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 java.awt.BorderLayout;
  24 import java.awt.Component;
  25 import java.awt.Rectangle;
  26 import java.awt.Toolkit;
  27 import java.awt.datatransfer.Clipboard;
  28 import java.awt.datatransfer.DataFlavor;
  29 import java.awt.datatransfer.StringSelection;
  30 import java.awt.datatransfer.Transferable;
  31 import java.awt.dnd.DnDConstants;
  32 import java.awt.dnd.DropTargetDragEvent;
  33 import java.awt.dnd.DropTargetDropEvent;
  34 import java.awt.dnd.DropTargetEvent;
  35 import java.awt.dnd.DropTargetListener;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.FocusAdapter;
  39 import java.awt.event.FocusEvent;
  40 import java.awt.event.ItemEvent;
  41 import java.awt.event.ItemListener;
  42 import java.awt.event.KeyAdapter;
  43 import java.awt.event.KeyEvent;
  44 import java.awt.event.MouseEvent;
  45 import java.awt.print.PageFormat;
  46 import java.awt.print.PrinterJob;
  47 import java.beans.PropertyChangeEvent;
  48 import java.io.File;
  49 import java.io.FileWriter;
  50 import java.io.IOException;
  51 import java.io.PrintWriter;
  52 import java.net.URL;
  53 import java.util.ArrayList;
  54 import java.util.Arrays;
  55 import java.util.Deque;
  56 import java.util.Enumeration;
  57 import java.util.Hashtable;
  58 import java.util.List;
  59 import java.util.Vector;
  60
  61 import javax.swing.ButtonGroup;
  62 import javax.swing.JCheckBoxMenuItem;
  63 import javax.swing.JEditorPane;
  64 import javax.swing.JInternalFrame;
  65 import javax.swing.JLayeredPane;
  66 import javax.swing.JMenu;
  67 import javax.swing.JMenuItem;
  68 import javax.swing.JScrollPane;
  69 import javax.swing.SwingUtilities;
  70
  71 import jalview.analysis.AlignmentSorter;
  72 import jalview.analysis.AlignmentUtils;
  73 import jalview.analysis.CrossRef;
  74 import jalview.analysis.Dna;
  75 import jalview.analysis.GeneticCodeI;
  76 import jalview.analysis.ParseProperties;
  77 import jalview.analysis.SequenceIdMatcher;
  78 import jalview.api.AlignExportSettingI;
  79 import jalview.api.AlignViewControllerGuiI;
  80 import jalview.api.AlignViewControllerI;
  81 import jalview.api.AlignViewportI;
  82 import jalview.api.AlignmentViewPanel;
  83 import jalview.api.FeatureSettingsControllerI;
  84 import jalview.api.FeatureSettingsModelI;
  85 import jalview.api.SplitContainerI;
  86 import jalview.api.ViewStyleI;
  87 import jalview.api.analysis.SimilarityParamsI;
  88 import jalview.bin.Cache;
  89 import jalview.bin.Jalview;
  90 import jalview.commands.CommandI;
  91 import jalview.commands.EditCommand;
  92 import jalview.commands.EditCommand.Action;
  93 import jalview.commands.OrderCommand;
  94 import jalview.commands.RemoveGapColCommand;
  95 import jalview.commands.RemoveGapsCommand;
  96 import jalview.commands.SlideSequencesCommand;
  97 import jalview.commands.TrimRegionCommand;
  98 import jalview.datamodel.AlignedCodonFrame;
  99 import jalview.datamodel.Alignment;
 100 import jalview.datamodel.AlignmentAnnotation;
 101 import jalview.datamodel.AlignmentExportData;
 102 import jalview.datamodel.AlignmentI;
 103 import jalview.datamodel.AlignmentOrder;
 104 import jalview.datamodel.AlignmentView;
 105 import jalview.datamodel.ColumnSelection;
 106 import jalview.datamodel.HiddenColumns;
 107 import jalview.datamodel.HiddenSequences;
 108 import jalview.datamodel.PDBEntry;
 109 import jalview.datamodel.SeqCigar;
 110 import jalview.datamodel.Sequence;
 111 import jalview.datamodel.SequenceGroup;
 112 import jalview.datamodel.SequenceI;
 113 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 114 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 115 import jalview.io.AlignmentProperties;
 116 import jalview.io.AnnotationFile;
 117 import jalview.io.BackupFiles;
 118 import jalview.io.BioJsHTMLOutput;
 119 import jalview.io.DataSourceType;
 120 import jalview.io.FileFormat;
 121 import jalview.io.FileFormatI;
 122 import jalview.io.FileFormats;
 123 import jalview.io.FileLoader;
 124 import jalview.io.FileParse;
 125 import jalview.io.FormatAdapter;
 126 import jalview.io.HtmlSvgOutput;
 127 import jalview.io.IdentifyFile;
 128 import jalview.io.JPredFile;
 129 import jalview.io.JalviewFileChooser;
 130 import jalview.io.JalviewFileView;
 131 import jalview.io.JnetAnnotationMaker;
 132 import jalview.io.NewickFile;
 133 import jalview.io.ScoreMatrixFile;
 134 import jalview.io.TCoffeeScoreFile;
 135 import jalview.io.vcf.VCFLoader;
 136 import jalview.jbgui.GAlignFrame;
 137 import jalview.schemes.ColourSchemeI;
 138 import jalview.schemes.ColourSchemes;
 139 import jalview.schemes.ResidueColourScheme;
 140 import jalview.schemes.TCoffeeColourScheme;
 141 import jalview.util.MessageManager;
 142 import jalview.util.Platform;
 143 import jalview.viewmodel.AlignmentViewport;
 144 import jalview.viewmodel.ViewportRanges;
 145 import jalview.ws.DBRefFetcher;
 146 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 147 import jalview.ws.jws1.Discoverer;
 148 import jalview.ws.jws2.Jws2Discoverer;
 149 import jalview.ws.jws2.jabaws2.Jws2Instance;
 150 import jalview.ws.seqfetcher.DbSourceProxy;
 151
 152 /**
 153  * DOCUMENT ME!
 154  *
 155  * @author $author$
 156  * @version $Revision$
 157  */
 158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 159         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 160 {
 161
 162   public static final int DEFAULT_WIDTH = 700;
 163
 164   public static final int DEFAULT_HEIGHT = 500;
 165
 166   /*
 167    * The currently displayed panel (selected tabbed view if more than one)
 168    */
 169   public AlignmentPanel alignPanel;
 170
 171   AlignViewport viewport;
 172
 173   public AlignViewControllerI avc;
 174
 175   List<AlignmentPanel> alignPanels = new ArrayList<>();
 176
 177   /**
 178    * Last format used to load or save alignments in this window
 179    */
 180   FileFormatI currentFileFormat = null;
 181
 182   /**
 183    * Current filename for this alignment
 184    */
 185   String fileName = null;
 186
 187   /**
 188    * Creates a new AlignFrame object with specific width and height.
 189    *
 190    * @param al
 191    * @param width
 192    * @param height
 193    */
 194   public AlignFrame(AlignmentI al, int width, int height)
 195   {
 196     this(al, null, width, height);
 197   }
 198
 199   /**
 200    * Creates a new AlignFrame object with specific width, height and
 201    * sequenceSetId
 202    *
 203    * @param al
 204    * @param width
 205    * @param height
 206    * @param sequenceSetId
 207    */
 208   public AlignFrame(AlignmentI al, int width, int height,
 209           String sequenceSetId)
 210   {
 211     this(al, null, width, height, sequenceSetId);
 212   }
 213
 214   /**
 215    * Creates a new AlignFrame object with specific width, height and
 216    * sequenceSetId
 217    *
 218    * @param al
 219    * @param width
 220    * @param height
 221    * @param sequenceSetId
 222    * @param viewId
 223    */
 224   public AlignFrame(AlignmentI al, int width, int height,
 225           String sequenceSetId, String viewId)
 226   {
 227     this(al, null, width, height, sequenceSetId, viewId);
 228   }
 229
 230   /**
 231    * new alignment window with hidden columns
 232    *
 233    * @param al
 234    *          AlignmentI
 235    * @param hiddenColumns
 236    *          ColumnSelection or null
 237    * @param width
 238    *          Width of alignment frame
 239    * @param height
 240    *          height of frame.
 241    */
 242   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 243           int height)
 244   {
 245     this(al, hiddenColumns, width, height, null);
 246   }
 247
 248   /**
 249    * Create alignment frame for al with hiddenColumns, a specific width and
 250    * height, and specific sequenceId
 251    *
 252    * @param al
 253    * @param hiddenColumns
 254    * @param width
 255    * @param height
 256    * @param sequenceSetId
 257    *          (may be null)
 258    */
 259   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 260           int height, String sequenceSetId)
 261   {
 262     this(al, hiddenColumns, width, height, sequenceSetId, null);
 263   }
 264
 265   /**
 266    * Create alignment frame for al with hiddenColumns, a specific width and
 267    * height, and specific sequenceId
 268    *
 269    * @param al
 270    * @param hiddenColumns
 271    * @param width
 272    * @param height
 273    * @param sequenceSetId
 274    *          (may be null)
 275    * @param viewId
 276    *          (may be null)
 277    */
 278   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 279           int height, String sequenceSetId, String viewId)
 280   {
 281     setSize(width, height);
 282
 283     if (al.getDataset() == null)
 284     {
 285       al.setDataset(null);
 286     }
 287
 288     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 289
 290     alignPanel = new AlignmentPanel(this, viewport);
 291
 292     addAlignmentPanel(alignPanel, true);
 293     init();
 294   }
 295
 296   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 297           HiddenColumns hiddenColumns, int width, int height)
 298   {
 299     setSize(width, height);
 300
 301     if (al.getDataset() == null)
 302     {
 303       al.setDataset(null);
 304     }
 305
 306     viewport = new AlignViewport(al, hiddenColumns);
 307
 308     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 309     {
 310       viewport.hideSequence(hiddenSeqs);
 311     }
 312     alignPanel = new AlignmentPanel(this, viewport);
 313     addAlignmentPanel(alignPanel, true);
 314     init();
 315   }
 316
 317   /**
 318    * Make a new AlignFrame from existing alignmentPanels
 319    *
 320    * @param ap
 321    *          AlignmentPanel
 322    * @param av
 323    *          AlignViewport
 324    */
 325   public AlignFrame(AlignmentPanel ap)
 326   {
 327     viewport = ap.av;
 328     alignPanel = ap;
 329     addAlignmentPanel(ap, false);
 330     init();
 331   }
 332
 333   /**
 334    * initalise the alignframe from the underlying viewport data and the
 335    * configurations
 336    */
 337   void init()
 338   {
 339     if (!Jalview.isHeadlessMode())
 340     {
 341       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 342     }
 343
 344     avc = new jalview.controller.AlignViewController(this, viewport,
 345             alignPanel);
 346     if (viewport.getAlignmentConservationAnnotation() == null)
 347     {
 348       // BLOSUM62Colour.setEnabled(false);
 349       conservationMenuItem.setEnabled(false);
 350       modifyConservation.setEnabled(false);
 351       // PIDColour.setEnabled(false);
 352       // abovePIDThreshold.setEnabled(false);
 353       // modifyPID.setEnabled(false);
 354     }
 355
 356     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 357             "No sort");
 358
 359     if (sortby.equals("Id"))
 360     {
 361       sortIDMenuItem_actionPerformed(null);
 362     }
 363     else if (sortby.equals("Pairwise Identity"))
 364     {
 365       sortPairwiseMenuItem_actionPerformed(null);
 366     }
 367
 368     this.alignPanel.av
 369             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 370
 371     setMenusFromViewport(viewport);
 372     buildSortByAnnotationScoresMenu();
 373     calculateTree.addActionListener(new ActionListener()
 374     {
 375
 376       @Override
 377       public void actionPerformed(ActionEvent e)
 378       {
 379         openTreePcaDialog();
 380       }
 381     });
 382     buildColourMenu();
 383
 384     if (Desktop.desktop != null)
 385     {
 386       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 387       addServiceListeners();
 388       setGUINucleotide();
 389     }
 390
 391     if (viewport.getWrapAlignment())
 392     {
 393       wrapMenuItem_actionPerformed(null);
 394     }
 395
 396     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 397     {
 398       this.overviewMenuItem_actionPerformed(null);
 399     }
 400
 401     addKeyListener();
 402
 403     final List<AlignmentPanel> selviews = new ArrayList<>();
 404     final List<AlignmentPanel> origview = new ArrayList<>();
 405     final String menuLabel = MessageManager
 406             .getString("label.copy_format_from");
 407     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 408             new ViewSetProvider()
 409             {
 410
 411               @Override
 412               public AlignmentPanel[] getAllAlignmentPanels()
 413               {
 414                 origview.clear();
 415                 origview.add(alignPanel);
 416                 // make an array of all alignment panels except for this one
 417                 List<AlignmentPanel> aps = new ArrayList<>(
 418                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 419                 aps.remove(AlignFrame.this.alignPanel);
 420                 return aps.toArray(new AlignmentPanel[aps.size()]);
 421               }
 422             }, selviews, new ItemListener()
 423             {
 424
 425               @Override
 426               public void itemStateChanged(ItemEvent e)
 427               {
 428                 if (origview.size() > 0)
 429                 {
 430                   final AlignmentPanel ap = origview.get(0);
 431
 432                   /*
 433                    * Copy the ViewStyle of the selected panel to 'this one'.
 434                    * Don't change value of 'scaleProteinAsCdna' unless copying
 435                    * from a SplitFrame.
 436                    */
 437                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 438                           .getViewStyle();
 439                   boolean fromSplitFrame = selviews.get(0)
 440                           .getAlignViewport().getCodingComplement() != null;
 441                   if (!fromSplitFrame)
 442                   {
 443                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 444                             .getViewStyle().isScaleProteinAsCdna());
 445                   }
 446                   ap.getAlignViewport().setViewStyle(vs);
 447
 448                   /*
 449                    * Also rescale ViewStyle of SplitFrame complement if there is
 450                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 451                    * the whole ViewStyle (allow cDNA protein to have different
 452                    * fonts)
 453                    */
 454                   AlignViewportI complement = ap.getAlignViewport()
 455                           .getCodingComplement();
 456                   if (complement != null && vs.isScaleProteinAsCdna())
 457                   {
 458                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 459                     ((SplitFrame) af.getSplitViewContainer())
 460                             .adjustLayout();
 461                     af.setMenusForViewport();
 462                   }
 463
 464                   ap.updateLayout();
 465                   ap.setSelected(true);
 466                   ap.alignFrame.setMenusForViewport();
 467
 468                 }
 469               }
 470             });
 471     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 472             .indexOf("devel") > -1
 473             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 474                     .indexOf("test") > -1)
 475     {
 476       formatMenu.add(vsel);
 477     }
 478     addFocusListener(new FocusAdapter()
 479     {
 480       @Override
 481       public void focusGained(FocusEvent e)
 482       {
 483         Jalview.setCurrentAlignFrame(AlignFrame.this);
 484       }
 485     });
 486
 487   }
 488
 489   /**
 490    * Change the filename and format for the alignment, and enable the 'reload'
 491    * button functionality.
 492    *
 493    * @param file
 494    *          valid filename
 495    * @param format
 496    *          format of file
 497    */
 498   public void setFileName(String file, FileFormatI format)
 499   {
 500     fileName = file;
 501     setFileFormat(format);
 502     reload.setEnabled(true);
 503   }
 504
 505   /**
 506    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 507    * events
 508    */
 509   void addKeyListener()
 510   {
 511     addKeyListener(new KeyAdapter()
 512     {
 513       @Override
 514       public void keyPressed(KeyEvent evt)
 515       {
 516         if (viewport.cursorMode
 517                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 518                         && evt.getKeyCode() <= KeyEvent.VK_9)
 519                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 520                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 521                 && Character.isDigit(evt.getKeyChar()))
 522         {
 523           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 524         }
 525
 526         switch (evt.getKeyCode())
 527         {
 528
 529         case 27: // escape key
 530           deselectAllSequenceMenuItem_actionPerformed(null);
 531
 532           break;
 533
 534         case KeyEvent.VK_DOWN:
 535           if (evt.isAltDown() || !viewport.cursorMode)
 536           {
 537             moveSelectedSequences(false);
 538           }
 539           if (viewport.cursorMode)
 540           {
 541             alignPanel.getSeqPanel().moveCursor(0, 1,
 542                     evt.isShiftDown() && !evt.isAltDown());
 543           }
 544           break;
 545
 546         case KeyEvent.VK_UP:
 547           if (evt.isAltDown() || !viewport.cursorMode)
 548           {
 549             moveSelectedSequences(true);
 550           }
 551           if (viewport.cursorMode)
 552           {
 553             alignPanel.getSeqPanel().moveCursor(0, -1,
 554                     evt.isShiftDown() && !evt.isAltDown());
 555           }
 556           break;
 557
 558         case KeyEvent.VK_LEFT:
 559           if (evt.isAltDown() || !viewport.cursorMode)
 560           {
 561             slideSequences(false,
 562                     alignPanel.getSeqPanel().getKeyboardNo1());
 563           }
 564           else
 565           {
 566             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 567           }
 568
 569           break;
 570
 571         case KeyEvent.VK_RIGHT:
 572           if (evt.isAltDown() || !viewport.cursorMode)
 573           {
 574             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 575           }
 576           else
 577           {
 578             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 579           }
 580           break;
 581
 582         case KeyEvent.VK_SPACE:
 583           if (viewport.cursorMode)
 584           {
 585             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 586                     || evt.isShiftDown() || evt.isAltDown());
 587           }
 588           break;
 589
 590         // case KeyEvent.VK_A:
 591         // if (viewport.cursorMode)
 592         // {
 593         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 594         // //System.out.println("A");
 595         // }
 596         // break;
 597         /*
 598          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 599          * System.out.println("closing bracket"); } break;
 600          */
 601         case KeyEvent.VK_DELETE:
 602         case KeyEvent.VK_BACK_SPACE:
 603           if (!viewport.cursorMode)
 604           {
 605             cut_actionPerformed(null);
 606           }
 607           else
 608           {
 609             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 610                     || evt.isShiftDown() || evt.isAltDown());
 611           }
 612
 613           break;
 614
 615         case KeyEvent.VK_S:
 616           if (viewport.cursorMode)
 617           {
 618             alignPanel.getSeqPanel().setCursorRow();
 619           }
 620           break;
 621         case KeyEvent.VK_C:
 622           if (viewport.cursorMode && !evt.isControlDown())
 623           {
 624             alignPanel.getSeqPanel().setCursorColumn();
 625           }
 626           break;
 627         case KeyEvent.VK_P:
 628           if (viewport.cursorMode)
 629           {
 630             alignPanel.getSeqPanel().setCursorPosition();
 631           }
 632           break;
 633
 634         case KeyEvent.VK_ENTER:
 635         case KeyEvent.VK_COMMA:
 636           if (viewport.cursorMode)
 637           {
 638             alignPanel.getSeqPanel().setCursorRowAndColumn();
 639           }
 640           break;
 641
 642         case KeyEvent.VK_Q:
 643           if (viewport.cursorMode)
 644           {
 645             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 646           }
 647           break;
 648         case KeyEvent.VK_M:
 649           if (viewport.cursorMode)
 650           {
 651             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 652           }
 653           break;
 654
 655         case KeyEvent.VK_F2:
 656           viewport.cursorMode = !viewport.cursorMode;
 657           statusBar.setText(MessageManager
 658                   .formatMessage("label.keyboard_editing_mode", new String[]
 659                   { (viewport.cursorMode ? "on" : "off") }));
 660           if (viewport.cursorMode)
 661           {
 662             ViewportRanges ranges = viewport.getRanges();
 663             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 664                     .getStartRes();
 665             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 666                     .getStartSeq();
 667           }
 668           alignPanel.getSeqPanel().seqCanvas.repaint();
 669           break;
 670
 671         case KeyEvent.VK_F1:
 672           try
 673           {
 674             Help.showHelpWindow();
 675           } catch (Exception ex)
 676           {
 677             ex.printStackTrace();
 678           }
 679           break;
 680         case KeyEvent.VK_H:
 681         {
 682           boolean toggleSeqs = !evt.isControlDown();
 683           boolean toggleCols = !evt.isShiftDown();
 684           toggleHiddenRegions(toggleSeqs, toggleCols);
 685           break;
 686         }
 687         case KeyEvent.VK_B:
 688         {
 689           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 690           boolean modifyExisting = true; // always modify, don't clear
 691                                          // evt.isShiftDown();
 692           boolean invertHighlighted = evt.isAltDown();
 693           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 694                   toggleSel);
 695           break;
 696         }
 697         case KeyEvent.VK_PAGE_UP:
 698           viewport.getRanges().pageUp();
 699           break;
 700         case KeyEvent.VK_PAGE_DOWN:
 701           viewport.getRanges().pageDown();
 702           break;
 703         }
 704       }
 705
 706       @Override
 707       public void keyReleased(KeyEvent evt)
 708       {
 709         switch (evt.getKeyCode())
 710         {
 711         case KeyEvent.VK_LEFT:
 712           if (evt.isAltDown() || !viewport.cursorMode)
 713           {
 714             viewport.firePropertyChange("alignment", null,
 715                     viewport.getAlignment().getSequences());
 716           }
 717           break;
 718
 719         case KeyEvent.VK_RIGHT:
 720           if (evt.isAltDown() || !viewport.cursorMode)
 721           {
 722             viewport.firePropertyChange("alignment", null,
 723                     viewport.getAlignment().getSequences());
 724           }
 725           break;
 726         }
 727       }
 728     });
 729   }
 730
 731   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 732   {
 733     ap.alignFrame = this;
 734     avc = new jalview.controller.AlignViewController(this, viewport,
 735             alignPanel);
 736
 737     alignPanels.add(ap);
 738
 739     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 740
 741     int aSize = alignPanels.size();
 742
 743     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 744
 745     if (aSize == 1 && ap.av.getViewName() == null)
 746     {
 747       this.getContentPane().add(ap, BorderLayout.CENTER);
 748     }
 749     else
 750     {
 751       if (aSize == 2)
 752       {
 753         setInitialTabVisible();
 754       }
 755
 756       expandViews.setEnabled(true);
 757       gatherViews.setEnabled(true);
 758       tabbedPane.addTab(ap.av.getViewName(), ap);
 759
 760       ap.setVisible(false);
 761     }
 762
 763     if (newPanel)
 764     {
 765       if (ap.av.isPadGaps())
 766       {
 767         ap.av.getAlignment().padGaps();
 768       }
 769       ap.av.updateConservation(ap);
 770       ap.av.updateConsensus(ap);
 771       ap.av.updateStrucConsensus(ap);
 772     }
 773   }
 774
 775   public void setInitialTabVisible()
 776   {
 777     expandViews.setEnabled(true);
 778     gatherViews.setEnabled(true);
 779     tabbedPane.setVisible(true);
 780     AlignmentPanel first = alignPanels.get(0);
 781     tabbedPane.addTab(first.av.getViewName(), first);
 782     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 783   }
 784
 785   public AlignViewport getViewport()
 786   {
 787     return viewport;
 788   }
 789
 790   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 791   private void addServiceListeners()
 792   {
 793     final java.beans.PropertyChangeListener thisListener;
 794     Desktop.instance.addJalviewPropertyChangeListener("services",
 795             thisListener = new java.beans.PropertyChangeListener()
 796             {
 797               @Override
 798               public void propertyChange(PropertyChangeEvent evt)
 799               {
 800                 // // System.out.println("Discoverer property change.");
 801                 // if (evt.getPropertyName().equals("services"))
 802                 {
 803                   SwingUtilities.invokeLater(new Runnable()
 804                   {
 805
 806                     @Override
 807                     public void run()
 808                     {
 809                       System.err.println(
 810                               "Rebuild WS Menu for service change");
 811                       BuildWebServiceMenu();
 812                     }
 813
 814                   });
 815                 }
 816               }
 817             });
 818     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 819     {
 820       @Override
 821       public void internalFrameClosed(
 822               javax.swing.event.InternalFrameEvent evt)
 823       {
 824         // System.out.println("deregistering discoverer listener");
 825         Desktop.instance.removeJalviewPropertyChangeListener("services",
 826                 thisListener);
 827         closeMenuItem_actionPerformed(true);
 828       };
 829     });
 830     // Finally, build the menu once to get current service state
 831     new Thread(new Runnable()
 832     {
 833       @Override
 834       public void run()
 835       {
 836         BuildWebServiceMenu();
 837       }
 838     }).start();
 839   }
 840
 841   /**
 842    * Configure menu items that vary according to whether the alignment is
 843    * nucleotide or protein
 844    */
 845   public void setGUINucleotide()
 846   {
 847     AlignmentI al = getViewport().getAlignment();
 848     boolean nucleotide = al.isNucleotide();
 849
 850     loadVcf.setVisible(nucleotide);
 851     showTranslation.setVisible(nucleotide);
 852     showReverse.setVisible(nucleotide);
 853     showReverseComplement.setVisible(nucleotide);
 854     conservationMenuItem.setEnabled(!nucleotide);
 855     modifyConservation
 856             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 857     showGroupConservation.setEnabled(!nucleotide);
 858
 859     showComplementMenuItem
 860             .setText(nucleotide ? MessageManager.getString("label.protein")
 861                     : MessageManager.getString("label.nucleotide"));
 862   }
 863
 864   /**
 865    * set up menus for the current viewport. This may be called after any
 866    * operation that affects the data in the current view (selection changed,
 867    * etc) to update the menus to reflect the new state.
