
4300    * Decides what is submitted to a secondary structure prediction service: the
4301    * first sequence in the alignment, or in the current selection, or, if the
4302    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4303    * region or the whole alignment. (where the first sequence in the set is the
4304    * one that the prediction will be for).
4305    */
4306   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4307   {
4308     AlignmentView seqs = null;
4309
4310     if ((viewport.getSelectionGroup() != null)
4311             && (viewport.getSelectionGroup().getSize() > 0))
4312     {
4313       seqs = viewport.getAlignmentView(true);
4314     }
4315     else
4316     {
4317       seqs = viewport.getAlignmentView(false);
4318     }
4319     // limit sequences - JBPNote in future - could spawn multiple prediction
4320     // jobs
4321     // TODO: viewport.getAlignment().isAligned is a global state - the local
4322     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4323     if (!viewport.getAlignment().isAligned(false))
4324     {
4325       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4326       // TODO: if seqs.getSequences().length>1 then should really have warned
4327       // user!
4328
4329     }
4330     return seqs;
4331   }
4332
4333   /**
4334    * DOCUMENT ME!
4335    *
4336    * @param e
4337    *          DOCUMENT ME!
4338    */
4339   @Override
4340   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4341   {
4342     // Pick the tree file
4343     JalviewFileChooser chooser = new JalviewFileChooser(
4344             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4345     chooser.setFileView(new JalviewFileView());
4346     chooser.setDialogTitle(MessageManager
4347             .getString("label.select_newick_like_tree_file"));
4348     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4349
4350     int value = chooser.showOpenDialog(null);
4351
4352     if (value == JalviewFileChooser.APPROVE_OPTION)
4353     {
4354       String choice = chooser.getSelectedFile().getPath();
4355       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4356       jalview.io.NewickFile fin = null;
4357       try
4358       {
4359         fin = new jalview.io.NewickFile(choice, "File");
4360         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4361       } catch (Exception ex)
4362       {
4363         JOptionPane
4364                 .showMessageDialog(
4365                         Desktop.desktop,
4366                         ex.getMessage(),
4367                         MessageManager
4368                                 .getString("label.problem_reading_tree_file"),
4369                         JOptionPane.WARNING_MESSAGE);
4370         ex.printStackTrace();
4371       }
4372       if (fin != null && fin.hasWarningMessage())
4373       {
4374         JOptionPane.showMessageDialog(Desktop.desktop, fin
4375                 .getWarningMessage(), MessageManager
4376                 .getString("label.possible_problem_with_tree_file"),
4377                 JOptionPane.WARNING_MESSAGE);
4378       }
4379     }
4380   }
4381
4382   @Override
4383   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4384   {
4385     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4386   }
4387
4388   public TreePanel ShowNewickTree(NewickFile nf, String title)
4389   {
4390     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4391   }
4392
4393   public TreePanel ShowNewickTree(NewickFile nf, String title,
4394           AlignmentView input)
4395   {
4396     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4397   }
4398
4399   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4400           int h, int x, int y)
4401   {
4402     return ShowNewickTree(nf, title, null, w, h, x, y);
4403   }
4404
4405   /**
4406    * Add a treeviewer for the tree extracted from a newick file object to the
4407    * current alignment view
4408    *
4409    * @param nf
4410    *          the tree
4411    * @param title
4412    *          tree viewer title
4413    * @param input
4414    *          Associated alignment input data (or null)
4415    * @param w
4416    *          width
4417    * @param h
4418    *          height
4419    * @param x
4420    *          position
4421    * @param y
4422    *          position
4423    * @return TreePanel handle
4424    */
4425   public TreePanel ShowNewickTree(NewickFile nf, String title,
4426           AlignmentView input, int w, int h, int x, int y)
4427   {
4428     TreePanel tp = null;
4429
4430     try
4431     {
4432       nf.parse();
4433
4434       if (nf.getTree() != null)
4435       {
4436         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4437
4438         tp.setSize(w, h);
4439
4440         if (x > 0 && y > 0)
4441         {
4442           tp.setLocation(x, y);
4443         }
4444
4445         Desktop.addInternalFrame(tp, title, w, h);
4446       }
4447     } catch (Exception ex)
4448     {
4449       ex.printStackTrace();
4450     }
4451
4452     return tp;
4453   }
4454
4455   private boolean buildingMenu = false;
4456
4457   /**
4458    * Generates menu items and listener event actions for web service clients
4459    *
4460    */
4461   public void BuildWebServiceMenu()
4462   {
4463     while (buildingMenu)
4464     {
4465       try
4466       {
4467         System.err.println("Waiting for building menu to finish.");
4468         Thread.sleep(10);
4469       } catch (Exception e)
4470       {
4471       }
4472     }
4473     final AlignFrame me = this;
4474     buildingMenu = true;
4475     new Thread(new Runnable()
4476     {
4477       @Override
4478       public void run()
4479       {
4480         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4481         try
4482         {
4483           // System.err.println("Building ws menu again "
4484           // + Thread.currentThread());
4485           // TODO: add support for context dependent disabling of services based
4486           // on
4487           // alignment and current selection
4488           // TODO: add additional serviceHandle parameter to specify abstract
4489           // handler
4490           // class independently of AbstractName
4491           // TODO: add in rediscovery GUI function to restart discoverer
4492           // TODO: group services by location as well as function and/or
4493           // introduce
4494           // object broker mechanism.
4495           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4496           final IProgressIndicator af = me;
4497           final JMenu msawsmenu = new JMenu("Alignment");
4498           final JMenu secstrmenu = new JMenu(
4499                   "Secondary Structure Prediction");
4500           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4501           final JMenu analymenu = new JMenu("Analysis");
4502           final JMenu dismenu = new JMenu("Protein Disorder");
4503           // final JMenu msawsmenu = new
4504           // JMenu(MessageManager.getString("label.alignment"));
4505           // final JMenu secstrmenu = new
4506           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4507           // final JMenu seqsrchmenu = new
4508           // JMenu(MessageManager.getString("label.sequence_database_search"));
4509           // final JMenu analymenu = new
4510           // JMenu(MessageManager.getString("label.analysis"));
4511           // final JMenu dismenu = new
4512           // JMenu(MessageManager.getString("label.protein_disorder"));
4513           // JAL-940 - only show secondary structure prediction services from
4514           // the legacy server
4515           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4516               // &&
4517           Discoverer.services != null && (Discoverer.services.size() > 0))
4518           {
4519             // TODO: refactor to allow list of AbstractName/Handler bindings to
4520             // be
4521             // stored or retrieved from elsewhere
4522             // No MSAWS used any more:
4523             // Vector msaws = null; // (Vector)
4524             // Discoverer.services.get("MsaWS");
4525             Vector secstrpr = (Vector) Discoverer.services
4526                     .get("SecStrPred");
4527             if (secstrpr != null)
4528             {
4529               // Add any secondary structure prediction services
4530               for (int i = 0, j = secstrpr.size(); i < j; i++)
4531               {
4532                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4533                         .get(i);
4534                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4535                         .getServiceClient(sh);
4536                 int p = secstrmenu.getItemCount();
4537                 impl.attachWSMenuEntry(secstrmenu, me);
4538                 int q = secstrmenu.getItemCount();
4539                 for (int litm = p; litm < q; litm++)
4540                 {
4541                   legacyItems.add(secstrmenu.getItem(litm));
4542                 }
4543               }
4544             }
4545           }
4546
4547           // Add all submenus in the order they should appear on the web
4548           // services menu
4549           wsmenu.add(msawsmenu);
4550           wsmenu.add(secstrmenu);
4551           wsmenu.add(dismenu);
4552           wsmenu.add(analymenu);
4553           // No search services yet
4554           // wsmenu.add(seqsrchmenu);
4555
4556           javax.swing.SwingUtilities.invokeLater(new Runnable()
4557           {
4558             @Override
4559             public void run()
4560             {
4561               try
4562               {
4563                 webService.removeAll();
4564                 // first, add discovered services onto the webservices menu
4565                 if (wsmenu.size() > 0)
4566                 {
4567                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4568                   {
4569                     webService.add(wsmenu.get(i));
4570                   }
4571                 }
4572                 else
4573                 {
4574                   webService.add(me.webServiceNoServices);
4575                 }
4576                 // TODO: move into separate menu builder class.
