src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  64 import jalview.io.AlignmentProperties;
  65 import jalview.io.AnnotationFile;
  66 import jalview.io.BioJsHTMLOutput;
  67 import jalview.io.DataSourceType;
  68 import jalview.io.FileFormat;
  69 import jalview.io.FileFormatI;
  70 import jalview.io.FileFormats;
  71 import jalview.io.FileLoader;
  72 import jalview.io.FileParse;
  73 import jalview.io.FormatAdapter;
  74 import jalview.io.HtmlSvgOutput;
  75 import jalview.io.IdentifyFile;
  76 import jalview.io.JPredFile;
  77 import jalview.io.JalviewFileChooser;
  78 import jalview.io.JalviewFileView;
  79 import jalview.io.JnetAnnotationMaker;
  80 import jalview.io.NewickFile;
  81 import jalview.io.ScoreMatrixFile;
  82 import jalview.io.TCoffeeScoreFile;
  83 import jalview.jbgui.GAlignFrame;
  84 import jalview.schemes.ColourSchemeI;
  85 import jalview.schemes.ColourSchemes;
  86 import jalview.schemes.ResidueColourScheme;
  87 import jalview.schemes.TCoffeeColourScheme;
  88 import jalview.util.MessageManager;
  89 import jalview.viewmodel.AlignmentViewport;
  90 import jalview.viewmodel.ViewportRanges;
  91 import jalview.ws.DBRefFetcher;
  92 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  93 import jalview.ws.jws1.Discoverer;
  94 import jalview.ws.jws2.Jws2Discoverer;
  95 import jalview.ws.jws2.jabaws2.Jws2Instance;
  96 import jalview.ws.seqfetcher.DbSourceProxy;
  97
  98 import java.awt.BorderLayout;
  99 import java.awt.Component;
 100 import java.awt.Rectangle;
 101 import java.awt.Toolkit;
 102 import java.awt.datatransfer.Clipboard;
 103 import java.awt.datatransfer.DataFlavor;
 104 import java.awt.datatransfer.StringSelection;
 105 import java.awt.datatransfer.Transferable;
 106 import java.awt.dnd.DnDConstants;
 107 import java.awt.dnd.DropTargetDragEvent;
 108 import java.awt.dnd.DropTargetDropEvent;
 109 import java.awt.dnd.DropTargetEvent;
 110 import java.awt.dnd.DropTargetListener;
 111 import java.awt.event.ActionEvent;
 112 import java.awt.event.ActionListener;
 113 import java.awt.event.FocusAdapter;
 114 import java.awt.event.FocusEvent;
 115 import java.awt.event.ItemEvent;
 116 import java.awt.event.ItemListener;
 117 import java.awt.event.KeyAdapter;
 118 import java.awt.event.KeyEvent;
 119 import java.awt.event.MouseEvent;
 120 import java.awt.print.PageFormat;
 121 import java.awt.print.PrinterJob;
 122 import java.beans.PropertyChangeEvent;
 123 import java.io.File;
 124 import java.io.FileWriter;
 125 import java.io.PrintWriter;
 126 import java.net.URL;
 127 import java.util.ArrayList;
 128 import java.util.Arrays;
 129 import java.util.Deque;
 130 import java.util.Enumeration;
 131 import java.util.Hashtable;
 132 import java.util.List;
 133 import java.util.Vector;
 134
 135 import javax.swing.JCheckBoxMenuItem;
 136 import javax.swing.JEditorPane;
 137 import javax.swing.JInternalFrame;
 138 import javax.swing.JLayeredPane;
 139 import javax.swing.JMenu;
 140 import javax.swing.JMenuItem;
 141 import javax.swing.JScrollPane;
 142 import javax.swing.SwingUtilities;
 143
 144 /**
 145  * DOCUMENT ME!
 146  *
 147  * @author $author$
 148  * @version $Revision$
 149  */
 150 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 151         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 152 {
 153
 154   public static final int DEFAULT_WIDTH = 700;
 155
 156   public static final int DEFAULT_HEIGHT = 500;
 157
 158   /*
 159    * The currently displayed panel (selected tabbed view if more than one)
 160    */
 161   public AlignmentPanel alignPanel;
 162
 163   AlignViewport viewport;
 164
 165   ViewportRanges vpRanges;
 166
 167   public AlignViewControllerI avc;
 168
 169   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 170
 171   /**
 172    * Last format used to load or save alignments in this window
 173    */
 174   FileFormatI currentFileFormat = null;
 175
 176   /**
 177    * Current filename for this alignment
 178    */
 179   String fileName = null;
 180
 181   /**
 182    * Creates a new AlignFrame object with specific width and height.
 183    *
 184    * @param al
 185    * @param width
 186    * @param height
 187    */
 188   public AlignFrame(AlignmentI al, int width, int height)
 189   {
 190     this(al, null, width, height);
 191   }
 192
 193   /**
 194    * Creates a new AlignFrame object with specific width, height and
 195    * sequenceSetId
 196    *
 197    * @param al
 198    * @param width
 199    * @param height
 200    * @param sequenceSetId
 201    */
 202   public AlignFrame(AlignmentI al, int width, int height,
 203           String sequenceSetId)
 204   {
 205     this(al, null, width, height, sequenceSetId);
 206   }
 207
 208   /**
 209    * Creates a new AlignFrame object with specific width, height and
 210    * sequenceSetId
 211    *
 212    * @param al
 213    * @param width
 214    * @param height
 215    * @param sequenceSetId
 216    * @param viewId
 217    */
 218   public AlignFrame(AlignmentI al, int width, int height,
 219           String sequenceSetId, String viewId)
 220   {
 221     this(al, null, width, height, sequenceSetId, viewId);
 222   }
 223
 224   /**
 225    * new alignment window with hidden columns
 226    *
 227    * @param al
 228    *          AlignmentI
 229    * @param hiddenColumns
 230    *          ColumnSelection or null
 231    * @param width
 232    *          Width of alignment frame
 233    * @param height
 234    *          height of frame.
 235    */
 236   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 237           int width, int height)
 238   {
 239     this(al, hiddenColumns, width, height, null);
 240   }
 241
 242   /**
 243    * Create alignment frame for al with hiddenColumns, a specific width and
 244    * height, and specific sequenceId
 245    *
 246    * @param al
 247    * @param hiddenColumns
 248    * @param width
 249    * @param height
 250    * @param sequenceSetId
 251    *          (may be null)
 252    */
 253   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 254           int width, int height, String sequenceSetId)
 255   {
 256     this(al, hiddenColumns, width, height, sequenceSetId, null);
 257   }
 258
 259   /**
 260    * Create alignment frame for al with hiddenColumns, a specific width and
 261    * height, and specific sequenceId
 262    *
 263    * @param al
 264    * @param hiddenColumns
 265    * @param width
 266    * @param height
 267    * @param sequenceSetId
 268    *          (may be null)
 269    * @param viewId
 270    *          (may be null)
 271    */
 272   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 273           int width, int height, String sequenceSetId, String viewId)
 274   {
 275     setSize(width, height);
 276
 277     if (al.getDataset() == null)
 278     {
 279       al.setDataset(null);
 280     }
 281
 282     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 283
 284     alignPanel = new AlignmentPanel(this, viewport);
 285
 286     addAlignmentPanel(alignPanel, true);
 287     init();
 288   }
 289
 290   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 291           ColumnSelection hiddenColumns, int width, int height)
 292   {
 293     setSize(width, height);
 294
 295     if (al.getDataset() == null)
 296     {
 297       al.setDataset(null);
 298     }
 299
 300     viewport = new AlignViewport(al, hiddenColumns);
 301
 302     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 303     {
 304       viewport.hideSequence(hiddenSeqs);
 305     }
 306     alignPanel = new AlignmentPanel(this, viewport);
 307     addAlignmentPanel(alignPanel, true);
 308     init();
 309   }
 310
 311   /**
 312    * Make a new AlignFrame from existing alignmentPanels
 313    *
 314    * @param ap
 315    *          AlignmentPanel
 316    * @param av
 317    *          AlignViewport
 318    */
 319   public AlignFrame(AlignmentPanel ap)
 320   {
 321     viewport = ap.av;
 322     alignPanel = ap;
 323     addAlignmentPanel(ap, false);
 324     init();
 325   }
 326
 327   /**
 328    * initalise the alignframe from the underlying viewport data and the
 329    * configurations
 330    */
 331   void init()
 332   {
 333     if (!Jalview.isHeadlessMode())
 334     {
 335       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 336     }
 337
 338     vpRanges = viewport.getRanges();
 339     avc = new jalview.controller.AlignViewController(this, viewport,
 340             alignPanel);
 341     if (viewport.getAlignmentConservationAnnotation() == null)
 342     {
 343       // BLOSUM62Colour.setEnabled(false);
 344       conservationMenuItem.setEnabled(false);
 345       modifyConservation.setEnabled(false);
 346       // PIDColour.setEnabled(false);
 347       // abovePIDThreshold.setEnabled(false);
 348       // modifyPID.setEnabled(false);
 349     }
 350
 351     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 352             "No sort");
 353
 354     if (sortby.equals("Id"))
 355     {
 356       sortIDMenuItem_actionPerformed(null);
 357     }
 358     else if (sortby.equals("Pairwise Identity"))
 359     {
 360       sortPairwiseMenuItem_actionPerformed(null);
 361     }
 362
 363     this.alignPanel.av
 364             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 365
 366     setMenusFromViewport(viewport);
 367     buildSortByAnnotationScoresMenu();
 368     calculateTree.addActionListener(new ActionListener()
 369     {
 370
 371       @Override
 372       public void actionPerformed(ActionEvent e)
 373       {
 374         openTreePcaDialog();
 375       }
 376     });
 377     buildColourMenu();
 378
 379     if (Desktop.desktop != null)
 380     {
 381       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 382       addServiceListeners();
 383       setGUINucleotide();
 384     }
 385
 386     if (viewport.getWrapAlignment())
 387     {
 388       wrapMenuItem_actionPerformed(null);
 389     }
 390
 391     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 392     {
 393       this.overviewMenuItem_actionPerformed(null);
 394     }
 395
 396     addKeyListener();
 397
 398     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 399     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 400     final String menuLabel = MessageManager
 401             .getString("label.copy_format_from");
 402     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 403             new ViewSetProvider()
 404             {
 405
 406               @Override
 407               public AlignmentPanel[] getAllAlignmentPanels()
 408               {
 409                 origview.clear();
 410                 origview.add(alignPanel);
 411                 // make an array of all alignment panels except for this one
 412                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 413                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 414                 aps.remove(AlignFrame.this.alignPanel);
 415                 return aps.toArray(new AlignmentPanel[aps.size()]);
 416               }
 417             }, selviews, new ItemListener()
 418             {
 419
 420               @Override
 421               public void itemStateChanged(ItemEvent e)
 422               {
 423                 if (origview.size() > 0)
 424                 {
 425                   final AlignmentPanel ap = origview.get(0);
 426
 427                   /*
 428                    * Copy the ViewStyle of the selected panel to 'this one'.
 429                    * Don't change value of 'scaleProteinAsCdna' unless copying
 430                    * from a SplitFrame.
 431                    */
 432                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 433                           .getViewStyle();
 434                   boolean fromSplitFrame = selviews.get(0)
 435                           .getAlignViewport().getCodingComplement() != null;
 436                   if (!fromSplitFrame)
 437                   {
 438                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 439                             .getViewStyle().isScaleProteinAsCdna());
 440                   }
 441                   ap.getAlignViewport().setViewStyle(vs);
 442
 443                   /*
 444                    * Also rescale ViewStyle of SplitFrame complement if there is
 445                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 446                    * the whole ViewStyle (allow cDNA protein to have different
 447                    * fonts)
 448                    */
 449                   AlignViewportI complement = ap.getAlignViewport()
 450                           .getCodingComplement();
 451                   if (complement != null && vs.isScaleProteinAsCdna())
 452                   {
 453                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 454                     ((SplitFrame) af.getSplitViewContainer())
 455                             .adjustLayout();
 456                     af.setMenusForViewport();
 457                   }
 458
 459                   ap.updateLayout();
 460                   ap.setSelected(true);
 461                   ap.alignFrame.setMenusForViewport();
 462
 463                 }
 464               }
 465             });
 466     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 467             .indexOf("devel") > -1
 468             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 469                     .indexOf("test") > -1)
 470     {
 471       formatMenu.add(vsel);
 472     }
 473     addFocusListener(new FocusAdapter()
 474     {
 475       @Override
 476       public void focusGained(FocusEvent e)
 477       {
 478         Jalview.setCurrentAlignFrame(AlignFrame.this);
 479       }
 480     });
 481
 482   }
 483
 484   /**
 485    * Change the filename and format for the alignment, and enable the 'reload'
 486    * button functionality.
 487    *
 488    * @param file
 489    *          valid filename
 490    * @param format
 491    *          format of file
 492    */
 493   public void setFileName(String file, FileFormatI format)
 494   {
 495     fileName = file;
 496     setFileFormat(format);
 497     reload.setEnabled(true);
 498   }
 499
 500   /**
 501    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 502    * events
 503    */
 504   void addKeyListener()
 505   {
 506     addKeyListener(new KeyAdapter()
 507     {
 508       @Override
 509       public void keyPressed(KeyEvent evt)
 510       {
 511         if (viewport.cursorMode
 512                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 513                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 514                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 515                 && Character.isDigit(evt.getKeyChar()))
 516         {
 517           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 518         }
 519
 520         switch (evt.getKeyCode())
 521         {
 522
 523         case 27: // escape key
 524           deselectAllSequenceMenuItem_actionPerformed(null);
 525
 526           break;
 527
 528         case KeyEvent.VK_DOWN:
 529           if (evt.isAltDown() || !viewport.cursorMode)
 530           {
 531             moveSelectedSequences(false);
 532           }
 533           if (viewport.cursorMode)
 534           {
 535             alignPanel.getSeqPanel().moveCursor(0, 1);
 536           }
 537           break;
 538
 539         case KeyEvent.VK_UP:
 540           if (evt.isAltDown() || !viewport.cursorMode)
 541           {
 542             moveSelectedSequences(true);
 543           }
 544           if (viewport.cursorMode)
 545           {
 546             alignPanel.getSeqPanel().moveCursor(0, -1);
 547           }
 548
 549           break;
 550
 551         case KeyEvent.VK_LEFT:
 552           if (evt.isAltDown() || !viewport.cursorMode)
 553           {
 554             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 555           }
 556           else
 557           {
 558             alignPanel.getSeqPanel().moveCursor(-1, 0);
 559           }
 560
 561           break;
 562
 563         case KeyEvent.VK_RIGHT:
 564           if (evt.isAltDown() || !viewport.cursorMode)
 565           {
 566             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 567           }
 568           else
 569           {
 570             alignPanel.getSeqPanel().moveCursor(1, 0);
 571           }
 572           break;
 573
 574         case KeyEvent.VK_SPACE:
 575           if (viewport.cursorMode)
 576           {
 577             alignPanel.getSeqPanel().insertGapAtCursor(
 578                     evt.isControlDown() || evt.isShiftDown()
 579                             || evt.isAltDown());
 580           }
 581           break;
 582
 583         // case KeyEvent.VK_A:
 584         // if (viewport.cursorMode)
 585         // {
 586         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 587         // //System.out.println("A");
 588         // }
 589         // break;
 590         /*
 591          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 592          * System.out.println("closing bracket"); } break;
 593          */
 594         case KeyEvent.VK_DELETE:
 595         case KeyEvent.VK_BACK_SPACE:
 596           if (!viewport.cursorMode)
 597           {
 598             cut_actionPerformed(null);
 599           }
 600           else
 601           {
 602             alignPanel.getSeqPanel().deleteGapAtCursor(
 603                     evt.isControlDown() || evt.isShiftDown()
 604                             || evt.isAltDown());
 605           }
 606
 607           break;
 608
 609         case KeyEvent.VK_S:
 610           if (viewport.cursorMode)
 611           {
 612             alignPanel.getSeqPanel().setCursorRow();
 613           }
 614           break;
 615         case KeyEvent.VK_C:
 616           if (viewport.cursorMode && !evt.isControlDown())
 617           {
 618             alignPanel.getSeqPanel().setCursorColumn();
 619           }
 620           break;
 621         case KeyEvent.VK_P:
 622           if (viewport.cursorMode)
 623           {
 624             alignPanel.getSeqPanel().setCursorPosition();
 625           }
 626           break;
 627
 628         case KeyEvent.VK_ENTER:
 629         case KeyEvent.VK_COMMA:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().setCursorRowAndColumn();
 633           }
 634           break;
 635
 636         case KeyEvent.VK_Q:
 637           if (viewport.cursorMode)
 638           {
 639             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 640           }
 641           break;
 642         case KeyEvent.VK_M:
 643           if (viewport.cursorMode)
 644           {
 645             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 646           }
 647           break;
 648
 649         case KeyEvent.VK_F2:
 650           viewport.cursorMode = !viewport.cursorMode;
 651           statusBar.setText(MessageManager.formatMessage(
 652                   "label.keyboard_editing_mode",
 653                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 654           if (viewport.cursorMode)
 655           {
 656             alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
 657                     .getStartRes();
 658             alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
 659                     .getStartSeq();
 660           }
 661           alignPanel.getSeqPanel().seqCanvas.repaint();
 662           break;
 663
 664         case KeyEvent.VK_F1:
 665           try
 666           {
 667             Help.showHelpWindow();
 668           } catch (Exception ex)
 669           {
 670             ex.printStackTrace();
 671           }
 672           break;
 673         case KeyEvent.VK_H:
 674         {
 675           boolean toggleSeqs = !evt.isControlDown();
 676           boolean toggleCols = !evt.isShiftDown();
 677           toggleHiddenRegions(toggleSeqs, toggleCols);
 678           break;
 679         }
 680         case KeyEvent.VK_B:
 681         {
 682           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 683           boolean modifyExisting = true; // always modify, don't clear
 684                                          // evt.isShiftDown();
 685           boolean invertHighlighted = evt.isAltDown();
 686           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 687                   toggleSel);
 688           break;
 689         }
 690         case KeyEvent.VK_PAGE_UP:
 691           if (viewport.getWrapAlignment())
 692           {
 693             alignPanel.scrollUp(true);
 694           }
 695           else
 696           {
 697             alignPanel.setScrollValues(vpRanges.getStartRes(),
 698                     2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
 699           }
 700           break;
 701         case KeyEvent.VK_PAGE_DOWN:
 702           if (viewport.getWrapAlignment())
 703           {
 704             alignPanel.scrollUp(false);
 705           }
 706           else
 707           {
 708             alignPanel.setScrollValues(vpRanges.getStartRes(),
 709                     vpRanges.getEndSeq());
 710           }
 711           break;
 712         }
 713       }
 714
 715       @Override
 716       public void keyReleased(KeyEvent evt)
 717       {
 718         switch (evt.getKeyCode())
 719         {
 720         case KeyEvent.VK_LEFT:
 721           if (evt.isAltDown() || !viewport.cursorMode)
 722           {
 723             viewport.firePropertyChange("alignment", null, viewport
 724                     .getAlignment().getSequences());
 725           }
 726           break;
 727
 728         case KeyEvent.VK_RIGHT:
 729           if (evt.isAltDown() || !viewport.cursorMode)
 730           {
 731             viewport.firePropertyChange("alignment", null, viewport
 732                     .getAlignment().getSequences());
 733           }
 734           break;
 735         }
 736       }
 737     });
 738   }
 739
 740   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 741   {
 742     ap.alignFrame = this;
 743     avc = new jalview.controller.AlignViewController(this, viewport,
 744             alignPanel);
 745
 746     alignPanels.add(ap);
 747
 748     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 749
 750     int aSize = alignPanels.size();
 751
 752     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 753
 754     if (aSize == 1 && ap.av.viewName == null)
 755     {
 756       this.getContentPane().add(ap, BorderLayout.CENTER);
 757     }
 758     else
 759     {
 760       if (aSize == 2)
 761       {
 762         setInitialTabVisible();
 763       }
 764
 765       expandViews.setEnabled(true);
 766       gatherViews.setEnabled(true);
 767       tabbedPane.addTab(ap.av.viewName, ap);
 768
 769       ap.setVisible(false);
 770     }
 771
 772     if (newPanel)
 773     {
 774       if (ap.av.isPadGaps())
 775       {
 776         ap.av.getAlignment().padGaps();
 777       }
 778       ap.av.updateConservation(ap);
 779       ap.av.updateConsensus(ap);
 780       ap.av.updateStrucConsensus(ap);
 781     }
 782   }
 783
 784   public void setInitialTabVisible()
 785   {
 786     expandViews.setEnabled(true);
 787     gatherViews.setEnabled(true);
 788     tabbedPane.setVisible(true);
 789     AlignmentPanel first = alignPanels.get(0);
 790     tabbedPane.addTab(first.av.viewName, first);
 791     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 792   }
 793
 794   public AlignViewport getViewport()
 795   {
 796     return viewport;
 797   }
 798
 799   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 800   private void addServiceListeners()
 801   {
 802     final java.beans.PropertyChangeListener thisListener;
 803     Desktop.instance.addJalviewPropertyChangeListener("services",
 804             thisListener = new java.beans.PropertyChangeListener()
 805             {
 806               @Override
 807               public void propertyChange(PropertyChangeEvent evt)
 808               {
 809                 // // System.out.println("Discoverer property change.");
 810                 // if (evt.getPropertyName().equals("services"))
 811                 {
 812                   SwingUtilities.invokeLater(new Runnable()
 813                   {
 814
 815                     @Override
 816                     public void run()
 817                     {
 818                       System.err
 819                               .println("Rebuild WS Menu for service change");
 820                       BuildWebServiceMenu();
 821                     }
 822
 823                   });
 824                 }
 825               }
 826             });
 827     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 828     {
 829       @Override
 830       public void internalFrameClosed(
 831               javax.swing.event.InternalFrameEvent evt)
 832       {
 833         // System.out.println("deregistering discoverer listener");
 834         Desktop.instance.removeJalviewPropertyChangeListener("services",
 835                 thisListener);
 836         closeMenuItem_actionPerformed(true);
 837       };
 838     });
 839     // Finally, build the menu once to get current service state
 840     new Thread(new Runnable()
 841     {
 842       @Override
 843       public void run()
 844       {
 845         BuildWebServiceMenu();
 846       }
 847     }).start();
 848   }
 849
 850   /**
 851    * Configure menu items that vary according to whether the alignment is
 852    * nucleotide or protein
 853    */
 854   public void setGUINucleotide()
 855   {
 856     AlignmentI al = getViewport().getAlignment();
 857     boolean nucleotide = al.isNucleotide();
 858
 859     showTranslation.setVisible(nucleotide);
 860     showReverse.setVisible(nucleotide);
 861     showReverseComplement.setVisible(nucleotide);
 862     conservationMenuItem.setEnabled(!nucleotide);
 863     modifyConservation.setEnabled(!nucleotide
 864             && conservationMenuItem.isSelected());
 865     showGroupConservation.setEnabled(!nucleotide);
 866
 867     showComplementMenuItem.setText(nucleotide ? MessageManager
 868             .getString("label.protein") : MessageManager
 869             .getString("label.nucleotide"));
 870   }
 871
 872   /**
 873    * set up menus for the current viewport. This may be called after any
 874    * operation that affects the data in the current view (selection changed,
 875    * etc) to update the menus to reflect the new state.