 868    */
 869   @Override
 870   public void setMenusForViewport()
 871   {
 872     setMenusFromViewport(viewport);
 873   }
 874
 875   /**
 876    * Need to call this method when tabs are selected for multiple views, or when
 877    * loading from Jalview2XML.java
 878    *
 879    * @param av
 880    *          AlignViewport
 881    */
 882   public void setMenusFromViewport(AlignViewport av)
 883   {
 884     padGapsMenuitem.setSelected(av.isPadGaps());
 885     colourTextMenuItem.setSelected(av.isShowColourText());
 886     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 887     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 888     conservationMenuItem.setSelected(av.getConservationSelected());
 889     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 890     seqLimits.setSelected(av.getShowJVSuffix());
 891     idRightAlign.setSelected(av.isRightAlignIds());
 892     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 893     renderGapsMenuItem.setSelected(av.isRenderGaps());
 894     wrapMenuItem.setSelected(av.getWrapAlignment());
 895     scaleAbove.setVisible(av.getWrapAlignment());
 896     scaleLeft.setVisible(av.getWrapAlignment());
 897     scaleRight.setVisible(av.getWrapAlignment());
 898     annotationPanelMenuItem.setState(av.isShowAnnotation());
 899     /*
 900      * Show/hide annotations only enabled if annotation panel is shown
 901      */
 902     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 903     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 904     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 905     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 906     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 907     viewTextMenuItem.setSelected(av.getShowText());
 908     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 909     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 910     showGroupConservation.setSelected(av.isShowGroupConservation());
 911     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 912     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 913     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 914
 915     ColourMenuHelper.setColourSelected(colourMenu,
 916             av.getGlobalColourScheme());
 917
 918     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 919     hiddenMarkers.setState(av.getShowHiddenMarkers());
 920     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 921     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 922     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 923     autoCalculate.setSelected(av.autoCalculateConsensus);
 924     sortByTree.setSelected(av.sortByTree);
 925     listenToViewSelections.setSelected(av.followSelection);
 926
 927     showProducts.setEnabled(canShowProducts());
 928     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 929
 930     updateEditMenuBar();
 931   }
 932
 933   /**
 934    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 935    *
 936    * @param b
 937    */
 938   public void setGroovyEnabled(boolean b)
 939   {
 940     runGroovy.setEnabled(b);
 941   }
 942
 943   private IProgressIndicator progressBar;
 944
 945   /*
 946    * (non-Javadoc)
 947    *
 948    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 949    */
 950   @Override
 951   public void setProgressBar(String message, long id)
 952   {
 953     progressBar.setProgressBar(message, id);
 954   }
 955
 956   @Override
 957   public void registerHandler(final long id,
 958           final IProgressIndicatorHandler handler)
 959   {
 960     progressBar.registerHandler(id, handler);
 961   }
 962
 963   /**
 964    *
 965    * @return true if any progress bars are still active
 966    */
 967   @Override
 968   public boolean operationInProgress()
 969   {
 970     return progressBar.operationInProgress();
 971   }
 972
 973   /**
 974    * Sets the text of the status bar. Note that setting a null or empty value
 975    * will cause the status bar to be hidden, with possibly undesirable flicker
 976    * of the screen layout.
 977    */
 978   @Override
 979   public void setStatus(String text)
 980   {
 981     statusBar.setText(text == null || text.isEmpty() ? " " : text);
 982   }
 983
 984   /*
 985    * Added so Castor Mapping file can obtain Jalview Version
 986    */
 987   public String getVersion()
 988   {
 989     return jalview.bin.Cache.getProperty("VERSION");
 990   }
 991
 992   public FeatureRenderer getFeatureRenderer()
 993   {
 994     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 995   }
 996
 997   @Override
 998   public void fetchSequence_actionPerformed(ActionEvent e)
 999   {
1000     new jalview.gui.SequenceFetcher(this);
1001   }
1002
1003   @Override
1004   public void addFromFile_actionPerformed(ActionEvent e)
1005   {
1006     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1007   }
1008
1009   @Override
1010   public void reload_actionPerformed(ActionEvent e)
1011   {
1012     if (fileName != null)
1013     {
1014       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1015       // originating file's format
1016       // TODO: work out how to recover feature settings for correct view(s) when
1017       // file is reloaded.
1018       if (FileFormat.Jalview.equals(currentFileFormat))
1019       {
1020         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1021         for (int i = 0; i < frames.length; i++)
1022         {
1023           if (frames[i] instanceof AlignFrame && frames[i] != this
1024                   && ((AlignFrame) frames[i]).fileName != null
1025                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1026           {
1027             try
1028             {
1029               frames[i].setSelected(true);
1030               Desktop.instance.closeAssociatedWindows();
1031             } catch (java.beans.PropertyVetoException ex)
1032             {
1033             }
1034           }
1035
1036         }
1037         Desktop.instance.closeAssociatedWindows();
1038
1039         FileLoader loader = new FileLoader();
1040         DataSourceType protocol = fileName.startsWith("http:")
1041                 ? DataSourceType.URL
1042                 : DataSourceType.FILE;
1043         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1044       }
1045       else
1046       {
1047         Rectangle bounds = this.getBounds();
1048
1049         FileLoader loader = new FileLoader();
1050         DataSourceType protocol = fileName.startsWith("http:")
1051                 ? DataSourceType.URL
1052                 : DataSourceType.FILE;
1053         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1054                 protocol, currentFileFormat);
1055
1056         newframe.setBounds(bounds);
1057         if (featureSettings != null && featureSettings.isShowing())
1058         {
1059           final Rectangle fspos = featureSettings.frame.getBounds();
1060           // TODO: need a 'show feature settings' function that takes bounds -
1061           // need to refactor Desktop.addFrame
1062           newframe.featureSettings_actionPerformed(null);
1063           final FeatureSettings nfs = newframe.featureSettings;
1064           SwingUtilities.invokeLater(new Runnable()
1065           {
1066             @Override
1067             public void run()
1068             {
1069               nfs.frame.setBounds(fspos);
1070             }
1071           });
1072           this.featureSettings.close();
1073           this.featureSettings = null;
1074         }
1075         this.closeMenuItem_actionPerformed(true);
1076       }
1077     }
1078   }
1079
1080   @Override
1081   public void addFromText_actionPerformed(ActionEvent e)
1082   {
1083     Desktop.instance
1084             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1085   }
1086
1087   @Override
1088   public void addFromURL_actionPerformed(ActionEvent e)
1089   {
1090     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1091   }
1092
1093   @Override
1094   public void save_actionPerformed(ActionEvent e)
1095   {
1096     if (fileName == null || (currentFileFormat == null)
1097             || fileName.startsWith("http"))
1098     {
1099       saveAs_actionPerformed(null);
1100     }
1101     else
1102     {
1103       saveAlignment(fileName, currentFileFormat);
1104     }
1105   }
1106
1107   /**
1108    * DOCUMENT ME!
1109    *
1110    * @param e
1111    *          DOCUMENT ME!
1112    */
1113   @Override
1114   public void saveAs_actionPerformed(ActionEvent e)
1115   {
1116     String format = currentFileFormat == null ? null
1117             : currentFileFormat.getName();
1118     JalviewFileChooser chooser = JalviewFileChooser
1119             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1120
1121     chooser.setFileView(new JalviewFileView());
1122     chooser.setDialogTitle(
1123             MessageManager.getString("label.save_alignment_to_file"));
1124     chooser.setToolTipText(MessageManager.getString("action.save"));
1125
1126     int value = chooser.showSaveDialog(this);
1127
1128     if (value == JalviewFileChooser.APPROVE_OPTION)
1129     {
1130       currentFileFormat = chooser.getSelectedFormat();
1131       while (currentFileFormat == null)
1132       {
1133         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1134                 MessageManager.getString(
1135                         "label.select_file_format_before_saving"),
1136                 MessageManager.getString("label.file_format_not_specified"),
1137                 JvOptionPane.WARNING_MESSAGE);
1138         currentFileFormat = chooser.getSelectedFormat();
1139         value = chooser.showSaveDialog(this);
1140         if (value != JalviewFileChooser.APPROVE_OPTION)
1141         {
1142           return;
1143         }
1144       }
1145
1146       fileName = chooser.getSelectedFile().getPath();
1147
1148       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1149
1150       Cache.setProperty("LAST_DIRECTORY", fileName);
1151       saveAlignment(fileName, currentFileFormat);
1152     }
1153   }
1154
1155   public boolean saveAlignment(String file, FileFormatI format)
1156   {
1157     boolean success = true;
1158
1159     if (FileFormat.Jalview.equals(format))
1160     {
1161       String shortName = title;
1162
1163       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1164       {
1165         shortName = shortName.substring(
1166                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1167       }
1168
1169       success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1170               shortName);
1171
1172       statusBar.setText(MessageManager.formatMessage(
1173               "label.successfully_saved_to_file_in_format", new Object[]
1174               { file, format }));
1175
1176     }
1177     else
1178     {
1179       AlignmentExportData exportData = getAlignmentForExport(format,
1180               viewport, null);
1181       if (exportData.getSettings().isCancelled())
1182       {
1183         return false;
1184       }
1185       FormatAdapter f = new FormatAdapter(alignPanel,
1186               exportData.getSettings());
1187       String output = f.formatSequences(format, exportData.getAlignment(), // class
1188                                                                            // cast
1189                                                                            // exceptions
1190                                                                            // will
1191               // occur in the distant future
1192               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1193               f.getCacheSuffixDefault(format),
1194               viewport.getAlignment().getHiddenColumns());
1195
1196       if (output == null)
1197       {
1198         success = false;
1199       }
1200       else
1201       {
1202         // create backupfiles object and get new temp filename destination
1203         Cache.log.debug("ALIGNFRAME making backupfiles object for " + file);
1204         BackupFiles backupfiles = new BackupFiles(file);
1205
1206         try
1207         {
1208           String tempFilePath = backupfiles.getTempFilePath();
1209           Cache.log.debug(
1210                   "ALIGNFRAME setting PrintWriter to " + tempFilePath);
1211           PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1212
1213           Cache.log.debug(
1214                   "ALIGNFRAME about to write to temp file " + tempFilePath);
1215
1216           out.print(output);
1217           Cache.log.debug("ALIGNFRAME about to close file");
1218           out.close();
1219           Cache.log.debug("ALIGNFRAME closed file");
1220           this.setTitle(file);
1221           statusBar.setText(MessageManager.formatMessage(
1222                   "label.successfully_saved_to_file_in_format", new Object[]
1223                   { file, format.getName() }));
1224         } catch (IOException e)
1225         {
1226           success = false;
1227           Cache.log.error(
1228                   "ALIGNFRAME Something happened writing the temp file");
1229           Cache.log.error(e.getMessage());
1230           Cache.log.debug(Cache.getStackTraceString(e));
1231
1232         } catch (Exception ex)
1233         {
1234           success = false;
1235           Cache.log.error(
1236                   "ALIGNFRAME Something else happened writing the temp file");
1237           Cache.log.error(ex.getMessage());
1238           Cache.log.debug(Cache.getStackTraceString(ex));
1239         }
1240
1241         backupfiles.setWriteSuccess(success);
1242         Cache.log.debug("ALIGNFRAME writing temp file was "
1243                 + (success ? "" : "NOT ") + "successful");
1244         // do the backup file roll and rename the temp file to actual file
1245         Cache.log.debug("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1246         success = backupfiles.rollBackupsAndRenameTempFile();
1247         Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1248                 + (success ? "" : "un") + "successfully");
1249
1250       }
1251     }
1252
1253     if (!success)
1254     {
1255       if (!Platform.isHeadless())
1256       {
1257         JvOptionPane.showInternalMessageDialog(this, MessageManager
1258                 .formatMessage("label.couldnt_save_file", new Object[]
1259                 { file }),
1260                 MessageManager.getString("label.error_saving_file"),
1261                 JvOptionPane.WARNING_MESSAGE);
1262       }
1263     }
1264
1265     return success;
1266   }
1267
1268   private void warningMessage(String warning, String title)
1269   {
1270     if (new jalview.util.Platform().isHeadless())
1271     {
1272       System.err.println("Warning: " + title + "\nWarning: " + warning);
1273
1274     }
1275     else
1276     {
1277       JvOptionPane.showInternalMessageDialog(this, warning, title,
1278               JvOptionPane.WARNING_MESSAGE);
1279     }
1280     return;
1281   }
1282
1283   /**
1284    * DOCUMENT ME!
1285    *
1286    * @param e
1287    *          DOCUMENT ME!
1288    */
1289   @Override
1290   protected void outputText_actionPerformed(ActionEvent e)
1291   {
1292     FileFormatI fileFormat = FileFormats.getInstance()
1293             .forName(e.getActionCommand());
1294     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1295             viewport, null);
1296     if (exportData.getSettings().isCancelled())
1297     {
1298       return;
1299     }
1300     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1301     cap.setForInput(null);
1302     try
1303     {
1304       FileFormatI format = fileFormat;
1305       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1306               .formatSequences(format, exportData.getAlignment(),
1307                       exportData.getOmitHidden(),
1308                       exportData.getStartEndPostions(),
1309                       viewport.getAlignment().getHiddenColumns()));
1310       Desktop.addInternalFrame(cap, MessageManager
1311               .formatMessage("label.alignment_output_command", new Object[]
1312               { e.getActionCommand() }), 600, 500);
1313     } catch (OutOfMemoryError oom)
1314     {
1315       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1316               oom);
1317       cap.dispose();
1318     }
1319
1320   }
1321
1322   public static AlignmentExportData getAlignmentForExport(
1323           FileFormatI format, AlignViewportI viewport,
1324           AlignExportSettingI exportSettings)
1325   {
1326     AlignmentI alignmentToExport = null;
1327     AlignExportSettingI settings = exportSettings;
1328     String[] omitHidden = null;
1329
1330     HiddenSequences hiddenSeqs = viewport.getAlignment()
1331             .getHiddenSequences();
1332
1333     alignmentToExport = viewport.getAlignment();
1334
1335     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1336     if (settings == null)
1337     {
1338       settings = new AlignExportSettings(hasHiddenSeqs,
1339               viewport.hasHiddenColumns(), format);
1340     }
1341     // settings.isExportAnnotations();
1342
1343     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1344     {
1345       omitHidden = viewport.getViewAsString(false,
1346               settings.isExportHiddenSequences());
1347     }
1348
1349     int[] alignmentStartEnd = new int[2];
1350     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1351     {
1352       alignmentToExport = hiddenSeqs.getFullAlignment();
1353     }
1354     else
1355     {
1356       alignmentToExport = viewport.getAlignment();
1357     }
1358     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1359             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1360     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1361             omitHidden, alignmentStartEnd, settings);
1362     return ed;
1363   }
1364
1365   /**
1366    * DOCUMENT ME!
1367    *
1368    * @param e
1369    *          DOCUMENT ME!
1370    */
1371   @Override
1372   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1373   {
1374     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1375     htmlSVG.exportHTML(null);
1376   }
1377
1378   @Override
1379   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1380   {
1381     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1382     bjs.exportHTML(null);
1383   }
1384
1385   public void createImageMap(File file, String image)
1386   {
1387     alignPanel.makePNGImageMap(file, image);
1388   }
1389
1390   /**
1391    * DOCUMENT ME!
1392    *
1393    * @param e
1394    *          DOCUMENT ME!