4577                 boolean new_sspred = false;
4578                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4579                 {
4580                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4581                   if (jws2servs != null)
4582                   {
4583                     if (jws2servs.hasServices())
4584                     {
4585                       jws2servs.attachWSMenuEntry(webService, me);
4586                       for (Jws2Instance sv : jws2servs.getServices())
4587                       {
4588                         if (sv.description.toLowerCase().contains("jpred"))
4589                         {
4590                           for (JMenuItem jmi : legacyItems)
4591                           {
4592                             jmi.setVisible(false);
4593                           }
4594                         }
4595                       }
4596
4597                     }
4598                     if (jws2servs.isRunning())
4599                     {
4600                       JMenuItem tm = new JMenuItem(
4601                               "Still discovering JABA Services");
4602                       tm.setEnabled(false);
4603                       webService.add(tm);
4604                     }
4605                   }
4606                 }
4607                 build_urlServiceMenu(me.webService);
4608                 build_fetchdbmenu(webService);
4609                 for (JMenu item : wsmenu)
4610                 {
4611                   if (item.getItemCount() == 0)
4612                   {
4613                     item.setEnabled(false);
4614                   }
4615                   else
4616                   {
4617                     item.setEnabled(true);
4618                   }
4619                 }
4620               } catch (Exception e)
4621               {
4622                 Cache.log
4623                         .debug("Exception during web service menu building process.",
4624                                 e);
4625               }
4626             }
4627           });
4628         } catch (Exception e)
4629         {
4630         }
4631         buildingMenu = false;
4632       }
4633     }).start();
4634
4635   }
4636
4637   /**
4638    * construct any groupURL type service menu entries.
4639    *
4640    * @param webService
4641    */
4642   private void build_urlServiceMenu(JMenu webService)
4643   {
4644     // TODO: remove this code when 2.7 is released
4645     // DEBUG - alignmentView
4646     /*
4647      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4648      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4649      *
4650      * @Override public void actionPerformed(ActionEvent e) {
4651      * jalview.datamodel.AlignmentView
4652      * .testSelectionViews(af.viewport.getAlignment(),
4653      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4654      *
4655      * }); webService.add(testAlView);
4656      */
4657     // TODO: refactor to RestClient discoverer and merge menu entries for
4658     // rest-style services with other types of analysis/calculation service
4659     // SHmmr test client - still being implemented.
4660     // DEBUG - alignmentView
4661
4662     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4663             .getRestClients())
4664     {
4665       client.attachWSMenuEntry(
4666               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4667               this);
4668     }
4669   }
4670
4671   /**
4672    * Searches selected sequences for xRef products and builds the Show
4673    * Cross-References menu (formerly called Show Products)
4674    *
4675    * @return true if Show Cross-references menu should be enabled.
4676    */
4677   public boolean canShowProducts()
4678   {
4679     SequenceI[] selection = viewport.getSequenceSelection();
4680     AlignmentI dataset = viewport.getAlignment().getDataset();
4681     boolean showp = false;
4682     try
4683     {
4684       showProducts.removeAll();
4685       final boolean dna = viewport.getAlignment().isNucleotide();
4686       String[] ptypes = (selection == null || selection.length == 0) ? null
4687               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4688
4689       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4690       {
4691         showp = true;
4692         final AlignFrame af = this;
4693         final String source = ptypes[t];
4694         JMenuItem xtype = new JMenuItem(ptypes[t]);
4695         xtype.addActionListener(new ActionListener()
4696         {
4697
4698           @Override
4699           public void actionPerformed(ActionEvent e)
4700           {
4701             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4702           }
4703
4704         });
4705         showProducts.add(xtype);
4706       }
4707       showProducts.setVisible(showp);
4708       showProducts.setEnabled(showp);
4709     } catch (Exception e)
4710     {
4711       jalview.bin.Cache.log
4712               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4713                       e);
4714       return false;
4715     }
4716     return showp;
4717   }
4718
4719   protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4720           final String source)
4721   {
4722     Runnable foo = new Runnable()
4723     {
4724
4725       @Override
4726       public void run()
4727       {
4728         final long sttime = System.currentTimeMillis();
4729         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4730                 "status.searching_for_sequences_from",
4731                 new Object[] { source }), sttime);
4732         try
4733         {
4734           AlignmentI alignment = AlignFrame.this.getViewport()
4735                   .getAlignment();
4736           AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4737                   alignment);
4738           if (xrefs != null)
4739           {
4740             /*
4741              * get display scheme (if any) to apply to features
4742              */
4743             FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4744                     .getFeatureColourScheme(source);
4745
4746             AlignmentI al = makeCrossReferencesAlignment(
4747                     alignment.getDataset(), xrefs);
4748
4749             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4750                     DEFAULT_HEIGHT);
4751             String newtitle = String.format("%s %s %s",
4752                     MessageManager.getString(dna ? "label.proteins"
4753                             : "label.nucleotides"), MessageManager
4754                             .getString("label.for"), getTitle());
4755             newFrame.setTitle(newtitle);
4756
4757             if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4758             {
4759               /*
4760                * split frame display is turned off in preferences file
4761                */
4762               Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4763                       DEFAULT_HEIGHT);
4764               return; // via finally clause
4765             }
4766
4767             /*
4768              * Make a copy of this alignment (sharing the same dataset
4769              * sequences). If we are DNA, drop introns and update mappings
4770              */
4771             AlignmentI copyAlignment = null;
4772             final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4773                     .getSequenceSelection();
4774             List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4775             boolean copyAlignmentIsAligned = false;
4776             if (dna)
4777             {
4778               copyAlignment = AlignmentUtils.makeCdsAlignment(
4779                       sequenceSelection, cf, alignment);
4780               if (copyAlignment.getHeight() == 0)
4781               {
4782                 System.err.println("Failed to make CDS alignment");
4783               }
4784               al.getCodonFrames().clear();
4785               al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
4786
4787               /*
4788                * pending getting Embl transcripts to 'align',
4789                * we are only doing this for Ensembl
4790                */
4791               // TODO proper criteria for 'can align as cdna'
4792               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4793                       || AlignmentUtils.looksLikeEnsembl(alignment))
4794               {
4795                 copyAlignment.alignAs(alignment);
4796                 copyAlignmentIsAligned = true;
4797               }
4798             }
4799             else
4800             {
4801               copyAlignment = AlignmentUtils.makeCopyAlignment(
4802                       sequenceSelection, xrefs.getSequencesArray());
4803               copyAlignment.getCodonFrames().addAll(cf);
4804             }
4805             copyAlignment.setGapCharacter(AlignFrame.this.viewport
4806                     .getGapCharacter());
4807
4808             StructureSelectionManager ssm = StructureSelectionManager
4809                     .getStructureSelectionManager(Desktop.instance);
4810             ssm.registerMappings(cf);
4811
4812             if (copyAlignment.getHeight() <= 0)
4813             {
4814               System.err.println("No Sequences generated for xRef type "
4815                       + source);
4816               return;
4817             }
4818             /*
4819              * align protein to dna
4820              */
4821             if (dna && copyAlignmentIsAligned)
4822             {
4823               al.alignAs(copyAlignment);
4824             }
4825             else
4826             {
4827               /*
4828                * align cdna to protein - currently only if
4829                * fetching and aligning Ensembl transcripts!