 876    */
 877   @Override
 878   public void setMenusForViewport()
 879   {
 880     setMenusFromViewport(viewport);
 881   }
 882
 883   /**
 884    * Need to call this method when tabs are selected for multiple views, or when
 885    * loading from Jalview2XML.java
 886    *
 887    * @param av
 888    *          AlignViewport
 889    */
 890   void setMenusFromViewport(AlignViewport av)
 891   {
 892     padGapsMenuitem.setSelected(av.isPadGaps());
 893     colourTextMenuItem.setSelected(av.isShowColourText());
 894     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 895     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 896     conservationMenuItem.setSelected(av.getConservationSelected());
 897     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 898     seqLimits.setSelected(av.getShowJVSuffix());
 899     idRightAlign.setSelected(av.isRightAlignIds());
 900     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 901     renderGapsMenuItem.setSelected(av.isRenderGaps());
 902     wrapMenuItem.setSelected(av.getWrapAlignment());
 903     scaleAbove.setVisible(av.getWrapAlignment());
 904     scaleLeft.setVisible(av.getWrapAlignment());
 905     scaleRight.setVisible(av.getWrapAlignment());
 906     annotationPanelMenuItem.setState(av.isShowAnnotation());
 907     /*
 908      * Show/hide annotations only enabled if annotation panel is shown
 909      */
 910     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 911     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 912     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 913     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 914     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 915     viewTextMenuItem.setSelected(av.getShowText());
 916     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 917     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 918     showGroupConservation.setSelected(av.isShowGroupConservation());
 919     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 920     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 921     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 922
 923     ColourMenuHelper.setColourSelected(colourMenu,
 924             av.getGlobalColourScheme());
 925
 926     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 927     hiddenMarkers.setState(av.getShowHiddenMarkers());
 928     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 929     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 930     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 931     autoCalculate.setSelected(av.autoCalculateConsensus);
 932     sortByTree.setSelected(av.sortByTree);
 933     listenToViewSelections.setSelected(av.followSelection);
 934
 935     showProducts.setEnabled(canShowProducts());
 936     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 937
 938     updateEditMenuBar();
 939   }
 940
 941   /**
 942    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 943    *
 944    * @param b
 945    */
 946   public void setGroovyEnabled(boolean b)
 947   {
 948     runGroovy.setEnabled(b);
 949   }
 950
 951   private IProgressIndicator progressBar;
 952
 953   /*
 954    * (non-Javadoc)
 955    *
 956    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 957    */
 958   @Override
 959   public void setProgressBar(String message, long id)
 960   {
 961     progressBar.setProgressBar(message, id);
 962   }
 963
 964   @Override
 965   public void registerHandler(final long id,
 966           final IProgressIndicatorHandler handler)
 967   {
 968     progressBar.registerHandler(id, handler);
 969   }
 970
 971   /**
 972    *
 973    * @return true if any progress bars are still active
 974    */
 975   @Override
 976   public boolean operationInProgress()
 977   {
 978     return progressBar.operationInProgress();
 979   }
 980
 981   @Override
 982   public void setStatus(String text)
 983   {
 984     statusBar.setText(text);
 985   }
 986
 987   /*
 988    * Added so Castor Mapping file can obtain Jalview Version
 989    */
 990   public String getVersion()
 991   {
 992     return jalview.bin.Cache.getProperty("VERSION");
 993   }
 994
 995   public FeatureRenderer getFeatureRenderer()
 996   {
 997     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 998   }
 999
1000   @Override
1001   public void fetchSequence_actionPerformed(ActionEvent e)
1002   {
1003     new jalview.gui.SequenceFetcher(this);
1004   }
1005
1006   @Override
1007   public void addFromFile_actionPerformed(ActionEvent e)
1008   {
1009     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1010   }
1011
1012   @Override
1013   public void reload_actionPerformed(ActionEvent e)
1014   {
1015     if (fileName != null)
1016     {
1017       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1018       // originating file's format
1019       // TODO: work out how to recover feature settings for correct view(s) when
1020       // file is reloaded.
1021       if (FileFormat.Jalview.equals(currentFileFormat))
1022       {
1023         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1024         for (int i = 0; i < frames.length; i++)
1025         {
1026           if (frames[i] instanceof AlignFrame && frames[i] != this
1027                   && ((AlignFrame) frames[i]).fileName != null
1028                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1029           {
1030             try
1031             {
1032               frames[i].setSelected(true);
1033               Desktop.instance.closeAssociatedWindows();
1034             } catch (java.beans.PropertyVetoException ex)
1035             {
1036             }
1037           }
1038
1039         }
1040         Desktop.instance.closeAssociatedWindows();
1041
1042         FileLoader loader = new FileLoader();
1043         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1044                 : DataSourceType.FILE;
1045         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1046       }
1047       else
1048       {
1049         Rectangle bounds = this.getBounds();
1050
1051         FileLoader loader = new FileLoader();
1052         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1053                 : DataSourceType.FILE;
1054         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1055                 protocol, currentFileFormat);
1056
1057         newframe.setBounds(bounds);
1058         if (featureSettings != null && featureSettings.isShowing())
1059         {
1060           final Rectangle fspos = featureSettings.frame.getBounds();
1061           // TODO: need a 'show feature settings' function that takes bounds -
1062           // need to refactor Desktop.addFrame
1063           newframe.featureSettings_actionPerformed(null);
1064           final FeatureSettings nfs = newframe.featureSettings;
1065           SwingUtilities.invokeLater(new Runnable()
1066           {
1067             @Override
1068             public void run()
1069             {
1070               nfs.frame.setBounds(fspos);
1071             }
1072           });
1073           this.featureSettings.close();
1074           this.featureSettings = null;
1075         }
1076         this.closeMenuItem_actionPerformed(true);
1077       }
1078     }
1079   }
1080
1081   @Override
1082   public void addFromText_actionPerformed(ActionEvent e)
1083   {
1084     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1085             .getAlignPanel());
1086   }
1087
1088   @Override
1089   public void addFromURL_actionPerformed(ActionEvent e)
1090   {
1091     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1092   }
1093
1094   @Override
1095   public void save_actionPerformed(ActionEvent e)
1096   {
1097     if (fileName == null || (currentFileFormat == null)
1098             || fileName.startsWith("http"))
1099     {
1100       saveAs_actionPerformed(null);
1101     }
1102     else
1103     {
1104       saveAlignment(fileName, currentFileFormat);
1105     }
1106   }
1107
1108   /**
1109    * DOCUMENT ME!
1110    *
1111    * @param e
1112    *          DOCUMENT ME!
1113    */
1114   @Override
1115   public void saveAs_actionPerformed(ActionEvent e)
1116   {
1117     String format = currentFileFormat == null ? null : currentFileFormat
1118             .getName();
1119     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1120             Cache.getProperty("LAST_DIRECTORY"), format);
1121
1122     chooser.setFileView(new JalviewFileView());
1123     chooser.setDialogTitle(MessageManager
1124             .getString("label.save_alignment_to_file"));
1125     chooser.setToolTipText(MessageManager.getString("action.save"));
1126
1127     int value = chooser.showSaveDialog(this);
1128
1129     if (value == JalviewFileChooser.APPROVE_OPTION)
1130     {
1131       currentFileFormat = chooser.getSelectedFormat();
1132       while (currentFileFormat == null)
1133       {
1134         JvOptionPane
1135                 .showInternalMessageDialog(
1136                         Desktop.desktop,
1137                         MessageManager
1138                                 .getString("label.select_file_format_before_saving"),
1139                         MessageManager
1140                                 .getString("label.file_format_not_specified"),
1141                         JvOptionPane.WARNING_MESSAGE);
1142         currentFileFormat = chooser.getSelectedFormat();
1143         value = chooser.showSaveDialog(this);
1144         if (value != JalviewFileChooser.APPROVE_OPTION)
1145         {
1146           return;
1147         }
1148       }
1149
1150       fileName = chooser.getSelectedFile().getPath();
1151
1152       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1153
1154       Cache.setProperty("LAST_DIRECTORY", fileName);
1155       saveAlignment(fileName, currentFileFormat);
1156     }
1157   }
1158
1159   public boolean saveAlignment(String file, FileFormatI format)
1160   {
1161     boolean success = true;
1162
1163     if (FileFormat.Jalview.equals(format))
1164     {
1165       String shortName = title;
1166
1167       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1168       {
1169         shortName = shortName.substring(shortName
1170                 .lastIndexOf(java.io.File.separatorChar) + 1);
1171       }
1172
1173       success = new Jalview2XML().saveAlignment(this, file, shortName);
1174
1175       statusBar.setText(MessageManager.formatMessage(
1176               "label.successfully_saved_to_file_in_format", new Object[] {
1177                   fileName, format }));
1178
1179     }
1180     else
1181     {
1182       AlignmentExportData exportData = getAlignmentForExport(format,
1183               viewport, null);
1184       if (exportData.getSettings().isCancelled())
1185       {
1186         return false;
1187       }
1188       FormatAdapter f = new FormatAdapter(alignPanel,
1189               exportData.getSettings());
1190       String output = f.formatSequences(
1191               format,
1192               exportData.getAlignment(), // class cast exceptions will
1193               // occur in the distant future
1194               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1195               f.getCacheSuffixDefault(format),
1196               viewport.getColumnSelection());
1197
1198       if (output == null)
1199       {
1200         success = false;
1201       }
1202       else
1203       {
1204         try
1205         {
1206           PrintWriter out = new PrintWriter(new FileWriter(file));
1207
1208           out.print(output);
1209           out.close();
1210           this.setTitle(file);
1211           statusBar.setText(MessageManager.formatMessage(
1212                   "label.successfully_saved_to_file_in_format",
1213                   new Object[] { fileName, format.getName() }));
1214         } catch (Exception ex)
1215         {
1216           success = false;
1217           ex.printStackTrace();
1218         }
1219       }
1220     }
1221
1222     if (!success)
1223     {
1224       JvOptionPane.showInternalMessageDialog(this, MessageManager
1225               .formatMessage("label.couldnt_save_file",
1226                       new Object[] { fileName }), MessageManager
1227               .getString("label.error_saving_file"),
1228               JvOptionPane.WARNING_MESSAGE);
1229     }
1230
1231     return success;
1232   }
1233
1234   private void warningMessage(String warning, String title)
1235   {
1236     if (new jalview.util.Platform().isHeadless())
1237     {
1238       System.err.println("Warning: " + title + "\nWarning: " + warning);
1239
1240     }
1241     else
1242     {
1243       JvOptionPane.showInternalMessageDialog(this, warning, title,
1244               JvOptionPane.WARNING_MESSAGE);
1245     }
1246     return;
1247   }
1248
1249   /**
1250    * DOCUMENT ME!
1251    *
1252    * @param e
1253    *          DOCUMENT ME!
1254    */
1255   @Override
1256   protected void outputText_actionPerformed(ActionEvent e)
1257   {
1258     FileFormatI fileFormat = FileFormats.getInstance().forName(
1259             e.getActionCommand());
1260     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1261             viewport, null);
1262     if (exportData.getSettings().isCancelled())
1263     {
1264       return;
1265     }
1266     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1267     cap.setForInput(null);
1268     try
1269     {
1270       FileFormatI format = fileFormat;
1271       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1272               .formatSequences(format, exportData.getAlignment(),
1273                       exportData.getOmitHidden(),
1274                       exportData.getStartEndPostions(),
1275                       viewport.getColumnSelection()));
1276       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1277               "label.alignment_output_command",
1278               new Object[] { e.getActionCommand() }), 600, 500);
1279     } catch (OutOfMemoryError oom)
1280     {
1281       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1282       cap.dispose();
1283     }
1284
1285   }
1286
1287   public static AlignmentExportData getAlignmentForExport(
1288           FileFormatI format, AlignViewportI viewport,
1289           AlignExportSettingI exportSettings)
1290   {
1291     AlignmentI alignmentToExport = null;
1292     AlignExportSettingI settings = exportSettings;
1293     String[] omitHidden = null;
1294
1295     HiddenSequences hiddenSeqs = viewport.getAlignment()
1296             .getHiddenSequences();
1297
1298     alignmentToExport = viewport.getAlignment();
1299
1300     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1301     if (settings == null)
1302     {
1303       settings = new AlignExportSettings(hasHiddenSeqs,
1304               viewport.hasHiddenColumns(), format);
1305     }
1306     // settings.isExportAnnotations();
1307
1308     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1309     {
1310       omitHidden = viewport.getViewAsString(false,
1311               settings.isExportHiddenSequences());
1312     }
1313
1314     int[] alignmentStartEnd = new int[2];
1315     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1316     {
1317       alignmentToExport = hiddenSeqs.getFullAlignment();
1318     }
1319     else
1320     {
1321       alignmentToExport = viewport.getAlignment();
1322     }
1323     alignmentStartEnd = alignmentToExport
1324             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1325                     .getHiddenColumns());
1326     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1327             omitHidden, alignmentStartEnd, settings);
1328     return ed;
1329   }
1330
1331   /**
1332    * DOCUMENT ME!
1333    *
1334    * @param e
1335    *          DOCUMENT ME!
1336    */
1337   @Override
1338   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1339   {
1340     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1341     htmlSVG.exportHTML(null);
1342   }
1343
1344   @Override
1345   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1346   {
1347     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1348     bjs.exportHTML(null);
1349   }
1350
1351   public void createImageMap(File file, String image)
1352   {
1353     alignPanel.makePNGImageMap(file, image);
1354   }
1355
1356   /**
1357    * DOCUMENT ME!
1358    *
1359    * @param e
1360    *          DOCUMENT ME!
1361    */
1362   @Override
1363   public void createPNG(File f)
1364   {
1365     alignPanel.makePNG(f);
1366   }
1367
1368   /**
1369    * DOCUMENT ME!
1370    *
1371    * @param e
1372    *          DOCUMENT ME!
1373    */
1374   @Override
1375   public void createEPS(File f)
1376   {
1377     alignPanel.makeEPS(f);
1378   }
1379
1380   @Override
1381   public void createSVG(File f)
1382   {
1383     alignPanel.makeSVG(f);
1384   }
1385
1386   @Override
1387   public void pageSetup_actionPerformed(ActionEvent e)
1388   {
1389     PrinterJob printJob = PrinterJob.getPrinterJob();
1390     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1391   }
1392
1393   /**
1394    * DOCUMENT ME!
1395    *
1396    * @param e
1397    *          DOCUMENT ME!
1398    */
1399   @Override
1400   public void printMenuItem_actionPerformed(ActionEvent e)
1401   {
1402     // Putting in a thread avoids Swing painting problems
1403     PrintThread thread = new PrintThread(alignPanel);
1404     thread.start();
1405   }
1406
1407   @Override
1408   public void exportFeatures_actionPerformed(ActionEvent e)
1409   {
1410     new AnnotationExporter().exportFeatures(alignPanel);
1411   }
1412
1413   @Override
1414   public void exportAnnotations_actionPerformed(ActionEvent e)
1415   {
1416     new AnnotationExporter().exportAnnotations(alignPanel);
1417   }
1418
1419   @Override
1420   public void associatedData_actionPerformed(ActionEvent e)
1421   {
1422     // Pick the tree file
1423     JalviewFileChooser chooser = new JalviewFileChooser(
1424             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1425     chooser.setFileView(new JalviewFileView());
1426     chooser.setDialogTitle(MessageManager
1427             .getString("label.load_jalview_annotations"));
1428     chooser.setToolTipText(MessageManager
1429             .getString("label.load_jalview_annotations"));
1430
1431     int value = chooser.showOpenDialog(null);
1432
1433     if (value == JalviewFileChooser.APPROVE_OPTION)
1434     {
1435       String choice = chooser.getSelectedFile().getPath();
1436       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1437       loadJalviewDataFile(choice, null, null, null);
1438     }
1439
1440   }
1441
1442   /**
1443    * Close the current view or all views in the alignment frame. If the frame
1444    * only contains one view then the alignment will be removed from memory.