1395    */
1396   @Override
1397   public void createPNG(File f)
1398   {
1399     alignPanel.makePNG(f);
1400   }
1401
1402   /**
1403    * DOCUMENT ME!
1404    *
1405    * @param e
1406    *          DOCUMENT ME!
1407    */
1408   @Override
1409   public void createEPS(File f)
1410   {
1411     alignPanel.makeEPS(f);
1412   }
1413
1414   @Override
1415   public void createSVG(File f)
1416   {
1417     alignPanel.makeSVG(f);
1418   }
1419
1420   @Override
1421   public void pageSetup_actionPerformed(ActionEvent e)
1422   {
1423     PrinterJob printJob = PrinterJob.getPrinterJob();
1424     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1425   }
1426
1427   /**
1428    * DOCUMENT ME!
1429    *
1430    * @param e
1431    *          DOCUMENT ME!
1432    */
1433   @Override
1434   public void printMenuItem_actionPerformed(ActionEvent e)
1435   {
1436     // Putting in a thread avoids Swing painting problems
1437     PrintThread thread = new PrintThread(alignPanel);
1438     thread.start();
1439   }
1440
1441   @Override
1442   public void exportFeatures_actionPerformed(ActionEvent e)
1443   {
1444     new AnnotationExporter(alignPanel).exportFeatures();
1445   }
1446
1447   @Override
1448   public void exportAnnotations_actionPerformed(ActionEvent e)
1449   {
1450     new AnnotationExporter(alignPanel).exportAnnotations();
1451   }
1452
1453   @Override
1454   public void associatedData_actionPerformed(ActionEvent e)
1455   {
1456     // Pick the tree file
1457     JalviewFileChooser chooser = new JalviewFileChooser(
1458             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1459     chooser.setFileView(new JalviewFileView());
1460     chooser.setDialogTitle(
1461             MessageManager.getString("label.load_jalview_annotations"));
1462     chooser.setToolTipText(
1463             MessageManager.getString("label.load_jalview_annotations"));
1464
1465     int value = chooser.showOpenDialog(null);
1466
1467     if (value == JalviewFileChooser.APPROVE_OPTION)
1468     {
1469       String choice = chooser.getSelectedFile().getPath();
1470       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1471       loadJalviewDataFile(choice, null, null, null);
1472     }
1473
1474   }
1475
1476   /**
1477    * Close the current view or all views in the alignment frame. If the frame
1478    * only contains one view then the alignment will be removed from memory.
1479    *
1480    * @param closeAllTabs
1481    */
1482   @Override
1483   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1484   {
1485     if (alignPanels != null && alignPanels.size() < 2)
1486     {
1487       closeAllTabs = true;
1488     }
1489
1490     try
1491     {
1492       if (alignPanels != null)
1493       {
1494         if (closeAllTabs)
1495         {
1496           if (this.isClosed())
1497           {
1498             // really close all the windows - otherwise wait till
1499             // setClosed(true) is called
1500             for (int i = 0; i < alignPanels.size(); i++)
1501             {
1502               AlignmentPanel ap = alignPanels.get(i);
1503               ap.closePanel();
1504             }
1505           }
1506         }
1507         else
1508         {
1509           closeView(alignPanel);
1510         }
1511       }
1512       if (closeAllTabs)
1513       {
1514         if (featureSettings != null && featureSettings.isOpen())
1515         {
1516           featureSettings.close();
1517           featureSettings = null;
1518         }
1519         /*
1520          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1521          * be called recursively, with the frame now in 'closed' state
1522          */
1523         this.setClosed(true);
1524       }
1525     } catch (Exception ex)
1526     {
1527       ex.printStackTrace();
1528     }
1529   }
1530
1531   /**
1532    * Close the specified panel and close up tabs appropriately.
1533    *
1534    * @param panelToClose
1535    */
1536   public void closeView(AlignmentPanel panelToClose)
1537   {
1538     int index = tabbedPane.getSelectedIndex();
1539     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1540     alignPanels.remove(panelToClose);
1541     panelToClose.closePanel();
1542     panelToClose = null;
1543
1544     tabbedPane.removeTabAt(closedindex);
1545     tabbedPane.validate();
1546
1547     if (index > closedindex || index == tabbedPane.getTabCount())
1548     {
1549       // modify currently selected tab index if necessary.
1550       index--;
1551     }
1552
1553     this.tabSelectionChanged(index);
1554   }
1555
1556   /**
1557    * DOCUMENT ME!
1558    */
1559   void updateEditMenuBar()
1560   {
1561
1562     if (viewport.getHistoryList().size() > 0)
1563     {
1564       undoMenuItem.setEnabled(true);
1565       CommandI command = viewport.getHistoryList().peek();
1566       undoMenuItem.setText(MessageManager
1567               .formatMessage("label.undo_command", new Object[]
1568               { command.getDescription() }));
1569     }
1570     else
1571     {
1572       undoMenuItem.setEnabled(false);
1573       undoMenuItem.setText(MessageManager.getString("action.undo"));
1574     }
1575
1576     if (viewport.getRedoList().size() > 0)
1577     {
1578       redoMenuItem.setEnabled(true);
1579
1580       CommandI command = viewport.getRedoList().peek();
1581       redoMenuItem.setText(MessageManager
1582               .formatMessage("label.redo_command", new Object[]
1583               { command.getDescription() }));
1584     }
1585     else
1586     {
1587       redoMenuItem.setEnabled(false);
1588       redoMenuItem.setText(MessageManager.getString("action.redo"));
1589     }
1590   }
1591
1592   @Override
1593   public void addHistoryItem(CommandI command)
1594   {
1595     if (command.getSize() > 0)
1596     {
1597       viewport.addToHistoryList(command);
1598       viewport.clearRedoList();
1599       updateEditMenuBar();
1600       viewport.updateHiddenColumns();
1601       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1602       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1603       // viewport.getColumnSelection()
1604       // .getHiddenColumns().size() > 0);
1605     }
1606   }
1607
1608   /**
1609    *
1610    * @return alignment objects for all views
1611    */
1612   AlignmentI[] getViewAlignments()
1613   {
1614     if (alignPanels != null)
1615     {
1616       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1617       int i = 0;
1618       for (AlignmentPanel ap : alignPanels)
1619       {
1620         als[i++] = ap.av.getAlignment();
1621       }
1622       return als;
1623     }
1624     if (viewport != null)
1625     {
1626       return new AlignmentI[] { viewport.getAlignment() };
1627     }
1628     return null;
1629   }
1630
1631   /**
1632    * DOCUMENT ME!
1633    *
1634    * @param e
1635    *          DOCUMENT ME!
1636    */
1637   @Override
1638   protected void undoMenuItem_actionPerformed(ActionEvent e)
1639   {
1640     if (viewport.getHistoryList().isEmpty())
1641     {
1642       return;
1643     }
1644     CommandI command = viewport.getHistoryList().pop();
1645     viewport.addToRedoList(command);
1646     command.undoCommand(getViewAlignments());
1647
1648     AlignmentViewport originalSource = getOriginatingSource(command);
1649     updateEditMenuBar();
1650
1651     if (originalSource != null)
1652     {
1653       if (originalSource != viewport)
1654       {
1655         Cache.log.warn(
1656                 "Implementation worry: mismatch of viewport origin for undo");
1657       }
1658       originalSource.updateHiddenColumns();
1659       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1660       // null
1661       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1662       // viewport.getColumnSelection()
1663       // .getHiddenColumns().size() > 0);
1664       originalSource.firePropertyChange("alignment", null,
1665               originalSource.getAlignment().getSequences());
1666     }
1667   }
1668
1669   /**
1670    * DOCUMENT ME!
1671    *
1672    * @param e
1673    *          DOCUMENT ME!
1674    */
1675   @Override
1676   protected void redoMenuItem_actionPerformed(ActionEvent e)
1677   {
1678     if (viewport.getRedoList().size() < 1)
1679     {
1680       return;
1681     }
1682
1683     CommandI command = viewport.getRedoList().pop();
1684     viewport.addToHistoryList(command);
1685     command.doCommand(getViewAlignments());
1686
1687     AlignmentViewport originalSource = getOriginatingSource(command);
1688     updateEditMenuBar();
1689
1690     if (originalSource != null)
1691     {
1692
1693       if (originalSource != viewport)
1694       {
1695         Cache.log.warn(
1696                 "Implementation worry: mismatch of viewport origin for redo");
1697       }
1698       originalSource.updateHiddenColumns();
1699       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1700       // null
1701       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1702       // viewport.getColumnSelection()
1703       // .getHiddenColumns().size() > 0);
1704       originalSource.firePropertyChange("alignment", null,
1705               originalSource.getAlignment().getSequences());
1706     }
1707   }
1708
1709   AlignmentViewport getOriginatingSource(CommandI command)
1710   {
1711     AlignmentViewport originalSource = null;
1712     // For sequence removal and addition, we need to fire
1713     // the property change event FROM the viewport where the
1714     // original alignment was altered
1715     AlignmentI al = null;
1716     if (command instanceof EditCommand)
1717     {
1718       EditCommand editCommand = (EditCommand) command;
1719       al = editCommand.getAlignment();
1720       List<Component> comps = PaintRefresher.components
1721               .get(viewport.getSequenceSetId());
1722
1723       for (Component comp : comps)
1724       {
1725         if (comp instanceof AlignmentPanel)
1726         {
1727           if (al == ((AlignmentPanel) comp).av.getAlignment())
1728           {
1729             originalSource = ((AlignmentPanel) comp).av;
1730             break;
1731           }
1732         }
1733       }
1734     }
1735
1736     if (originalSource == null)
1737     {
1738       // The original view is closed, we must validate
1739       // the current view against the closed view first
1740       if (al != null)
1741       {
1742         PaintRefresher.validateSequences(al, viewport.getAlignment());
1743       }
1744
1745       originalSource = viewport;
1746     }
1747
1748     return originalSource;
1749   }
1750
1751   /**
1752    * DOCUMENT ME!
1753    *
1754    * @param up
1755    *          DOCUMENT ME!
1756    */
1757   public void moveSelectedSequences(boolean up)
1758   {
1759     SequenceGroup sg = viewport.getSelectionGroup();
1760
1761     if (sg == null)
1762     {
1763       return;
1764     }
1765     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1766             viewport.getHiddenRepSequences(), up);
1767     alignPanel.paintAlignment(true, false);
1768   }
1769
1770   synchronized void slideSequences(boolean right, int size)
1771   {
1772     List<SequenceI> sg = new ArrayList<>();
1773     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
1774             .getSize() != viewport.getAlignment().getHeight())
1775     {
1776       sg = viewport.getSelectionGroup()
1777               .getSequences(viewport.getHiddenRepSequences());
1778     }
1779
1780     if (sg.size() == 0 && viewport.cursorMode)
1781     {
1782       sg.add(viewport.getAlignment()
1783               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1784     }
1785
1786     if (sg.size() < 1)
1787     {
1788       return;
1789     }
1790
1791     List<SequenceI> invertGroup = new ArrayList<>();
1792
1793     for (SequenceI seq : viewport.getAlignment().getSequences())
1794     {
1795       if (!sg.contains(seq))
1796       {
1797         invertGroup.add(seq);
1798       }
1799     }
1800
1801     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1802
1803     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1804     for (int i = 0; i < invertGroup.size(); i++)
1805     {
1806       seqs2[i] = invertGroup.get(i);
1807     }
1808
1809     SlideSequencesCommand ssc;
1810     if (right)
1811     {
1812       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1813               viewport.getGapCharacter());
1814     }
1815     else
1816     {
1817       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1818               viewport.getGapCharacter());
1819     }
1820
1821     int groupAdjustment = 0;
1822     if (ssc.getGapsInsertedBegin() && right)
1823     {
1824       if (viewport.cursorMode)
1825       {
1826         alignPanel.getSeqPanel().moveCursor(size, 0);
1827       }
1828       else
1829       {
1830         groupAdjustment = size;
1831       }
1832     }
1833     else if (!ssc.getGapsInsertedBegin() && !right)
1834     {
1835       if (viewport.cursorMode)
1836       {
1837         alignPanel.getSeqPanel().moveCursor(-size, 0);
1838       }
1839       else
1840       {
1841         groupAdjustment = -size;
1842       }
1843     }
1844
1845     if (groupAdjustment != 0)
1846     {
1847       viewport.getSelectionGroup().setStartRes(
1848               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1849       viewport.getSelectionGroup().setEndRes(
1850               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1851     }
1852
1853     /*
1854      * just extend the last slide command if compatible; but not if in
1855      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1856      */
1857     boolean appendHistoryItem = false;
1858     Deque<CommandI> historyList = viewport.getHistoryList();
1859     boolean inSplitFrame = getSplitViewContainer() != null;
1860     if (!inSplitFrame && historyList != null && historyList.size() > 0
1861             && historyList.peek() instanceof SlideSequencesCommand)
1862     {
1863       appendHistoryItem = ssc.appendSlideCommand(
1864               (SlideSequencesCommand) historyList.peek());
1865     }
1866
1867     if (!appendHistoryItem)
1868     {
1869       addHistoryItem(ssc);
1870     }
1871
1872     repaint();
1873   }
1874
1875   /**
1876    * DOCUMENT ME!
1877    *
1878    * @param e
1879    *          DOCUMENT ME!
1880    */
1881   @Override
1882   protected void copy_actionPerformed(ActionEvent e)
1883   {
1884     if (viewport.getSelectionGroup() == null)
1885     {
1886       return;
1887     }
1888     // TODO: preserve the ordering of displayed alignment annotation in any
1889     // internal paste (particularly sequence associated annotation)
1890     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1891     String[] omitHidden = null;
1892
1893     if (viewport.hasHiddenColumns())
1894     {
1895       omitHidden = viewport.getViewAsString(true);
1896     }
1897
1898     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1899             seqs, omitHidden, null);
1900
1901     StringSelection ss = new StringSelection(output);
1902
1903     try
1904     {
1905       jalview.gui.Desktop.internalCopy = true;
1906       // Its really worth setting the clipboard contents
1907       // to empty before setting the large StringSelection!!
1908       Toolkit.getDefaultToolkit().getSystemClipboard()
1909               .setContents(new StringSelection(""), null);
1910
1911       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1912               Desktop.instance);
1913     } catch (OutOfMemoryError er)
1914     {
1915       new OOMWarning("copying region", er);
1916       return;
1917     }
1918
1919     HiddenColumns hiddenColumns = null;
1920     if (viewport.hasHiddenColumns())
1921     {
1922       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1923       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1924
1925       // create new HiddenColumns object with copy of hidden regions
1926       // between startRes and endRes, offset by startRes
1927       hiddenColumns = new HiddenColumns(
1928               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1929               hiddenCutoff, hiddenOffset);
1930     }
1931
1932     Desktop.jalviewClipboard = new Object[] { seqs,
1933         viewport.getAlignment().getDataset(), hiddenColumns };
1934     statusBar.setText(MessageManager.formatMessage(
1935             "label.copied_sequences_to_clipboard", new Object[]
1936             { Integer.valueOf(seqs.length).toString() }));
1937   }
1938
1939   /**
1940    * DOCUMENT ME!
1941    *
1942    * @param e
1943    *          DOCUMENT ME!
1944    */
1945   @Override
1946   protected void pasteNew_actionPerformed(ActionEvent e)
1947   {
1948     paste(true);
1949   }
1950
1951   /**
1952    * DOCUMENT ME!
1953    *
1954    * @param e
1955    *          DOCUMENT ME!
1956    */
1957   @Override
1958   protected void pasteThis_actionPerformed(ActionEvent e)
1959   {
1960     paste(false);
1961   }
1962
1963   /**
1964    * Paste contents of Jalview clipboard
1965    *
1966    * @param newAlignment
1967    *          true to paste to a new alignment, otherwise add to this.
1968    */
1969   void paste(boolean newAlignment)
1970   {
1971     boolean externalPaste = true;
1972     try
1973     {
1974       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1975       Transferable contents = c.getContents(this);
1976
1977       if (contents == null)
1978       {
1979         return;
1980       }
1981
1982       String str;
1983       FileFormatI format;
1984       try
1985       {
1986         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1987         if (str.length() < 1)
1988         {
1989           return;
1990         }
1991
1992         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1993
1994       } catch (OutOfMemoryError er)
1995       {
1996         new OOMWarning("Out of memory pasting sequences!!", er);
1997         return;
1998       }
1999
2000       SequenceI[] sequences;
2001       boolean annotationAdded = false;
2002       AlignmentI alignment = null;
2003
2004       if (Desktop.jalviewClipboard != null)
2005       {
2006         // The clipboard was filled from within Jalview, we must use the
2007         // sequences
2008         // And dataset from the copied alignment
2009         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2010         // be doubly sure that we create *new* sequence objects.
2011         sequences = new SequenceI[newseq.length];
2012         for (int i = 0; i < newseq.length; i++)
2013         {
2014           sequences[i] = new Sequence(newseq[i]);
2015         }
2016         alignment = new Alignment(sequences);
2017         externalPaste = false;
2018       }
2019       else
2020       {
2021         // parse the clipboard as an alignment.
2022         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2023                 format);
2024         sequences = alignment.getSequencesArray();
2025       }
2026
2027       int alwidth = 0;
2028       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2029       int fgroup = -1;
2030
2031       if (newAlignment)
2032       {
2033
2034         if (Desktop.jalviewClipboard != null)
2035         {
2036           // dataset is inherited
2037           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2038         }
2039         else
2040         {
2041           // new dataset is constructed
2042           alignment.setDataset(null);
2043         }
2044         alwidth = alignment.getWidth() + 1;
2045       }
2046       else
2047       {
2048         AlignmentI pastedal = alignment; // preserve pasted alignment object
2049         // Add pasted sequences and dataset into existing alignment.
2050         alignment = viewport.getAlignment();
2051         alwidth = alignment.getWidth() + 1;
2052         // decide if we need to import sequences from an existing dataset
2053         boolean importDs = Desktop.jalviewClipboard != null
2054                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2055         // importDs==true instructs us to copy over new dataset sequences from
2056         // an existing alignment
2057         Vector newDs = (importDs) ? new Vector() : null; // used to create
2058         // minimum dataset set
2059
2060         for (int i = 0; i < sequences.length; i++)
2061         {
2062           if (importDs)
2063           {
2064             newDs.addElement(null);
2065           }
2066           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2067           // paste
2068           if (importDs && ds != null)
2069           {
2070             if (!newDs.contains(ds))
2071             {
2072               newDs.setElementAt(ds, i);
2073               ds = new Sequence(ds);
2074               // update with new dataset sequence
2075               sequences[i].setDatasetSequence(ds);
2076             }
2077             else
2078             {
2079               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2080             }
2081           }
2082           else
2083           {
2084             // copy and derive new dataset sequence
2085             sequences[i] = sequences[i].deriveSequence();
2086             alignment.getDataset()
2087                     .addSequence(sequences[i].getDatasetSequence());
2088             // TODO: avoid creation of duplicate dataset sequences with a
2089             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2090           }
2091           alignment.addSequence(sequences[i]); // merges dataset
2092         }
2093         if (newDs != null)
2094         {
2095           newDs.clear(); // tidy up
2096         }
2097         if (alignment.getAlignmentAnnotation() != null)
2098         {
2099           for (AlignmentAnnotation alan : alignment
2100                   .getAlignmentAnnotation())
2101           {
2102             if (alan.graphGroup > fgroup)
2103             {
2104               fgroup = alan.graphGroup;
2105             }
2106           }
2107         }
2108         if (pastedal.getAlignmentAnnotation() != null)
2109         {
2110           // Add any annotation attached to alignment.
