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