1445    *
1446    * @param closeAllTabs
1447    */
1448   @Override
1449   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1450   {
1451     if (alignPanels != null && alignPanels.size() < 2)
1452     {
1453       closeAllTabs = true;
1454     }
1455
1456     try
1457     {
1458       if (alignPanels != null)
1459       {
1460         if (closeAllTabs)
1461         {
1462           if (this.isClosed())
1463           {
1464             // really close all the windows - otherwise wait till
1465             // setClosed(true) is called
1466             for (int i = 0; i < alignPanels.size(); i++)
1467             {
1468               AlignmentPanel ap = alignPanels.get(i);
1469               ap.closePanel();
1470             }
1471           }
1472         }
1473         else
1474         {
1475           closeView(alignPanel);
1476         }
1477       }
1478
1479       if (closeAllTabs)
1480       {
1481         /*
1482          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1483          * be called recursively, with the frame now in 'closed' state
1484          */
1485         this.setClosed(true);
1486       }
1487     } catch (Exception ex)
1488     {
1489       ex.printStackTrace();
1490     }
1491   }
1492
1493   /**
1494    * Close the specified panel and close up tabs appropriately.
1495    *
1496    * @param panelToClose
1497    */
1498   public void closeView(AlignmentPanel panelToClose)
1499   {
1500     int index = tabbedPane.getSelectedIndex();
1501     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1502     alignPanels.remove(panelToClose);
1503     panelToClose.closePanel();
1504     panelToClose = null;
1505
1506     tabbedPane.removeTabAt(closedindex);
1507     tabbedPane.validate();
1508
1509     if (index > closedindex || index == tabbedPane.getTabCount())
1510     {
1511       // modify currently selected tab index if necessary.
1512       index--;
1513     }
1514
1515     this.tabSelectionChanged(index);
1516   }
1517
1518   /**
1519    * DOCUMENT ME!
1520    */
1521   void updateEditMenuBar()
1522   {
1523
1524     if (viewport.getHistoryList().size() > 0)
1525     {
1526       undoMenuItem.setEnabled(true);
1527       CommandI command = viewport.getHistoryList().peek();
1528       undoMenuItem.setText(MessageManager.formatMessage(
1529               "label.undo_command",
1530               new Object[] { command.getDescription() }));
1531     }
1532     else
1533     {
1534       undoMenuItem.setEnabled(false);
1535       undoMenuItem.setText(MessageManager.getString("action.undo"));
1536     }
1537
1538     if (viewport.getRedoList().size() > 0)
1539     {
1540       redoMenuItem.setEnabled(true);
1541
1542       CommandI command = viewport.getRedoList().peek();
1543       redoMenuItem.setText(MessageManager.formatMessage(
1544               "label.redo_command",
1545               new Object[] { command.getDescription() }));
1546     }
1547     else
1548     {
1549       redoMenuItem.setEnabled(false);
1550       redoMenuItem.setText(MessageManager.getString("action.redo"));
1551     }
1552   }
1553
1554   @Override
1555   public void addHistoryItem(CommandI command)
1556   {
1557     if (command.getSize() > 0)
1558     {
1559       viewport.addToHistoryList(command);
1560       viewport.clearRedoList();
1561       updateEditMenuBar();
1562       viewport.updateHiddenColumns();
1563       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1564       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1565       // viewport.getColumnSelection()
1566       // .getHiddenColumns().size() > 0);
1567     }
1568   }
1569
1570   /**
1571    *
1572    * @return alignment objects for all views
1573    */
1574   AlignmentI[] getViewAlignments()
1575   {
1576     if (alignPanels != null)
1577     {
1578       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1579       int i = 0;
1580       for (AlignmentPanel ap : alignPanels)
1581       {
1582         als[i++] = ap.av.getAlignment();
1583       }
1584       return als;
1585     }
1586     if (viewport != null)
1587     {
1588       return new AlignmentI[] { viewport.getAlignment() };
1589     }
1590     return null;
1591   }
1592
1593   /**
1594    * DOCUMENT ME!
1595    *
1596    * @param e
1597    *          DOCUMENT ME!
1598    */
1599   @Override
1600   protected void undoMenuItem_actionPerformed(ActionEvent e)
1601   {
1602     if (viewport.getHistoryList().isEmpty())
1603     {
1604       return;
1605     }
1606     CommandI command = viewport.getHistoryList().pop();
1607     viewport.addToRedoList(command);
1608     command.undoCommand(getViewAlignments());
1609
1610     AlignmentViewport originalSource = getOriginatingSource(command);
1611     updateEditMenuBar();
1612
1613     if (originalSource != null)
1614     {
1615       if (originalSource != viewport)
1616       {
1617         Cache.log
1618                 .warn("Implementation worry: mismatch of viewport origin for undo");
1619       }
1620       originalSource.updateHiddenColumns();
1621       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1622       // null
1623       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1624       // viewport.getColumnSelection()
1625       // .getHiddenColumns().size() > 0);
1626       originalSource.firePropertyChange("alignment", null, originalSource
1627               .getAlignment().getSequences());
1628     }
1629   }
1630
1631   /**
1632    * DOCUMENT ME!
1633    *
1634    * @param e
1635    *          DOCUMENT ME!
1636    */
1637   @Override
1638   protected void redoMenuItem_actionPerformed(ActionEvent e)
1639   {
1640     if (viewport.getRedoList().size() < 1)
1641     {
1642       return;
1643     }
1644
1645     CommandI command = viewport.getRedoList().pop();
1646     viewport.addToHistoryList(command);
1647     command.doCommand(getViewAlignments());
1648
1649     AlignmentViewport originalSource = getOriginatingSource(command);
1650     updateEditMenuBar();
1651
1652     if (originalSource != null)
1653     {
1654
1655       if (originalSource != viewport)
1656       {
1657         Cache.log
1658                 .warn("Implementation worry: mismatch of viewport origin for redo");
1659       }
1660       originalSource.updateHiddenColumns();
1661       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1662       // null
1663       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1664       // viewport.getColumnSelection()
1665       // .getHiddenColumns().size() > 0);
1666       originalSource.firePropertyChange("alignment", null, originalSource
1667               .getAlignment().getSequences());
1668     }
1669   }
1670
1671   AlignmentViewport getOriginatingSource(CommandI command)
1672   {
1673     AlignmentViewport originalSource = null;
1674     // For sequence removal and addition, we need to fire
1675     // the property change event FROM the viewport where the
1676     // original alignment was altered
1677     AlignmentI al = null;
1678     if (command instanceof EditCommand)
1679     {
1680       EditCommand editCommand = (EditCommand) command;
1681       al = editCommand.getAlignment();
1682       List<Component> comps = PaintRefresher.components.get(viewport
1683               .getSequenceSetId());
1684
1685       for (Component comp : comps)
1686       {
1687         if (comp instanceof AlignmentPanel)
1688         {
1689           if (al == ((AlignmentPanel) comp).av.getAlignment())
1690           {
1691             originalSource = ((AlignmentPanel) comp).av;
1692             break;
1693           }
1694         }
1695       }
1696     }
1697
1698     if (originalSource == null)
1699     {
1700       // The original view is closed, we must validate
1701       // the current view against the closed view first
1702       if (al != null)
1703       {
1704         PaintRefresher.validateSequences(al, viewport.getAlignment());
1705       }
1706
1707       originalSource = viewport;
1708     }
1709
1710     return originalSource;
1711   }
1712
1713   /**
1714    * DOCUMENT ME!
1715    *
1716    * @param up
1717    *          DOCUMENT ME!
1718    */
1719   public void moveSelectedSequences(boolean up)
1720   {
1721     SequenceGroup sg = viewport.getSelectionGroup();
1722
1723     if (sg == null)
1724     {
1725       return;
1726     }
1727     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1728             viewport.getHiddenRepSequences(), up);
1729     alignPanel.paintAlignment(true);
1730   }
1731
1732   synchronized void slideSequences(boolean right, int size)
1733   {
1734     List<SequenceI> sg = new ArrayList<SequenceI>();
1735     if (viewport.cursorMode)
1736     {
1737       sg.add(viewport.getAlignment().getSequenceAt(
1738               alignPanel.getSeqPanel().seqCanvas.cursorY));
1739     }
1740     else if (viewport.getSelectionGroup() != null
1741             && viewport.getSelectionGroup().getSize() != viewport
1742                     .getAlignment().getHeight())
1743     {
1744       sg = viewport.getSelectionGroup().getSequences(
1745               viewport.getHiddenRepSequences());
1746     }
1747
1748     if (sg.size() < 1)
1749     {
1750       return;
1751     }
1752
1753     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1754
1755     for (SequenceI seq : viewport.getAlignment().getSequences())
1756     {
1757       if (!sg.contains(seq))
1758       {
1759         invertGroup.add(seq);
1760       }
1761     }
1762
1763     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1764
1765     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1766     for (int i = 0; i < invertGroup.size(); i++)
1767     {
1768       seqs2[i] = invertGroup.get(i);
1769     }
1770
1771     SlideSequencesCommand ssc;
1772     if (right)
1773     {
1774       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1775               size, viewport.getGapCharacter());
1776     }
1777     else
1778     {
1779       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1780               size, viewport.getGapCharacter());
1781     }
1782
1783     int groupAdjustment = 0;
1784     if (ssc.getGapsInsertedBegin() && right)
1785     {
1786       if (viewport.cursorMode)
1787       {
1788         alignPanel.getSeqPanel().moveCursor(size, 0);
1789       }
1790       else
1791       {
1792         groupAdjustment = size;
1793       }
1794     }
1795     else if (!ssc.getGapsInsertedBegin() && !right)
1796     {
1797       if (viewport.cursorMode)
1798       {
1799         alignPanel.getSeqPanel().moveCursor(-size, 0);
1800       }
1801       else
1802       {
1803         groupAdjustment = -size;
1804       }
1805     }
1806
1807     if (groupAdjustment != 0)
1808     {
1809       viewport.getSelectionGroup().setStartRes(
1810               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1811       viewport.getSelectionGroup().setEndRes(
1812               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1813     }
1814
1815     /*
1816      * just extend the last slide command if compatible; but not if in
1817      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1818      */
1819     boolean appendHistoryItem = false;
1820     Deque<CommandI> historyList = viewport.getHistoryList();
1821     boolean inSplitFrame = getSplitViewContainer() != null;
1822     if (!inSplitFrame && historyList != null && historyList.size() > 0
1823             && historyList.peek() instanceof SlideSequencesCommand)
1824     {
1825       appendHistoryItem = ssc
1826               .appendSlideCommand((SlideSequencesCommand) historyList
1827                       .peek());
1828     }
1829
1830     if (!appendHistoryItem)
1831     {
1832       addHistoryItem(ssc);
1833     }
1834
1835     repaint();
1836   }
1837
1838   /**
1839    * DOCUMENT ME!
1840    *
1841    * @param e
1842    *          DOCUMENT ME!
1843    */
1844   @Override
1845   protected void copy_actionPerformed(ActionEvent e)
1846   {
1847     System.gc();
1848     if (viewport.getSelectionGroup() == null)
1849     {
1850       return;
1851     }
1852     // TODO: preserve the ordering of displayed alignment annotation in any
1853     // internal paste (particularly sequence associated annotation)
1854     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1855     String[] omitHidden = null;
1856
1857     if (viewport.hasHiddenColumns())
1858     {
1859       omitHidden = viewport.getViewAsString(true);
1860     }
1861
1862     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1863             seqs, omitHidden, null);
1864
1865     StringSelection ss = new StringSelection(output);
1866
1867     try
1868     {
1869       jalview.gui.Desktop.internalCopy = true;
1870       // Its really worth setting the clipboard contents
1871       // to empty before setting the large StringSelection!!
1872       Toolkit.getDefaultToolkit().getSystemClipboard()
1873               .setContents(new StringSelection(""), null);
1874
1875       Toolkit.getDefaultToolkit().getSystemClipboard()
1876               .setContents(ss, Desktop.instance);
1877     } catch (OutOfMemoryError er)
1878     {
1879       new OOMWarning("copying region", er);
1880       return;
1881     }
1882
1883     ArrayList<int[]> hiddenColumns = null;
1884     if (viewport.hasHiddenColumns())
1885     {
1886       hiddenColumns = new ArrayList<int[]>();
1887       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1888               .getSelectionGroup().getEndRes();
1889       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1890       {
1891         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1892         {
1893           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1894               region[1] - hiddenOffset });
1895         }
1896       }
1897     }
1898
1899     Desktop.jalviewClipboard = new Object[] { seqs,
1900         viewport.getAlignment().getDataset(), hiddenColumns };
1901     statusBar.setText(MessageManager.formatMessage(
1902             "label.copied_sequences_to_clipboard", new Object[] { Integer
1903                     .valueOf(seqs.length).toString() }));
1904   }
1905
1906   /**
1907    * DOCUMENT ME!
1908    *
1909    * @param e
1910    *          DOCUMENT ME!
1911    */
1912   @Override
1913   protected void pasteNew_actionPerformed(ActionEvent e)
1914   {
1915     paste(true);
1916   }
1917
1918   /**
1919    * DOCUMENT ME!
1920    *
1921    * @param e
1922    *          DOCUMENT ME!
1923    */
1924   @Override
1925   protected void pasteThis_actionPerformed(ActionEvent e)
1926   {
1927     paste(false);
1928   }
1929
1930   /**
1931    * Paste contents of Jalview clipboard
1932    *
1933    * @param newAlignment
1934    *          true to paste to a new alignment, otherwise add to this.
1935    */
1936   void paste(boolean newAlignment)
1937   {
1938     boolean externalPaste = true;
1939     try
1940     {
1941       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1942       Transferable contents = c.getContents(this);
1943
1944       if (contents == null)
1945       {
1946         return;
1947       }
1948
1949       String str;
1950       FileFormatI format;
1951       try
1952       {
1953         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1954         if (str.length() < 1)
1955         {
1956           return;
1957         }
1958
1959         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1960
1961       } catch (OutOfMemoryError er)
1962       {
1963         new OOMWarning("Out of memory pasting sequences!!", er);
1964         return;
1965       }
1966
1967       SequenceI[] sequences;
1968       boolean annotationAdded = false;
1969       AlignmentI alignment = null;
1970
1971       if (Desktop.jalviewClipboard != null)
1972       {
1973         // The clipboard was filled from within Jalview, we must use the
1974         // sequences
1975         // And dataset from the copied alignment
1976         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1977         // be doubly sure that we create *new* sequence objects.
1978         sequences = new SequenceI[newseq.length];
1979         for (int i = 0; i < newseq.length; i++)
1980         {
1981           sequences[i] = new Sequence(newseq[i]);
1982         }
1983         alignment = new Alignment(sequences);
1984         externalPaste = false;
1985       }
1986       else
1987       {
1988         // parse the clipboard as an alignment.
1989         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1990                 format);
1991         sequences = alignment.getSequencesArray();
1992       }
1993
1994       int alwidth = 0;
1995       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1996       int fgroup = -1;
1997
1998       if (newAlignment)
1999       {
2000
2001         if (Desktop.jalviewClipboard != null)
2002         {
2003           // dataset is inherited
2004           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2005         }
2006         else
2007         {
2008           // new dataset is constructed
2009           alignment.setDataset(null);
2010         }
2011         alwidth = alignment.getWidth() + 1;
2012       }
2013       else
2014       {
2015         AlignmentI pastedal = alignment; // preserve pasted alignment object
2016         // Add pasted sequences and dataset into existing alignment.
2017         alignment = viewport.getAlignment();
2018         alwidth = alignment.getWidth() + 1;
2019         // decide if we need to import sequences from an existing dataset
2020         boolean importDs = Desktop.jalviewClipboard != null
2021                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2022         // importDs==true instructs us to copy over new dataset sequences from
2023         // an existing alignment
2024         Vector newDs = (importDs) ? new Vector() : null; // used to create
2025         // minimum dataset set
2026
2027         for (int i = 0; i < sequences.length; i++)
2028         {
2029           if (importDs)
2030           {
2031             newDs.addElement(null);
2032           }
2033           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2034           // paste
2035           if (importDs && ds != null)
2036           {
2037             if (!newDs.contains(ds))
2038             {
2039               newDs.setElementAt(ds, i);
2040               ds = new Sequence(ds);
2041               // update with new dataset sequence
2042               sequences[i].setDatasetSequence(ds);
2043             }
2044             else
2045             {
2046               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2047             }
2048           }
2049           else
2050           {
2051             // copy and derive new dataset sequence
2052             sequences[i] = sequences[i].deriveSequence();
2053             alignment.getDataset().addSequence(
2054                     sequences[i].getDatasetSequence());
2055             // TODO: avoid creation of duplicate dataset sequences with a
2056             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2057           }
2058           alignment.addSequence(sequences[i]); // merges dataset
2059         }
2060         if (newDs != null)
2061         {
2062           newDs.clear(); // tidy up
2063         }
2064         if (alignment.getAlignmentAnnotation() != null)
2065         {
2066           for (AlignmentAnnotation alan : alignment
2067                   .getAlignmentAnnotation())
2068           {
2069             if (alan.graphGroup > fgroup)
2070             {
2071               fgroup = alan.graphGroup;
2072             }
2073           }
2074         }
2075         if (pastedal.getAlignmentAnnotation() != null)
2076         {
2077           // Add any annotation attached to alignment.
2078           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2079           for (int i = 0; i < alann.length; i++)
2080           {
2081             annotationAdded = true;
2082             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2083             {
2084               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2085               if (newann.graphGroup > -1)
2086               {
2087                 if (newGraphGroups.size() <= newann.graphGroup
2088                         || newGraphGroups.get(newann.graphGroup) == null)
2089                 {
2090                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2091                   {
2092                     newGraphGroups.add(q, null);
2093                   }
2094                   newGraphGroups.set(newann.graphGroup, new Integer(
2095                           ++fgroup));
2096                 }
2097                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2098                         .intValue();
2099               }
2100
2101               newann.padAnnotation(alwidth);
2102               alignment.addAnnotation(newann);
2103             }
2104           }
2105         }
2106       }
2107       if (!newAlignment)
2108       {
2109         // /////
2110         // ADD HISTORY ITEM
2111         //
2112         addHistoryItem(new EditCommand(
2113                 MessageManager.getString("label.add_sequences"),
2114                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2115       }
2116       // Add any annotations attached to sequences
2117       for (int i = 0; i < sequences.length; i++)
2118       {
2119         if (sequences[i].getAnnotation() != null)
2120         {
2121           AlignmentAnnotation newann;
2122           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2123           {
2124             annotationAdded = true;
2125             newann = sequences[i].getAnnotation()[a];
2126             newann.adjustForAlignment();
2127             newann.padAnnotation(alwidth);
2128             if (newann.graphGroup > -1)
2129             {
2130               if (newann.graphGroup > -1)
2131               {
2132                 if (newGraphGroups.size() <= newann.graphGroup
2133                         || newGraphGroups.get(newann.graphGroup) == null)
2134                 {
2135                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2136                   {
2137                     newGraphGroups.add(q, null);
2138                   }
2139                   newGraphGroups.set(newann.graphGroup, new Integer(
2140                           ++fgroup));
2141                 }
2142                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2143                         .intValue();
2144               }
2145             }
2146             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2147             // was
2148             // duplicated
2149             // earlier
2150             alignment
2151                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2152           }
2153         }
2154       }
2155       if (!newAlignment)
2156       {
2157
2158         // propagate alignment changed.