2111           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2112           for (int i = 0; i < alann.length; i++)
2113           {
2114             annotationAdded = true;
2115             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2116             {
2117               AlignmentAnnotation newann = new AlignmentAnnotation(
2118                       alann[i]);
2119               if (newann.graphGroup > -1)
2120               {
2121                 if (newGraphGroups.size() <= newann.graphGroup
2122                         || newGraphGroups.get(newann.graphGroup) == null)
2123                 {
2124                   for (int q = newGraphGroups
2125                           .size(); q <= newann.graphGroup; q++)
2126                   {
2127                     newGraphGroups.add(q, null);
2128                   }
2129                   newGraphGroups.set(newann.graphGroup,
2130                           Integer.valueOf(++fgroup));
2131                 }
2132                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2133                         .intValue();
2134               }
2135
2136               newann.padAnnotation(alwidth);
2137               alignment.addAnnotation(newann);
2138             }
2139           }
2140         }
2141       }
2142       if (!newAlignment)
2143       {
2144         // /////
2145         // ADD HISTORY ITEM
2146         //
2147         addHistoryItem(new EditCommand(
2148                 MessageManager.getString("label.add_sequences"),
2149                 Action.PASTE, sequences, 0, alignment.getWidth(),
2150                 alignment));
2151       }
2152       // Add any annotations attached to sequences
2153       for (int i = 0; i < sequences.length; i++)
2154       {
2155         if (sequences[i].getAnnotation() != null)
2156         {
2157           AlignmentAnnotation newann;
2158           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2159           {
2160             annotationAdded = true;
2161             newann = sequences[i].getAnnotation()[a];
2162             newann.adjustForAlignment();
2163             newann.padAnnotation(alwidth);
2164             if (newann.graphGroup > -1)
2165             {
2166               if (newann.graphGroup > -1)
2167               {
2168                 if (newGraphGroups.size() <= newann.graphGroup
2169                         || newGraphGroups.get(newann.graphGroup) == null)
2170                 {
2171                   for (int q = newGraphGroups
2172                           .size(); q <= newann.graphGroup; q++)
2173                   {
2174                     newGraphGroups.add(q, null);
2175                   }
2176                   newGraphGroups.set(newann.graphGroup,
2177                           Integer.valueOf(++fgroup));
2178                 }
2179                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2180                         .intValue();
2181               }
2182             }
2183             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2184             // was
2185             // duplicated
2186             // earlier
2187             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2188                     a);
2189           }
2190         }
2191       }
2192       if (!newAlignment)
2193       {
2194
2195         // propagate alignment changed.
2196         viewport.getRanges().setEndSeq(alignment.getHeight());
2197         if (annotationAdded)
2198         {
2199           // Duplicate sequence annotation in all views.
2200           AlignmentI[] alview = this.getViewAlignments();
2201           for (int i = 0; i < sequences.length; i++)
2202           {
2203             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2204             if (sann == null)
2205             {
2206               continue;
2207             }
2208             for (int avnum = 0; avnum < alview.length; avnum++)
2209             {
2210               if (alview[avnum] != alignment)
2211               {
2212                 // duplicate in a view other than the one with input focus
2213                 int avwidth = alview[avnum].getWidth() + 1;
2214                 // this relies on sann being preserved after we
2215                 // modify the sequence's annotation array for each duplication
2216                 for (int a = 0; a < sann.length; a++)
2217                 {
2218                   AlignmentAnnotation newann = new AlignmentAnnotation(
2219                           sann[a]);
2220                   sequences[i].addAlignmentAnnotation(newann);
2221                   newann.padAnnotation(avwidth);
2222                   alview[avnum].addAnnotation(newann); // annotation was
2223                   // duplicated earlier
2224                   // TODO JAL-1145 graphGroups are not updated for sequence
2225                   // annotation added to several views. This may cause
2226                   // strangeness
2227                   alview[avnum].setAnnotationIndex(newann, a);
2228                 }
2229               }
2230             }
2231           }
2232           buildSortByAnnotationScoresMenu();
2233         }
2234         viewport.firePropertyChange("alignment", null,
2235                 alignment.getSequences());
2236         if (alignPanels != null)
2237         {
2238           for (AlignmentPanel ap : alignPanels)
2239           {
2240             ap.validateAnnotationDimensions(false);
2241           }
2242         }
2243         else
2244         {
2245           alignPanel.validateAnnotationDimensions(false);
2246         }
2247
2248       }
2249       else
2250       {
2251         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2252                 DEFAULT_HEIGHT);
2253         String newtitle = new String("Copied sequences");
2254
2255         if (Desktop.jalviewClipboard != null
2256                 && Desktop.jalviewClipboard[2] != null)
2257         {
2258           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2259           af.viewport.setHiddenColumns(hc);
2260         }
2261
2262         // >>>This is a fix for the moment, until a better solution is
2263         // found!!<<<
2264         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2265                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2266                         .getFeatureRenderer());
2267
2268         // TODO: maintain provenance of an alignment, rather than just make the
2269         // title a concatenation of operations.
2270         if (!externalPaste)
2271         {
2272           if (title.startsWith("Copied sequences"))
2273           {
2274             newtitle = title;
2275           }
2276           else
2277           {
2278             newtitle = newtitle.concat("- from " + title);
2279           }
2280         }
2281         else
2282         {
2283           newtitle = new String("Pasted sequences");
2284         }
2285
2286         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2287                 DEFAULT_HEIGHT);
2288
2289       }
2290
2291     } catch (Exception ex)
2292     {
2293       ex.printStackTrace();
2294       System.out.println("Exception whilst pasting: " + ex);
2295       // could be anything being pasted in here
2296     }
2297
2298   }
2299
2300   @Override
2301   protected void expand_newalign(ActionEvent e)
2302   {
2303     try
2304     {
2305       AlignmentI alignment = AlignmentUtils
2306               .expandContext(getViewport().getAlignment(), -1);
2307       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2308               DEFAULT_HEIGHT);
2309       String newtitle = new String("Flanking alignment");
2310
2311       if (Desktop.jalviewClipboard != null
2312               && Desktop.jalviewClipboard[2] != null)
2313       {
2314         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2315         af.viewport.setHiddenColumns(hc);
2316       }
2317
2318       // >>>This is a fix for the moment, until a better solution is
2319       // found!!<<<
2320       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2321               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2322                       .getFeatureRenderer());
2323
2324       // TODO: maintain provenance of an alignment, rather than just make the
2325       // title a concatenation of operations.
2326       {
2327         if (title.startsWith("Copied sequences"))
2328         {
2329           newtitle = title;
2330         }
2331         else
2332         {
2333           newtitle = newtitle.concat("- from " + title);
2334         }
2335       }
2336
2337       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2338
2339     } catch (Exception ex)
2340     {
2341       ex.printStackTrace();
2342       System.out.println("Exception whilst pasting: " + ex);
2343       // could be anything being pasted in here
2344     } catch (OutOfMemoryError oom)
2345     {
2346       new OOMWarning("Viewing flanking region of alignment", oom);
2347     }
2348   }
2349
2350   /**
2351    * DOCUMENT ME!
2352    *
2353    * @param e
2354    *          DOCUMENT ME!
2355    */
2356   @Override
2357   protected void cut_actionPerformed(ActionEvent e)
2358   {
2359     copy_actionPerformed(null);
2360     delete_actionPerformed(null);
2361   }
2362
2363   /**
2364    * DOCUMENT ME!
2365    *
2366    * @param e
2367    *          DOCUMENT ME!
2368    */
2369   @Override
2370   protected void delete_actionPerformed(ActionEvent evt)
2371   {
2372
2373     SequenceGroup sg = viewport.getSelectionGroup();
2374     if (sg == null)
2375     {
2376       return;
2377     }
2378
2379     /*
2380      * If the cut affects all sequences, warn, remove highlighted columns
2381      */
2382     if (sg.getSize() == viewport.getAlignment().getHeight())
2383     {
2384       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2385               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2386       if (isEntireAlignWidth)
2387       {
2388         int confirm = JvOptionPane.showConfirmDialog(this,
2389                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2390                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2391                 JvOptionPane.OK_CANCEL_OPTION);
2392
2393         if (confirm == JvOptionPane.CANCEL_OPTION
2394                 || confirm == JvOptionPane.CLOSED_OPTION)
2395         {
2396           return;
2397         }
2398       }
2399       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2400               sg.getEndRes() + 1);
2401     }
2402     SequenceI[] cut = sg.getSequences()
2403             .toArray(new SequenceI[sg.getSize()]);
2404
2405     addHistoryItem(new EditCommand(
2406             MessageManager.getString("label.cut_sequences"), Action.CUT,
2407             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2408             viewport.getAlignment()));
2409
2410     viewport.setSelectionGroup(null);
2411     viewport.sendSelection();
2412     viewport.getAlignment().deleteGroup(sg);
2413
2414     viewport.firePropertyChange("alignment", null,
2415             viewport.getAlignment().getSequences());
2416     if (viewport.getAlignment().getHeight() < 1)
2417     {
2418       try
2419       {
2420         this.setClosed(true);
2421       } catch (Exception ex)
2422       {
2423       }
2424     }
2425   }
2426
2427   /**
2428    * DOCUMENT ME!
2429    *
2430    * @param e
2431    *          DOCUMENT ME!
2432    */
2433   @Override
2434   protected void deleteGroups_actionPerformed(ActionEvent e)
2435   {
2436     if (avc.deleteGroups())
2437     {
2438       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2439       alignPanel.updateAnnotation();
2440       alignPanel.paintAlignment(true, true);
2441     }
2442   }
2443
2444   /**
2445    * DOCUMENT ME!
2446    *
2447    * @param e
2448    *          DOCUMENT ME!
2449    */
2450   @Override
2451   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2452   {
2453     SequenceGroup sg = new SequenceGroup(
2454             viewport.getAlignment().getSequences());
2455
2456     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2457     viewport.setSelectionGroup(sg);
2458     viewport.isSelectionGroupChanged(true);
2459     viewport.sendSelection();
2460     // JAL-2034 - should delegate to
2461     // alignPanel to decide if overview needs
2462     // updating.
2463     alignPanel.paintAlignment(false, false);
2464     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2465   }
2466
2467   /**
2468    * DOCUMENT ME!
2469    *
2470    * @param e
2471    *          DOCUMENT ME!
2472    */
2473   @Override
2474   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2475   {
2476     if (viewport.cursorMode)
2477     {
2478       alignPanel.getSeqPanel().keyboardNo1 = null;
2479       alignPanel.getSeqPanel().keyboardNo2 = null;
2480     }
2481     viewport.setSelectionGroup(null);
2482     viewport.getColumnSelection().clear();
2483     viewport.setSearchResults(null);
2484     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2485     // JAL-2034 - should delegate to
2486     // alignPanel to decide if overview needs
2487     // updating.
2488     alignPanel.paintAlignment(false, false);
2489     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2490     viewport.sendSelection();
2491   }
2492
2493   /**
2494    * DOCUMENT ME!
2495    *
2496    * @param e
2497    *          DOCUMENT ME!
2498    */
2499   @Override
2500   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2501   {
2502     SequenceGroup sg = viewport.getSelectionGroup();
2503
2504     if (sg == null)
2505     {
2506       selectAllSequenceMenuItem_actionPerformed(null);
2507
2508       return;
2509     }
2510
2511     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2512     {
2513       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2514     }
2515     // JAL-2034 - should delegate to
2516     // alignPanel to decide if overview needs
2517     // updating.
2518
2519     alignPanel.paintAlignment(true, false);
2520     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2521     viewport.sendSelection();
2522   }
2523
2524   @Override
2525   public void invertColSel_actionPerformed(ActionEvent e)
2526   {
2527     viewport.invertColumnSelection();
2528     alignPanel.paintAlignment(true, false);
2529     viewport.sendSelection();
2530   }
2531
2532   /**
2533    * DOCUMENT ME!
2534    *
2535    * @param e
2536    *          DOCUMENT ME!
2537    */
2538   @Override
2539   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2540   {
2541     trimAlignment(true);
2542   }
2543
2544   /**
2545    * DOCUMENT ME!
2546    *
2547    * @param e
2548    *          DOCUMENT ME!
2549    */
2550   @Override
2551   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2552   {
2553     trimAlignment(false);
2554   }
2555
2556   void trimAlignment(boolean trimLeft)
2557   {
2558     ColumnSelection colSel = viewport.getColumnSelection();
2559     int column;
2560
2561     if (!colSel.isEmpty())
2562     {
2563       if (trimLeft)
2564       {
2565         column = colSel.getMin();
2566       }
2567       else
2568       {
2569         column = colSel.getMax();
2570       }
2571
2572       SequenceI[] seqs;
2573       if (viewport.getSelectionGroup() != null)
2574       {
2575         seqs = viewport.getSelectionGroup()
2576                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2577       }
2578       else
2579       {
2580         seqs = viewport.getAlignment().getSequencesArray();
2581       }
2582
2583       TrimRegionCommand trimRegion;
2584       if (trimLeft)
2585       {
2586         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2587                 column, viewport.getAlignment());
2588         viewport.getRanges().setStartRes(0);
2589       }
2590       else
2591       {
2592         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2593                 column, viewport.getAlignment());
2594       }
2595
2596       statusBar.setText(MessageManager
2597               .formatMessage("label.removed_columns", new String[]
2598               { Integer.valueOf(trimRegion.getSize()).toString() }));
2599
2600       addHistoryItem(trimRegion);
2601
2602       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2603       {
2604         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2605                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2606         {
2607           viewport.getAlignment().deleteGroup(sg);
2608         }
2609       }
2610
2611       viewport.firePropertyChange("alignment", null,
2612               viewport.getAlignment().getSequences());
2613     }
2614   }
2615
2616   /**
2617    * DOCUMENT ME!
2618    *
2619    * @param e
2620    *          DOCUMENT ME!
2621    */
2622   @Override
2623   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2624   {
2625     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2626
2627     SequenceI[] seqs;
2628     if (viewport.getSelectionGroup() != null)
2629     {
2630       seqs = viewport.getSelectionGroup()
2631               .getSequencesAsArray(viewport.getHiddenRepSequences());
2632       start = viewport.getSelectionGroup().getStartRes();
2633       end = viewport.getSelectionGroup().getEndRes();
2634     }
2635     else
2636     {
2637       seqs = viewport.getAlignment().getSequencesArray();
2638     }
2639
2640     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2641             "Remove Gapped Columns", seqs, start, end,
2642             viewport.getAlignment());
2643
2644     addHistoryItem(removeGapCols);
2645
2646     statusBar.setText(MessageManager
2647             .formatMessage("label.removed_empty_columns", new Object[]
2648             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2649
2650     // This is to maintain viewport position on first residue
2651     // of first sequence
2652     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2653     ViewportRanges ranges = viewport.getRanges();
2654     int startRes = seq.findPosition(ranges.getStartRes());
2655     // ShiftList shifts;
2656     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2657     // edit.alColumnChanges=shifts.getInverse();
2658     // if (viewport.hasHiddenColumns)
2659     // viewport.getColumnSelection().compensateForEdits(shifts);
2660     ranges.setStartRes(seq.findIndex(startRes) - 1);
2661     viewport.firePropertyChange("alignment", null,
2662             viewport.getAlignment().getSequences());
2663
2664   }
2665
2666   /**
2667    * DOCUMENT ME!
2668    *
2669    * @param e
2670    *          DOCUMENT ME!
2671    */
2672   @Override
2673   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2674   {
2675     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2676
2677     SequenceI[] seqs;
2678     if (viewport.getSelectionGroup() != null)
2679     {
2680       seqs = viewport.getSelectionGroup()
2681               .getSequencesAsArray(viewport.getHiddenRepSequences());
2682       start = viewport.getSelectionGroup().getStartRes();
2683       end = viewport.getSelectionGroup().getEndRes();
2684     }
2685     else
2686     {
2687       seqs = viewport.getAlignment().getSequencesArray();
2688     }
2689
2690     // This is to maintain viewport position on first residue
2691     // of first sequence
2692     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2693     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2694
2695     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2696             viewport.getAlignment()));
2697
2698     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2699
2700     viewport.firePropertyChange("alignment", null,
2701             viewport.getAlignment().getSequences());
2702
2703   }
2704
2705   /**
2706    * DOCUMENT ME!
2707    *
2708    * @param e
2709    *          DOCUMENT ME!
2710    */
2711   @Override
2712   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2713   {
2714     viewport.setPadGaps(padGapsMenuitem.isSelected());
2715     viewport.firePropertyChange("alignment", null,
2716             viewport.getAlignment().getSequences());
2717   }
2718
2719   /**
2720    * DOCUMENT ME!
2721    *
2722    * @param e
2723    *          DOCUMENT ME!
2724    */
2725   @Override
2726   public void findMenuItem_actionPerformed(ActionEvent e)
2727   {
2728     new Finder();
2729   }
2730
2731   /**
2732    * Create a new view of the current alignment.
2733    */
2734   @Override
2735   public void newView_actionPerformed(ActionEvent e)
2736   {
2737     newView(null, true);
2738   }
2739
2740   /**
2741    * Creates and shows a new view of the current alignment.
2742    *
2743    * @param viewTitle
2744    *          title of newly created view; if null, one will be generated
2745    * @param copyAnnotation
2746    *          if true then duplicate all annnotation, groups and settings
2747    * @return new alignment panel, already displayed.
2748    */
2749   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2750   {
2751     /*
2752      * Create a new AlignmentPanel (with its own, new Viewport)
2753      */
2754     AlignmentPanel newap = new jalview.project.Jalview2XML()
2755             .copyAlignPanel(alignPanel);
2756     if (!copyAnnotation)
2757     {
2758       /*
2759        * remove all groups and annotation except for the automatic stuff
2760        */
2761       newap.av.getAlignment().deleteAllGroups();
2762       newap.av.getAlignment().deleteAllAnnotations(false);
2763     }
2764
2765     newap.av.setGatherViewsHere(false);
2766
2767     if (viewport.getViewName() == null)
2768     {
2769       viewport.setViewName(
2770               MessageManager.getString("label.view_name_original"));
2771     }
2772
2773     /*
2774      * Views share the same edits undo and redo stacks
2775      */
2776     newap.av.setHistoryList(viewport.getHistoryList());
2777     newap.av.setRedoList(viewport.getRedoList());
2778
2779     /*
2780      * copy any visualisation settings that are not saved in the project
2781      */
2782     newap.av.setColourAppliesToAllGroups(
2783             viewport.getColourAppliesToAllGroups());
2784
2785     /*
2786      * Views share the same mappings; need to deregister any new mappings
2787      * created by copyAlignPanel, and register the new reference to the shared
2788      * mappings
2789      */
2790     newap.av.replaceMappings(viewport.getAlignment());
2791
2792     /*
2793      * start up cDNA consensus (if applicable) now mappings are in place
2794      */
2795     if (newap.av.initComplementConsensus())
2796     {
2797       newap.refresh(true); // adjust layout of annotations
2798     }
2799
2800     newap.av.setViewName(getNewViewName(viewTitle));
2801
2802     addAlignmentPanel(newap, true);
2803     newap.alignmentChanged();
2804
2805     if (alignPanels.size() == 2)
2806     {
2807       viewport.setGatherViewsHere(true);
2808     }
2809     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2810     return newap;
2811   }
2812
2813   /**
2814    * Make a new name for the view, ensuring it is unique within the current
2815    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2816    * these now use viewId. Unique view names are still desirable for usability.)
2817    *
2818    * @param viewTitle
2819    * @return
2820    */
2821   protected String getNewViewName(String viewTitle)
2822   {
2823     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2824     boolean addFirstIndex = false;
2825     if (viewTitle == null || viewTitle.trim().length() == 0)
2826     {
2827       viewTitle = MessageManager.getString("action.view");
2828       addFirstIndex = true;
2829     }
2830     else
2831     {
2832       index = 1;// we count from 1 if given a specific name
2833     }
2834     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2835
2836     List<Component> comps = PaintRefresher.components
2837             .get(viewport.getSequenceSetId());
2838
2839     List<String> existingNames = getExistingViewNames(comps);
2840
2841     while (existingNames.contains(newViewName))
2842     {
2843       newViewName = viewTitle + " " + (++index);
2844     }
2845     return newViewName;
2846   }
2847
2848   /**
2849    * Returns a list of distinct view names found in the given list of
2850    * components. View names are held on the viewport of an AlignmentPanel.
2851    *
2852    * @param comps
2853    * @return
2854    */
2855   protected List<String> getExistingViewNames(List<Component> comps)
2856   {
2857     List<String> existingNames = new ArrayList<>();
2858     for (Component comp : comps)
2859     {
2860       if (comp instanceof AlignmentPanel)
2861       {
2862         AlignmentPanel ap = (AlignmentPanel) comp;
2863         if (!existingNames.contains(ap.av.getViewName()))
2864         {
2865           existingNames.add(ap.av.getViewName());
2866         }
2867       }
2868     }
2869     return existingNames;
2870   }
2871
2872   /**
2873    * Explode tabbed views into separate windows.
2874    */
2875   @Override
2876   public void expandViews_actionPerformed(ActionEvent e)
2877   {
2878     Desktop.explodeViews(this);
2879   }
2880
2881   /**
2882    * Gather views in separate windows back into a tabbed presentation.