4830                */
4831               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4832               {
4833                 copyAlignment.alignAs(al);
4834               }
4835             }
4836
4837             AlignFrame copyThis = new AlignFrame(copyAlignment,
4838                     AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4839             copyThis.setTitle(AlignFrame.this.getTitle());
4840
4841             boolean showSequenceFeatures = viewport
4842                     .isShowSequenceFeatures();
4843             newFrame.setShowSeqFeatures(showSequenceFeatures);
4844             copyThis.setShowSeqFeatures(showSequenceFeatures);
4845             FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4846                     .getFeatureRenderer();
4847
4848             /*
4849              * copy feature rendering settings to split frame
4850              */
4851             newFrame.alignPanel.getSeqPanel().seqCanvas
4852                     .getFeatureRenderer()
4853                     .transferSettings(myFeatureStyling);
4854             copyThis.alignPanel.getSeqPanel().seqCanvas
4855                     .getFeatureRenderer()
4856                     .transferSettings(myFeatureStyling);
4857
4858             /*
4859              * apply 'database source' feature configuration
4860              * if any was found
4861              */
4862             // TODO is this the feature colouring for the original
4863             // alignment or the fetched xrefs? either could be Ensembl
4864             newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4865             copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4866
4867             SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4868                     dna ? newFrame : copyThis);
4869             newFrame.setVisible(true);
4870             copyThis.setVisible(true);
4871             String linkedTitle = MessageManager
4872                     .getString("label.linked_view_title");
4873             Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4874             sf.adjustDivider();
4875           }
4876         } catch (Exception e)
4877         {
4878           Cache.log.error(
4879                   "Exception when finding crossreferences", e);
4880         } catch (OutOfMemoryError e)
4881         {
4882           new OOMWarning("whilst fetching crossreferences", e);
4883         } catch (Throwable e)
4884         {
4885           Cache.log.error("Error when finding crossreferences",
4886                   e);
4887         } finally
4888         {
4889           AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4890                   "status.finished_searching_for_sequences_from",
4891                   new Object[] { source }), sttime);
4892         }
4893       }
4894
4895       /**
4896        * Makes an alignment containing the given sequences. If this is of the
4897        * same type as the given dataset (nucleotide/protein), then the new
4898        * alignment shares the same dataset, and its dataset sequences are added
4899        * to it. Otherwise a new dataset sequence is created for the
4900        * cross-references.
4901        *
4902        * @param dataset
4903        * @param seqs
4904        * @return
4905        */
4906       protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4907               AlignmentI seqs)
4908       {
4909         boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4910
4911         SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4912         for (int s = 0; s < sprods.length; s++)
4913         {
4914           sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4915           if (sameType)
4916           {
4917             if (dataset.getSequences() == null
4918                     || !dataset.getSequences().contains(
4919                             sprods[s].getDatasetSequence()))
4920             {
4921               dataset.addSequence(sprods[s].getDatasetSequence());
4922             }
4923           }
4924           sprods[s].updatePDBIds();
4925         }
4926         Alignment al = new Alignment(sprods);
4927         if (sameType)
4928         {
4929           al.setDataset((Alignment) dataset);
4930         }
4931         else
4932         {
4933           al.createDatasetAlignment();
4934         }
4935         return al;
4936       }
4937
4938     };
4939     Thread frunner = new Thread(foo);
4940     frunner.start();
4941   }
4942
4943   /**
4944    * Construct and display a new frame containing the translation of this
4945    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4946    */
4947   @Override
4948   public void showTranslation_actionPerformed(ActionEvent e)
4949   {
4950     AlignmentI al = null;
4951     try
4952     {
4953       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4954
4955       al = dna.translateCdna();
4956     } catch (Exception ex)
4957     {
4958       jalview.bin.Cache.log.error(
4959               "Exception during translation. Please report this !", ex);
4960       final String msg = MessageManager
4961               .getString("label.error_when_translating_sequences_submit_bug_report");
4962       final String errorTitle = MessageManager
4963               .getString("label.implementation_error")
4964               + MessageManager.getString("translation_failed");
4965       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4966               JOptionPane.ERROR_MESSAGE);
4967       return;
4968     }
4969     if (al == null || al.getHeight() == 0)
4970     {
4971       final String msg = MessageManager
4972               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4973       final String errorTitle = MessageManager
4974               .getString("label.translation_failed");
4975       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4976               JOptionPane.WARNING_MESSAGE);
4977     }
4978     else
4979     {
4980       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4981       af.setFileFormat(this.currentFileFormat);
4982       final String newTitle = MessageManager.formatMessage(
4983               "label.translation_of_params",
4984               new Object[] { this.getTitle() });
4985       af.setTitle(newTitle);
4986       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4987       {
4988         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4989         viewport.openSplitFrame(af, new Alignment(seqs));
4990       }
4991       else
4992       {
4993         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4994                 DEFAULT_HEIGHT);
4995       }
4996     }
4997   }
4998
4999   /**
5000    * Set the file format
5001    *
5002    * @param fileFormat
5003    */
5004   public void setFileFormat(String fileFormat)
5005   {
5006     this.currentFileFormat = fileFormat;
5007   }
5008
5009   /**
5010    * Try to load a features file onto the alignment.