2159         vpRanges.setEndSeq(alignment.getHeight());
2160         if (annotationAdded)
2161         {
2162           // Duplicate sequence annotation in all views.
2163           AlignmentI[] alview = this.getViewAlignments();
2164           for (int i = 0; i < sequences.length; i++)
2165           {
2166             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2167             if (sann == null)
2168             {
2169               continue;
2170             }
2171             for (int avnum = 0; avnum < alview.length; avnum++)
2172             {
2173               if (alview[avnum] != alignment)
2174               {
2175                 // duplicate in a view other than the one with input focus
2176                 int avwidth = alview[avnum].getWidth() + 1;
2177                 // this relies on sann being preserved after we
2178                 // modify the sequence's annotation array for each duplication
2179                 for (int a = 0; a < sann.length; a++)
2180                 {
2181                   AlignmentAnnotation newann = new AlignmentAnnotation(
2182                           sann[a]);
2183                   sequences[i].addAlignmentAnnotation(newann);
2184                   newann.padAnnotation(avwidth);
2185                   alview[avnum].addAnnotation(newann); // annotation was
2186                   // duplicated earlier
2187                   // TODO JAL-1145 graphGroups are not updated for sequence
2188                   // annotation added to several views. This may cause
2189                   // strangeness
2190                   alview[avnum].setAnnotationIndex(newann, a);
2191                 }
2192               }
2193             }
2194           }
2195           buildSortByAnnotationScoresMenu();
2196         }
2197         viewport.firePropertyChange("alignment", null,
2198                 alignment.getSequences());
2199         if (alignPanels != null)
2200         {
2201           for (AlignmentPanel ap : alignPanels)
2202           {
2203             ap.validateAnnotationDimensions(false);
2204           }
2205         }
2206         else
2207         {
2208           alignPanel.validateAnnotationDimensions(false);
2209         }
2210
2211       }
2212       else
2213       {
2214         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2215                 DEFAULT_HEIGHT);
2216         String newtitle = new String("Copied sequences");
2217
2218         if (Desktop.jalviewClipboard != null
2219                 && Desktop.jalviewClipboard[2] != null)
2220         {
2221           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2222           for (int[] region : hc)
2223           {
2224             af.viewport.hideColumns(region[0], region[1]);
2225           }
2226         }
2227
2228         // >>>This is a fix for the moment, until a better solution is
2229         // found!!<<<
2230         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2231                 .transferSettings(
2232                         alignPanel.getSeqPanel().seqCanvas
2233                                 .getFeatureRenderer());
2234
2235         // TODO: maintain provenance of an alignment, rather than just make the
2236         // title a concatenation of operations.
2237         if (!externalPaste)
2238         {
2239           if (title.startsWith("Copied sequences"))
2240           {
2241             newtitle = title;
2242           }
2243           else
2244           {
2245             newtitle = newtitle.concat("- from " + title);
2246           }
2247         }
2248         else
2249         {
2250           newtitle = new String("Pasted sequences");
2251         }
2252
2253         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2254                 DEFAULT_HEIGHT);
2255
2256       }
2257
2258     } catch (Exception ex)
2259     {
2260       ex.printStackTrace();
2261       System.out.println("Exception whilst pasting: " + ex);
2262       // could be anything being pasted in here
2263     }
2264
2265   }
2266
2267   @Override
2268   protected void expand_newalign(ActionEvent e)
2269   {
2270     try
2271     {
2272       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2273               .getAlignment(), -1);
2274       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2275               DEFAULT_HEIGHT);
2276       String newtitle = new String("Flanking alignment");
2277
2278       if (Desktop.jalviewClipboard != null
2279               && Desktop.jalviewClipboard[2] != null)
2280       {
2281         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2282         for (int region[] : hc)
2283         {
2284           af.viewport.hideColumns(region[0], region[1]);
2285         }
2286       }
2287
2288       // >>>This is a fix for the moment, until a better solution is
2289       // found!!<<<
2290       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2291               .transferSettings(
2292                       alignPanel.getSeqPanel().seqCanvas
2293                               .getFeatureRenderer());
2294
2295       // TODO: maintain provenance of an alignment, rather than just make the
2296       // title a concatenation of operations.
2297       {
2298         if (title.startsWith("Copied sequences"))
2299         {
2300           newtitle = title;
2301         }
2302         else
2303         {
2304           newtitle = newtitle.concat("- from " + title);
2305         }
2306       }
2307
2308       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2309
2310     } catch (Exception ex)
2311     {
2312       ex.printStackTrace();
2313       System.out.println("Exception whilst pasting: " + ex);
2314       // could be anything being pasted in here
2315     } catch (OutOfMemoryError oom)
2316     {
2317       new OOMWarning("Viewing flanking region of alignment", oom);
2318     }
2319   }
2320
2321   /**
2322    * DOCUMENT ME!
2323    *
2324    * @param e
2325    *          DOCUMENT ME!
2326    */
2327   @Override
2328   protected void cut_actionPerformed(ActionEvent e)
2329   {
2330     copy_actionPerformed(null);
2331     delete_actionPerformed(null);
2332   }
2333
2334   /**
2335    * DOCUMENT ME!
2336    *
2337    * @param e
2338    *          DOCUMENT ME!
2339    */
2340   @Override
2341   protected void delete_actionPerformed(ActionEvent evt)
2342   {
2343
2344     SequenceGroup sg = viewport.getSelectionGroup();
2345     if (sg == null)
2346     {
2347       return;
2348     }
2349
2350     /*
2351      * If the cut affects all sequences, warn, remove highlighted columns
2352      */
2353     if (sg.getSize() == viewport.getAlignment().getHeight())
2354     {
2355       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2356               .getAlignment().getWidth()) ? true : false;
2357       if (isEntireAlignWidth)
2358       {
2359         int confirm = JvOptionPane.showConfirmDialog(this,
2360                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2361                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2362                 JvOptionPane.OK_CANCEL_OPTION);
2363
2364         if (confirm == JvOptionPane.CANCEL_OPTION
2365                 || confirm == JvOptionPane.CLOSED_OPTION)
2366         {
2367           return;
2368         }
2369       }
2370       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2371               sg.getEndRes() + 1);
2372     }
2373     SequenceI[] cut = sg.getSequences()
2374             .toArray(new SequenceI[sg.getSize()]);
2375
2376     addHistoryItem(new EditCommand(
2377             MessageManager.getString("label.cut_sequences"), Action.CUT,
2378             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2379             viewport.getAlignment()));
2380
2381     viewport.setSelectionGroup(null);
2382     viewport.sendSelection();
2383     viewport.getAlignment().deleteGroup(sg);
2384
2385     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2386             .getSequences());
2387     if (viewport.getAlignment().getHeight() < 1)
2388     {
2389       try
2390       {
2391         this.setClosed(true);
2392       } catch (Exception ex)
2393       {
2394       }
2395     }
2396   }
2397
2398   /**
2399    * DOCUMENT ME!
2400    *
2401    * @param e
2402    *          DOCUMENT ME!
2403    */
2404   @Override
2405   protected void deleteGroups_actionPerformed(ActionEvent e)
2406   {
2407     if (avc.deleteGroups())
2408     {
2409       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2410       alignPanel.updateAnnotation();
2411       alignPanel.paintAlignment(true);
2412     }
2413   }
2414
2415   /**
2416    * DOCUMENT ME!
2417    *
2418    * @param e
2419    *          DOCUMENT ME!
2420    */
2421   @Override
2422   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2423   {
2424     SequenceGroup sg = new SequenceGroup();
2425
2426     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2427     {
2428       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2429     }
2430
2431     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2432     viewport.setSelectionGroup(sg);
2433     viewport.sendSelection();
2434     // JAL-2034 - should delegate to
2435     // alignPanel to decide if overview needs
2436     // updating.
2437     alignPanel.paintAlignment(false);
2438     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2439   }
2440
2441   /**
2442    * DOCUMENT ME!
2443    *
2444    * @param e
2445    *          DOCUMENT ME!
2446    */
2447   @Override
2448   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2449   {
2450     if (viewport.cursorMode)
2451     {
2452       alignPanel.getSeqPanel().keyboardNo1 = null;
2453       alignPanel.getSeqPanel().keyboardNo2 = null;
2454     }
2455     viewport.setSelectionGroup(null);
2456     viewport.getColumnSelection().clear();
2457     viewport.setSelectionGroup(null);
2458     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2459     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2460     // JAL-2034 - should delegate to
2461     // alignPanel to decide if overview needs
2462     // updating.
2463     alignPanel.paintAlignment(false);
2464     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2465     viewport.sendSelection();
2466   }
2467
2468   /**
2469    * DOCUMENT ME!
2470    *
2471    * @param e
2472    *          DOCUMENT ME!
2473    */
2474   @Override
2475   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2476   {
2477     SequenceGroup sg = viewport.getSelectionGroup();
2478
2479     if (sg == null)
2480     {
2481       selectAllSequenceMenuItem_actionPerformed(null);
2482
2483       return;
2484     }
2485
2486     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2487     {
2488       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2489     }
2490     // JAL-2034 - should delegate to
2491     // alignPanel to decide if overview needs
2492     // updating.
2493
2494     alignPanel.paintAlignment(true);
2495     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2496     viewport.sendSelection();
2497   }
2498
2499   @Override
2500   public void invertColSel_actionPerformed(ActionEvent e)
2501   {
2502     viewport.invertColumnSelection();
2503     alignPanel.paintAlignment(true);
2504     viewport.sendSelection();
2505   }
2506
2507   /**
2508    * DOCUMENT ME!
2509    *
2510    * @param e
2511    *          DOCUMENT ME!
2512    */
2513   @Override
2514   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2515   {
2516     trimAlignment(true);
2517   }
2518
2519   /**
2520    * DOCUMENT ME!
2521    *
2522    * @param e
2523    *          DOCUMENT ME!
2524    */
2525   @Override
2526   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2527   {
2528     trimAlignment(false);
2529   }
2530
2531   void trimAlignment(boolean trimLeft)
2532   {
2533     ColumnSelection colSel = viewport.getColumnSelection();
2534     int column;
2535
2536     if (!colSel.isEmpty())
2537     {
2538       if (trimLeft)
2539       {
2540         column = colSel.getMin();
2541       }
2542       else
2543       {
2544         column = colSel.getMax();
2545       }
2546
2547       SequenceI[] seqs;
2548       if (viewport.getSelectionGroup() != null)
2549       {
2550         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2551                 viewport.getHiddenRepSequences());
2552       }
2553       else
2554       {
2555         seqs = viewport.getAlignment().getSequencesArray();
2556       }
2557
2558       TrimRegionCommand trimRegion;
2559       if (trimLeft)
2560       {
2561         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2562                 column, viewport.getAlignment());
2563         vpRanges.setStartRes(0);
2564       }
2565       else
2566       {
2567         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2568                 column, viewport.getAlignment());
2569       }
2570
2571       statusBar.setText(MessageManager.formatMessage(
2572               "label.removed_columns",
2573               new String[] { Integer.valueOf(trimRegion.getSize())
2574                       .toString() }));
2575
2576       addHistoryItem(trimRegion);
2577
2578       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2579       {
2580         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2581                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2582         {
2583           viewport.getAlignment().deleteGroup(sg);
2584         }
2585       }
2586
2587       viewport.firePropertyChange("alignment", null, viewport
2588               .getAlignment().getSequences());
2589     }
2590   }
2591
2592   /**
2593    * DOCUMENT ME!
2594    *
2595    * @param e
2596    *          DOCUMENT ME!
2597    */
2598   @Override
2599   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2600   {
2601     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2602
2603     SequenceI[] seqs;
2604     if (viewport.getSelectionGroup() != null)
2605     {
2606       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2607               viewport.getHiddenRepSequences());
2608       start = viewport.getSelectionGroup().getStartRes();
2609       end = viewport.getSelectionGroup().getEndRes();
2610     }
2611     else
2612     {
2613       seqs = viewport.getAlignment().getSequencesArray();
2614     }
2615
2616     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2617             "Remove Gapped Columns", seqs, start, end,
2618             viewport.getAlignment());
2619
2620     addHistoryItem(removeGapCols);
2621
2622     statusBar.setText(MessageManager.formatMessage(
2623             "label.removed_empty_columns",
2624             new Object[] { Integer.valueOf(removeGapCols.getSize())
2625                     .toString() }));
2626
2627     // This is to maintain viewport position on first residue
2628     // of first sequence
2629     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2630     int startRes = seq.findPosition(vpRanges.getStartRes());
2631     // ShiftList shifts;
2632     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2633     // edit.alColumnChanges=shifts.getInverse();
2634     // if (viewport.hasHiddenColumns)
2635     // viewport.getColumnSelection().compensateForEdits(shifts);
2636     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2637     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2638             .getSequences());
2639
2640   }
2641
2642   /**
2643    * DOCUMENT ME!
2644    *
2645    * @param e
2646    *          DOCUMENT ME!
2647    */
2648   @Override
2649   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2650   {
2651     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2652
2653     SequenceI[] seqs;
2654     if (viewport.getSelectionGroup() != null)
2655     {
2656       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2657               viewport.getHiddenRepSequences());
2658       start = viewport.getSelectionGroup().getStartRes();
2659       end = viewport.getSelectionGroup().getEndRes();
2660     }
2661     else
2662     {
2663       seqs = viewport.getAlignment().getSequencesArray();
2664     }
2665
2666     // This is to maintain viewport position on first residue
2667     // of first sequence
2668     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2669     int startRes = seq.findPosition(vpRanges.getStartRes());
2670
2671     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2672             viewport.getAlignment()));
2673
2674     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2675
2676     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2677             .getSequences());
2678
2679   }
2680
2681   /**
2682    * DOCUMENT ME!
2683    *
2684    * @param e
2685    *          DOCUMENT ME!
2686    */
2687   @Override
2688   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2689   {
2690     viewport.setPadGaps(padGapsMenuitem.isSelected());
2691     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2692             .getSequences());
2693   }
2694
2695   /**
2696    * DOCUMENT ME!
2697    *
2698    * @param e
2699    *          DOCUMENT ME!
2700    */
2701   @Override
2702   public void findMenuItem_actionPerformed(ActionEvent e)
2703   {
2704     new Finder();
2705   }
2706
2707   /**
2708    * Create a new view of the current alignment.
2709    */
2710   @Override
2711   public void newView_actionPerformed(ActionEvent e)
2712   {
2713     newView(null, true);
2714   }
2715
2716   /**
2717    * Creates and shows a new view of the current alignment.
2718    *
2719    * @param viewTitle
2720    *          title of newly created view; if null, one will be generated
2721    * @param copyAnnotation
2722    *          if true then duplicate all annnotation, groups and settings
2723    * @return new alignment panel, already displayed.
2724    */
2725   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2726   {
2727     /*
2728      * Create a new AlignmentPanel (with its own, new Viewport)
2729      */
2730     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2731             true);
2732     if (!copyAnnotation)
2733     {
2734       /*
2735        * remove all groups and annotation except for the automatic stuff
2736        */
2737       newap.av.getAlignment().deleteAllGroups();
2738       newap.av.getAlignment().deleteAllAnnotations(false);
2739     }
2740
2741     newap.av.setGatherViewsHere(false);
2742
2743     if (viewport.viewName == null)
2744     {
2745       viewport.viewName = MessageManager
2746               .getString("label.view_name_original");
2747     }
2748
2749     /*
2750      * Views share the same edits undo and redo stacks
2751      */
2752     newap.av.setHistoryList(viewport.getHistoryList());
2753     newap.av.setRedoList(viewport.getRedoList());
2754
2755     /*
2756      * Views share the same mappings; need to deregister any new mappings
2757      * created by copyAlignPanel, and register the new reference to the shared
2758      * mappings
2759      */
2760     newap.av.replaceMappings(viewport.getAlignment());
2761
2762     /*
2763      * start up cDNA consensus (if applicable) now mappings are in place
2764      */
2765     if (newap.av.initComplementConsensus())
2766     {
2767       newap.refresh(true); // adjust layout of annotations
2768     }
2769
2770     newap.av.viewName = getNewViewName(viewTitle);
2771
2772     addAlignmentPanel(newap, true);
2773     newap.alignmentChanged();
2774
2775     if (alignPanels.size() == 2)
2776     {
2777       viewport.setGatherViewsHere(true);
2778     }
2779     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2780     return newap;
2781   }
2782
2783   /**
2784    * Make a new name for the view, ensuring it is unique within the current
2785    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2786    * these now use viewId. Unique view names are still desirable for usability.)
2787    *
2788    * @param viewTitle
2789    * @return
2790    */
2791   protected String getNewViewName(String viewTitle)
2792   {
2793     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2794     boolean addFirstIndex = false;
2795     if (viewTitle == null || viewTitle.trim().length() == 0)
2796     {
2797       viewTitle = MessageManager.getString("action.view");
2798       addFirstIndex = true;
2799     }
2800     else
2801     {
2802       index = 1;// we count from 1 if given a specific name
2803     }
2804     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2805
2806     List<Component> comps = PaintRefresher.components.get(viewport
2807             .getSequenceSetId());
2808
2809     List<String> existingNames = getExistingViewNames(comps);
2810
2811     while (existingNames.contains(newViewName))
2812     {
2813       newViewName = viewTitle + " " + (++index);
2814     }
2815     return newViewName;
2816   }
2817
2818   /**
2819    * Returns a list of distinct view names found in the given list of
2820    * components. View names are held on the viewport of an AlignmentPanel.
2821    *
2822    * @param comps
2823    * @return
2824    */
2825   protected List<String> getExistingViewNames(List<Component> comps)
2826   {
2827     List<String> existingNames = new ArrayList<String>();
2828     for (Component comp : comps)
2829     {
2830       if (comp instanceof AlignmentPanel)
2831       {
2832         AlignmentPanel ap = (AlignmentPanel) comp;
2833         if (!existingNames.contains(ap.av.viewName))
2834         {
2835           existingNames.add(ap.av.viewName);
2836         }
2837       }
2838     }
2839     return existingNames;
2840   }
2841
2842   /**
2843    * Explode tabbed views into separate windows.
2844    */
2845   @Override
2846   public void expandViews_actionPerformed(ActionEvent e)
2847   {
2848     Desktop.explodeViews(this);
2849   }
2850
2851   /**
2852    * Gather views in separate windows back into a tabbed presentation.