2883    */
2884   @Override
2885   public void gatherViews_actionPerformed(ActionEvent e)
2886   {
2887     Desktop.instance.gatherViews(this);
2888   }
2889
2890   /**
2891    * DOCUMENT ME!
2892    *
2893    * @param e
2894    *          DOCUMENT ME!
2895    */
2896   @Override
2897   public void font_actionPerformed(ActionEvent e)
2898   {
2899     new FontChooser(alignPanel);
2900   }
2901
2902   /**
2903    * DOCUMENT ME!
2904    *
2905    * @param e
2906    *          DOCUMENT ME!
2907    */
2908   @Override
2909   protected void seqLimit_actionPerformed(ActionEvent e)
2910   {
2911     viewport.setShowJVSuffix(seqLimits.isSelected());
2912
2913     alignPanel.getIdPanel().getIdCanvas()
2914             .setPreferredSize(alignPanel.calculateIdWidth());
2915     alignPanel.paintAlignment(true, false);
2916   }
2917
2918   @Override
2919   public void idRightAlign_actionPerformed(ActionEvent e)
2920   {
2921     viewport.setRightAlignIds(idRightAlign.isSelected());
2922     alignPanel.paintAlignment(false, false);
2923   }
2924
2925   @Override
2926   public void centreColumnLabels_actionPerformed(ActionEvent e)
2927   {
2928     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2929     alignPanel.paintAlignment(false, false);
2930   }
2931
2932   /*
2933    * (non-Javadoc)
2934    *
2935    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2936    */
2937   @Override
2938   protected void followHighlight_actionPerformed()
2939   {
2940     /*
2941      * Set the 'follow' flag on the Viewport (and scroll to position if now
2942      * true).
2943      */
2944     final boolean state = this.followHighlightMenuItem.getState();
2945     viewport.setFollowHighlight(state);
2946     if (state)
2947     {
2948       alignPanel.scrollToPosition(viewport.getSearchResults());
2949     }
2950   }
2951
2952   /**
2953    * DOCUMENT ME!
2954    *
2955    * @param e
2956    *          DOCUMENT ME!
2957    */
2958   @Override
2959   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2960   {
2961     viewport.setColourText(colourTextMenuItem.isSelected());
2962     alignPanel.paintAlignment(false, false);
2963   }
2964
2965   /**
2966    * DOCUMENT ME!
2967    *
2968    * @param e
2969    *          DOCUMENT ME!
2970    */
2971   @Override
2972   public void wrapMenuItem_actionPerformed(ActionEvent e)
2973   {
2974     scaleAbove.setVisible(wrapMenuItem.isSelected());
2975     scaleLeft.setVisible(wrapMenuItem.isSelected());
2976     scaleRight.setVisible(wrapMenuItem.isSelected());
2977     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2978     alignPanel.updateLayout();
2979   }
2980
2981   @Override
2982   public void showAllSeqs_actionPerformed(ActionEvent e)
2983   {
2984     viewport.showAllHiddenSeqs();
2985   }
2986
2987   @Override
2988   public void showAllColumns_actionPerformed(ActionEvent e)
2989   {
2990     viewport.showAllHiddenColumns();
2991     alignPanel.paintAlignment(true, true);
2992     viewport.sendSelection();
2993   }
2994
2995   @Override
2996   public void hideSelSequences_actionPerformed(ActionEvent e)
2997   {
2998     viewport.hideAllSelectedSeqs();
2999   }
3000
3001   /**
3002    * called by key handler and the hide all/show all menu items
3003    *
3004    * @param toggleSeqs
3005    * @param toggleCols
3006    */
3007   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3008   {
3009
3010     boolean hide = false;
3011     SequenceGroup sg = viewport.getSelectionGroup();
3012     if (!toggleSeqs && !toggleCols)
3013     {
3014       // Hide everything by the current selection - this is a hack - we do the
3015       // invert and then hide
3016       // first check that there will be visible columns after the invert.
3017       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3018               && sg.getStartRes() <= sg.getEndRes()))
3019       {
3020         // now invert the sequence set, if required - empty selection implies
3021         // that no hiding is required.
3022         if (sg != null)
3023         {
3024           invertSequenceMenuItem_actionPerformed(null);
3025           sg = viewport.getSelectionGroup();
3026           toggleSeqs = true;
3027
3028         }
3029         viewport.expandColSelection(sg, true);
3030         // finally invert the column selection and get the new sequence
3031         // selection.
3032         invertColSel_actionPerformed(null);
3033         toggleCols = true;
3034       }
3035     }
3036
3037     if (toggleSeqs)
3038     {
3039       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3040       {
3041         hideSelSequences_actionPerformed(null);
3042         hide = true;
3043       }
3044       else if (!(toggleCols && viewport.hasSelectedColumns()))
3045       {
3046         showAllSeqs_actionPerformed(null);
3047       }
3048     }
3049
3050     if (toggleCols)
3051     {
3052       if (viewport.hasSelectedColumns())
3053       {
3054         hideSelColumns_actionPerformed(null);
3055         if (!toggleSeqs)
3056         {
3057           viewport.setSelectionGroup(sg);
3058         }
3059       }
3060       else if (!hide)
3061       {
3062         showAllColumns_actionPerformed(null);
3063       }
3064     }
3065   }
3066
3067   /*
3068    * (non-Javadoc)
3069    *
3070    * @see
3071    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3072    * event.ActionEvent)
3073    */
3074   @Override
3075   public void hideAllButSelection_actionPerformed(ActionEvent e)
3076   {
3077     toggleHiddenRegions(false, false);
3078     viewport.sendSelection();
3079   }
3080
3081   /*
3082    * (non-Javadoc)
3083    *
3084    * @see
3085    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3086    * .ActionEvent)
3087    */
3088   @Override
3089   public void hideAllSelection_actionPerformed(ActionEvent e)
3090   {
3091     SequenceGroup sg = viewport.getSelectionGroup();
3092     viewport.expandColSelection(sg, false);
3093     viewport.hideAllSelectedSeqs();
3094     viewport.hideSelectedColumns();
3095     alignPanel.updateLayout();
3096     alignPanel.paintAlignment(true, true);
3097     viewport.sendSelection();
3098   }
3099
3100   /*
3101    * (non-Javadoc)
3102    *
3103    * @see
3104    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3105    * ActionEvent)
3106    */
3107   @Override
3108   public void showAllhidden_actionPerformed(ActionEvent e)
3109   {
3110     viewport.showAllHiddenColumns();
3111     viewport.showAllHiddenSeqs();
3112     alignPanel.paintAlignment(true, true);
3113     viewport.sendSelection();
3114   }
3115
3116   @Override
3117   public void hideSelColumns_actionPerformed(ActionEvent e)
3118   {
3119     viewport.hideSelectedColumns();
3120     alignPanel.updateLayout();
3121     alignPanel.paintAlignment(true, true);
3122     viewport.sendSelection();
3123   }
3124
3125   @Override
3126   public void hiddenMarkers_actionPerformed(ActionEvent e)
3127   {
3128     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3129     repaint();
3130   }
3131
3132   /**
3133    * DOCUMENT ME!
3134    *
3135    * @param e
3136    *          DOCUMENT ME!
3137    */
3138   @Override
3139   protected void scaleAbove_actionPerformed(ActionEvent e)
3140   {
3141     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3142     alignPanel.updateLayout();
3143     alignPanel.paintAlignment(true, false);
3144   }
3145
3146   /**
3147    * DOCUMENT ME!
3148    *
3149    * @param e
3150    *          DOCUMENT ME!
3151    */
3152   @Override
3153   protected void scaleLeft_actionPerformed(ActionEvent e)
3154   {
3155     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3156     alignPanel.updateLayout();
3157     alignPanel.paintAlignment(true, false);
3158   }
3159
3160   /**
3161    * DOCUMENT ME!
3162    *
3163    * @param e
3164    *          DOCUMENT ME!
3165    */
3166   @Override
3167   protected void scaleRight_actionPerformed(ActionEvent e)
3168   {
3169     viewport.setScaleRightWrapped(scaleRight.isSelected());
3170     alignPanel.updateLayout();
3171     alignPanel.paintAlignment(true, false);
3172   }
3173
3174   /**
3175    * DOCUMENT ME!
3176    *
3177    * @param e
3178    *          DOCUMENT ME!
3179    */
3180   @Override
3181   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3182   {
3183     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3184     alignPanel.paintAlignment(false, false);
3185   }
3186
3187   /**
3188    * DOCUMENT ME!
3189    *
3190    * @param e
3191    *          DOCUMENT ME!
3192    */
3193   @Override
3194   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3195   {
3196     viewport.setShowText(viewTextMenuItem.isSelected());
3197     alignPanel.paintAlignment(false, false);
3198   }
3199
3200   /**
3201    * DOCUMENT ME!
3202    *
3203    * @param e
3204    *          DOCUMENT ME!
3205    */
3206   @Override
3207   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3208   {
3209     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3210     alignPanel.paintAlignment(false, false);
3211   }
3212
3213   public FeatureSettings featureSettings;
3214
3215   @Override
3216   public FeatureSettingsControllerI getFeatureSettingsUI()
3217   {
3218     return featureSettings;
3219   }
3220
3221   @Override
3222   public void featureSettings_actionPerformed(ActionEvent e)
3223   {
3224     showFeatureSettingsUI();
3225   }
3226
3227   @Override
3228   public FeatureSettingsControllerI showFeatureSettingsUI()
3229   {
3230     if (featureSettings != null)
3231     {
3232       featureSettings.closeOldSettings();
3233       featureSettings = null;
3234     }
3235     if (!showSeqFeatures.isSelected())
3236     {
3237       // make sure features are actually displayed
3238       showSeqFeatures.setSelected(true);
3239       showSeqFeatures_actionPerformed(null);
3240     }
3241     featureSettings = new FeatureSettings(this);
3242     return featureSettings;
3243   }
3244
3245   /**
3246    * Set or clear 'Show Sequence Features'
3247    *
3248    * @param evt
3249    *          DOCUMENT ME!
3250    */
3251   @Override
3252   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3253   {
3254     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3255     alignPanel.paintAlignment(true, true);
3256   }
3257
3258   /**
3259    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3260    * the annotations panel as a whole.
3261    *
3262    * The options to show/hide all annotations should be enabled when the panel
3263    * is shown, and disabled when the panel is hidden.
3264    *
3265    * @param e
3266    */
3267   @Override
3268   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3269   {
3270     final boolean setVisible = annotationPanelMenuItem.isSelected();
3271     viewport.setShowAnnotation(setVisible);
3272     this.showAllSeqAnnotations.setEnabled(setVisible);
3273     this.hideAllSeqAnnotations.setEnabled(setVisible);
3274     this.showAllAlAnnotations.setEnabled(setVisible);
3275     this.hideAllAlAnnotations.setEnabled(setVisible);
3276     alignPanel.updateLayout();
3277   }
3278
3279   @Override
3280   public void alignmentProperties()
3281   {
3282     JEditorPane editPane = new JEditorPane("text/html", "");
3283     editPane.setEditable(false);
3284     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3285             .formatAsHtml();
3286     editPane.setText(
3287             MessageManager.formatMessage("label.html_content", new Object[]
3288             { contents.toString() }));
3289     JInternalFrame frame = new JInternalFrame();
3290     frame.getContentPane().add(new JScrollPane(editPane));
3291
3292     Desktop.addInternalFrame(frame, MessageManager
3293             .formatMessage("label.alignment_properties", new Object[]
3294             { getTitle() }), 500, 400);
3295   }
3296
3297   /**
3298    * DOCUMENT ME!
3299    *
3300    * @param e
3301    *          DOCUMENT ME!
3302    */
3303   @Override
3304   public void overviewMenuItem_actionPerformed(ActionEvent e)
3305   {
3306     if (alignPanel.overviewPanel != null)
3307     {
3308       return;
3309     }
3310
3311     JInternalFrame frame = new JInternalFrame();
3312     final OverviewPanel overview = new OverviewPanel(alignPanel);
3313     frame.setContentPane(overview);
3314     Desktop.addInternalFrame(frame, MessageManager
3315             .formatMessage("label.overview_params", new Object[]
3316             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3317             true, true);
3318     frame.pack();
3319     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3320     frame.addInternalFrameListener(
3321             new javax.swing.event.InternalFrameAdapter()
3322             {
3323               @Override
3324               public void internalFrameClosed(
3325                       javax.swing.event.InternalFrameEvent evt)
3326               {
3327                 overview.dispose();
3328                 alignPanel.setOverviewPanel(null);
3329               };
3330             });
3331     if (getKeyListeners().length > 0)
3332     {
3333       frame.addKeyListener(getKeyListeners()[0]);
3334     }
3335
3336     alignPanel.setOverviewPanel(overview);
3337   }
3338
3339   @Override
3340   public void textColour_actionPerformed()
3341   {
3342     new TextColourChooser().chooseColour(alignPanel, null);
3343   }
3344
3345   /*
3346    * public void covariationColour_actionPerformed() {
3347    * changeColour(new
3348    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3349    * ()[0])); }
3350    */
3351   @Override
3352   public void annotationColour_actionPerformed()
3353   {
3354     new AnnotationColourChooser(viewport, alignPanel);
3355   }
3356
3357   @Override
3358   public void annotationColumn_actionPerformed(ActionEvent e)
3359   {
3360     new AnnotationColumnChooser(viewport, alignPanel);
3361   }
3362
3363   /**
3364    * Action on the user checking or unchecking the option to apply the selected
3365    * colour scheme to all groups. If unchecked, groups may have their own
3366    * independent colour schemes.
3367    *
3368    * @param selected
3369    */
3370   @Override
3371   public void applyToAllGroups_actionPerformed(boolean selected)
3372   {
3373     viewport.setColourAppliesToAllGroups(selected);
3374   }
3375
3376   /**
3377    * Action on user selecting a colour from the colour menu
3378    *
3379    * @param name
3380    *          the name (not the menu item label!) of the colour scheme
3381    */
3382   @Override
3383   public void changeColour_actionPerformed(String name)
3384   {
3385     /*
3386      * 'User Defined' opens a panel to configure or load a
3387      * user-defined colour scheme
3388      */
3389     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3390     {
3391       new UserDefinedColours(alignPanel);
3392       return;
3393     }
3394
3395     /*
3396      * otherwise set the chosen colour scheme (or null for 'None')
3397      */
3398     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3399             viewport, viewport.getAlignment(),
3400             viewport.getHiddenRepSequences());
3401     changeColour(cs);
3402   }
3403
3404   /**
3405    * Actions on setting or changing the alignment colour scheme
3406    *
3407    * @param cs
3408    */
3409   @Override
3410   public void changeColour(ColourSchemeI cs)
3411   {
3412     // TODO: pull up to controller method
3413     ColourMenuHelper.setColourSelected(colourMenu, cs);
3414
3415     viewport.setGlobalColourScheme(cs);
3416
3417     alignPanel.paintAlignment(true, true);
3418   }
3419
3420   /**
3421    * Show the PID threshold slider panel
3422    */
3423   @Override
3424   protected void modifyPID_actionPerformed()
3425   {
3426     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3427             alignPanel.getViewName());
3428     SliderPanel.showPIDSlider();
3429   }
3430
3431   /**
3432    * Show the Conservation slider panel
3433    */
3434   @Override
3435   protected void modifyConservation_actionPerformed()
3436   {
3437     SliderPanel.setConservationSlider(alignPanel,
3438             viewport.getResidueShading(), alignPanel.getViewName());
3439     SliderPanel.showConservationSlider();
3440   }
3441
3442   /**
3443    * Action on selecting or deselecting (Colour) By Conservation
3444    */
3445   @Override
3446   public void conservationMenuItem_actionPerformed(boolean selected)
3447   {
3448     modifyConservation.setEnabled(selected);
3449     viewport.setConservationSelected(selected);
3450     viewport.getResidueShading().setConservationApplied(selected);
3451
3452     changeColour(viewport.getGlobalColourScheme());
3453     if (selected)
3454     {
3455       modifyConservation_actionPerformed();
3456     }
3457     else
3458     {
3459       SliderPanel.hideConservationSlider();
3460     }
3461   }
3462
3463   /**
3464    * Action on selecting or deselecting (Colour) Above PID Threshold
3465    */
3466   @Override
3467   public void abovePIDThreshold_actionPerformed(boolean selected)
3468   {
3469     modifyPID.setEnabled(selected);
3470     viewport.setAbovePIDThreshold(selected);
3471     if (!selected)
3472     {
3473       viewport.getResidueShading().setThreshold(0,
3474               viewport.isIgnoreGapsConsensus());
3475     }
3476
3477     changeColour(viewport.getGlobalColourScheme());
3478     if (selected)
3479     {
3480       modifyPID_actionPerformed();
3481     }
3482     else
3483     {
3484       SliderPanel.hidePIDSlider();
3485     }
3486   }
3487
3488   /**
3489    * DOCUMENT ME!
3490    *
3491    * @param e
3492    *          DOCUMENT ME!
3493    */
3494   @Override
3495   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3496   {
3497     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3498     AlignmentSorter.sortByPID(viewport.getAlignment(),
3499             viewport.getAlignment().getSequenceAt(0));
3500     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3501             viewport.getAlignment()));
3502     alignPanel.paintAlignment(true, false);
3503   }
3504
3505   /**
3506    * DOCUMENT ME!
3507    *
3508    * @param e
3509    *          DOCUMENT ME!
3510    */
3511   @Override
3512   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3513   {
3514     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3515     AlignmentSorter.sortByID(viewport.getAlignment());
3516     addHistoryItem(
3517             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3518     alignPanel.paintAlignment(true, false);
3519   }
3520
3521   /**
3522    * DOCUMENT ME!
3523    *
3524    * @param e
3525    *          DOCUMENT ME!
3526    */
3527   @Override
3528   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3529   {
3530     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3531     AlignmentSorter.sortByLength(viewport.getAlignment());
3532     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3533             viewport.getAlignment()));
3534     alignPanel.paintAlignment(true, false);
3535   }
3536
3537   /**
3538    * DOCUMENT ME!
3539    *
3540    * @param e
3541    *          DOCUMENT ME!
3542    */
3543   @Override
3544   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3545   {
3546     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3547     AlignmentSorter.sortByGroup(viewport.getAlignment());
3548     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3549             viewport.getAlignment()));
3550
3551     alignPanel.paintAlignment(true, false);
3552   }
3553
3554   /**
3555    * DOCUMENT ME!
3556    *
3557    * @param e
3558    *          DOCUMENT ME!
3559    */
3560   @Override
3561   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3562   {
3563     new RedundancyPanel(alignPanel, this);
3564   }
3565
3566   /**
3567    * DOCUMENT ME!
3568    *
3569    * @param e
3570    *          DOCUMENT ME!
3571    */
3572   @Override
3573   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3574   {
3575     if ((viewport.getSelectionGroup() == null)
3576             || (viewport.getSelectionGroup().getSize() < 2))
3577     {
3578       JvOptionPane.showInternalMessageDialog(this,
3579               MessageManager.getString(
3580                       "label.you_must_select_least_two_sequences"),
3581               MessageManager.getString("label.invalid_selection"),
3582               JvOptionPane.WARNING_MESSAGE);
3583     }
3584     else
3585     {
3586       JInternalFrame frame = new JInternalFrame();
3587       frame.setContentPane(new PairwiseAlignPanel(viewport));
3588       Desktop.addInternalFrame(frame,
3589               MessageManager.getString("action.pairwise_alignment"), 600,
3590               500);
3591     }
3592   }
3593
3594   @Override
3595   public void autoCalculate_actionPerformed(ActionEvent e)
3596   {
3597     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3598     if (viewport.autoCalculateConsensus)
3599     {
3600       viewport.firePropertyChange("alignment", null,
3601               viewport.getAlignment().getSequences());
3602     }
3603   }
3604
3605   @Override
3606   public void sortByTreeOption_actionPerformed(ActionEvent e)
3607   {
3608     viewport.sortByTree = sortByTree.isSelected();
3609   }
3610
3611   @Override
3612   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3613   {
3614     viewport.followSelection = listenToViewSelections.isSelected();
3615   }
3616
3617   /**
3618    * Constructs a tree panel and adds it to the desktop
3619    *
3620    * @param type
3621    *          tree type (NJ or AV)
3622    * @param modelName
3623    *          name of score model used to compute the tree
3624    * @param options
3625    *          parameters for the distance or similarity calculation
3626    */
3627   void newTreePanel(String type, String modelName,
3628           SimilarityParamsI options)
3629   {
3630     String frameTitle = "";
3631     TreePanel tp;
3632
3633     boolean onSelection = false;
3634     if (viewport.getSelectionGroup() != null
3635             && viewport.getSelectionGroup().getSize() > 0)
3636     {
3637       SequenceGroup sg = viewport.getSelectionGroup();
3638
3639       /* Decide if the selection is a column region */
3640       for (SequenceI _s : sg.getSequences())
3641       {
3642         if (_s.getLength() < sg.getEndRes())
3643         {
3644           JvOptionPane.showMessageDialog(Desktop.desktop,
3645                   MessageManager.getString(
3646                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3647                   MessageManager.getString(
3648                           "label.sequences_selection_not_aligned"),
3649                   JvOptionPane.WARNING_MESSAGE);
3650
3651           return;
3652         }
3653       }
3654       onSelection = true;
3655     }
3656     else
3657     {
3658       if (viewport.getAlignment().getHeight() < 2)
3659       {
3660         return;
3661       }
3662     }
3663
3664     tp = new TreePanel(alignPanel, type, modelName, options);
3665     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3666
3667     frameTitle += " from ";
3668
3669     if (viewport.getViewName() != null)
3670     {
3671       frameTitle += viewport.getViewName() + " of ";
3672     }
3673
3674     frameTitle += this.title;
3675
3676     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3677   }
3678
3679   /**
3680    * DOCUMENT ME!