5011    *
5012    * @param file
5013    *          contents or path to retrieve file
5014    * @param type
5015    *          access mode of file (see jalview.io.AlignFile)
5016    * @return true if features file was parsed correctly.
5017    */
5018   public boolean parseFeaturesFile(String file, String type)
5019   {
5020     return avc.parseFeaturesFile(file, type,
5021             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5022
5023   }
5024
5025   @Override
5026   public void refreshFeatureUI(boolean enableIfNecessary)
5027   {
5028     // note - currently this is only still here rather than in the controller
5029     // because of the featureSettings hard reference that is yet to be
5030     // abstracted
5031     if (enableIfNecessary)
5032     {
5033       viewport.setShowSequenceFeatures(true);
5034       showSeqFeatures.setSelected(true);
5035     }
5036
5037   }
5038
5039   @Override
5040   public void dragEnter(DropTargetDragEvent evt)
5041   {
5042   }
5043
5044   @Override
5045   public void dragExit(DropTargetEvent evt)
5046   {
5047   }
5048
5049   @Override
5050   public void dragOver(DropTargetDragEvent evt)
5051   {
5052   }
5053
5054   @Override
5055   public void dropActionChanged(DropTargetDragEvent evt)
5056   {
5057   }
5058
5059   @Override
5060   public void drop(DropTargetDropEvent evt)
5061   {
5062     Transferable t = evt.getTransferable();
5063     java.util.List files = null;
5064
5065     try
5066     {
5067       DataFlavor uriListFlavor = new DataFlavor(
5068               "text/uri-list;class=java.lang.String");
5069       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5070       {
5071         // Works on Windows and MacOSX
5072         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5073         files = (java.util.List) t
5074                 .getTransferData(DataFlavor.javaFileListFlavor);
5075       }
5076       else if (t.isDataFlavorSupported(uriListFlavor))
5077       {
5078         // This is used by Unix drag system
5079         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5080         String data = (String) t.getTransferData(uriListFlavor);
5081         files = new java.util.ArrayList(1);
5082         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5083                 data, "\r\n"); st.hasMoreTokens();)
5084         {
5085           String s = st.nextToken();
5086           if (s.startsWith("#"))
5087           {
5088             // the line is a comment (as per the RFC 2483)
5089             continue;
5090           }
5091
5092           java.net.URI uri = new java.net.URI(s);
5093           // check to see if we can handle this kind of URI
5094           if (uri.getScheme().toLowerCase().startsWith("http"))
5095           {
5096             files.add(uri.toString());
5097           }
5098           else
5099           {
5100             // otherwise preserve old behaviour: catch all for file objects
5101             java.io.File file = new java.io.File(uri);
5102             files.add(file.toString());
5103           }
5104         }
5105       }
5106     } catch (Exception e)
5107     {
5108       e.printStackTrace();
5109     }
5110     if (files != null)
5111     {
5112       try
5113       {
5114         // check to see if any of these files have names matching sequences in
5115         // the alignment
5116         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5117                 .getAlignment().getSequencesArray());
5118         /**
5119          * Object[] { String,SequenceI}
5120          */
5121         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5122         ArrayList<String> filesnotmatched = new ArrayList<String>();
5123         for (int i = 0; i < files.size(); i++)
5124         {
5125           String file = files.get(i).toString();
5126           String pdbfn = "";
5127           String protocol = FormatAdapter.checkProtocol(file);
5128           if (protocol == jalview.io.FormatAdapter.FILE)
5129           {
5130             File fl = new File(file);
5131             pdbfn = fl.getName();
5132           }
5133           else if (protocol == jalview.io.FormatAdapter.URL)
5134           {
5135             URL url = new URL(file);
5136             pdbfn = url.getFile();
5137           }
5138           if (pdbfn.length() > 0)
5139           {
5140             // attempt to find a match in the alignment
5141             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5142             int l = 0, c = pdbfn.indexOf(".");
5143             while (mtch == null && c != -1)
5144             {
5145               do
5146               {
5147                 l = c;
5148               } while ((c = pdbfn.indexOf(".", l)) > l);
5149               if (l > -1)
5150               {
5151                 pdbfn = pdbfn.substring(0, l);
5152               }
5153               mtch = idm.findAllIdMatches(pdbfn);
5154             }
5155             if (mtch != null)
5156             {
5157               String type = null;
5158               try
5159               {
5160                 type = new IdentifyFile().identify(file, protocol);
5161               } catch (Exception ex)
5162               {
5163                 type = null;
5164               }
5165               if (type != null)
5166               {
5167                 if (type.equalsIgnoreCase("PDB"))
5168                 {
5169                   filesmatched.add(new Object[] { file, protocol, mtch });
5170                   continue;
5171                 }
5172               }
5173             }
5174             // File wasn't named like one of the sequences or wasn't a PDB file.
5175             filesnotmatched.add(file);
5176           }
5177         }
5178         int assocfiles = 0;
5179         if (filesmatched.size() > 0)
5180         {
5181           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5182                   || JOptionPane
5183                           .showConfirmDialog(
5184                                   this,
5185                                   MessageManager
5186                                           .formatMessage(
5187                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5188                                                   new Object[] { Integer
5189                                                           .valueOf(
5190                                                                   filesmatched
5191                                                                           .size())
5192                                                           .toString() }),
5193                                   MessageManager
5194                                           .getString("label.automatically_associate_pdb_files_by_name"),
5195                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5196
5197           {
5198             for (Object[] fm : filesmatched)
5199             {
5200               // try and associate
5201               // TODO: may want to set a standard ID naming formalism for
5202               // associating PDB files which have no IDs.
5203               for (SequenceI toassoc : (SequenceI[]) fm[2])
5204               {
5205                 PDBEntry pe = new AssociatePdbFileWithSeq()
5206                         .associatePdbWithSeq((String) fm[0],
5207                                 (String) fm[1], toassoc, false,
5208                                 Desktop.instance);
5209                 if (pe != null)
5210                 {
5211                   System.err.println("Associated file : "
5212                           + ((String) fm[0]) + " with "
5213                           + toassoc.getDisplayId(true));
5214                   assocfiles++;
5215                 }
5216               }
5217               alignPanel.paintAlignment(true);
5218             }
5219           }
5220         }
5221         if (filesnotmatched.size() > 0)
5222         {
5223           if (assocfiles > 0
5224                   && (Cache.getDefault(
5225                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5226                           .showConfirmDialog(
5227                                   this,
5228                                   "<html>"
5229                                           + MessageManager
5230                                                   .formatMessage(
5231                                                           "label.ignore_unmatched_dropped_files_info",
5232                                                           new Object[] { Integer
5233                                                                   .valueOf(
5234                                                                           filesnotmatched
5235                                                                                   .size())
5236                                                                   .toString() })
5237                                           + "</html>",
5238                                   MessageManager
5239                                           .getString("label.ignore_unmatched_dropped_files"),
5240                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5241           {
5242             return;
5243           }
5244           for (String fn : filesnotmatched)
5245           {
5246             loadJalviewDataFile(fn, null, null, null);
5247           }
5248
5249         }
5250       } catch (Exception ex)
5251       {
5252         ex.printStackTrace();
5253       }
5254     }
5255   }
5256
5257   /**
5258    * Attempt to load a "dropped" file or URL string: First by testing whether
5259    * it's an Annotation file, then a JNet file, and finally a features file. If
5260    * all are false then the user may have dropped an alignment file onto this
5261    * AlignFrame.