2853    */
2854   @Override
2855   public void gatherViews_actionPerformed(ActionEvent e)
2856   {
2857     Desktop.instance.gatherViews(this);
2858   }
2859
2860   /**
2861    * DOCUMENT ME!
2862    *
2863    * @param e
2864    *          DOCUMENT ME!
2865    */
2866   @Override
2867   public void font_actionPerformed(ActionEvent e)
2868   {
2869     new FontChooser(alignPanel);
2870   }
2871
2872   /**
2873    * DOCUMENT ME!
2874    *
2875    * @param e
2876    *          DOCUMENT ME!
2877    */
2878   @Override
2879   protected void seqLimit_actionPerformed(ActionEvent e)
2880   {
2881     viewport.setShowJVSuffix(seqLimits.isSelected());
2882
2883     alignPanel.getIdPanel().getIdCanvas()
2884             .setPreferredSize(alignPanel.calculateIdWidth());
2885     alignPanel.paintAlignment(true);
2886   }
2887
2888   @Override
2889   public void idRightAlign_actionPerformed(ActionEvent e)
2890   {
2891     viewport.setRightAlignIds(idRightAlign.isSelected());
2892     alignPanel.paintAlignment(true);
2893   }
2894
2895   @Override
2896   public void centreColumnLabels_actionPerformed(ActionEvent e)
2897   {
2898     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2899     alignPanel.paintAlignment(true);
2900   }
2901
2902   /*
2903    * (non-Javadoc)
2904    *
2905    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2906    */
2907   @Override
2908   protected void followHighlight_actionPerformed()
2909   {
2910     /*
2911      * Set the 'follow' flag on the Viewport (and scroll to position if now
2912      * true).
2913      */
2914     final boolean state = this.followHighlightMenuItem.getState();
2915     viewport.setFollowHighlight(state);
2916     if (state)
2917     {
2918       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2919     }
2920   }
2921
2922   /**
2923    * DOCUMENT ME!
2924    *
2925    * @param e
2926    *          DOCUMENT ME!
2927    */
2928   @Override
2929   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2930   {
2931     viewport.setColourText(colourTextMenuItem.isSelected());
2932     alignPanel.paintAlignment(true);
2933   }
2934
2935   /**
2936    * DOCUMENT ME!
2937    *
2938    * @param e
2939    *          DOCUMENT ME!
2940    */
2941   @Override
2942   public void wrapMenuItem_actionPerformed(ActionEvent e)
2943   {
2944     scaleAbove.setVisible(wrapMenuItem.isSelected());
2945     scaleLeft.setVisible(wrapMenuItem.isSelected());
2946     scaleRight.setVisible(wrapMenuItem.isSelected());
2947     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2948     alignPanel.updateLayout();
2949   }
2950
2951   @Override
2952   public void showAllSeqs_actionPerformed(ActionEvent e)
2953   {
2954     viewport.showAllHiddenSeqs();
2955   }
2956
2957   @Override
2958   public void showAllColumns_actionPerformed(ActionEvent e)
2959   {
2960     viewport.showAllHiddenColumns();
2961     repaint();
2962     viewport.sendSelection();
2963   }
2964
2965   @Override
2966   public void hideSelSequences_actionPerformed(ActionEvent e)
2967   {
2968     viewport.hideAllSelectedSeqs();
2969     // alignPanel.paintAlignment(true);
2970   }
2971
2972   /**
2973    * called by key handler and the hide all/show all menu items
2974    *
2975    * @param toggleSeqs
2976    * @param toggleCols
2977    */
2978   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2979   {
2980
2981     boolean hide = false;
2982     SequenceGroup sg = viewport.getSelectionGroup();
2983     if (!toggleSeqs && !toggleCols)
2984     {
2985       // Hide everything by the current selection - this is a hack - we do the
2986       // invert and then hide
2987       // first check that there will be visible columns after the invert.
2988       if (viewport.hasSelectedColumns()
2989               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2990                       .getEndRes()))
2991       {
2992         // now invert the sequence set, if required - empty selection implies
2993         // that no hiding is required.
2994         if (sg != null)
2995         {
2996           invertSequenceMenuItem_actionPerformed(null);
2997           sg = viewport.getSelectionGroup();
2998           toggleSeqs = true;
2999
3000         }
3001         viewport.expandColSelection(sg, true);
3002         // finally invert the column selection and get the new sequence
3003         // selection.
3004         invertColSel_actionPerformed(null);
3005         toggleCols = true;
3006       }
3007     }
3008
3009     if (toggleSeqs)
3010     {
3011       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3012       {
3013         hideSelSequences_actionPerformed(null);
3014         hide = true;
3015       }
3016       else if (!(toggleCols && viewport.hasSelectedColumns()))
3017       {
3018         showAllSeqs_actionPerformed(null);
3019       }
3020     }
3021
3022     if (toggleCols)
3023     {
3024       if (viewport.hasSelectedColumns())
3025       {
3026         hideSelColumns_actionPerformed(null);
3027         if (!toggleSeqs)
3028         {
3029           viewport.setSelectionGroup(sg);
3030         }
3031       }
3032       else if (!hide)
3033       {
3034         showAllColumns_actionPerformed(null);
3035       }
3036     }
3037   }
3038
3039   /*
3040    * (non-Javadoc)
3041    *
3042    * @see
3043    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3044    * event.ActionEvent)
3045    */
3046   @Override
3047   public void hideAllButSelection_actionPerformed(ActionEvent e)
3048   {
3049     toggleHiddenRegions(false, false);
3050     viewport.sendSelection();
3051   }
3052
3053   /*
3054    * (non-Javadoc)
3055    *
3056    * @see
3057    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3058    * .ActionEvent)
3059    */
3060   @Override
3061   public void hideAllSelection_actionPerformed(ActionEvent e)
3062   {
3063     SequenceGroup sg = viewport.getSelectionGroup();
3064     viewport.expandColSelection(sg, false);
3065     viewport.hideAllSelectedSeqs();
3066     viewport.hideSelectedColumns();
3067     alignPanel.paintAlignment(true);
3068     viewport.sendSelection();
3069   }
3070
3071   /*
3072    * (non-Javadoc)
3073    *
3074    * @see
3075    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3076    * ActionEvent)
3077    */
3078   @Override
3079   public void showAllhidden_actionPerformed(ActionEvent e)
3080   {
3081     viewport.showAllHiddenColumns();
3082     viewport.showAllHiddenSeqs();
3083     alignPanel.paintAlignment(true);
3084     viewport.sendSelection();
3085   }
3086
3087   @Override
3088   public void hideSelColumns_actionPerformed(ActionEvent e)
3089   {
3090     viewport.hideSelectedColumns();
3091     alignPanel.paintAlignment(true);
3092     viewport.sendSelection();
3093   }
3094
3095   @Override
3096   public void hiddenMarkers_actionPerformed(ActionEvent e)
3097   {
3098     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3099     repaint();
3100   }
3101
3102   /**
3103    * DOCUMENT ME!
3104    *
3105    * @param e
3106    *          DOCUMENT ME!
3107    */
3108   @Override
3109   protected void scaleAbove_actionPerformed(ActionEvent e)
3110   {
3111     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3112     alignPanel.paintAlignment(true);
3113   }
3114
3115   /**
3116    * DOCUMENT ME!
3117    *
3118    * @param e
3119    *          DOCUMENT ME!
3120    */
3121   @Override
3122   protected void scaleLeft_actionPerformed(ActionEvent e)
3123   {
3124     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3125     alignPanel.paintAlignment(true);
3126   }
3127
3128   /**
3129    * DOCUMENT ME!
3130    *
3131    * @param e
3132    *          DOCUMENT ME!
3133    */
3134   @Override
3135   protected void scaleRight_actionPerformed(ActionEvent e)
3136   {
3137     viewport.setScaleRightWrapped(scaleRight.isSelected());
3138     alignPanel.paintAlignment(true);
3139   }
3140
3141   /**
3142    * DOCUMENT ME!
3143    *
3144    * @param e
3145    *          DOCUMENT ME!
3146    */
3147   @Override
3148   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3149   {
3150     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3151     alignPanel.paintAlignment(true);
3152   }
3153
3154   /**
3155    * DOCUMENT ME!
3156    *
3157    * @param e
3158    *          DOCUMENT ME!
3159    */
3160   @Override
3161   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3162   {
3163     viewport.setShowText(viewTextMenuItem.isSelected());
3164     alignPanel.paintAlignment(true);
3165   }
3166
3167   /**
3168    * DOCUMENT ME!
3169    *
3170    * @param e
3171    *          DOCUMENT ME!
3172    */
3173   @Override
3174   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3175   {
3176     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3177     alignPanel.paintAlignment(true);
3178   }
3179
3180   public FeatureSettings featureSettings;
3181
3182   @Override
3183   public FeatureSettingsControllerI getFeatureSettingsUI()
3184   {
3185     return featureSettings;
3186   }
3187
3188   @Override
3189   public void featureSettings_actionPerformed(ActionEvent e)
3190   {
3191     if (featureSettings != null)
3192     {
3193       featureSettings.close();
3194       featureSettings = null;
3195     }
3196     if (!showSeqFeatures.isSelected())
3197     {
3198       // make sure features are actually displayed
3199       showSeqFeatures.setSelected(true);
3200       showSeqFeatures_actionPerformed(null);
3201     }
3202     featureSettings = new FeatureSettings(this);
3203   }
3204
3205   /**
3206    * Set or clear 'Show Sequence Features'
3207    *
3208    * @param evt
3209    *          DOCUMENT ME!
3210    */
3211   @Override
3212   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3213   {
3214     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3215     alignPanel.paintAlignment(true);
3216     if (alignPanel.getOverviewPanel() != null)
3217     {
3218       alignPanel.getOverviewPanel().updateOverviewImage();
3219     }
3220   }
3221
3222   /**
3223    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3224    * the annotations panel as a whole.
3225    *
3226    * The options to show/hide all annotations should be enabled when the panel
3227    * is shown, and disabled when the panel is hidden.
3228    *
3229    * @param e
3230    */
3231   @Override
3232   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3233   {
3234     final boolean setVisible = annotationPanelMenuItem.isSelected();
3235     viewport.setShowAnnotation(setVisible);
3236     this.showAllSeqAnnotations.setEnabled(setVisible);
3237     this.hideAllSeqAnnotations.setEnabled(setVisible);
3238     this.showAllAlAnnotations.setEnabled(setVisible);
3239     this.hideAllAlAnnotations.setEnabled(setVisible);
3240     alignPanel.updateLayout();
3241   }
3242
3243   @Override
3244   public void alignmentProperties()
3245   {
3246     JEditorPane editPane = new JEditorPane("text/html", "");
3247     editPane.setEditable(false);
3248     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3249             .formatAsHtml();
3250     editPane.setText(MessageManager.formatMessage("label.html_content",
3251             new Object[] { contents.toString() }));
3252     JInternalFrame frame = new JInternalFrame();
3253     frame.getContentPane().add(new JScrollPane(editPane));
3254
3255     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3256             "label.alignment_properties", new Object[] { getTitle() }),
3257             500, 400);
3258   }
3259
3260   /**
3261    * DOCUMENT ME!
3262    *
3263    * @param e
3264    *          DOCUMENT ME!
3265    */
3266   @Override
3267   public void overviewMenuItem_actionPerformed(ActionEvent e)
3268   {
3269     if (alignPanel.overviewPanel != null)
3270     {
3271       return;
3272     }
3273
3274     JInternalFrame frame = new JInternalFrame();
3275     OverviewPanel overview = new OverviewPanel(alignPanel);
3276     frame.setContentPane(overview);
3277     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3278             "label.overview_params", new Object[] { this.getTitle() }),
3279             frame.getWidth(), frame.getHeight());
3280     frame.pack();
3281     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3282     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3283     {
3284       @Override
3285       public void internalFrameClosed(
3286               javax.swing.event.InternalFrameEvent evt)
3287       {
3288         alignPanel.setOverviewPanel(null);
3289       };
3290     });
3291
3292     alignPanel.setOverviewPanel(overview);
3293   }
3294
3295   @Override
3296   public void textColour_actionPerformed()
3297   {
3298     new TextColourChooser().chooseColour(alignPanel, null);
3299   }
3300
3301   /*
3302    * public void covariationColour_actionPerformed() {
3303    * changeColour(new
3304    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3305    * ()[0])); }
3306    */
3307   @Override
3308   public void annotationColour_actionPerformed()
3309   {
3310     new AnnotationColourChooser(viewport, alignPanel);
3311   }
3312
3313   @Override
3314   public void annotationColumn_actionPerformed(ActionEvent e)
3315   {
3316     new AnnotationColumnChooser(viewport, alignPanel);
3317   }
3318
3319   /**
3320    * Action on the user checking or unchecking the option to apply the selected
3321    * colour scheme to all groups. If unchecked, groups may have their own
3322    * independent colour schemes.
3323    *
3324    * @param selected
3325    */
3326   @Override
3327   public void applyToAllGroups_actionPerformed(boolean selected)
3328   {
3329     viewport.setColourAppliesToAllGroups(selected);
3330   }
3331
3332   /**
3333    * Action on user selecting a colour from the colour menu
3334    *
3335    * @param name
3336    *          the name (not the menu item label!) of the colour scheme
3337    */
3338   @Override
3339   public void changeColour_actionPerformed(String name)
3340   {
3341     /*
3342      * 'User Defined' opens a panel to configure or load a
3343      * user-defined colour scheme
3344      */
3345     if (ResidueColourScheme.USER_DEFINED.equals(name))
3346     {
3347       new UserDefinedColours(alignPanel);
3348       return;
3349     }
3350
3351     /*
3352      * otherwise set the chosen colour scheme (or null for 'None')
3353      */
3354     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3355             viewport.getAlignment(), viewport.getHiddenRepSequences());
3356     changeColour(cs);
3357   }
3358
3359   /**
3360    * Actions on setting or changing the alignment colour scheme
3361    *
3362    * @param cs
3363    */
3364   @Override
3365   public void changeColour(ColourSchemeI cs)
3366   {
3367     // TODO: pull up to controller method
3368     ColourMenuHelper.setColourSelected(colourMenu, cs);
3369
3370     viewport.setGlobalColourScheme(cs);
3371
3372     alignPanel.paintAlignment(true);
3373   }
3374
3375   /**
3376    * Show the PID threshold slider panel
3377    */
3378   @Override
3379   protected void modifyPID_actionPerformed()
3380   {
3381     SliderPanel.setPIDSliderSource(alignPanel,
3382             viewport.getResidueShading(), alignPanel.getViewName());
3383     SliderPanel.showPIDSlider();
3384   }
3385
3386   /**
3387    * Show the Conservation slider panel
3388    */
3389   @Override
3390   protected void modifyConservation_actionPerformed()
3391   {
3392     SliderPanel.setConservationSlider(alignPanel,
3393             viewport.getResidueShading(), alignPanel.getViewName());
3394     SliderPanel.showConservationSlider();
3395   }
3396
3397   /**
3398    * Action on selecting or deselecting (Colour) By Conservation
3399    */
3400   @Override
3401   public void conservationMenuItem_actionPerformed(boolean selected)
3402   {
3403     modifyConservation.setEnabled(selected);
3404     viewport.setConservationSelected(selected);
3405     viewport.getResidueShading().setConservationApplied(selected);
3406
3407     changeColour(viewport.getGlobalColourScheme());
3408     if (selected)
3409     {
3410       modifyConservation_actionPerformed();
3411     }
3412     else
3413     {
3414       SliderPanel.hideConservationSlider();
3415     }
3416   }
3417
3418   /**
3419    * Action on selecting or deselecting (Colour) Above PID Threshold
3420    */
3421   @Override
3422   public void abovePIDThreshold_actionPerformed(boolean selected)
3423   {
3424     modifyPID.setEnabled(selected);
3425     viewport.setAbovePIDThreshold(selected);
3426     if (!selected)
3427     {
3428       viewport.getResidueShading().setThreshold(0,
3429               viewport.isIgnoreGapsConsensus());
3430     }
3431
3432     changeColour(viewport.getGlobalColourScheme());
3433     if (selected)
3434     {
3435       modifyPID_actionPerformed();
3436     }
3437     else
3438     {
3439       SliderPanel.hidePIDSlider();
3440     }
3441   }
3442
3443   /**
3444    * DOCUMENT ME!
3445    *
3446    * @param e
3447    *          DOCUMENT ME!
3448    */
3449   @Override
3450   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3451   {
3452     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3453     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3454             .getAlignment().getSequenceAt(0));
3455     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3456             viewport.getAlignment()));
3457     alignPanel.paintAlignment(true);
3458   }
3459
3460   /**
3461    * DOCUMENT ME!
3462    *
3463    * @param e
3464    *          DOCUMENT ME!
3465    */
3466   @Override
3467   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3468   {
3469     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470     AlignmentSorter.sortByID(viewport.getAlignment());
3471     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3472             viewport.getAlignment()));
3473     alignPanel.paintAlignment(true);
3474   }
3475
3476   /**
3477    * DOCUMENT ME!
3478    *
3479    * @param e
3480    *          DOCUMENT ME!
3481    */
3482   @Override
3483   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3484   {
3485     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3486     AlignmentSorter.sortByLength(viewport.getAlignment());
3487     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3488             viewport.getAlignment()));
3489     alignPanel.paintAlignment(true);
3490   }
3491
3492   /**
3493    * DOCUMENT ME!
3494    *
3495    * @param e
3496    *          DOCUMENT ME!
3497    */
3498   @Override
3499   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3500   {
3501     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3502     AlignmentSorter.sortByGroup(viewport.getAlignment());
3503     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3504             viewport.getAlignment()));
3505
3506     alignPanel.paintAlignment(true);
3507   }
3508
3509   /**
3510    * DOCUMENT ME!
3511    *
3512    * @param e
3513    *          DOCUMENT ME!
3514    */
3515   @Override
3516   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3517   {
3518     new RedundancyPanel(alignPanel, this);
3519   }
3520
3521   /**
3522    * DOCUMENT ME!
3523    *
3524    * @param e
3525    *          DOCUMENT ME!