3681    *
3682    * @param title
3683    *          DOCUMENT ME!
3684    * @param order
3685    *          DOCUMENT ME!
3686    */
3687   public void addSortByOrderMenuItem(String title,
3688           final AlignmentOrder order)
3689   {
3690     final JMenuItem item = new JMenuItem(MessageManager
3691             .formatMessage("action.by_title_param", new Object[]
3692             { title }));
3693     sort.add(item);
3694     item.addActionListener(new java.awt.event.ActionListener()
3695     {
3696       @Override
3697       public void actionPerformed(ActionEvent e)
3698       {
3699         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3700
3701         // TODO: JBPNote - have to map order entries to curent SequenceI
3702         // pointers
3703         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3704
3705         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3706                 viewport.getAlignment()));
3707
3708         alignPanel.paintAlignment(true, false);
3709       }
3710     });
3711   }
3712
3713   /**
3714    * Add a new sort by annotation score menu item
3715    *
3716    * @param sort
3717    *          the menu to add the option to
3718    * @param scoreLabel
3719    *          the label used to retrieve scores for each sequence on the
3720    *          alignment
3721    */
3722   public void addSortByAnnotScoreMenuItem(JMenu sort,
3723           final String scoreLabel)
3724   {
3725     final JMenuItem item = new JMenuItem(scoreLabel);
3726     sort.add(item);
3727     item.addActionListener(new java.awt.event.ActionListener()
3728     {
3729       @Override
3730       public void actionPerformed(ActionEvent e)
3731       {
3732         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3733         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3734                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3735         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3736                 viewport.getAlignment()));
3737         alignPanel.paintAlignment(true, false);
3738       }
3739     });
3740   }
3741
3742   /**
3743    * last hash for alignment's annotation array - used to minimise cost of
3744    * rebuild.
3745    */
3746   protected int _annotationScoreVectorHash;
3747
3748   /**
3749    * search the alignment and rebuild the sort by annotation score submenu the
3750    * last alignment annotation vector hash is stored to minimize cost of
3751    * rebuilding in subsequence calls.
3752    *
3753    */
3754   @Override
3755   public void buildSortByAnnotationScoresMenu()
3756   {
3757     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3758     {
3759       return;
3760     }
3761
3762     if (viewport.getAlignment().getAlignmentAnnotation()
3763             .hashCode() != _annotationScoreVectorHash)
3764     {
3765       sortByAnnotScore.removeAll();
3766       // almost certainly a quicker way to do this - but we keep it simple
3767       Hashtable scoreSorts = new Hashtable();
3768       AlignmentAnnotation aann[];
3769       for (SequenceI sqa : viewport.getAlignment().getSequences())
3770       {
3771         aann = sqa.getAnnotation();
3772         for (int i = 0; aann != null && i < aann.length; i++)
3773         {
3774           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3775           {
3776             scoreSorts.put(aann[i].label, aann[i].label);
3777           }
3778         }
3779       }
3780       Enumeration labels = scoreSorts.keys();
3781       while (labels.hasMoreElements())
3782       {
3783         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3784                 (String) labels.nextElement());
3785       }
3786       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3787       scoreSorts.clear();
3788
3789       _annotationScoreVectorHash = viewport.getAlignment()
3790               .getAlignmentAnnotation().hashCode();
3791     }
3792   }
3793
3794   /**
3795    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3796    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3797    * call. Listeners are added to remove the menu item when the treePanel is
3798    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3799    * modified.
3800    */
3801   @Override
3802   public void buildTreeSortMenu()
3803   {
3804     sortByTreeMenu.removeAll();
3805
3806     List<Component> comps = PaintRefresher.components
3807             .get(viewport.getSequenceSetId());
3808     List<TreePanel> treePanels = new ArrayList<>();
3809     for (Component comp : comps)
3810     {
3811       if (comp instanceof TreePanel)
3812       {
3813         treePanels.add((TreePanel) comp);
3814       }
3815     }
3816
3817     if (treePanels.size() < 1)
3818     {
3819       sortByTreeMenu.setVisible(false);
3820       return;
3821     }
3822
3823     sortByTreeMenu.setVisible(true);
3824
3825     for (final TreePanel tp : treePanels)
3826     {
3827       final JMenuItem item = new JMenuItem(tp.getTitle());
3828       item.addActionListener(new java.awt.event.ActionListener()
3829       {
3830         @Override
3831         public void actionPerformed(ActionEvent e)
3832         {
3833           tp.sortByTree_actionPerformed();
3834           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3835
3836         }
3837       });
3838
3839       sortByTreeMenu.add(item);
3840     }
3841   }
3842
3843   public boolean sortBy(AlignmentOrder alorder, String undoname)
3844   {
3845     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3846     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3847     if (undoname != null)
3848     {
3849       addHistoryItem(new OrderCommand(undoname, oldOrder,
3850               viewport.getAlignment()));
3851     }
3852     alignPanel.paintAlignment(true, false);
3853     return true;
3854   }
3855
3856   /**
3857    * Work out whether the whole set of sequences or just the selected set will
3858    * be submitted for multiple alignment.
3859    *
3860    */
3861   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3862   {
3863     // Now, check we have enough sequences
3864     AlignmentView msa = null;
3865
3866     if ((viewport.getSelectionGroup() != null)
3867             && (viewport.getSelectionGroup().getSize() > 1))
3868     {
3869       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3870       // some common interface!
3871       /*
3872        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3873        * SequenceI[sz = seqs.getSize(false)];
3874        *
3875        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3876        * seqs.getSequenceAt(i); }
3877        */
3878       msa = viewport.getAlignmentView(true);
3879     }
3880     else if (viewport.getSelectionGroup() != null
3881             && viewport.getSelectionGroup().getSize() == 1)
3882     {
3883       int option = JvOptionPane.showConfirmDialog(this,
3884               MessageManager.getString("warn.oneseq_msainput_selection"),
3885               MessageManager.getString("label.invalid_selection"),
3886               JvOptionPane.OK_CANCEL_OPTION);
3887       if (option == JvOptionPane.OK_OPTION)
3888       {
3889         msa = viewport.getAlignmentView(false);
3890       }
3891     }
3892     else
3893     {
3894       msa = viewport.getAlignmentView(false);
3895     }
3896     return msa;
3897   }
3898
3899   /**
3900    * Decides what is submitted to a secondary structure prediction service: the
3901    * first sequence in the alignment, or in the current selection, or, if the
3902    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3903    * region or the whole alignment. (where the first sequence in the set is the
3904    * one that the prediction will be for).
3905    */
3906   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3907   {
3908     AlignmentView seqs = null;
3909
3910     if ((viewport.getSelectionGroup() != null)
3911             && (viewport.getSelectionGroup().getSize() > 0))
3912     {
3913       seqs = viewport.getAlignmentView(true);
3914     }
3915     else
3916     {
3917       seqs = viewport.getAlignmentView(false);
3918     }
3919     // limit sequences - JBPNote in future - could spawn multiple prediction
3920     // jobs
3921     // TODO: viewport.getAlignment().isAligned is a global state - the local
3922     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3923     if (!viewport.getAlignment().isAligned(false))
3924     {
3925       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3926       // TODO: if seqs.getSequences().length>1 then should really have warned
3927       // user!
3928
3929     }
3930     return seqs;
3931   }
3932
3933   /**
3934    * DOCUMENT ME!
3935    *
3936    * @param e
3937    *          DOCUMENT ME!
3938    */
3939   @Override
3940   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3941   {
3942     // Pick the tree file
3943     JalviewFileChooser chooser = new JalviewFileChooser(
3944             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3945     chooser.setFileView(new JalviewFileView());
3946     chooser.setDialogTitle(
3947             MessageManager.getString("label.select_newick_like_tree_file"));
3948     chooser.setToolTipText(
3949             MessageManager.getString("label.load_tree_file"));
3950
3951     int value = chooser.showOpenDialog(null);
3952
3953     if (value == JalviewFileChooser.APPROVE_OPTION)
3954     {
3955       String filePath = chooser.getSelectedFile().getPath();
3956       Cache.setProperty("LAST_DIRECTORY", filePath);
3957       NewickFile fin = null;
3958       try
3959       {
3960         fin = new NewickFile(filePath, DataSourceType.FILE);
3961         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3962       } catch (Exception ex)
3963       {
3964         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3965                 MessageManager.getString("label.problem_reading_tree_file"),
3966                 JvOptionPane.WARNING_MESSAGE);
3967         ex.printStackTrace();
3968       }
3969       if (fin != null && fin.hasWarningMessage())
3970       {
3971         JvOptionPane.showMessageDialog(Desktop.desktop,
3972                 fin.getWarningMessage(),
3973                 MessageManager
3974                         .getString("label.possible_problem_with_tree_file"),
3975                 JvOptionPane.WARNING_MESSAGE);
3976       }
3977     }
3978   }
3979
3980   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3981   {
3982     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3983   }
3984
3985   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3986           int h, int x, int y)
3987   {
3988     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3989   }
3990
3991   /**
3992    * Add a treeviewer for the tree extracted from a Newick file object to the
3993    * current alignment view
3994    *
3995    * @param nf
3996    *          the tree
3997    * @param title
3998    *          tree viewer title
3999    * @param input
4000    *          Associated alignment input data (or null)
4001    * @param w
4002    *          width
4003    * @param h
4004    *          height
4005    * @param x
4006    *          position
4007    * @param y
4008    *          position
4009    * @return TreePanel handle
4010    */
4011   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4012           AlignmentView input, int w, int h, int x, int y)
4013   {
4014     TreePanel tp = null;
4015
4016     try
4017     {
4018       nf.parse();
4019
4020       if (nf.getTree() != null)
4021       {
4022         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4023
4024         tp.setSize(w, h);
4025
4026         if (x > 0 && y > 0)
4027         {
4028           tp.setLocation(x, y);
4029         }
4030
4031         Desktop.addInternalFrame(tp, treeTitle, w, h);
4032       }
4033     } catch (Exception ex)
4034     {
4035       ex.printStackTrace();
4036     }
4037
4038     return tp;
4039   }
4040
4041   private boolean buildingMenu = false;
4042
4043   /**
4044    * Generates menu items and listener event actions for web service clients
4045    *
4046    */
4047   public void BuildWebServiceMenu()
4048   {
4049     while (buildingMenu)
4050     {
4051       try
4052       {
4053         System.err.println("Waiting for building menu to finish.");
4054         Thread.sleep(10);
4055       } catch (Exception e)
4056       {
4057       }
4058     }
4059     final AlignFrame me = this;
4060     buildingMenu = true;
4061     new Thread(new Runnable()
4062     {
4063       @Override
4064       public void run()
4065       {
4066         final List<JMenuItem> legacyItems = new ArrayList<>();
4067         try
4068         {
4069           // System.err.println("Building ws menu again "
4070           // + Thread.currentThread());
4071           // TODO: add support for context dependent disabling of services based
4072           // on
4073           // alignment and current selection
4074           // TODO: add additional serviceHandle parameter to specify abstract
4075           // handler
4076           // class independently of AbstractName
4077           // TODO: add in rediscovery GUI function to restart discoverer
4078           // TODO: group services by location as well as function and/or
4079           // introduce
4080           // object broker mechanism.
4081           final Vector<JMenu> wsmenu = new Vector<>();
4082           final IProgressIndicator af = me;
4083
4084           /*
4085            * do not i18n these strings - they are hard-coded in class
4086            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4087            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4088            */
4089           final JMenu msawsmenu = new JMenu("Alignment");
4090           final JMenu secstrmenu = new JMenu(
4091                   "Secondary Structure Prediction");
4092           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4093           final JMenu analymenu = new JMenu("Analysis");
4094           final JMenu dismenu = new JMenu("Protein Disorder");
4095           // JAL-940 - only show secondary structure prediction services from
4096           // the legacy server
4097           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4098               // &&
4099           Discoverer.services != null && (Discoverer.services.size() > 0))
4100           {
4101             // TODO: refactor to allow list of AbstractName/Handler bindings to
4102             // be
4103             // stored or retrieved from elsewhere
4104             // No MSAWS used any more:
4105             // Vector msaws = null; // (Vector)
4106             // Discoverer.services.get("MsaWS");
4107             Vector secstrpr = (Vector) Discoverer.services
4108                     .get("SecStrPred");
4109             if (secstrpr != null)
4110             {
4111               // Add any secondary structure prediction services
4112               for (int i = 0, j = secstrpr.size(); i < j; i++)
4113               {
4114                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4115                         .get(i);
4116                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4117                         .getServiceClient(sh);
4118                 int p = secstrmenu.getItemCount();
4119                 impl.attachWSMenuEntry(secstrmenu, me);
4120                 int q = secstrmenu.getItemCount();
4121                 for (int litm = p; litm < q; litm++)
4122                 {
4123                   legacyItems.add(secstrmenu.getItem(litm));
4124                 }
4125               }
4126             }
4127           }
4128
4129           // Add all submenus in the order they should appear on the web
4130           // services menu
4131           wsmenu.add(msawsmenu);
4132           wsmenu.add(secstrmenu);
4133           wsmenu.add(dismenu);
4134           wsmenu.add(analymenu);
4135           // No search services yet
4136           // wsmenu.add(seqsrchmenu);
4137
4138           javax.swing.SwingUtilities.invokeLater(new Runnable()
4139           {
4140             @Override
4141             public void run()
4142             {
4143               try
4144               {
4145                 webService.removeAll();
4146                 // first, add discovered services onto the webservices menu
4147                 if (wsmenu.size() > 0)
4148                 {
4149                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4150                   {
4151                     webService.add(wsmenu.get(i));
4152                   }
4153                 }
4154                 else
4155                 {
4156                   webService.add(me.webServiceNoServices);
4157                 }
4158                 // TODO: move into separate menu builder class.
4159                 boolean new_sspred = false;
4160                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4161                 {
4162                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4163                   if (jws2servs != null)
4164                   {
4165                     if (jws2servs.hasServices())
4166                     {
4167                       jws2servs.attachWSMenuEntry(webService, me);
4168                       for (Jws2Instance sv : jws2servs.getServices())
4169                       {
4170                         if (sv.description.toLowerCase().contains("jpred"))
4171                         {
4172                           for (JMenuItem jmi : legacyItems)
4173                           {
4174                             jmi.setVisible(false);
4175                           }
4176                         }
4177                       }
4178
4179                     }
4180                     if (jws2servs.isRunning())
4181                     {
4182                       JMenuItem tm = new JMenuItem(
4183                               "Still discovering JABA Services");
4184                       tm.setEnabled(false);
4185                       webService.add(tm);
4186                     }
4187                   }
4188                 }
4189                 build_urlServiceMenu(me.webService);
4190                 build_fetchdbmenu(webService);
4191                 for (JMenu item : wsmenu)
4192                 {
4193                   if (item.getItemCount() == 0)
4194                   {
4195                     item.setEnabled(false);
4196                   }
4197                   else
4198                   {
4199                     item.setEnabled(true);
4200                   }
4201                 }
4202               } catch (Exception e)
4203               {
4204                 Cache.log.debug(
4205                         "Exception during web service menu building process.",
4206                         e);
4207               }
4208             }
4209           });
4210         } catch (Exception e)
4211         {
4212         }
4213         buildingMenu = false;
4214       }
4215     }).start();
4216
4217   }
4218
4219   /**
4220    * construct any groupURL type service menu entries.
4221    *
4222    * @param webService
4223    */
4224   private void build_urlServiceMenu(JMenu webService)
4225   {
4226     // TODO: remove this code when 2.7 is released
4227     // DEBUG - alignmentView
4228     /*
4229      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4230      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4231      *
4232      * @Override public void actionPerformed(ActionEvent e) {
4233      * jalview.datamodel.AlignmentView
4234      * .testSelectionViews(af.viewport.getAlignment(),
4235      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4236      *
4237      * }); webService.add(testAlView);
4238      */
4239     // TODO: refactor to RestClient discoverer and merge menu entries for
4240     // rest-style services with other types of analysis/calculation service
4241     // SHmmr test client - still being implemented.
4242     // DEBUG - alignmentView
4243
4244     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4245             .getRestClients())
4246     {
4247       client.attachWSMenuEntry(
4248               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4249               this);
4250     }
4251   }
4252
4253   /**
4254    * Searches the alignment sequences for xRefs and builds the Show
4255    * Cross-References menu (formerly called Show Products), with database
4256    * sources for which cross-references are found (protein sources for a
4257    * nucleotide alignment and vice versa)
4258    *
4259    * @return true if Show Cross-references menu should be enabled
4260    */
4261   public boolean canShowProducts()
4262   {
4263     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4264     AlignmentI dataset = viewport.getAlignment().getDataset();
4265
4266     showProducts.removeAll();
4267     final boolean dna = viewport.getAlignment().isNucleotide();
4268
4269     if (seqs == null || seqs.length == 0)
4270     {
4271       // nothing to see here.
4272       return false;
4273     }
4274
4275     boolean showp = false;
4276     try
4277     {
4278       List<String> ptypes = new CrossRef(seqs, dataset)
4279               .findXrefSourcesForSequences(dna);
4280
4281       for (final String source : ptypes)
4282       {
4283         showp = true;
4284         final AlignFrame af = this;
4285         JMenuItem xtype = new JMenuItem(source);
4286         xtype.addActionListener(new ActionListener()
4287         {
4288           @Override
4289           public void actionPerformed(ActionEvent e)
4290           {
4291             showProductsFor(af.viewport.getSequenceSelection(), dna,
4292                     source);
4293           }
4294         });
4295         showProducts.add(xtype);
4296       }
4297       showProducts.setVisible(showp);
4298       showProducts.setEnabled(showp);
4299     } catch (Exception e)
4300     {
4301       Cache.log.warn(
4302               "canShowProducts threw an exception - please report to help@jalview.org",
4303               e);
4304       return false;
4305     }
4306     return showp;
4307   }
4308
4309   /**
4310    * Finds and displays cross-references for the selected sequences (protein
4311    * products for nucleotide sequences, dna coding sequences for peptides).