5262    *
5263    * @param file
5264    *          either a filename or a URL string.
5265    */
5266   public void loadJalviewDataFile(String file, String protocol,
5267           String format, SequenceI assocSeq)
5268   {
5269     try
5270     {
5271       if (protocol == null)
5272       {
5273         protocol = FormatAdapter.checkProtocol(file);
5274       }
5275       // if the file isn't identified, or not positively identified as some
5276       // other filetype (PFAM is default unidentified alignment file type) then
5277       // try to parse as annotation.
5278       boolean isAnnotation = (format == null || format
5279               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5280               .annotateAlignmentView(viewport, file, protocol) : false;
5281
5282       if (!isAnnotation)
5283       {
5284         // first see if its a T-COFFEE score file
5285         TCoffeeScoreFile tcf = null;
5286         try
5287         {
5288           tcf = new TCoffeeScoreFile(file, protocol);
5289           if (tcf.isValid())
5290           {
5291             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5292             {
5293               tcoffeeColour.setEnabled(true);
5294               tcoffeeColour.setSelected(true);
5295               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5296               isAnnotation = true;
5297               statusBar
5298                       .setText(MessageManager
5299                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5300             }
5301             else
5302             {
5303               // some problem - if no warning its probable that the ID matching
5304               // process didn't work
5305               JOptionPane
5306                       .showMessageDialog(
5307                               Desktop.desktop,
5308                               tcf.getWarningMessage() == null ? MessageManager
5309                                       .getString("label.check_file_matches_sequence_ids_alignment")
5310                                       : tcf.getWarningMessage(),
5311                               MessageManager
5312                                       .getString("label.problem_reading_tcoffee_score_file"),
5313                               JOptionPane.WARNING_MESSAGE);
5314             }
5315           }
5316           else
5317           {
5318             tcf = null;
5319           }
5320         } catch (Exception x)
5321         {
5322           Cache.log
5323                   .debug("Exception when processing data source as T-COFFEE score file",
5324                           x);
5325           tcf = null;
5326         }
5327         if (tcf == null)
5328         {
5329           // try to see if its a JNet 'concise' style annotation file *before*
5330           // we
5331           // try to parse it as a features file
5332           if (format == null)
5333           {
5334             format = new IdentifyFile().identify(file, protocol);
5335           }
5336           if (format.equalsIgnoreCase("JnetFile"))
5337           {
5338             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5339                     file, protocol);
5340             new JnetAnnotationMaker();
5341             JnetAnnotationMaker.add_annotation(predictions,
5342                     viewport.getAlignment(), 0, false);
5343             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5344             viewport.getAlignment().setSeqrep(repseq);
5345             ColumnSelection cs = new ColumnSelection();
5346             cs.hideInsertionsFor(repseq);
5347             viewport.setColumnSelection(cs);
5348             isAnnotation = true;
5349           }
5350           else if (IdentifyFile.FeaturesFile.equals(format))
5351           {
5352             if (parseFeaturesFile(file, protocol))
5353             {
5354               alignPanel.paintAlignment(true);
5355             }
5356           }
5357           else
5358           {
5359             new FileLoader().LoadFile(viewport, file, protocol, format);
5360           }
5361         }
5362       }
5363       if (isAnnotation)
5364       {
5365
5366         alignPanel.adjustAnnotationHeight();
5367         viewport.updateSequenceIdColours();
5368         buildSortByAnnotationScoresMenu();
5369         alignPanel.paintAlignment(true);
5370       }
5371     } catch (Exception ex)
5372     {
5373       ex.printStackTrace();
5374     } catch (OutOfMemoryError oom)
5375     {
5376       try
5377       {
5378         System.gc();
5379       } catch (Exception x)
5380       {
5381       }
5382       new OOMWarning(
5383               "loading data "
5384                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5385                               : "using " + protocol + " from " + file)
5386                               : ".")
5387                       + (format != null ? "(parsing as '" + format
5388                               + "' file)" : ""), oom, Desktop.desktop);
5389     }
5390   }
5391
5392   /**
5393    * Method invoked by the ChangeListener on the tabbed pane, in other words
5394    * when a different tabbed pane is selected by the user or programmatically.
5395    */
5396   @Override
5397   public void tabSelectionChanged(int index)
5398   {
5399     if (index > -1)
5400     {
5401       alignPanel = alignPanels.get(index);
5402       viewport = alignPanel.av;
5403       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5404       setMenusFromViewport(viewport);
5405     }
5406
5407     /*
5408      * If there is a frame linked to this one in a SplitPane, switch it to the
5409      * same view tab index. No infinite recursion of calls should happen, since
5410      * tabSelectionChanged() should not get invoked on setting the selected
5411      * index to an unchanged value. Guard against setting an invalid index
5412      * before the new view peer tab has been created.
5413      */
5414     final AlignViewportI peer = viewport.getCodingComplement();
5415     if (peer != null)
5416     {
5417       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5418       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5419       {
5420         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5421       }
5422     }
5423   }
5424
5425   /**
5426    * On right mouse click on view tab, prompt for and set new view name.
5427    */
5428   @Override
5429   public void tabbedPane_mousePressed(MouseEvent e)
5430   {
5431     if (SwingUtilities.isRightMouseButton(e))
5432     {
5433       String msg = MessageManager.getString("label.enter_view_name");
5434       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5435               JOptionPane.QUESTION_MESSAGE);
5436
5437       if (reply != null)
5438       {
5439         viewport.viewName = reply;
5440         // TODO warn if reply is in getExistingViewNames()?
5441         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5442       }
5443     }
5444   }
5445
5446   public AlignViewport getCurrentView()
5447   {
5448     return viewport;
5449   }
5450
5451   /**
5452    * Open the dialog for regex description parsing.