3526    */
3527   @Override
3528   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3529   {
3530     if ((viewport.getSelectionGroup() == null)
3531             || (viewport.getSelectionGroup().getSize() < 2))
3532     {
3533       JvOptionPane.showInternalMessageDialog(this, MessageManager
3534               .getString("label.you_must_select_least_two_sequences"),
3535               MessageManager.getString("label.invalid_selection"),
3536               JvOptionPane.WARNING_MESSAGE);
3537     }
3538     else
3539     {
3540       JInternalFrame frame = new JInternalFrame();
3541       frame.setContentPane(new PairwiseAlignPanel(viewport));
3542       Desktop.addInternalFrame(frame,
3543               MessageManager.getString("action.pairwise_alignment"), 600,
3544               500);
3545     }
3546   }
3547
3548   @Override
3549   public void autoCalculate_actionPerformed(ActionEvent e)
3550   {
3551     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3552     if (viewport.autoCalculateConsensus)
3553     {
3554       viewport.firePropertyChange("alignment", null, viewport
3555               .getAlignment().getSequences());
3556     }
3557   }
3558
3559   @Override
3560   public void sortByTreeOption_actionPerformed(ActionEvent e)
3561   {
3562     viewport.sortByTree = sortByTree.isSelected();
3563   }
3564
3565   @Override
3566   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3567   {
3568     viewport.followSelection = listenToViewSelections.isSelected();
3569   }
3570
3571   /**
3572    * Constructs a tree panel and adds it to the desktop
3573    *
3574    * @param type
3575    *          tree type (NJ or AV)
3576    * @param modelName
3577    *          name of score model used to compute the tree
3578    * @param options
3579    *          parameters for the distance or similarity calculation
3580    */
3581   void newTreePanel(String type, String modelName, SimilarityParamsI options)
3582   {
3583     String frameTitle = "";
3584     TreePanel tp;
3585
3586     boolean onSelection = false;
3587     if (viewport.getSelectionGroup() != null
3588             && viewport.getSelectionGroup().getSize() > 0)
3589     {
3590       SequenceGroup sg = viewport.getSelectionGroup();
3591
3592       /* Decide if the selection is a column region */
3593       for (SequenceI _s : sg.getSequences())
3594       {
3595         if (_s.getLength() < sg.getEndRes())
3596         {
3597           JvOptionPane
3598                   .showMessageDialog(
3599                           Desktop.desktop,
3600                           MessageManager
3601                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3602                           MessageManager
3603                                   .getString("label.sequences_selection_not_aligned"),
3604                           JvOptionPane.WARNING_MESSAGE);
3605
3606           return;
3607         }
3608       }
3609       onSelection = true;
3610     }
3611     else
3612     {
3613       if (viewport.getAlignment().getHeight() < 2)
3614       {
3615         return;
3616       }
3617     }
3618
3619     tp = new TreePanel(alignPanel, type, modelName, options);
3620     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3621
3622     frameTitle += " from ";
3623
3624     if (viewport.viewName != null)
3625     {
3626       frameTitle += viewport.viewName + " of ";
3627     }
3628
3629     frameTitle += this.title;
3630
3631     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3632   }
3633
3634   /**
3635    * DOCUMENT ME!
3636    *
3637    * @param title
3638    *          DOCUMENT ME!
3639    * @param order
3640    *          DOCUMENT ME!
3641    */
3642   public void addSortByOrderMenuItem(String title,
3643           final AlignmentOrder order)
3644   {
3645     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3646             "action.by_title_param", new Object[] { title }));
3647     sort.add(item);
3648     item.addActionListener(new java.awt.event.ActionListener()
3649     {
3650       @Override
3651       public void actionPerformed(ActionEvent e)
3652       {
3653         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3654
3655         // TODO: JBPNote - have to map order entries to curent SequenceI
3656         // pointers
3657         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3658
3659         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3660                 .getAlignment()));
3661
3662         alignPanel.paintAlignment(true);
3663       }
3664     });
3665   }
3666
3667   /**
3668    * Add a new sort by annotation score menu item
3669    *
3670    * @param sort
3671    *          the menu to add the option to
3672    * @param scoreLabel
3673    *          the label used to retrieve scores for each sequence on the
3674    *          alignment
3675    */
3676   public void addSortByAnnotScoreMenuItem(JMenu sort,
3677           final String scoreLabel)
3678   {
3679     final JMenuItem item = new JMenuItem(scoreLabel);
3680     sort.add(item);
3681     item.addActionListener(new java.awt.event.ActionListener()
3682     {
3683       @Override
3684       public void actionPerformed(ActionEvent e)
3685       {
3686         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3687         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3688                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3689         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3690                 viewport.getAlignment()));
3691         alignPanel.paintAlignment(true);
3692       }
3693     });
3694   }
3695
3696   /**
3697    * last hash for alignment's annotation array - used to minimise cost of
3698    * rebuild.
3699    */
3700   protected int _annotationScoreVectorHash;
3701
3702   /**
3703    * search the alignment and rebuild the sort by annotation score submenu the
3704    * last alignment annotation vector hash is stored to minimize cost of
3705    * rebuilding in subsequence calls.
3706    *
3707    */
3708   @Override
3709   public void buildSortByAnnotationScoresMenu()
3710   {
3711     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3712     {
3713       return;
3714     }
3715
3716     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3717     {
3718       sortByAnnotScore.removeAll();
3719       // almost certainly a quicker way to do this - but we keep it simple
3720       Hashtable scoreSorts = new Hashtable();
3721       AlignmentAnnotation aann[];
3722       for (SequenceI sqa : viewport.getAlignment().getSequences())
3723       {
3724         aann = sqa.getAnnotation();
3725         for (int i = 0; aann != null && i < aann.length; i++)
3726         {
3727           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3728           {
3729             scoreSorts.put(aann[i].label, aann[i].label);
3730           }
3731         }
3732       }
3733       Enumeration labels = scoreSorts.keys();
3734       while (labels.hasMoreElements())
3735       {
3736         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3737                 (String) labels.nextElement());
3738       }
3739       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3740       scoreSorts.clear();
3741
3742       _annotationScoreVectorHash = viewport.getAlignment()
3743               .getAlignmentAnnotation().hashCode();
3744     }
3745   }
3746
3747   /**
3748    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3749    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3750    * call. Listeners are added to remove the menu item when the treePanel is
3751    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3752    * modified.
3753    */
3754   @Override
3755   public void buildTreeSortMenu()
3756   {
3757     sortByTreeMenu.removeAll();
3758
3759     List<Component> comps = PaintRefresher.components.get(viewport
3760             .getSequenceSetId());
3761     List<TreePanel> treePanels = new ArrayList<TreePanel>();
3762     for (Component comp : comps)
3763     {
3764       if (comp instanceof TreePanel)
3765       {
3766         treePanels.add((TreePanel) comp);
3767       }
3768     }
3769
3770     if (treePanels.size() < 1)
3771     {
3772       sortByTreeMenu.setVisible(false);
3773       return;
3774     }
3775
3776     sortByTreeMenu.setVisible(true);
3777
3778     for (final TreePanel tp : treePanels)
3779     {
3780       final JMenuItem item = new JMenuItem(tp.getTitle());
3781       item.addActionListener(new java.awt.event.ActionListener()
3782       {
3783         @Override
3784         public void actionPerformed(ActionEvent e)
3785         {
3786           tp.sortByTree_actionPerformed();
3787           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3788
3789         }
3790       });
3791
3792       sortByTreeMenu.add(item);
3793     }
3794   }
3795
3796   public boolean sortBy(AlignmentOrder alorder, String undoname)
3797   {
3798     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3799     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3800     if (undoname != null)
3801     {
3802       addHistoryItem(new OrderCommand(undoname, oldOrder,
3803               viewport.getAlignment()));
3804     }
3805     alignPanel.paintAlignment(true);
3806     return true;
3807   }
3808
3809   /**
3810    * Work out whether the whole set of sequences or just the selected set will
3811    * be submitted for multiple alignment.
3812    *
3813    */
3814   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3815   {
3816     // Now, check we have enough sequences
3817     AlignmentView msa = null;
3818
3819     if ((viewport.getSelectionGroup() != null)
3820             && (viewport.getSelectionGroup().getSize() > 1))
3821     {
3822       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3823       // some common interface!
3824       /*
3825        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3826        * SequenceI[sz = seqs.getSize(false)];
3827        *
3828        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3829        * seqs.getSequenceAt(i); }
3830        */
3831       msa = viewport.getAlignmentView(true);
3832     }
3833     else if (viewport.getSelectionGroup() != null
3834             && viewport.getSelectionGroup().getSize() == 1)
3835     {
3836       int option = JvOptionPane.showConfirmDialog(this,
3837               MessageManager.getString("warn.oneseq_msainput_selection"),
3838               MessageManager.getString("label.invalid_selection"),
3839               JvOptionPane.OK_CANCEL_OPTION);
3840       if (option == JvOptionPane.OK_OPTION)
3841       {
3842         msa = viewport.getAlignmentView(false);
3843       }
3844     }
3845     else
3846     {
3847       msa = viewport.getAlignmentView(false);
3848     }
3849     return msa;
3850   }
3851
3852   /**
3853    * Decides what is submitted to a secondary structure prediction service: the
3854    * first sequence in the alignment, or in the current selection, or, if the
3855    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3856    * region or the whole alignment. (where the first sequence in the set is the
3857    * one that the prediction will be for).
3858    */
3859   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3860   {
3861     AlignmentView seqs = null;
3862
3863     if ((viewport.getSelectionGroup() != null)
3864             && (viewport.getSelectionGroup().getSize() > 0))
3865     {
3866       seqs = viewport.getAlignmentView(true);
3867     }
3868     else
3869     {
3870       seqs = viewport.getAlignmentView(false);
3871     }
3872     // limit sequences - JBPNote in future - could spawn multiple prediction
3873     // jobs
3874     // TODO: viewport.getAlignment().isAligned is a global state - the local
3875     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3876     if (!viewport.getAlignment().isAligned(false))
3877     {
3878       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3879       // TODO: if seqs.getSequences().length>1 then should really have warned
3880       // user!
3881
3882     }
3883     return seqs;
3884   }
3885
3886   /**
3887    * DOCUMENT ME!
3888    *
3889    * @param e
3890    *          DOCUMENT ME!
3891    */
3892   @Override
3893   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3894   {
3895     // Pick the tree file
3896     JalviewFileChooser chooser = new JalviewFileChooser(
3897             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3898     chooser.setFileView(new JalviewFileView());
3899     chooser.setDialogTitle(MessageManager
3900             .getString("label.select_newick_like_tree_file"));
3901     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3902
3903     int value = chooser.showOpenDialog(null);
3904
3905     if (value == JalviewFileChooser.APPROVE_OPTION)
3906     {
3907       String filePath = chooser.getSelectedFile().getPath();
3908       Cache.setProperty("LAST_DIRECTORY", filePath);
3909       NewickFile fin = null;
3910       try
3911       {
3912         fin = new NewickFile(filePath, DataSourceType.FILE);
3913         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3914       } catch (Exception ex)
3915       {
3916         JvOptionPane
3917                 .showMessageDialog(
3918                         Desktop.desktop,
3919                         ex.getMessage(),
3920                         MessageManager
3921                                 .getString("label.problem_reading_tree_file"),
3922                         JvOptionPane.WARNING_MESSAGE);
3923         ex.printStackTrace();
3924       }
3925       if (fin != null && fin.hasWarningMessage())
3926       {
3927         JvOptionPane.showMessageDialog(Desktop.desktop, fin
3928                 .getWarningMessage(), MessageManager
3929                 .getString("label.possible_problem_with_tree_file"),
3930                 JvOptionPane.WARNING_MESSAGE);
3931       }
3932     }
3933   }
3934
3935   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3936   {
3937     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3938   }
3939
3940   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3941           int h, int x, int y)
3942   {
3943     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3944   }
3945
3946   /**
3947    * Add a treeviewer for the tree extracted from a Newick file object to the
3948    * current alignment view
3949    *
3950    * @param nf
3951    *          the tree
3952    * @param title
3953    *          tree viewer title
3954    * @param input
3955    *          Associated alignment input data (or null)
3956    * @param w
3957    *          width
3958    * @param h
3959    *          height
3960    * @param x
3961    *          position
3962    * @param y
3963    *          position
3964    * @return TreePanel handle
3965    */
3966   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3967           AlignmentView input, int w, int h, int x, int y)
3968   {
3969     TreePanel tp = null;
3970
3971     try
3972     {
3973       nf.parse();
3974
3975       if (nf.getTree() != null)
3976       {
3977         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3978
3979         tp.setSize(w, h);
3980
3981         if (x > 0 && y > 0)
3982         {
3983           tp.setLocation(x, y);
3984         }
3985
3986         Desktop.addInternalFrame(tp, treeTitle, w, h);
3987       }
3988     } catch (Exception ex)
3989     {
3990       ex.printStackTrace();
3991     }
3992
3993     return tp;
3994   }
3995
3996   private boolean buildingMenu = false;
3997
3998   /**
3999    * Generates menu items and listener event actions for web service clients
4000    *
4001    */
4002   public void BuildWebServiceMenu()
4003   {
4004     while (buildingMenu)
4005     {
4006       try
4007       {
4008         System.err.println("Waiting for building menu to finish.");
4009         Thread.sleep(10);
4010       } catch (Exception e)
4011       {
4012       }
4013     }
4014     final AlignFrame me = this;
4015     buildingMenu = true;
4016     new Thread(new Runnable()
4017     {
4018       @Override
4019       public void run()
4020       {
4021         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4022         try
4023         {
4024           // System.err.println("Building ws menu again "
4025           // + Thread.currentThread());
4026           // TODO: add support for context dependent disabling of services based
4027           // on
4028           // alignment and current selection
4029           // TODO: add additional serviceHandle parameter to specify abstract
4030           // handler
4031           // class independently of AbstractName
4032           // TODO: add in rediscovery GUI function to restart discoverer
4033           // TODO: group services by location as well as function and/or
4034           // introduce
4035           // object broker mechanism.
4036           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4037           final IProgressIndicator af = me;
4038
4039           /*
4040            * do not i18n these strings - they are hard-coded in class
4041            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4042            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4043            */
4044           final JMenu msawsmenu = new JMenu("Alignment");
4045           final JMenu secstrmenu = new JMenu(
4046                   "Secondary Structure Prediction");
4047           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4048           final JMenu analymenu = new JMenu("Analysis");
4049           final JMenu dismenu = new JMenu("Protein Disorder");
4050           // JAL-940 - only show secondary structure prediction services from
4051           // the legacy server
4052           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4053               // &&
4054           Discoverer.services != null && (Discoverer.services.size() > 0))
4055           {
4056             // TODO: refactor to allow list of AbstractName/Handler bindings to
4057             // be
4058             // stored or retrieved from elsewhere
4059             // No MSAWS used any more:
4060             // Vector msaws = null; // (Vector)
4061             // Discoverer.services.get("MsaWS");
4062             Vector secstrpr = (Vector) Discoverer.services
4063                     .get("SecStrPred");
4064             if (secstrpr != null)
4065             {
4066               // Add any secondary structure prediction services
4067               for (int i = 0, j = secstrpr.size(); i < j; i++)
4068               {
4069                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4070                         .get(i);
4071                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4072                         .getServiceClient(sh);
4073                 int p = secstrmenu.getItemCount();
4074                 impl.attachWSMenuEntry(secstrmenu, me);
4075                 int q = secstrmenu.getItemCount();
4076                 for (int litm = p; litm < q; litm++)
4077                 {
4078                   legacyItems.add(secstrmenu.getItem(litm));
4079                 }
4080               }
4081             }
4082           }
4083
4084           // Add all submenus in the order they should appear on the web
4085           // services menu
4086           wsmenu.add(msawsmenu);
4087           wsmenu.add(secstrmenu);
4088           wsmenu.add(dismenu);
4089           wsmenu.add(analymenu);
4090           // No search services yet
4091           // wsmenu.add(seqsrchmenu);
4092
4093           javax.swing.SwingUtilities.invokeLater(new Runnable()
4094           {
4095             @Override
4096             public void run()
4097             {
4098               try
4099               {
4100                 webService.removeAll();
4101                 // first, add discovered services onto the webservices menu
4102                 if (wsmenu.size() > 0)
4103                 {
4104                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4105                   {
4106                     webService.add(wsmenu.get(i));
4107                   }
4108                 }
4109                 else
4110                 {
4111                   webService.add(me.webServiceNoServices);
4112                 }
4113                 // TODO: move into separate menu builder class.
4114                 boolean new_sspred = false;
4115                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4116                 {
4117                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4118                   if (jws2servs != null)
4119                   {
4120                     if (jws2servs.hasServices())
4121                     {
4122                       jws2servs.attachWSMenuEntry(webService, me);
4123                       for (Jws2Instance sv : jws2servs.getServices())
4124                       {
4125                         if (sv.description.toLowerCase().contains("jpred"))
4126                         {
4127                           for (JMenuItem jmi : legacyItems)
4128                           {
4129                             jmi.setVisible(false);
4130                           }
4131                         }
4132                       }
4133
4134                     }
4135                     if (jws2servs.isRunning())
4136                     {
4137                       JMenuItem tm = new JMenuItem(
4138                               "Still discovering JABA Services");
4139                       tm.setEnabled(false);
4140                       webService.add(tm);
4141                     }
4142                   }
4143                 }
4144                 build_urlServiceMenu(me.webService);
4145                 build_fetchdbmenu(webService);
4146                 for (JMenu item : wsmenu)
4147                 {
4148                   if (item.getItemCount() == 0)
4149                   {
4150                     item.setEnabled(false);
4151                   }
4152                   else
4153                   {
4154                     item.setEnabled(true);
4155                   }
4156                 }
4157               } catch (Exception e)
4158               {
4159                 Cache.log
4160                         .debug("Exception during web service menu building process.",
4161                                 e);
4162               }
4163             }
4164           });
4165         } catch (Exception e)
4166         {
4167         }
4168         buildingMenu = false;
4169       }
4170     }).start();
4171
4172   }
4173
4174   /**
4175    * construct any groupURL type service menu entries.
4176    *
4177    * @param webService
4178    */
4179   private void build_urlServiceMenu(JMenu webService)
4180   {
4181     // TODO: remove this code when 2.7 is released
4182     // DEBUG - alignmentView
4183     /*
4184      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4185      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4186      *
4187      * @Override public void actionPerformed(ActionEvent e) {
4188      * jalview.datamodel.AlignmentView
4189      * .testSelectionViews(af.viewport.getAlignment(),
4190      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4191      *
4192      * }); webService.add(testAlView);
4193      */
4194     // TODO: refactor to RestClient discoverer and merge menu entries for
4195     // rest-style services with other types of analysis/calculation service
4196     // SHmmr test client - still being implemented.
4197     // DEBUG - alignmentView
4198
4199     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4200             .getRestClients())
4201     {
4202       client.attachWSMenuEntry(
4203               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4204               this);
4205     }
4206   }
4207
4208   /**
4209    * Searches the alignment sequences for xRefs and builds the Show
4210    * Cross-References menu (formerly called Show Products), with database
4211    * sources for which cross-references are found (protein sources for a
4212    * nucleotide alignment and vice versa)
4213    *
4214    * @return true if Show Cross-references menu should be enabled
4215    */
4216   public boolean canShowProducts()
4217   {
4218     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4219     AlignmentI dataset = viewport.getAlignment().getDataset();
4220
4221     showProducts.removeAll();
4222     final boolean dna = viewport.getAlignment().isNucleotide();
4223
4224     if (seqs == null || seqs.length == 0)
4225     {
4226       // nothing to see here.
4227       return false;
4228     }
4229
4230     boolean showp = false;
4231     try
4232     {
4233       List<String> ptypes = new CrossRef(seqs, dataset)
4234               .findXrefSourcesForSequences(dna);
4235
4236       for (final String source : ptypes)
4237       {
4238         showp = true;
4239         final AlignFrame af = this;
4240         JMenuItem xtype = new JMenuItem(source);
4241         xtype.addActionListener(new ActionListener()
4242         {
4243           @Override
4244           public void actionPerformed(ActionEvent e)
4245           {
4246             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4247           }
4248         });
4249         showProducts.add(xtype);
4250       }
4251       showProducts.setVisible(showp);
4252       showProducts.setEnabled(showp);
4253     } catch (Exception e)
4254     {
4255       Cache.log
4256               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4257                       e);
4258       return false;
4259     }
4260     return showp;
4261   }
4262
4263   /**
4264    * Finds and displays cross-references for the selected sequences (protein
4265    * products for nucleotide sequences, dna coding sequences for peptides).