4312    *
4313    * @param sel
4314    *          the sequences to show cross-references for
4315    * @param dna
4316    *          true if from a nucleotide alignment (so showing proteins)
4317    * @param source
4318    *          the database to show cross-references for
4319    */
4320   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4321           final String source)
4322   {
4323     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4324             .start();
4325   }
4326
4327   /**
4328    * Construct and display a new frame containing the translation of this
4329    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4330    */
4331   @Override
4332   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4333   {
4334     AlignmentI al = null;
4335     try
4336     {
4337       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4338
4339       al = dna.translateCdna(codeTable);
4340     } catch (Exception ex)
4341     {
4342       jalview.bin.Cache.log.error(
4343               "Exception during translation. Please report this !", ex);
4344       final String msg = MessageManager.getString(
4345               "label.error_when_translating_sequences_submit_bug_report");
4346       final String errorTitle = MessageManager
4347               .getString("label.implementation_error")
4348               + MessageManager.getString("label.translation_failed");
4349       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4350               JvOptionPane.ERROR_MESSAGE);
4351       return;
4352     }
4353     if (al == null || al.getHeight() == 0)
4354     {
4355       final String msg = MessageManager.getString(
4356               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4357       final String errorTitle = MessageManager
4358               .getString("label.translation_failed");
4359       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4360               JvOptionPane.WARNING_MESSAGE);
4361     }
4362     else
4363     {
4364       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4365       af.setFileFormat(this.currentFileFormat);
4366       final String newTitle = MessageManager
4367               .formatMessage("label.translation_of_params", new Object[]
4368               { this.getTitle(), codeTable.getId() });
4369       af.setTitle(newTitle);
4370       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4371       {
4372         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4373         viewport.openSplitFrame(af, new Alignment(seqs));
4374       }
4375       else
4376       {
4377         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4378                 DEFAULT_HEIGHT);
4379       }
4380     }
4381   }
4382
4383   /**
4384    * Set the file format
4385    *
4386    * @param format
4387    */
4388   public void setFileFormat(FileFormatI format)
4389   {
4390     this.currentFileFormat = format;
4391   }
4392
4393   /**
4394    * Try to load a features file onto the alignment.
4395    *
4396    * @param file
4397    *          contents or path to retrieve file
4398    * @param sourceType
4399    *          access mode of file (see jalview.io.AlignFile)
4400    * @return true if features file was parsed correctly.
4401    */
4402   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4403   {
4404     return avc.parseFeaturesFile(file, sourceType,
4405             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4406
4407   }
4408
4409   @Override
4410   public void refreshFeatureUI(boolean enableIfNecessary)
4411   {
4412     // note - currently this is only still here rather than in the controller
4413     // because of the featureSettings hard reference that is yet to be
4414     // abstracted
4415     if (enableIfNecessary)
4416     {
4417       viewport.setShowSequenceFeatures(true);
4418       showSeqFeatures.setSelected(true);
4419     }
4420
4421   }
4422
4423   @Override
4424   public void dragEnter(DropTargetDragEvent evt)
4425   {
4426   }
4427
4428   @Override
4429   public void dragExit(DropTargetEvent evt)
4430   {
4431   }
4432
4433   @Override
4434   public void dragOver(DropTargetDragEvent evt)
4435   {
4436   }
4437
4438   @Override
4439   public void dropActionChanged(DropTargetDragEvent evt)
4440   {
4441   }
4442
4443   @Override
4444   public void drop(DropTargetDropEvent evt)
4445   {
4446     // JAL-1552 - acceptDrop required before getTransferable call for
4447     // Java's Transferable for native dnd
4448     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4449     Transferable t = evt.getTransferable();
4450     final AlignFrame thisaf = this;
4451     final List<String> files = new ArrayList<>();
4452     List<DataSourceType> protocols = new ArrayList<>();
4453
4454     try
4455     {
4456       Desktop.transferFromDropTarget(files, protocols, evt, t);
4457     } catch (Exception e)
4458     {
4459       e.printStackTrace();
4460     }
4461     if (files != null)
4462     {
4463       new Thread(new Runnable()
4464       {
4465         @Override
4466         public void run()
4467         {
4468           try
4469           {
4470             // check to see if any of these files have names matching sequences
4471             // in
4472             // the alignment
4473             SequenceIdMatcher idm = new SequenceIdMatcher(
4474                     viewport.getAlignment().getSequencesArray());
4475             /**
4476              * Object[] { String,SequenceI}
4477              */
4478             ArrayList<Object[]> filesmatched = new ArrayList<>();
4479             ArrayList<String> filesnotmatched = new ArrayList<>();
4480             for (int i = 0; i < files.size(); i++)
4481             {
4482               String file = files.get(i).toString();
4483               String pdbfn = "";
4484               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4485               if (protocol == DataSourceType.FILE)
4486               {
4487                 File fl = new File(file);
4488                 pdbfn = fl.getName();
4489               }
4490               else if (protocol == DataSourceType.URL)
4491               {
4492                 URL url = new URL(file);
4493                 pdbfn = url.getFile();
4494               }
4495               if (pdbfn.length() > 0)
4496               {
4497                 // attempt to find a match in the alignment
4498                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4499                 int l = 0, c = pdbfn.indexOf(".");
4500                 while (mtch == null && c != -1)
4501                 {
4502                   do
4503                   {
4504                     l = c;
4505                   } while ((c = pdbfn.indexOf(".", l)) > l);
4506                   if (l > -1)
4507                   {
4508                     pdbfn = pdbfn.substring(0, l);
4509                   }
4510                   mtch = idm.findAllIdMatches(pdbfn);
4511                 }
4512                 if (mtch != null)
4513                 {
4514                   FileFormatI type = null;
4515                   try
4516                   {
4517                     type = new IdentifyFile().identify(file, protocol);
4518                   } catch (Exception ex)
4519                   {
4520                     type = null;
4521                   }
4522                   if (type != null && type.isStructureFile())
4523                   {
4524                     filesmatched.add(new Object[] { file, protocol, mtch });
4525                     continue;
4526                   }
4527                 }
4528                 // File wasn't named like one of the sequences or wasn't a PDB
4529                 // file.
4530                 filesnotmatched.add(file);
4531               }
4532             }
4533             int assocfiles = 0;
4534             if (filesmatched.size() > 0)
4535             {
4536               boolean autoAssociate = Cache
4537                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4538               if (!autoAssociate)
4539               {
4540                 String msg = MessageManager.formatMessage(
4541                         "label.automatically_associate_structure_files_with_sequences_same_name",
4542                         new Object[]
4543                         { Integer.valueOf(filesmatched.size())
4544                                 .toString() });
4545                 String ttl = MessageManager.getString(
4546                         "label.automatically_associate_structure_files_by_name");
4547                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4548                         ttl, JvOptionPane.YES_NO_OPTION);
4549                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4550               }
4551               if (autoAssociate)
4552               {
4553                 for (Object[] fm : filesmatched)
4554                 {
4555                   // try and associate
4556                   // TODO: may want to set a standard ID naming formalism for
4557                   // associating PDB files which have no IDs.
4558                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4559                   {
4560                     PDBEntry pe = new AssociatePdbFileWithSeq()
4561                             .associatePdbWithSeq((String) fm[0],
4562                                     (DataSourceType) fm[1], toassoc, false,
4563                                     Desktop.instance);
4564                     if (pe != null)
4565                     {
4566                       System.err.println("Associated file : "
4567                               + ((String) fm[0]) + " with "
4568                               + toassoc.getDisplayId(true));
4569                       assocfiles++;
4570                     }
4571                   }
4572                   // TODO: do we need to update overview ? only if features are
4573                   // shown I guess
4574                   alignPanel.paintAlignment(true, false);
4575                 }
4576               }
4577               else
4578               {
4579                 /*
4580                  * add declined structures as sequences
4581                  */
4582                 for (Object[] o : filesmatched)
4583                 {
4584                   filesnotmatched.add((String) o[0]);
4585                 }
4586               }
4587             }
4588             if (filesnotmatched.size() > 0)
4589             {
4590               if (assocfiles > 0 && (Cache.getDefault(
4591                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4592                       || JvOptionPane.showConfirmDialog(thisaf,
4593                               "<html>" + MessageManager.formatMessage(
4594                                       "label.ignore_unmatched_dropped_files_info",
4595                                       new Object[]
4596                                       { Integer.valueOf(
4597                                               filesnotmatched.size())
4598                                               .toString() })
4599                                       + "</html>",
4600                               MessageManager.getString(
4601                                       "label.ignore_unmatched_dropped_files"),
4602                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4603               {
4604                 return;
4605               }
4606               for (String fn : filesnotmatched)
4607               {
4608                 loadJalviewDataFile(fn, null, null, null);
4609               }
4610
4611             }
4612           } catch (Exception ex)
4613           {
4614             ex.printStackTrace();
4615           }
4616         }
4617       }).start();
4618     }
4619   }
4620
4621   /**
4622    * Attempt to load a "dropped" file or URL string, by testing in turn for
4623    * <ul>
4624    * <li>an Annotation file</li>
4625    * <li>a JNet file</li>
4626    * <li>a features file</li>
4627    * <li>else try to interpret as an alignment file</li>
4628    * </ul>
4629    *
4630    * @param file
4631    *          either a filename or a URL string.
4632    */
4633   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4634           FileFormatI format, SequenceI assocSeq)
4635   {
4636     try
4637     {
4638       if (sourceType == null)
4639       {
4640         sourceType = FormatAdapter.checkProtocol(file);
4641       }
4642       // if the file isn't identified, or not positively identified as some
4643       // other filetype (PFAM is default unidentified alignment file type) then
4644       // try to parse as annotation.
4645       boolean isAnnotation = (format == null
4646               || FileFormat.Pfam.equals(format))
4647                       ? new AnnotationFile().annotateAlignmentView(viewport,
4648                               file, sourceType)
4649                       : false;
4650
4651       if (!isAnnotation)
4652       {
4653         // first see if its a T-COFFEE score file
4654         TCoffeeScoreFile tcf = null;
4655         try
4656         {
4657           tcf = new TCoffeeScoreFile(file, sourceType);
4658           if (tcf.isValid())
4659           {
4660             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4661             {
4662               buildColourMenu();
4663               changeColour(
4664                       new TCoffeeColourScheme(viewport.getAlignment()));
4665               isAnnotation = true;
4666               statusBar.setText(MessageManager.getString(
4667                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4668             }
4669             else
4670             {
4671               // some problem - if no warning its probable that the ID matching
4672               // process didn't work
4673               JvOptionPane.showMessageDialog(Desktop.desktop,
4674                       tcf.getWarningMessage() == null
4675                               ? MessageManager.getString(
4676                                       "label.check_file_matches_sequence_ids_alignment")
4677                               : tcf.getWarningMessage(),
4678                       MessageManager.getString(
4679                               "label.problem_reading_tcoffee_score_file"),
4680                       JvOptionPane.WARNING_MESSAGE);
4681             }
4682           }
4683           else
4684           {
4685             tcf = null;
4686           }
4687         } catch (Exception x)
4688         {
4689           Cache.log.debug(
4690                   "Exception when processing data source as T-COFFEE score file",
4691                   x);
4692           tcf = null;
4693         }
4694         if (tcf == null)
4695         {
4696           // try to see if its a JNet 'concise' style annotation file *before*
4697           // we
4698           // try to parse it as a features file
4699           if (format == null)
4700           {
4701             format = new IdentifyFile().identify(file, sourceType);
4702           }
4703           if (FileFormat.ScoreMatrix == format)
4704           {
4705             ScoreMatrixFile sm = new ScoreMatrixFile(
4706                     new FileParse(file, sourceType));
4707             sm.parse();
4708             // todo: i18n this message
4709             statusBar.setText(MessageManager.formatMessage(
4710                     "label.successfully_loaded_matrix",
4711                     sm.getMatrixName()));
4712           }
4713           else if (FileFormat.Jnet.equals(format))
4714           {
4715             JPredFile predictions = new JPredFile(file, sourceType);
4716             new JnetAnnotationMaker();
4717             JnetAnnotationMaker.add_annotation(predictions,
4718                     viewport.getAlignment(), 0, false);
4719             viewport.getAlignment().setupJPredAlignment();
4720             isAnnotation = true;
4721           }
4722           // else if (IdentifyFile.FeaturesFile.equals(format))
4723           else if (FileFormat.Features.equals(format))
4724           {
4725             if (parseFeaturesFile(file, sourceType))
4726             {
4727               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4728               if (splitFrame != null)
4729               {
4730                 splitFrame.repaint();
4731               }
4732               else
4733               {
4734                 alignPanel.paintAlignment(true, true);
4735               }
4736             }
4737           }
4738           else
4739           {
4740             new FileLoader().LoadFile(viewport, file, sourceType, format);
4741           }
4742         }
4743       }
4744       if (isAnnotation)
4745       {
4746
4747         alignPanel.adjustAnnotationHeight();
4748         viewport.updateSequenceIdColours();
4749         buildSortByAnnotationScoresMenu();
4750         alignPanel.paintAlignment(true, true);
4751       }
4752     } catch (Exception ex)
4753     {
4754       ex.printStackTrace();
4755     } catch (OutOfMemoryError oom)
4756     {
4757       try
4758       {
4759         System.gc();
4760       } catch (Exception x)
4761       {
4762       }
4763       new OOMWarning(
4764               "loading data "
4765                       + (sourceType != null
4766                               ? (sourceType == DataSourceType.PASTE
4767                                       ? "from clipboard."
4768                                       : "using " + sourceType + " from "
4769                                               + file)
4770                               : ".")
4771                       + (format != null
4772                               ? "(parsing as '" + format + "' file)"
4773                               : ""),
4774               oom, Desktop.desktop);
4775     }
4776   }
4777
4778   /**
4779    * Method invoked by the ChangeListener on the tabbed pane, in other words
4780    * when a different tabbed pane is selected by the user or programmatically.
4781    */
4782   @Override
4783   public void tabSelectionChanged(int index)
4784   {
4785     if (index > -1)
4786     {
4787       alignPanel = alignPanels.get(index);
4788       viewport = alignPanel.av;
4789       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4790       setMenusFromViewport(viewport);
4791       if (featureSettings != null && featureSettings.isOpen()
4792               && featureSettings.fr.getViewport() != viewport)
4793       {
4794         if (viewport.isShowSequenceFeatures())
4795         {
4796           // refresh the featureSettings to reflect UI change
4797           showFeatureSettingsUI();
4798         }
4799         else
4800         {
4801           // close feature settings for this view.
4802           featureSettings.close();
4803         }
4804       }
4805
4806     }
4807
4808     /*
4809      * 'focus' any colour slider that is open to the selected viewport
4810      */
4811     if (viewport.getConservationSelected())
4812     {
4813       SliderPanel.setConservationSlider(alignPanel,
4814               viewport.getResidueShading(), alignPanel.getViewName());
4815     }
4816     else
4817     {
4818       SliderPanel.hideConservationSlider();
4819     }
4820     if (viewport.getAbovePIDThreshold())
4821     {
4822       SliderPanel.setPIDSliderSource(alignPanel,
4823               viewport.getResidueShading(), alignPanel.getViewName());
4824     }
4825     else
4826     {
4827       SliderPanel.hidePIDSlider();
4828     }
4829
4830     /*
4831      * If there is a frame linked to this one in a SplitPane, switch it to the
4832      * same view tab index. No infinite recursion of calls should happen, since
4833      * tabSelectionChanged() should not get invoked on setting the selected
4834      * index to an unchanged value. Guard against setting an invalid index
4835      * before the new view peer tab has been created.
4836      */
4837     final AlignViewportI peer = viewport.getCodingComplement();
4838     if (peer != null)
4839     {
4840       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4841               .getAlignPanel().alignFrame;
4842       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4843       {
4844         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4845       }
4846     }
4847   }
4848
4849   /**
4850    * On right mouse click on view tab, prompt for and set new view name.
4851    */
4852   @Override
4853   public void tabbedPane_mousePressed(MouseEvent e)
4854   {
4855     if (e.isPopupTrigger())
4856     {
4857       String msg = MessageManager.getString("label.enter_view_name");
4858       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4859               JvOptionPane.QUESTION_MESSAGE);
4860
4861       if (reply != null)
4862       {
4863         viewport.setViewName(reply);
4864         // TODO warn if reply is in getExistingViewNames()?
4865         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4866       }
4867     }
4868   }
4869
4870   public AlignViewport getCurrentView()
4871   {
4872     return viewport;
4873   }
4874
4875   /**
4876    * Open the dialog for regex description parsing.
4877    */
4878   @Override
4879   protected void extractScores_actionPerformed(ActionEvent e)
4880   {
4881     ParseProperties pp = new jalview.analysis.ParseProperties(
4882             viewport.getAlignment());
4883     // TODO: verify regex and introduce GUI dialog for version 2.5
4884     // if (pp.getScoresFromDescription("col", "score column ",
4885     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4886     // true)>0)
4887     if (pp.getScoresFromDescription("description column",
4888             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4889     {
4890       buildSortByAnnotationScoresMenu();
4891     }
4892   }
4893
4894   /*
4895    * (non-Javadoc)
4896    *
4897    * @see
4898    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4899    * )
4900    */
4901   @Override
4902   protected void showDbRefs_actionPerformed(ActionEvent e)
4903   {
4904     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4905   }
4906
4907   /*
4908    * (non-Javadoc)
4909    *
4910    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4911    * ActionEvent)
4912    */
4913   @Override
4914   protected void showNpFeats_actionPerformed(ActionEvent e)
4915   {
4916     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4917   }
4918
4919   /**
4920    * find the viewport amongst the tabs in this alignment frame and close that
4921    * tab
4922    *
4923    * @param av
4924    */
4925   public boolean closeView(AlignViewportI av)
4926   {
4927     if (viewport == av)
4928     {
4929       this.closeMenuItem_actionPerformed(false);
4930       return true;
4931     }
4932     Component[] comp = tabbedPane.getComponents();
4933     for (int i = 0; comp != null && i < comp.length; i++)
4934     {
4935       if (comp[i] instanceof AlignmentPanel)
4936       {
4937         if (((AlignmentPanel) comp[i]).av == av)
4938         {
4939           // close the view.
4940           closeView((AlignmentPanel) comp[i]);
4941           return true;
4942         }
4943       }
4944     }
4945     return false;
4946   }
4947
4948   protected void build_fetchdbmenu(JMenu webService)
4949   {
4950     // Temporary hack - DBRef Fetcher always top level ws entry.