5453    */
5454   @Override
5455   protected void extractScores_actionPerformed(ActionEvent e)
5456   {
5457     ParseProperties pp = new jalview.analysis.ParseProperties(
5458             viewport.getAlignment());
5459     // TODO: verify regex and introduce GUI dialog for version 2.5
5460     // if (pp.getScoresFromDescription("col", "score column ",
5461     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5462     // true)>0)
5463     if (pp.getScoresFromDescription("description column",
5464             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5465     {
5466       buildSortByAnnotationScoresMenu();
5467     }
5468   }
5469
5470   /*
5471    * (non-Javadoc)
5472    *
5473    * @see
5474    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5475    * )
5476    */
5477   @Override
5478   protected void showDbRefs_actionPerformed(ActionEvent e)
5479   {
5480     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5481   }
5482
5483   /*
5484    * (non-Javadoc)
5485    *
5486    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5487    * ActionEvent)
5488    */
5489   @Override
5490   protected void showNpFeats_actionPerformed(ActionEvent e)
5491   {
5492     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5493   }
5494
5495   /**
5496    * find the viewport amongst the tabs in this alignment frame and close that
5497    * tab
5498    *
5499    * @param av
5500    */
5501   public boolean closeView(AlignViewportI av)
5502   {
5503     if (viewport == av)
5504     {
5505       this.closeMenuItem_actionPerformed(false);
5506       return true;
5507     }
5508     Component[] comp = tabbedPane.getComponents();
5509     for (int i = 0; comp != null && i < comp.length; i++)
5510     {
5511       if (comp[i] instanceof AlignmentPanel)
5512       {
5513         if (((AlignmentPanel) comp[i]).av == av)
5514         {
5515           // close the view.
5516           closeView((AlignmentPanel) comp[i]);
5517           return true;
5518         }
5519       }
5520     }
5521     return false;
5522   }
5523
5524   protected void build_fetchdbmenu(JMenu webService)
5525   {
5526     // Temporary hack - DBRef Fetcher always top level ws entry.
5527     // TODO We probably want to store a sequence database checklist in
5528     // preferences and have checkboxes.. rather than individual sources selected
5529     // here
5530     final JMenu rfetch = new JMenu(
5531             MessageManager.getString("action.fetch_db_references"));
5532     rfetch.setToolTipText(MessageManager
5533             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5534     webService.add(rfetch);
5535
5536     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5537             MessageManager.getString("option.trim_retrieved_seqs"));
5538     trimrs.setToolTipText(MessageManager
5539             .getString("label.trim_retrieved_sequences"));
5540     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5541     trimrs.addActionListener(new ActionListener()
5542     {
5543       @Override
5544       public void actionPerformed(ActionEvent e)
5545       {
5546         trimrs.setSelected(trimrs.isSelected());
5547         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5548                 Boolean.valueOf(trimrs.isSelected()).toString());
5549       };
5550     });
5551     rfetch.add(trimrs);
5552     JMenuItem fetchr = new JMenuItem(
5553             MessageManager.getString("label.standard_databases"));
5554     fetchr.setToolTipText(MessageManager
5555             .getString("label.fetch_embl_uniprot"));
5556     fetchr.addActionListener(new ActionListener()
5557     {
5558
5559       @Override
5560       public void actionPerformed(ActionEvent e)
5561       {
5562         new Thread(new Runnable()
5563         {
5564           @Override
5565           public void run()
5566           {
5567             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5568                     .getAlignment().isNucleotide();
5569             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5570                     .getSequenceSelection(), alignPanel.alignFrame, null,
5571                     alignPanel.alignFrame.featureSettings, isNucleotide);
5572             dbRefFetcher.addListener(new FetchFinishedListenerI()
5573             {
5574               @Override
5575               public void finished()
5576               {
5577                 AlignFrame.this.setMenusForViewport();
5578               }
5579             });
5580             dbRefFetcher
5581                     .fetchDBRefs(false);
5582           }
5583         }).start();
5584
5585       }
5586
5587     });
5588     rfetch.add(fetchr);
5589     final AlignFrame me = this;
5590     new Thread(new Runnable()
5591     {
5592       @Override
5593       public void run()
5594       {
5595         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5596                 .getSequenceFetcherSingleton(me);
5597         javax.swing.SwingUtilities.invokeLater(new Runnable()
5598         {
5599           @Override
5600           public void run()
5601           {
5602             String[] dbclasses = sf.getOrderedSupportedSources();
5603             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5604             // jalview.util.QuickSort.sort(otherdb, otherdb);
5605             List<DbSourceProxy> otherdb;
5606             JMenu dfetch = new JMenu();
5607             JMenu ifetch = new JMenu();
5608             JMenuItem fetchr = null;
5609             int comp = 0, icomp = 0, mcomp = 15;
5610             String mname = null;
5611             int dbi = 0;
5612             for (String dbclass : dbclasses)
5613             {
5614               otherdb = sf.getSourceProxy(dbclass);
5615               // add a single entry for this class, or submenu allowing 'fetch
5616               // all' or pick one
5617               if (otherdb == null || otherdb.size() < 1)
5618               {
5619                 continue;
5620               }
5621               // List<DbSourceProxy> dbs=otherdb;
5622               // otherdb=new ArrayList<DbSourceProxy>();
5623               // for (DbSourceProxy db:dbs)
5624               // {
5625               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5626               // }
5627               if (mname == null)
5628               {
5629                 mname = "From " + dbclass;
5630               }
5631               if (otherdb.size() == 1)
5632               {
5633                 final DbSourceProxy[] dassource = otherdb
5634                         .toArray(new DbSourceProxy[0]);
5635                 DbSourceProxy src = otherdb.get(0);
5636                 fetchr = new JMenuItem(src.getDbSource());
5637                 fetchr.addActionListener(new ActionListener()
5638                 {
5639
5640                   @Override
5641                   public void actionPerformed(ActionEvent e)
5642                   {
5643                     new Thread(new Runnable()
5644                     {
5645
5646                       @Override
5647                       public void run()
5648                       {
5649                         boolean isNucleotide = alignPanel.alignFrame
5650                                 .getViewport().getAlignment()
5651                                 .isNucleotide();
5652                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5653                                 alignPanel.av.getSequenceSelection(),
5654                                 alignPanel.alignFrame, dassource,
5655                                 alignPanel.alignFrame.featureSettings,
5656                                 isNucleotide);
5657                         dbRefFetcher
5658                                 .addListener(new FetchFinishedListenerI()
5659                                 {
5660                                   @Override
5661                                   public void finished()