4266    *
4267    * @param sel
4268    *          the sequences to show cross-references for
4269    * @param dna
4270    *          true if from a nucleotide alignment (so showing proteins)
4271    * @param source
4272    *          the database to show cross-references for
4273    */
4274   protected void showProductsFor(final SequenceI[] sel,
4275           final boolean _odna, final String source)
4276   {
4277     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4278             .start();
4279   }
4280
4281   /**
4282    * Construct and display a new frame containing the translation of this
4283    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4284    */
4285   @Override
4286   public void showTranslation_actionPerformed(ActionEvent e)
4287   {
4288     AlignmentI al = null;
4289     try
4290     {
4291       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4292
4293       al = dna.translateCdna();
4294     } catch (Exception ex)
4295     {
4296       jalview.bin.Cache.log.error(
4297               "Exception during translation. Please report this !", ex);
4298       final String msg = MessageManager
4299               .getString("label.error_when_translating_sequences_submit_bug_report");
4300       final String errorTitle = MessageManager
4301               .getString("label.implementation_error")
4302               + MessageManager.getString("label.translation_failed");
4303       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4304               JvOptionPane.ERROR_MESSAGE);
4305       return;
4306     }
4307     if (al == null || al.getHeight() == 0)
4308     {
4309       final String msg = MessageManager
4310               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4311       final String errorTitle = MessageManager
4312               .getString("label.translation_failed");
4313       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4314               JvOptionPane.WARNING_MESSAGE);
4315     }
4316     else
4317     {
4318       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4319       af.setFileFormat(this.currentFileFormat);
4320       final String newTitle = MessageManager.formatMessage(
4321               "label.translation_of_params",
4322               new Object[] { this.getTitle() });
4323       af.setTitle(newTitle);
4324       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4325       {
4326         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4327         viewport.openSplitFrame(af, new Alignment(seqs));
4328       }
4329       else
4330       {
4331         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4332                 DEFAULT_HEIGHT);
4333       }
4334     }
4335   }
4336
4337   /**
4338    * Set the file format
4339    *
4340    * @param format
4341    */
4342   public void setFileFormat(FileFormatI format)
4343   {
4344     this.currentFileFormat = format;
4345   }
4346
4347   /**
4348    * Try to load a features file onto the alignment.
4349    *
4350    * @param file
4351    *          contents or path to retrieve file
4352    * @param sourceType
4353    *          access mode of file (see jalview.io.AlignFile)
4354    * @return true if features file was parsed correctly.
4355    */
4356   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4357   {
4358     return avc.parseFeaturesFile(file, sourceType,
4359             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4360
4361   }
4362
4363   @Override
4364   public void refreshFeatureUI(boolean enableIfNecessary)
4365   {
4366     // note - currently this is only still here rather than in the controller
4367     // because of the featureSettings hard reference that is yet to be
4368     // abstracted
4369     if (enableIfNecessary)
4370     {
4371       viewport.setShowSequenceFeatures(true);
4372       showSeqFeatures.setSelected(true);
4373     }
4374
4375   }
4376
4377   @Override
4378   public void dragEnter(DropTargetDragEvent evt)
4379   {
4380   }
4381
4382   @Override
4383   public void dragExit(DropTargetEvent evt)
4384   {
4385   }
4386
4387   @Override
4388   public void dragOver(DropTargetDragEvent evt)
4389   {
4390   }
4391
4392   @Override
4393   public void dropActionChanged(DropTargetDragEvent evt)
4394   {
4395   }
4396
4397   @Override
4398   public void drop(DropTargetDropEvent evt)
4399   {
4400     // JAL-1552 - acceptDrop required before getTransferable call for
4401     // Java's Transferable for native dnd
4402     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4403     Transferable t = evt.getTransferable();
4404     List<String> files = new ArrayList<String>();
4405     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4406
4407     try
4408     {
4409       Desktop.transferFromDropTarget(files, protocols, evt, t);
4410     } catch (Exception e)
4411     {
4412       e.printStackTrace();
4413     }
4414     if (files != null)
4415     {
4416       try
4417       {
4418         // check to see if any of these files have names matching sequences in
4419         // the alignment
4420         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4421                 .getAlignment().getSequencesArray());
4422         /**
4423          * Object[] { String,SequenceI}
4424          */
4425         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4426         ArrayList<String> filesnotmatched = new ArrayList<String>();
4427         for (int i = 0; i < files.size(); i++)
4428         {
4429           String file = files.get(i).toString();
4430           String pdbfn = "";
4431           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4432           if (protocol == DataSourceType.FILE)
4433           {
4434             File fl = new File(file);
4435             pdbfn = fl.getName();
4436           }
4437           else if (protocol == DataSourceType.URL)
4438           {
4439             URL url = new URL(file);
4440             pdbfn = url.getFile();
4441           }
4442           if (pdbfn.length() > 0)
4443           {
4444             // attempt to find a match in the alignment
4445             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4446             int l = 0, c = pdbfn.indexOf(".");
4447             while (mtch == null && c != -1)
4448             {
4449               do
4450               {
4451                 l = c;
4452               } while ((c = pdbfn.indexOf(".", l)) > l);
4453               if (l > -1)
4454               {
4455                 pdbfn = pdbfn.substring(0, l);
4456               }
4457               mtch = idm.findAllIdMatches(pdbfn);
4458             }
4459             if (mtch != null)
4460             {
4461               FileFormatI type = null;
4462               try
4463               {
4464                 type = new IdentifyFile().identify(file, protocol);
4465               } catch (Exception ex)
4466               {
4467                 type = null;
4468               }
4469               if (type != null && type.isStructureFile())
4470               {
4471                 filesmatched.add(new Object[] { file, protocol, mtch });
4472                 continue;
4473               }
4474             }
4475             // File wasn't named like one of the sequences or wasn't a PDB file.
4476             filesnotmatched.add(file);
4477           }
4478         }
4479         int assocfiles = 0;
4480         if (filesmatched.size() > 0)
4481         {
4482           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4483                   || JvOptionPane
4484                           .showConfirmDialog(
4485                                   this,
4486                                   MessageManager
4487                                           .formatMessage(
4488                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4489                                                   new Object[] { Integer
4490                                                           .valueOf(
4491                                                                   filesmatched
4492                                                                           .size())
4493                                                           .toString() }),
4494                                   MessageManager
4495                                           .getString("label.automatically_associate_structure_files_by_name"),
4496                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4497
4498           {
4499             for (Object[] fm : filesmatched)
4500             {
4501               // try and associate
4502               // TODO: may want to set a standard ID naming formalism for
4503               // associating PDB files which have no IDs.
4504               for (SequenceI toassoc : (SequenceI[]) fm[2])
4505               {
4506                 PDBEntry pe = new AssociatePdbFileWithSeq()
4507                         .associatePdbWithSeq((String) fm[0],
4508                                 (DataSourceType) fm[1], toassoc, false,
4509                                 Desktop.instance);
4510                 if (pe != null)
4511                 {
4512                   System.err.println("Associated file : "
4513                           + ((String) fm[0]) + " with "
4514                           + toassoc.getDisplayId(true));
4515                   assocfiles++;
4516                 }
4517               }
4518               alignPanel.paintAlignment(true);
4519             }
4520           }
4521         }
4522         if (filesnotmatched.size() > 0)
4523         {
4524           if (assocfiles > 0
4525                   && (Cache.getDefault(
4526                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4527                           .showConfirmDialog(
4528                                   this,
4529                                   "<html>"
4530                                           + MessageManager
4531                                                   .formatMessage(
4532                                                           "label.ignore_unmatched_dropped_files_info",
4533                                                           new Object[] { Integer
4534                                                                   .valueOf(
4535                                                                           filesnotmatched
4536                                                                                   .size())
4537                                                                   .toString() })
4538                                           + "</html>",
4539                                   MessageManager
4540                                           .getString("label.ignore_unmatched_dropped_files"),
4541                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4542           {
4543             return;
4544           }
4545           for (String fn : filesnotmatched)
4546           {
4547             loadJalviewDataFile(fn, null, null, null);
4548           }
4549
4550         }
4551       } catch (Exception ex)
4552       {
4553         ex.printStackTrace();
4554       }
4555     }
4556   }
4557
4558   /**
4559    * Attempt to load a "dropped" file or URL string, by testing in turn for
4560    * <ul>
4561    * <li>an Annotation file</li>
4562    * <li>a JNet file</li>
4563    * <li>a features file</li>
4564    * <li>else try to interpret as an alignment file</li>
4565    * </ul>
4566    *
4567    * @param file
4568    *          either a filename or a URL string.
4569    */
4570   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4571           FileFormatI format, SequenceI assocSeq)
4572   {
4573     try
4574     {
4575       if (sourceType == null)
4576       {
4577         sourceType = FormatAdapter.checkProtocol(file);
4578       }
4579       // if the file isn't identified, or not positively identified as some
4580       // other filetype (PFAM is default unidentified alignment file type) then
4581       // try to parse as annotation.
4582       boolean isAnnotation = (format == null || FileFormat.Pfam
4583               .equals(format)) ? new AnnotationFile()
4584               .annotateAlignmentView(viewport, file, sourceType) : false;
4585
4586       if (!isAnnotation)
4587       {
4588         // first see if its a T-COFFEE score file
4589         TCoffeeScoreFile tcf = null;
4590         try
4591         {
4592           tcf = new TCoffeeScoreFile(file, sourceType);
4593           if (tcf.isValid())
4594           {
4595             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4596             {
4597               buildColourMenu();
4598               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4599               isAnnotation = true;
4600               statusBar
4601                       .setText(MessageManager
4602                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4603             }
4604             else
4605             {
4606               // some problem - if no warning its probable that the ID matching
4607               // process didn't work
4608               JvOptionPane
4609                       .showMessageDialog(
4610                               Desktop.desktop,
4611                               tcf.getWarningMessage() == null ? MessageManager
4612                                       .getString("label.check_file_matches_sequence_ids_alignment")
4613                                       : tcf.getWarningMessage(),
4614                               MessageManager
4615                                       .getString("label.problem_reading_tcoffee_score_file"),
4616                               JvOptionPane.WARNING_MESSAGE);
4617             }
4618           }
4619           else
4620           {
4621             tcf = null;
4622           }
4623         } catch (Exception x)
4624         {
4625           Cache.log
4626                   .debug("Exception when processing data source as T-COFFEE score file",
4627                           x);
4628           tcf = null;
4629         }
4630         if (tcf == null)
4631         {
4632           // try to see if its a JNet 'concise' style annotation file *before*
4633           // we
4634           // try to parse it as a features file
4635           if (format == null)
4636           {
4637             format = new IdentifyFile().identify(file, sourceType);
4638           }
4639           if (FileFormat.ScoreMatrix == format)
4640           {
4641             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4642                     sourceType));
4643             sm.parse();
4644             // todo: i18n this message
4645             statusBar
4646                     .setText(MessageManager.formatMessage(
4647                             "label.successfully_loaded_matrix",
4648                             sm.getMatrixName()));
4649           }
4650           else if (FileFormat.Jnet.equals(format))
4651           {
4652             JPredFile predictions = new JPredFile(file, sourceType);
4653             new JnetAnnotationMaker();
4654             JnetAnnotationMaker.add_annotation(predictions,
4655                     viewport.getAlignment(), 0, false);
4656             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4657             viewport.getAlignment().setSeqrep(repseq);
4658             ColumnSelection cs = new ColumnSelection();
4659             cs.hideInsertionsFor(repseq);
4660             viewport.setColumnSelection(cs);
4661             isAnnotation = true;
4662           }
4663           // else if (IdentifyFile.FeaturesFile.equals(format))
4664           else if (FileFormat.Features.equals(format))
4665           {
4666             if (parseFeaturesFile(file, sourceType))
4667             {
4668               alignPanel.paintAlignment(true);
4669             }
4670           }
4671           else
4672           {
4673             new FileLoader().LoadFile(viewport, file, sourceType, format);
4674           }
4675         }
4676       }
4677       if (isAnnotation)
4678       {
4679
4680         alignPanel.adjustAnnotationHeight();
4681         viewport.updateSequenceIdColours();
4682         buildSortByAnnotationScoresMenu();
4683         alignPanel.paintAlignment(true);
4684       }
4685     } catch (Exception ex)
4686     {
4687       ex.printStackTrace();
4688     } catch (OutOfMemoryError oom)
4689     {
4690       try
4691       {
4692         System.gc();
4693       } catch (Exception x)
4694       {
4695       }
4696       new OOMWarning(
4697               "loading data "
4698                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4699                               : "using " + sourceType + " from " + file)
4700                               : ".")
4701                       + (format != null ? "(parsing as '" + format
4702                               + "' file)" : ""), oom, Desktop.desktop);
4703     }
4704   }
4705
4706   /**
4707    * Method invoked by the ChangeListener on the tabbed pane, in other words
4708    * when a different tabbed pane is selected by the user or programmatically.
4709    */
4710   @Override
4711   public void tabSelectionChanged(int index)
4712   {
4713     if (index > -1)
4714     {
4715       alignPanel = alignPanels.get(index);
4716       viewport = alignPanel.av;
4717       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4718       setMenusFromViewport(viewport);
4719     }
4720
4721     /*
4722      * 'focus' any colour slider that is open to the selected viewport
4723      */
4724     if (viewport.getConservationSelected())
4725     {
4726       SliderPanel.setConservationSlider(alignPanel,
4727               viewport.getResidueShading(), alignPanel.getViewName());
4728     }
4729     else
4730     {
4731       SliderPanel.hideConservationSlider();
4732     }
4733     if (viewport.getAbovePIDThreshold())
4734     {
4735       SliderPanel.setPIDSliderSource(alignPanel,
4736               viewport.getResidueShading(), alignPanel.getViewName());
4737     }
4738     else
4739     {
4740       SliderPanel.hidePIDSlider();
4741     }
4742
4743     /*
4744      * If there is a frame linked to this one in a SplitPane, switch it to the
4745      * same view tab index. No infinite recursion of calls should happen, since
4746      * tabSelectionChanged() should not get invoked on setting the selected
4747      * index to an unchanged value. Guard against setting an invalid index
4748      * before the new view peer tab has been created.
4749      */
4750     final AlignViewportI peer = viewport.getCodingComplement();
4751     if (peer != null)
4752     {
4753       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4754       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4755       {
4756         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4757       }
4758     }
4759   }
4760
4761   /**
4762    * On right mouse click on view tab, prompt for and set new view name.
4763    */
4764   @Override
4765   public void tabbedPane_mousePressed(MouseEvent e)
4766   {
4767     if (e.isPopupTrigger())
4768     {
4769       String msg = MessageManager.getString("label.enter_view_name");
4770       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4771               JvOptionPane.QUESTION_MESSAGE);
4772
4773       if (reply != null)
4774       {
4775         viewport.viewName = reply;
4776         // TODO warn if reply is in getExistingViewNames()?
4777         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4778       }
4779     }
4780   }
4781
4782   public AlignViewport getCurrentView()
4783   {
4784     return viewport;
4785   }
4786
4787   /**
4788    * Open the dialog for regex description parsing.
4789    */
4790   @Override
4791   protected void extractScores_actionPerformed(ActionEvent e)
4792   {
4793     ParseProperties pp = new jalview.analysis.ParseProperties(
4794             viewport.getAlignment());
4795     // TODO: verify regex and introduce GUI dialog for version 2.5
4796     // if (pp.getScoresFromDescription("col", "score column ",
4797     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4798     // true)>0)
4799     if (pp.getScoresFromDescription("description column",
4800             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4801     {
4802       buildSortByAnnotationScoresMenu();
4803     }
4804   }
4805
4806   /*
4807    * (non-Javadoc)
4808    *
4809    * @see
4810    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4811    * )
4812    */
4813   @Override
4814   protected void showDbRefs_actionPerformed(ActionEvent e)
4815   {
4816     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4817   }
4818
4819   /*
4820    * (non-Javadoc)
4821    *
4822    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4823    * ActionEvent)
4824    */
4825   @Override
4826   protected void showNpFeats_actionPerformed(ActionEvent e)
4827   {
4828     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4829   }
4830
4831   /**
4832    * find the viewport amongst the tabs in this alignment frame and close that
4833    * tab
4834    *
4835    * @param av
4836    */
4837   public boolean closeView(AlignViewportI av)
4838   {
4839     if (viewport == av)
4840     {
4841       this.closeMenuItem_actionPerformed(false);
4842       return true;
4843     }
4844     Component[] comp = tabbedPane.getComponents();
4845     for (int i = 0; comp != null && i < comp.length; i++)
4846     {
4847       if (comp[i] instanceof AlignmentPanel)
4848       {
4849         if (((AlignmentPanel) comp[i]).av == av)
4850         {
4851           // close the view.
4852           closeView((AlignmentPanel) comp[i]);
4853           return true;
4854         }
4855       }
4856     }
4857     return false;
4858   }
4859
4860   protected void build_fetchdbmenu(JMenu webService)
4861   {
4862     // Temporary hack - DBRef Fetcher always top level ws entry.