4951     // TODO We probably want to store a sequence database checklist in
4952     // preferences and have checkboxes.. rather than individual sources selected
4953     // here
4954     final JMenu rfetch = new JMenu(
4955             MessageManager.getString("action.fetch_db_references"));
4956     rfetch.setToolTipText(MessageManager.getString(
4957             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4958     webService.add(rfetch);
4959
4960     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4961             MessageManager.getString("option.trim_retrieved_seqs"));
4962     trimrs.setToolTipText(
4963             MessageManager.getString("label.trim_retrieved_sequences"));
4964     trimrs.setSelected(
4965             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4966     trimrs.addActionListener(new ActionListener()
4967     {
4968       @Override
4969       public void actionPerformed(ActionEvent e)
4970       {
4971         trimrs.setSelected(trimrs.isSelected());
4972         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4973                 Boolean.valueOf(trimrs.isSelected()).toString());
4974       };
4975     });
4976     rfetch.add(trimrs);
4977     JMenuItem fetchr = new JMenuItem(
4978             MessageManager.getString("label.standard_databases"));
4979     fetchr.setToolTipText(
4980             MessageManager.getString("label.fetch_embl_uniprot"));
4981     fetchr.addActionListener(new ActionListener()
4982     {
4983
4984       @Override
4985       public void actionPerformed(ActionEvent e)
4986       {
4987         new Thread(new Runnable()
4988         {
4989           @Override
4990           public void run()
4991           {
4992             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4993                     .getAlignment().isNucleotide();
4994             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4995                     alignPanel.av.getSequenceSelection(),
4996                     alignPanel.alignFrame, null,
4997                     alignPanel.alignFrame.featureSettings, isNucleotide);
4998             dbRefFetcher.addListener(new FetchFinishedListenerI()
4999             {
5000               @Override
5001               public void finished()
5002               {
5003
5004                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5005                         .getFeatureSettingsModels())
5006                 {
5007
5008                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5009                 }
5010                 AlignFrame.this.setMenusForViewport();
5011               }
5012             });
5013             dbRefFetcher.fetchDBRefs(false);
5014           }
5015         }).start();
5016
5017       }
5018
5019     });
5020     rfetch.add(fetchr);
5021     final AlignFrame me = this;
5022     new Thread(new Runnable()
5023     {
5024       @Override
5025       public void run()
5026       {
5027         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5028                 .getSequenceFetcherSingleton(me);
5029         javax.swing.SwingUtilities.invokeLater(new Runnable()
5030         {
5031           @Override
5032           public void run()
5033           {
5034             String[] dbclasses = sf.getOrderedSupportedSources();
5035             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5036             // jalview.util.QuickSort.sort(otherdb, otherdb);
5037             List<DbSourceProxy> otherdb;
5038             JMenu dfetch = new JMenu();
5039             JMenu ifetch = new JMenu();
5040             JMenuItem fetchr = null;
5041             int comp = 0, icomp = 0, mcomp = 15;
5042             String mname = null;
5043             int dbi = 0;
5044             for (String dbclass : dbclasses)
5045             {
5046               otherdb = sf.getSourceProxy(dbclass);
5047               // add a single entry for this class, or submenu allowing 'fetch
5048               // all' or pick one
5049               if (otherdb == null || otherdb.size() < 1)
5050               {
5051                 continue;
5052               }
5053               // List<DbSourceProxy> dbs=otherdb;
5054               // otherdb=new ArrayList<DbSourceProxy>();
5055               // for (DbSourceProxy db:dbs)
5056               // {
5057               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5058               // }
5059               if (mname == null)
5060               {
5061                 mname = "From " + dbclass;
5062               }
5063               if (otherdb.size() == 1)
5064               {
5065                 final DbSourceProxy[] dassource = otherdb
5066                         .toArray(new DbSourceProxy[0]);
5067                 DbSourceProxy src = otherdb.get(0);
5068                 fetchr = new JMenuItem(src.getDbSource());
5069                 fetchr.addActionListener(new ActionListener()
5070                 {
5071
5072                   @Override
5073                   public void actionPerformed(ActionEvent e)
5074                   {
5075                     new Thread(new Runnable()
5076                     {
5077
5078                       @Override
5079                       public void run()
5080                       {
5081                         boolean isNucleotide = alignPanel.alignFrame
5082                                 .getViewport().getAlignment()
5083                                 .isNucleotide();
5084                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5085                                 alignPanel.av.getSequenceSelection(),
5086                                 alignPanel.alignFrame, dassource,
5087                                 alignPanel.alignFrame.featureSettings,
5088                                 isNucleotide);
5089                         dbRefFetcher
5090                                 .addListener(new FetchFinishedListenerI()
5091                                 {
5092                                   @Override
5093                                   public void finished()
5094                                   {
5095                                     FeatureSettingsModelI srcSettings = dassource[0]
5096                                             .getFeatureColourScheme();
5097                                     alignPanel.av.mergeFeaturesStyle(
5098                                             srcSettings);
5099                                     AlignFrame.this.setMenusForViewport();
5100                                   }
5101                                 });
5102                         dbRefFetcher.fetchDBRefs(false);
5103                       }
5104                     }).start();
5105                   }
5106
5107                 });
5108                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5109                         MessageManager.formatMessage(
5110                                 "label.fetch_retrieve_from", new Object[]
5111                                 { src.getDbName() })));
5112                 dfetch.add(fetchr);
5113                 comp++;
5114               }
5115               else
5116               {
5117                 final DbSourceProxy[] dassource = otherdb
5118                         .toArray(new DbSourceProxy[0]);
5119                 // fetch all entry
5120                 DbSourceProxy src = otherdb.get(0);
5121                 fetchr = new JMenuItem(MessageManager
5122                         .formatMessage("label.fetch_all_param", new Object[]
5123                         { src.getDbSource() }));
5124                 fetchr.addActionListener(new ActionListener()
5125                 {
5126                   @Override
5127                   public void actionPerformed(ActionEvent e)
5128                   {
5129                     new Thread(new Runnable()
5130                     {
5131
5132                       @Override
5133                       public void run()
5134                       {
5135                         boolean isNucleotide = alignPanel.alignFrame
5136                                 .getViewport().getAlignment()
5137                                 .isNucleotide();
5138                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5139                                 alignPanel.av.getSequenceSelection(),
5140                                 alignPanel.alignFrame, dassource,
5141                                 alignPanel.alignFrame.featureSettings,
5142                                 isNucleotide);
5143                         dbRefFetcher
5144                                 .addListener(new FetchFinishedListenerI()
5145                                 {
5146                                   @Override
5147                                   public void finished()
5148                                   {
5149                                     AlignFrame.this.setMenusForViewport();
5150                                   }
5151                                 });
5152                         dbRefFetcher.fetchDBRefs(false);
5153                       }
5154                     }).start();
5155                   }
5156                 });
5157
5158                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5159                         MessageManager.formatMessage(
5160                                 "label.fetch_retrieve_from_all_sources",
5161                                 new Object[]
5162                                 { Integer.valueOf(otherdb.size())
5163                                         .toString(),
5164                                     src.getDbSource(), src.getDbName() })));
5165                 dfetch.add(fetchr);
5166                 comp++;
5167                 // and then build the rest of the individual menus
5168                 ifetch = new JMenu(MessageManager.formatMessage(
5169                         "label.source_from_db_source", new Object[]
5170                         { src.getDbSource() }));
5171                 icomp = 0;
5172                 String imname = null;
5173                 int i = 0;
5174                 for (DbSourceProxy sproxy : otherdb)
5175                 {
5176                   String dbname = sproxy.getDbName();
5177                   String sname = dbname.length() > 5
5178                           ? dbname.substring(0, 5) + "..."
5179                           : dbname;
5180                   String msname = dbname.length() > 10
5181                           ? dbname.substring(0, 10) + "..."
5182                           : dbname;
5183                   if (imname == null)
5184                   {
5185                     imname = MessageManager
5186                             .formatMessage("label.from_msname", new Object[]
5187                             { sname });
5188                   }
5189                   fetchr = new JMenuItem(msname);
5190                   final DbSourceProxy[] dassrc = { sproxy };
5191                   fetchr.addActionListener(new ActionListener()
5192                   {
5193
5194                     @Override
5195                     public void actionPerformed(ActionEvent e)
5196                     {
5197                       new Thread(new Runnable()
5198                       {
5199
5200                         @Override
5201                         public void run()
5202                         {
5203                           boolean isNucleotide = alignPanel.alignFrame
5204                                   .getViewport().getAlignment()
5205                                   .isNucleotide();
5206                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5207                                   alignPanel.av.getSequenceSelection(),
5208                                   alignPanel.alignFrame, dassrc,
5209                                   alignPanel.alignFrame.featureSettings,
5210                                   isNucleotide);
5211                           dbRefFetcher
5212                                   .addListener(new FetchFinishedListenerI()
5213                                   {
5214                                     @Override
5215                                     public void finished()
5216                                     {
5217                                       AlignFrame.this.setMenusForViewport();
5218                                     }
5219                                   });
5220                           dbRefFetcher.fetchDBRefs(false);
5221                         }
5222                       }).start();
5223                     }
5224
5225                   });
5226                   fetchr.setToolTipText(
5227                           "<html>" + MessageManager.formatMessage(
5228                                   "label.fetch_retrieve_from", new Object[]
5229                                   { dbname }));
5230                   ifetch.add(fetchr);
5231                   ++i;
5232                   if (++icomp >= mcomp || i == (otherdb.size()))
5233                   {
5234                     ifetch.setText(MessageManager.formatMessage(
5235                             "label.source_to_target", imname, sname));
5236                     dfetch.add(ifetch);
5237                     ifetch = new JMenu();
5238                     imname = null;
5239                     icomp = 0;
5240                     comp++;
5241                   }
5242                 }
5243               }
5244               ++dbi;
5245               if (comp >= mcomp || dbi >= (dbclasses.length))
5246               {
5247                 dfetch.setText(MessageManager.formatMessage(
5248                         "label.source_to_target", mname, dbclass));
5249                 rfetch.add(dfetch);
5250                 dfetch = new JMenu();
5251                 mname = null;
5252                 comp = 0;
5253               }
5254             }
5255           }
5256         });
5257       }
5258     }).start();
5259
5260   }
5261
5262   /**
5263    * Left justify the whole alignment.
5264    */
5265   @Override
5266   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5267   {
5268     AlignmentI al = viewport.getAlignment();
5269     al.justify(false);
5270     viewport.firePropertyChange("alignment", null, al);
5271   }
5272
5273   /**
5274    * Right justify the whole alignment.
5275    */
5276   @Override
5277   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5278   {
5279     AlignmentI al = viewport.getAlignment();
5280     al.justify(true);
5281     viewport.firePropertyChange("alignment", null, al);
5282   }
5283
5284   @Override
5285   public void setShowSeqFeatures(boolean b)
5286   {
5287     showSeqFeatures.setSelected(b);
5288     viewport.setShowSequenceFeatures(b);
5289   }
5290
5291   /*
5292    * (non-Javadoc)
5293    *
5294    * @see
5295    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5296    * awt.event.ActionEvent)
5297    */
5298   @Override
5299   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5300   {
5301     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5302     alignPanel.paintAlignment(false, false);
5303   }
5304
5305   /*
5306    * (non-Javadoc)
5307    *
5308    * @see
5309    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5310    * .ActionEvent)
5311    */
5312   @Override
5313   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5314   {
5315     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5316     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5317
5318   }
5319
5320   /*
5321    * (non-Javadoc)
5322    *
5323    * @see
5324    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5325    * .event.ActionEvent)
5326    */
5327   @Override
5328   protected void showGroupConservation_actionPerformed(ActionEvent e)
5329   {
5330     viewport.setShowGroupConservation(showGroupConservation.getState());
5331     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5332   }
5333
5334   /*
5335    * (non-Javadoc)
5336    *
5337    * @see
5338    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5339    * .event.ActionEvent)
5340    */
5341   @Override
5342   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5343   {
5344     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5345     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5346   }
5347
5348   /*
5349    * (non-Javadoc)
5350    *
5351    * @see
5352    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5353    * .event.ActionEvent)
5354    */
5355   @Override
5356   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5357   {
5358     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5359     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5360   }
5361
5362   @Override
5363   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5364   {
5365     showSequenceLogo.setState(true);
5366     viewport.setShowSequenceLogo(true);
5367     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5368     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5369   }
5370
5371   @Override
5372   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5373   {
5374     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5375   }
5376
5377   /*
5378    * (non-Javadoc)
5379    *
5380    * @see
5381    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5382    * .event.ActionEvent)
5383    */
5384   @Override
5385   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5386   {
5387     if (avc.makeGroupsFromSelection())
5388     {
5389       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5390       alignPanel.updateAnnotation();
5391       alignPanel.paintAlignment(true,
5392               viewport.needToUpdateStructureViews());
5393     }
5394   }
5395
5396   public void clearAlignmentSeqRep()
5397   {
5398     // TODO refactor alignmentseqrep to controller
5399     if (viewport.getAlignment().hasSeqrep())
5400     {
5401       viewport.getAlignment().setSeqrep(null);
5402       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5403       alignPanel.updateAnnotation();
5404       alignPanel.paintAlignment(true, true);
5405     }
5406   }
5407
5408   @Override
5409   protected void createGroup_actionPerformed(ActionEvent e)
5410   {
5411     if (avc.createGroup())
5412     {
5413       if (applyAutoAnnotationSettings.isSelected())
5414       {
5415         alignPanel.updateAnnotation(true, false);
5416       }
5417       alignPanel.alignmentChanged();
5418     }
5419   }
5420
5421   @Override
5422   protected void unGroup_actionPerformed(ActionEvent e)
5423   {
5424     if (avc.unGroup())
5425     {
5426       alignPanel.alignmentChanged();
5427     }
5428   }
5429
5430   /**
5431    * make the given alignmentPanel the currently selected tab
5432    *
5433    * @param alignmentPanel
5434    */
5435   public void setDisplayedView(AlignmentPanel alignmentPanel)
5436   {
5437     if (!viewport.getSequenceSetId()
5438             .equals(alignmentPanel.av.getSequenceSetId()))
5439     {
5440       throw new Error(MessageManager.getString(
5441               "error.implementation_error_cannot_show_view_alignment_frame"));
5442     }
5443     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5444             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5445     {
5446       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5447     }
5448   }
5449
5450   /**
5451    * Action on selection of menu options to Show or Hide annotations.
5452    *
5453    * @param visible
5454    * @param forSequences
5455    *          update sequence-related annotations
5456    * @param forAlignment
5457    *          update non-sequence-related annotations
5458    */
5459   @Override
5460   protected void setAnnotationsVisibility(boolean visible,
5461           boolean forSequences, boolean forAlignment)
5462   {
5463     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5464             .getAlignmentAnnotation();
5465     if (anns == null)
5466     {
5467       return;
5468     }
5469     for (AlignmentAnnotation aa : anns)
5470     {
5471       /*
5472        * don't display non-positional annotations on an alignment
5473        */
5474       if (aa.annotations == null)
5475       {
5476         continue;
5477       }
5478       boolean apply = (aa.sequenceRef == null && forAlignment)
5479               || (aa.sequenceRef != null && forSequences);
5480       if (apply)
5481       {
5482         aa.visible = visible;
5483       }
5484     }
5485     alignPanel.validateAnnotationDimensions(true);
5486     alignPanel.alignmentChanged();
5487   }
5488
5489   /**
5490    * Store selected annotation sort order for the view and repaint.
5491    */
5492   @Override
5493   protected void sortAnnotations_actionPerformed()
5494   {
5495     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5496     this.alignPanel.av
5497             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5498     alignPanel.paintAlignment(false, false);
5499   }
5500
5501   /**
5502    *
5503    * @return alignment panels in this alignment frame
5504    */
5505   public List<? extends AlignmentViewPanel> getAlignPanels()
5506   {
5507     // alignPanels is never null
5508     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5509     return alignPanels;
5510   }
5511
5512   /**
5513    * Open a new alignment window, with the cDNA associated with this (protein)
5514    * alignment, aligned as is the protein.
5515    */
5516   protected void viewAsCdna_actionPerformed()
5517   {
5518     // TODO no longer a menu action - refactor as required
5519     final AlignmentI alignment = getViewport().getAlignment();
5520     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5521     if (mappings == null)
5522     {
5523       return;
5524     }
5525     List<SequenceI> cdnaSeqs = new ArrayList<>();
5526     for (SequenceI aaSeq : alignment.getSequences())
5527     {
5528       for (AlignedCodonFrame acf : mappings)
5529       {
5530         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5531         if (dnaSeq != null)
5532         {
5533           /*
5534            * There is a cDNA mapping for this protein sequence - add to new
5535            * alignment. It will share the same dataset sequence as other mapped
5536            * cDNA (no new mappings need to be created).
5537            */
5538           final Sequence newSeq = new Sequence(dnaSeq);
5539           newSeq.setDatasetSequence(dnaSeq);
5540           cdnaSeqs.add(newSeq);
5541         }
5542       }
5543     }
5544     if (cdnaSeqs.size() == 0)
5545     {
5546       // show a warning dialog no mapped cDNA
5547       return;
5548     }
5549     AlignmentI cdna = new Alignment(
5550             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5551     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5552             AlignFrame.DEFAULT_HEIGHT);
5553     cdna.alignAs(alignment);
5554     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5555             + this.title;
5556     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5557             AlignFrame.DEFAULT_HEIGHT);
5558   }
5559
5560   /**
5561    * Set visibility of dna/protein complement view (available when shown in a
5562    * split frame).
5563    *
5564    * @param show
5565    */
5566   @Override
5567   protected void showComplement_actionPerformed(boolean show)
5568   {
5569     SplitContainerI sf = getSplitViewContainer();
5570     if (sf != null)
5571     {
5572       sf.setComplementVisible(this, show);
5573     }
5574   }
5575
5576   /**
5577    * Generate the reverse (optionally complemented) of the selected sequences,
5578    * and add them to the alignment
5579    */
5580   @Override
5581   protected void showReverse_actionPerformed(boolean complement)
5582   {
5583     AlignmentI al = null;
5584     try
5585     {
5586       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5587       al = dna.reverseCdna(complement);
5588       viewport.addAlignment(al, "");
5589       addHistoryItem(new EditCommand(
5590               MessageManager.getString("label.add_sequences"), Action.PASTE,
5591               al.getSequencesArray(), 0, al.getWidth(),
5592               viewport.getAlignment()));
5593     } catch (Exception ex)
5594     {
5595       System.err.println(ex.getMessage());
5596       return;
5597     }
5598   }
5599
5600   /**
5601    * Try to run a script in the Groovy console, having first ensured that this
5602    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5603    * be targeted at this alignment.
5604    */
5605   @Override
5606   protected void runGroovy_actionPerformed()
5607   {
5608     Jalview.setCurrentAlignFrame(this);
5609     groovy.ui.Console console = Desktop.getGroovyConsole();
5610     if (console != null)
5611     {
5612       try
5613       {
5614         console.runScript();
5615       } catch (Exception ex)
5616       {
5617         System.err.println((ex.toString()));
5618         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5619                 MessageManager.getString("label.couldnt_run_groovy_script"),
5620                 MessageManager.getString("label.groovy_support_failed"),
5621                 JvOptionPane.ERROR_MESSAGE);
5622       }
5623     }
5624     else
5625     {
5626       System.err.println("Can't run Groovy script as console not found");
5627     }
5628   }
5629
5630   /**
5631    * Hides columns containing (or not containing) a specified feature, provided
5632    * that would not leave all columns hidden
5633    *
5634    * @param featureType
5635    * @param columnsContaining
5636    * @return
5637    */
5638   public boolean hideFeatureColumns(String featureType,
5639           boolean columnsContaining)
5640   {
5641     boolean notForHiding = avc.markColumnsContainingFeatures(
5642             columnsContaining, false, false, featureType);
5643     if (notForHiding)
5644     {
5645       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5646               false, featureType))
5647       {
5648         getViewport().hideSelectedColumns();
5649         return true;
5650       }
5651     }
5652     return false;
5653   }
5654
5655   @Override
5656   protected void selectHighlightedColumns_actionPerformed(
5657           ActionEvent actionEvent)
5658   {
5659     // include key modifier check in case user selects from menu
5660     avc.markHighlightedColumns(
5661             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5662             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5663                     | ActionEvent.CTRL_MASK)) != 0);
5664   }
5665
5666   /**
5667    * Rebuilds the Colour menu, including any user-defined colours which have
5668    * been loaded either on startup or during the session
5669    */
5670   public void buildColourMenu()
5671   {
5672     colourMenu.removeAll();
5673
5674     colourMenu.add(applyToAllGroups);
5675     colourMenu.add(textColour);
5676     colourMenu.addSeparator();
5677
5678     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5679             viewport.getAlignment(), false);
5680
5681     colourMenu.add(annotationColour);
5682     bg.add(annotationColour);
5683     colourMenu.addSeparator();
5684     colourMenu.add(conservationMenuItem);
5685     colourMenu.add(modifyConservation);
5686     colourMenu.add(abovePIDThreshold);
5687     colourMenu.add(modifyPID);
5688
5689     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5690     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5691   }
5692
5693   /**
5694    * Open a dialog (if not already open) that allows the user to select and
5695    * calculate PCA or Tree analysis
5696    */
5697   protected void openTreePcaDialog()
5698   {
5699     if (alignPanel.getCalculationDialog() == null)
5700     {
5701       new CalculationChooser(AlignFrame.this);
5702     }
5703   }
5704
5705   @Override
5706   protected void loadVcf_actionPerformed()
5707   {
5708     JalviewFileChooser chooser = new JalviewFileChooser(
5709             Cache.getProperty("LAST_DIRECTORY"));
5710     chooser.setFileView(new JalviewFileView());
5711     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5712     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5713
5714     int value = chooser.showOpenDialog(null);
5715
5716     if (value == JalviewFileChooser.APPROVE_OPTION)
5717     {
5718       String choice = chooser.getSelectedFile().getPath();
5719       Cache.setProperty("LAST_DIRECTORY", choice);
5720       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5721       new VCFLoader(choice).loadVCF(seqs, this);
5722     }
5723
5724   }
5725
5726   private Rectangle lastFeatureSettingsBounds = null;
5727
5728   @Override
5729   public void setFeatureSettingsGeometry(Rectangle bounds)
5730   {
5731     lastFeatureSettingsBounds = bounds;
5732   }
5733
5734   @Override
5735   public Rectangle getFeatureSettingsGeometry()
5736   {
5737     return lastFeatureSettingsBounds;
5738   }
5739 }
5740
5741 class PrintThread extends Thread
5742 {
5743   AlignmentPanel ap;
5744
5745   public PrintThread(AlignmentPanel ap)
5746   {
5747     this.ap = ap;
5748   }
5749
5750   static PageFormat pf;
5751
5752   @Override
5753   public void run()
5754   {
5755     PrinterJob printJob = PrinterJob.getPrinterJob();
5756
5757     if (pf != null)
5758     {
5759       printJob.setPrintable(ap, pf);
5760     }
5761     else
5762     {
5763       printJob.setPrintable(ap);
5764     }
5765
5766     if (printJob.printDialog())
5767     {
5768       try
5769       {
5770         printJob.print();
5771       } catch (Exception PrintException)
5772       {
5773         PrintException.printStackTrace();
5774       }
5775     }
5776   }
5777 }