5662                                   {
5663                                     AlignFrame.this.setMenusForViewport();
5664                                   }
5665                                 });
5666                         dbRefFetcher.fetchDBRefs(false);
5667                       }
5668                     }).start();
5669                   }
5670
5671                 });
5672                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5673                         MessageManager.formatMessage(
5674                                 "label.fetch_retrieve_from",
5675                                 new Object[] { src.getDbName() })));
5676                 dfetch.add(fetchr);
5677                 comp++;
5678               }
5679               else
5680               {
5681                 final DbSourceProxy[] dassource = otherdb
5682                         .toArray(new DbSourceProxy[0]);
5683                 // fetch all entry
5684                 DbSourceProxy src = otherdb.get(0);
5685                 fetchr = new JMenuItem(MessageManager.formatMessage(
5686                         "label.fetch_all_param",
5687                         new Object[] { src.getDbSource() }));
5688                 fetchr.addActionListener(new ActionListener()
5689                 {
5690                   @Override
5691                   public void actionPerformed(ActionEvent e)
5692                   {
5693                     new Thread(new Runnable()
5694                     {
5695
5696                       @Override
5697                       public void run()
5698                       {
5699                         boolean isNucleotide = alignPanel.alignFrame
5700                                 .getViewport().getAlignment()
5701                                 .isNucleotide();
5702                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5703                                 alignPanel.av.getSequenceSelection(),
5704                                 alignPanel.alignFrame, dassource,
5705                                 alignPanel.alignFrame.featureSettings,
5706                                 isNucleotide);
5707                         dbRefFetcher
5708                                 .addListener(new FetchFinishedListenerI()
5709                                 {
5710                                   @Override
5711                                   public void finished()
5712                                   {
5713                                     AlignFrame.this.setMenusForViewport();
5714                                   }
5715                                 });
5716                         dbRefFetcher.fetchDBRefs(false);
5717                       }
5718                     }).start();
5719                   }
5720                 });
5721
5722                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5723                         MessageManager.formatMessage(
5724                                 "label.fetch_retrieve_from_all_sources",
5725                                 new Object[] {
5726                                     Integer.valueOf(otherdb.size())
5727                                             .toString(), src.getDbSource(),
5728                                     src.getDbName() })));
5729                 dfetch.add(fetchr);
5730                 comp++;
5731                 // and then build the rest of the individual menus
5732                 ifetch = new JMenu(MessageManager.formatMessage(
5733                         "label.source_from_db_source",
5734                         new Object[] { src.getDbSource() }));
5735                 icomp = 0;
5736                 String imname = null;
5737                 int i = 0;
5738                 for (DbSourceProxy sproxy : otherdb)
5739                 {
5740                   String dbname = sproxy.getDbName();
5741                   String sname = dbname.length() > 5 ? dbname.substring(0,
5742                           5) + "..." : dbname;
5743                   String msname = dbname.length() > 10 ? dbname.substring(
5744                           0, 10) + "..." : dbname;
5745                   if (imname == null)
5746                   {
5747                     imname = MessageManager.formatMessage(
5748                             "label.from_msname", new Object[] { sname });
5749                   }
5750                   fetchr = new JMenuItem(msname);
5751                   final DbSourceProxy[] dassrc = { sproxy };
5752                   fetchr.addActionListener(new ActionListener()
5753                   {
5754
5755                     @Override
5756                     public void actionPerformed(ActionEvent e)
5757                     {
5758                       new Thread(new Runnable()
5759                       {
5760
5761                         @Override
5762                         public void run()
5763                         {
5764                           boolean isNucleotide = alignPanel.alignFrame
5765                                   .getViewport().getAlignment()
5766                                   .isNucleotide();
5767                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5768                                   alignPanel.av.getSequenceSelection(),
5769                                   alignPanel.alignFrame, dassrc,
5770                                   alignPanel.alignFrame.featureSettings,
5771                                   isNucleotide);
5772                           dbRefFetcher
5773                                   .addListener(new FetchFinishedListenerI()
5774                                   {
5775                                     @Override
5776                                     public void finished()
5777                                     {
5778                                       AlignFrame.this.setMenusForViewport();
5779                                     }
5780                                   });
5781                           dbRefFetcher.fetchDBRefs(false);
5782                         }
5783                       }).start();
5784                     }
5785
5786                   });
5787                   fetchr.setToolTipText("<html>"
5788                           + MessageManager.formatMessage(
5789                                   "label.fetch_retrieve_from", new Object[]
5790                                   { dbname }));
5791                   ifetch.add(fetchr);
5792                   ++i;
5793                   if (++icomp >= mcomp || i == (otherdb.size()))
5794                   {
5795                     ifetch.setText(MessageManager.formatMessage(
5796                             "label.source_to_target", imname, sname));
5797                     dfetch.add(ifetch);
5798                     ifetch = new JMenu();
5799                     imname = null;
5800                     icomp = 0;
5801                     comp++;
5802                   }
5803                 }
5804               }
5805               ++dbi;
5806               if (comp >= mcomp || dbi >= (dbclasses.length))
5807               {
5808                 dfetch.setText(MessageManager.formatMessage(
5809                         "label.source_to_target", mname, dbclass));
5810                 rfetch.add(dfetch);
5811                 dfetch = new JMenu();
5812                 mname = null;
5813                 comp = 0;
5814               }
5815             }
5816           }
5817         });
5818       }
5819     }).start();
5820
5821   }
5822
5823   /**
5824    * Left justify the whole alignment.
5825    */
5826   @Override
5827   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5828   {
5829     AlignmentI al = viewport.getAlignment();
5830     al.justify(false);
5831     viewport.firePropertyChange("alignment", null, al);
5832   }
5833
5834   /**
5835    * Right justify the whole alignment.