4863     // TODO We probably want to store a sequence database checklist in
4864     // preferences and have checkboxes.. rather than individual sources selected
4865     // here
4866     final JMenu rfetch = new JMenu(
4867             MessageManager.getString("action.fetch_db_references"));
4868     rfetch.setToolTipText(MessageManager
4869             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4870     webService.add(rfetch);
4871
4872     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4873             MessageManager.getString("option.trim_retrieved_seqs"));
4874     trimrs.setToolTipText(MessageManager
4875             .getString("label.trim_retrieved_sequences"));
4876     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4877     trimrs.addActionListener(new ActionListener()
4878     {
4879       @Override
4880       public void actionPerformed(ActionEvent e)
4881       {
4882         trimrs.setSelected(trimrs.isSelected());
4883         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4884                 Boolean.valueOf(trimrs.isSelected()).toString());
4885       };
4886     });
4887     rfetch.add(trimrs);
4888     JMenuItem fetchr = new JMenuItem(
4889             MessageManager.getString("label.standard_databases"));
4890     fetchr.setToolTipText(MessageManager
4891             .getString("label.fetch_embl_uniprot"));
4892     fetchr.addActionListener(new ActionListener()
4893     {
4894
4895       @Override
4896       public void actionPerformed(ActionEvent e)
4897       {
4898         new Thread(new Runnable()
4899         {
4900           @Override
4901           public void run()
4902           {
4903             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4904                     .getAlignment().isNucleotide();
4905             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4906                     .getSequenceSelection(), alignPanel.alignFrame, null,
4907                     alignPanel.alignFrame.featureSettings, isNucleotide);
4908             dbRefFetcher.addListener(new FetchFinishedListenerI()
4909             {
4910               @Override
4911               public void finished()
4912               {
4913                 AlignFrame.this.setMenusForViewport();
4914               }
4915             });
4916             dbRefFetcher.fetchDBRefs(false);
4917           }
4918         }).start();
4919
4920       }
4921
4922     });
4923     rfetch.add(fetchr);
4924     final AlignFrame me = this;
4925     new Thread(new Runnable()
4926     {
4927       @Override
4928       public void run()
4929       {
4930         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4931                 .getSequenceFetcherSingleton(me);
4932         javax.swing.SwingUtilities.invokeLater(new Runnable()
4933         {
4934           @Override
4935           public void run()
4936           {
4937             String[] dbclasses = sf.getOrderedSupportedSources();
4938             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4939             // jalview.util.QuickSort.sort(otherdb, otherdb);
4940             List<DbSourceProxy> otherdb;
4941             JMenu dfetch = new JMenu();
4942             JMenu ifetch = new JMenu();
4943             JMenuItem fetchr = null;
4944             int comp = 0, icomp = 0, mcomp = 15;
4945             String mname = null;
4946             int dbi = 0;
4947             for (String dbclass : dbclasses)
4948             {
4949               otherdb = sf.getSourceProxy(dbclass);
4950               // add a single entry for this class, or submenu allowing 'fetch
4951               // all' or pick one
4952               if (otherdb == null || otherdb.size() < 1)
4953               {
4954                 continue;
4955               }
4956               // List<DbSourceProxy> dbs=otherdb;
4957               // otherdb=new ArrayList<DbSourceProxy>();
4958               // for (DbSourceProxy db:dbs)
4959               // {
4960               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4961               // }
4962               if (mname == null)
4963               {
4964                 mname = "From " + dbclass;
4965               }
4966               if (otherdb.size() == 1)
4967               {
4968                 final DbSourceProxy[] dassource = otherdb
4969                         .toArray(new DbSourceProxy[0]);
4970                 DbSourceProxy src = otherdb.get(0);
4971                 fetchr = new JMenuItem(src.getDbSource());
4972                 fetchr.addActionListener(new ActionListener()
4973                 {
4974
4975                   @Override
4976                   public void actionPerformed(ActionEvent e)
4977                   {
4978                     new Thread(new Runnable()
4979                     {
4980
4981                       @Override
4982                       public void run()
4983                       {
4984                         boolean isNucleotide = alignPanel.alignFrame
4985                                 .getViewport().getAlignment()
4986                                 .isNucleotide();
4987                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4988                                 alignPanel.av.getSequenceSelection(),
4989                                 alignPanel.alignFrame, dassource,
4990                                 alignPanel.alignFrame.featureSettings,
4991                                 isNucleotide);
4992                         dbRefFetcher
4993                                 .addListener(new FetchFinishedListenerI()
4994                                 {
4995                                   @Override
4996                                   public void finished()
4997                                   {
4998                                     AlignFrame.this.setMenusForViewport();
4999                                   }
5000                                 });
5001                         dbRefFetcher.fetchDBRefs(false);
5002                       }
5003                     }).start();
5004                   }
5005
5006                 });
5007                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5008                         MessageManager.formatMessage(
5009                                 "label.fetch_retrieve_from",
5010                                 new Object[] { src.getDbName() })));
5011                 dfetch.add(fetchr);
5012                 comp++;
5013               }
5014               else
5015               {
5016                 final DbSourceProxy[] dassource = otherdb
5017                         .toArray(new DbSourceProxy[0]);
5018                 // fetch all entry
5019                 DbSourceProxy src = otherdb.get(0);
5020                 fetchr = new JMenuItem(MessageManager.formatMessage(
5021                         "label.fetch_all_param",
5022                         new Object[] { src.getDbSource() }));
5023                 fetchr.addActionListener(new ActionListener()
5024                 {
5025                   @Override
5026                   public void actionPerformed(ActionEvent e)
5027                   {
5028                     new Thread(new Runnable()
5029                     {
5030
5031                       @Override
5032                       public void run()
5033                       {
5034                         boolean isNucleotide = alignPanel.alignFrame
5035                                 .getViewport().getAlignment()
5036                                 .isNucleotide();
5037                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5038                                 alignPanel.av.getSequenceSelection(),
5039                                 alignPanel.alignFrame, dassource,
5040                                 alignPanel.alignFrame.featureSettings,
5041                                 isNucleotide);
5042                         dbRefFetcher
5043                                 .addListener(new FetchFinishedListenerI()
5044                                 {
5045                                   @Override
5046                                   public void finished()
5047                                   {
5048                                     AlignFrame.this.setMenusForViewport();
5049                                   }
5050                                 });
5051                         dbRefFetcher.fetchDBRefs(false);
5052                       }
5053                     }).start();
5054                   }
5055                 });
5056
5057                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5058                         MessageManager.formatMessage(
5059                                 "label.fetch_retrieve_from_all_sources",
5060                                 new Object[] {
5061                                     Integer.valueOf(otherdb.size())
5062                                             .toString(), src.getDbSource(),
5063                                     src.getDbName() })));
5064                 dfetch.add(fetchr);
5065                 comp++;
5066                 // and then build the rest of the individual menus
5067                 ifetch = new JMenu(MessageManager.formatMessage(
5068                         "label.source_from_db_source",
5069                         new Object[] { src.getDbSource() }));
5070                 icomp = 0;
5071                 String imname = null;
5072                 int i = 0;
5073                 for (DbSourceProxy sproxy : otherdb)
5074                 {
5075                   String dbname = sproxy.getDbName();
5076                   String sname = dbname.length() > 5 ? dbname.substring(0,
5077                           5) + "..." : dbname;
5078                   String msname = dbname.length() > 10 ? dbname.substring(
5079                           0, 10) + "..." : dbname;
5080                   if (imname == null)
5081                   {
5082                     imname = MessageManager.formatMessage(
5083                             "label.from_msname", new Object[] { sname });
5084                   }
5085                   fetchr = new JMenuItem(msname);
5086                   final DbSourceProxy[] dassrc = { sproxy };
5087                   fetchr.addActionListener(new ActionListener()
5088                   {
5089
5090                     @Override
5091                     public void actionPerformed(ActionEvent e)
5092                     {
5093                       new Thread(new Runnable()
5094                       {
5095
5096                         @Override
5097                         public void run()
5098                         {
5099                           boolean isNucleotide = alignPanel.alignFrame
5100                                   .getViewport().getAlignment()
5101                                   .isNucleotide();
5102                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5103                                   alignPanel.av.getSequenceSelection(),
5104                                   alignPanel.alignFrame, dassrc,
5105                                   alignPanel.alignFrame.featureSettings,
5106                                   isNucleotide);
5107                           dbRefFetcher
5108                                   .addListener(new FetchFinishedListenerI()
5109                                   {
5110                                     @Override
5111                                     public void finished()
5112                                     {
5113                                       AlignFrame.this.setMenusForViewport();
5114                                     }
5115                                   });
5116                           dbRefFetcher.fetchDBRefs(false);
5117                         }
5118                       }).start();
5119                     }
5120
5121                   });
5122                   fetchr.setToolTipText("<html>"
5123                           + MessageManager.formatMessage(
5124                                   "label.fetch_retrieve_from", new Object[]
5125                                   { dbname }));
5126                   ifetch.add(fetchr);
5127                   ++i;
5128                   if (++icomp >= mcomp || i == (otherdb.size()))
5129                   {
5130                     ifetch.setText(MessageManager.formatMessage(
5131                             "label.source_to_target", imname, sname));
5132                     dfetch.add(ifetch);
5133                     ifetch = new JMenu();
5134                     imname = null;
5135                     icomp = 0;
5136                     comp++;
5137                   }
5138                 }
5139               }
5140               ++dbi;
5141               if (comp >= mcomp || dbi >= (dbclasses.length))
5142               {
5143                 dfetch.setText(MessageManager.formatMessage(
5144                         "label.source_to_target", mname, dbclass));
5145                 rfetch.add(dfetch);
5146                 dfetch = new JMenu();
5147                 mname = null;
5148                 comp = 0;
5149               }
5150             }
5151           }
5152         });
5153       }
5154     }).start();
5155
5156   }
5157
5158   /**
5159    * Left justify the whole alignment.
5160    */
5161   @Override
5162   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5163   {
5164     AlignmentI al = viewport.getAlignment();
5165     al.justify(false);
5166     viewport.firePropertyChange("alignment", null, al);
5167   }
5168
5169   /**
5170    * Right justify the whole alignment.
5171    */
5172   @Override
5173   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5174   {
5175     AlignmentI al = viewport.getAlignment();
5176     al.justify(true);
5177     viewport.firePropertyChange("alignment", null, al);
5178   }
5179
5180   @Override
5181   public void setShowSeqFeatures(boolean b)
5182   {
5183     showSeqFeatures.setSelected(b);
5184     viewport.setShowSequenceFeatures(b);
5185   }
5186
5187   /*
5188    * (non-Javadoc)
5189    *
5190    * @see
5191    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5192    * awt.event.ActionEvent)
5193    */
5194   @Override
5195   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5196   {
5197     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5198     alignPanel.paintAlignment(true);
5199   }
5200
5201   /*
5202    * (non-Javadoc)
5203    *
5204    * @see
5205    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5206    * .ActionEvent)
5207    */
5208   @Override
5209   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5210   {
5211     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5212     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5213
5214   }
5215
5216   /*
5217    * (non-Javadoc)
5218    *
5219    * @see
5220    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5221    * .event.ActionEvent)
5222    */
5223   @Override
5224   protected void showGroupConservation_actionPerformed(ActionEvent e)
5225   {
5226     viewport.setShowGroupConservation(showGroupConservation.getState());
5227     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5228   }
5229
5230   /*
5231    * (non-Javadoc)
5232    *
5233    * @see
5234    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5235    * .event.ActionEvent)
5236    */
5237   @Override
5238   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5239   {
5240     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5241     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5242   }
5243
5244   /*
5245    * (non-Javadoc)
5246    *
5247    * @see
5248    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5249    * .event.ActionEvent)
5250    */
5251   @Override
5252   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5253   {
5254     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5255     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5256   }
5257
5258   @Override
5259   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5260   {
5261     showSequenceLogo.setState(true);
5262     viewport.setShowSequenceLogo(true);
5263     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5264     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5265   }
5266
5267   @Override
5268   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5269   {
5270     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5271   }
5272
5273   /*
5274    * (non-Javadoc)
5275    *
5276    * @see
5277    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5278    * .event.ActionEvent)
5279    */
5280   @Override
5281   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5282   {
5283     if (avc.makeGroupsFromSelection())
5284     {
5285       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5286       alignPanel.updateAnnotation();
5287       alignPanel.paintAlignment(true);
5288     }
5289   }
5290
5291   public void clearAlignmentSeqRep()
5292   {
5293     // TODO refactor alignmentseqrep to controller
5294     if (viewport.getAlignment().hasSeqrep())
5295     {
5296       viewport.getAlignment().setSeqrep(null);
5297       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5298       alignPanel.updateAnnotation();
5299       alignPanel.paintAlignment(true);
5300     }
5301   }
5302
5303   @Override
5304   protected void createGroup_actionPerformed(ActionEvent e)
5305   {
5306     if (avc.createGroup())
5307     {
5308       alignPanel.alignmentChanged();
5309     }
5310   }
5311
5312   @Override
5313   protected void unGroup_actionPerformed(ActionEvent e)
5314   {
5315     if (avc.unGroup())
5316     {
5317       alignPanel.alignmentChanged();
5318     }
5319   }
5320
5321   /**
5322    * make the given alignmentPanel the currently selected tab
5323    *
5324    * @param alignmentPanel
5325    */
5326   public void setDisplayedView(AlignmentPanel alignmentPanel)
5327   {
5328     if (!viewport.getSequenceSetId().equals(
5329             alignmentPanel.av.getSequenceSetId()))
5330     {
5331       throw new Error(
5332               MessageManager
5333                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5334     }
5335     if (tabbedPane != null
5336             && tabbedPane.getTabCount() > 0
5337             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5338                     .getSelectedIndex())
5339     {
5340       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5341     }
5342   }
5343
5344   /**
5345    * Action on selection of menu options to Show or Hide annotations.
5346    *
5347    * @param visible
5348    * @param forSequences
5349    *          update sequence-related annotations
5350    * @param forAlignment
5351    *          update non-sequence-related annotations
5352    */
5353   @Override
5354   protected void setAnnotationsVisibility(boolean visible,
5355           boolean forSequences, boolean forAlignment)
5356   {
5357     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5358             .getAlignmentAnnotation();
5359     if (anns == null)
5360     {
5361       return;
5362     }
5363     for (AlignmentAnnotation aa : anns)
5364     {
5365       /*
5366        * don't display non-positional annotations on an alignment
5367        */
5368       if (aa.annotations == null)
5369       {
5370         continue;
5371       }
5372       boolean apply = (aa.sequenceRef == null && forAlignment)
5373               || (aa.sequenceRef != null && forSequences);
5374       if (apply)
5375       {
5376         aa.visible = visible;
5377       }
5378     }
5379     alignPanel.validateAnnotationDimensions(true);
5380     alignPanel.alignmentChanged();
5381   }
5382
5383   /**
5384    * Store selected annotation sort order for the view and repaint.
5385    */
5386   @Override
5387   protected void sortAnnotations_actionPerformed()
5388   {
5389     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5390     this.alignPanel.av
5391             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5392     alignPanel.paintAlignment(true);
5393   }
5394
5395   /**
5396    *
5397    * @return alignment panels in this alignment frame
5398    */
5399   public List<? extends AlignmentViewPanel> getAlignPanels()
5400   {
5401     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5402   }
5403
5404   /**
5405    * Open a new alignment window, with the cDNA associated with this (protein)
5406    * alignment, aligned as is the protein.
5407    */
5408   protected void viewAsCdna_actionPerformed()
5409   {
5410     // TODO no longer a menu action - refactor as required
5411     final AlignmentI alignment = getViewport().getAlignment();
5412     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5413     if (mappings == null)
5414     {
5415       return;
5416     }
5417     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5418     for (SequenceI aaSeq : alignment.getSequences())
5419     {
5420       for (AlignedCodonFrame acf : mappings)
5421       {
5422         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5423         if (dnaSeq != null)
5424         {
5425           /*
5426            * There is a cDNA mapping for this protein sequence - add to new
5427            * alignment. It will share the same dataset sequence as other mapped
5428            * cDNA (no new mappings need to be created).
5429            */
5430           final Sequence newSeq = new Sequence(dnaSeq);
5431           newSeq.setDatasetSequence(dnaSeq);
5432           cdnaSeqs.add(newSeq);
5433         }
5434       }
5435     }
5436     if (cdnaSeqs.size() == 0)
5437     {
5438       // show a warning dialog no mapped cDNA
5439       return;
5440     }
5441     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5442             .size()]));
5443     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5444             AlignFrame.DEFAULT_HEIGHT);
5445     cdna.alignAs(alignment);
5446     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5447             + this.title;
5448     Desktop.addInternalFrame(alignFrame, newtitle,
5449             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5450   }
5451
5452   /**
5453    * Set visibility of dna/protein complement view (available when shown in a
5454    * split frame).
5455    *
5456    * @param show
5457    */
5458   @Override
5459   protected void showComplement_actionPerformed(boolean show)
5460   {
5461     SplitContainerI sf = getSplitViewContainer();
5462     if (sf != null)
5463     {
5464       sf.setComplementVisible(this, show);
5465     }
5466   }
5467
5468   /**
5469    * Generate the reverse (optionally complemented) of the selected sequences,
5470    * and add them to the alignment
5471    */
5472   @Override
5473   protected void showReverse_actionPerformed(boolean complement)
5474   {
5475     AlignmentI al = null;
5476     try
5477     {
5478       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5479       al = dna.reverseCdna(complement);
5480       viewport.addAlignment(al, "");
5481       addHistoryItem(new EditCommand(
5482               MessageManager.getString("label.add_sequences"),
5483               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5484               viewport.getAlignment()));
5485     } catch (Exception ex)
5486     {
5487       System.err.println(ex.getMessage());
5488       return;
5489     }
5490   }
5491
5492   /**
5493    * Try to run a script in the Groovy console, having first ensured that this
5494    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5495    * be targeted at this alignment.
5496    */
5497   @Override
5498   protected void runGroovy_actionPerformed()
5499   {
5500     Jalview.setCurrentAlignFrame(this);
5501     groovy.ui.Console console = Desktop.getGroovyConsole();
5502     if (console != null)
5503     {
5504       try
5505       {
5506         console.runScript();
5507       } catch (Exception ex)
5508       {
5509         System.err.println((ex.toString()));
5510         JvOptionPane
5511                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5512                         .getString("label.couldnt_run_groovy_script"),
5513                         MessageManager
5514                                 .getString("label.groovy_support_failed"),
5515                         JvOptionPane.ERROR_MESSAGE);
5516       }
5517     }
5518     else
5519     {
5520       System.err.println("Can't run Groovy script as console not found");
5521     }
5522   }
5523
5524   /**
5525    * Hides columns containing (or not containing) a specified feature, provided
5526    * that would not leave all columns hidden
5527    *
5528    * @param featureType
5529    * @param columnsContaining
5530    * @return
5531    */
5532   public boolean hideFeatureColumns(String featureType,
5533           boolean columnsContaining)
5534   {
5535     boolean notForHiding = avc.markColumnsContainingFeatures(
5536             columnsContaining, false, false, featureType);
5537     if (notForHiding)
5538     {
5539       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5540               false, featureType))
5541       {
5542         getViewport().hideSelectedColumns();
5543         return true;
5544       }
5545     }
5546     return false;
5547   }
5548
5549   @Override
5550   protected void selectHighlightedColumns_actionPerformed(
5551           ActionEvent actionEvent)
5552   {
5553     // include key modifier check in case user selects from menu
5554     avc.markHighlightedColumns(
5555             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5556             true,
5557             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5558   }
5559
5560   /**
5561    * Rebuilds the Colour menu, including any user-defined colours which have
5562    * been loaded either on startup or during the session
5563    */
5564   public void buildColourMenu()
5565   {
5566     colourMenu.removeAll();
5567
5568     colourMenu.add(applyToAllGroups);
5569     colourMenu.add(textColour);
5570     colourMenu.addSeparator();
5571
5572     ColourMenuHelper.addMenuItems(colourMenu, this,
5573             viewport.getAlignment(), false);
5574
5575     colourMenu.addSeparator();
5576     colourMenu.add(conservationMenuItem);
5577     colourMenu.add(modifyConservation);
5578     colourMenu.add(abovePIDThreshold);
5579     colourMenu.add(modifyPID);
5580     colourMenu.add(annotationColour);
5581
5582     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5583     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5584   }
5585
5586   /**
5587    * Open a dialog (if not already open) that allows the user to select and
5588    * calculate PCA or Tree analysis
5589    */
5590   protected void openTreePcaDialog()
5591   {
5592     if (alignPanel.getCalculationDialog() == null)
5593     {
5594       new CalculationChooser(AlignFrame.this);
5595     }
5596   }
5597 }
5598
5599 class PrintThread extends Thread
5600 {
5601   AlignmentPanel ap;
5602
5603   public PrintThread(AlignmentPanel ap)
5604   {
5605     this.ap = ap;
5606   }
5607
5608   static PageFormat pf;
5609
5610   @Override
5611   public void run()
5612   {
5613     PrinterJob printJob = PrinterJob.getPrinterJob();
5614
5615     if (pf != null)
5616     {
5617       printJob.setPrintable(ap, pf);
5618     }
5619     else
5620     {
5621       printJob.setPrintable(ap);
5622     }
5623
5624     if (printJob.printDialog())
5625     {
5626       try
5627       {
5628         printJob.print();
5629       } catch (Exception PrintException)
5630       {
5631         PrintException.printStackTrace();
5632       }
5633     }
5634   }
5635 }