5836    */
5837   @Override
5838   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5839   {
5840     AlignmentI al = viewport.getAlignment();
5841     al.justify(true);
5842     viewport.firePropertyChange("alignment", null, al);
5843   }
5844
5845   @Override
5846   public void setShowSeqFeatures(boolean b)
5847   {
5848     showSeqFeatures.setSelected(b);
5849     viewport.setShowSequenceFeatures(b);
5850   }
5851
5852   /*
5853    * (non-Javadoc)
5854    *
5855    * @see
5856    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5857    * awt.event.ActionEvent)
5858    */
5859   @Override
5860   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5861   {
5862     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5863     alignPanel.paintAlignment(true);
5864   }
5865
5866   /*
5867    * (non-Javadoc)
5868    *
5869    * @see
5870    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5871    * .ActionEvent)
5872    */
5873   @Override
5874   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5875   {
5876     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5877     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5878
5879   }
5880
5881   /*
5882    * (non-Javadoc)
5883    *
5884    * @see
5885    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5886    * .event.ActionEvent)
5887    */
5888   @Override
5889   protected void showGroupConservation_actionPerformed(ActionEvent e)
5890   {
5891     viewport.setShowGroupConservation(showGroupConservation.getState());
5892     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5893   }
5894
5895   /*
5896    * (non-Javadoc)
5897    *
5898    * @see
5899    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5900    * .event.ActionEvent)
5901    */
5902   @Override
5903   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5904   {
5905     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5906     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5907   }
5908
5909   /*
5910    * (non-Javadoc)
5911    *
5912    * @see
5913    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5914    * .event.ActionEvent)
5915    */
5916   @Override
5917   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5918   {
5919     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5920     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5921   }
5922
5923   @Override
5924   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5925   {
5926     showSequenceLogo.setState(true);
5927     viewport.setShowSequenceLogo(true);
5928     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5929     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5930   }
5931
5932   @Override
5933   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5934   {
5935     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5936   }
5937
5938   /*
5939    * (non-Javadoc)
5940    *
5941    * @see
5942    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5943    * .event.ActionEvent)
5944    */
5945   @Override
5946   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5947   {
5948     if (avc.makeGroupsFromSelection())
5949     {
5950       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5951       alignPanel.updateAnnotation();
5952       alignPanel.paintAlignment(true);
5953     }
5954   }
5955
5956   public void clearAlignmentSeqRep()
5957   {
5958     // TODO refactor alignmentseqrep to controller
5959     if (viewport.getAlignment().hasSeqrep())
5960     {
5961       viewport.getAlignment().setSeqrep(null);
5962       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5963       alignPanel.updateAnnotation();
5964       alignPanel.paintAlignment(true);
5965     }
5966   }
5967
5968   @Override
5969   protected void createGroup_actionPerformed(ActionEvent e)
5970   {
5971     if (avc.createGroup())
5972     {
5973       alignPanel.alignmentChanged();
5974     }
5975   }
5976
5977   @Override
5978   protected void unGroup_actionPerformed(ActionEvent e)
5979   {
5980     if (avc.unGroup())
5981     {
5982       alignPanel.alignmentChanged();
5983     }
5984   }
5985
5986   /**
5987    * make the given alignmentPanel the currently selected tab
5988    *
5989    * @param alignmentPanel
5990    */
5991   public void setDisplayedView(AlignmentPanel alignmentPanel)
5992   {
5993     if (!viewport.getSequenceSetId().equals(
5994             alignmentPanel.av.getSequenceSetId()))
5995     {
5996       throw new Error(
5997               MessageManager
5998                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5999     }
6000     if (tabbedPane != null
6001             && tabbedPane.getTabCount() > 0
6002             && alignPanels.indexOf(alignmentPanel) != tabbedPane
6003                     .getSelectedIndex())
6004     {
6005       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
6006     }
6007   }
6008
6009   /**
6010    * Action on selection of menu options to Show or Hide annotations.
6011    *
6012    * @param visible
6013    * @param forSequences
6014    *          update sequence-related annotations
6015    * @param forAlignment
6016    *          update non-sequence-related annotations
6017    */
6018   @Override
6019   protected void setAnnotationsVisibility(boolean visible,
6020           boolean forSequences, boolean forAlignment)
6021   {
6022     for (AlignmentAnnotation aa : alignPanel.getAlignment()
6023             .getAlignmentAnnotation())
6024     {
6025       /*
6026        * don't display non-positional annotations on an alignment
6027        */
6028       if (aa.annotations == null)
6029       {
6030         continue;
6031       }
6032       boolean apply = (aa.sequenceRef == null && forAlignment)
6033               || (aa.sequenceRef != null && forSequences);
6034       if (apply)
6035       {
6036         aa.visible = visible;
6037       }
6038     }
6039     alignPanel.validateAnnotationDimensions(true);
6040     alignPanel.alignmentChanged();
6041   }
6042
6043   /**
6044    * Store selected annotation sort order for the view and repaint.
6045    */
6046   @Override
6047   protected void sortAnnotations_actionPerformed()
6048   {
6049     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6050     this.alignPanel.av
6051             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6052     alignPanel.paintAlignment(true);
6053   }
6054
6055   /**
6056    *
6057    * @return alignment panels in this alignment frame
6058    */
6059   public List<? extends AlignmentViewPanel> getAlignPanels()
6060   {
6061     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6062   }
6063
6064   /**
6065    * Open a new alignment window, with the cDNA associated with this (protein)
6066    * alignment, aligned as is the protein.
6067    */
6068   protected void viewAsCdna_actionPerformed()
6069   {
6070     // TODO no longer a menu action - refactor as required
6071     final AlignmentI alignment = getViewport().getAlignment();
6072     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6073     if (mappings == null)
6074     {
6075       return;
6076     }
6077     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6078     for (SequenceI aaSeq : alignment.getSequences())
6079     {
6080       for (AlignedCodonFrame acf : mappings)
6081       {
6082         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6083         if (dnaSeq != null)
6084         {
6085           /*
6086            * There is a cDNA mapping for this protein sequence - add to new
6087            * alignment. It will share the same dataset sequence as other mapped
6088            * cDNA (no new mappings need to be created).
6089            */
6090           final Sequence newSeq = new Sequence(dnaSeq);
6091           newSeq.setDatasetSequence(dnaSeq);
6092           cdnaSeqs.add(newSeq);
6093         }
6094       }
6095     }
6096     if (cdnaSeqs.size() == 0)
6097     {
6098       // show a warning dialog no mapped cDNA
6099       return;
6100     }
6101     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6102             .size()]));
6103     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6104             AlignFrame.DEFAULT_HEIGHT);
6105     cdna.alignAs(alignment);
6106     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6107             + this.title;
6108     Desktop.addInternalFrame(alignFrame, newtitle,
6109             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6110   }
6111
6112   /**
6113    * Set visibility of dna/protein complement view (available when shown in a
6114    * split frame).
6115    *
6116    * @param show
6117    */
6118   @Override
6119   protected void showComplement_actionPerformed(boolean show)
6120   {
6121     SplitContainerI sf = getSplitViewContainer();
6122     if (sf != null)
6123     {
6124       sf.setComplementVisible(this, show);
6125     }
6126   }
6127
6128   /**
6129    * Generate the reverse (optionally complemented) of the selected sequences,
6130    * and add them to the alignment
6131    */
6132   @Override
6133   protected void showReverse_actionPerformed(boolean complement)
6134   {
6135     AlignmentI al = null;
6136     try
6137     {
6138       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6139
6140       al = dna.reverseCdna(complement);
6141       viewport.addAlignment(al, "");
6142     } catch (Exception ex)
6143     {
6144       System.err.println(ex.getMessage());
6145       return;
6146     }
6147   }
6148 }
6149
6150 class PrintThread extends Thread
6151 {
6152   AlignmentPanel ap;
6153
6154   public PrintThread(AlignmentPanel ap)
6155   {
6156     this.ap = ap;
6157   }
6158
6159   static PageFormat pf;
6160
6161   @Override
6162   public void run()
6163   {
6164     PrinterJob printJob = PrinterJob.getPrinterJob();
6165
6166     if (pf != null)
6167     {
6168       printJob.setPrintable(ap, pf);
6169     }
6170     else
6171     {
6172       printJob.setPrintable(ap);
6173     }
6174
6175     if (printJob.printDialog())
6176     {
6177       try
6178       {
6179         printJob.print();
6180       } catch (Exception PrintException)
6181       {
6182         PrintException.printStackTrace();
6183       }
6184     }
6185   }
6186 }