src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignExportSettingBeanI;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.HiddenColumns;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileFormats;
  72 import jalview.io.FileLoader;
  73 import jalview.io.FileParse;
  74 import jalview.io.FormatAdapter;
  75 import jalview.io.HtmlSvgOutput;
  76 import jalview.io.IdentifyFile;
  77 import jalview.io.JPredFile;
  78 import jalview.io.JalviewFileChooser;
  79 import jalview.io.JalviewFileView;
  80 import jalview.io.JnetAnnotationMaker;
  81 import jalview.io.NewickFile;
  82 import jalview.io.ScoreMatrixFile;
  83 import jalview.io.TCoffeeScoreFile;
  84 import jalview.io.vcf.VCFLoader;
  85 import jalview.jbgui.GAlignFrame;
  86 import jalview.schemes.ColourSchemeI;
  87 import jalview.schemes.ColourSchemes;
  88 import jalview.schemes.ResidueColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.util.MessageManager;
  91 import jalview.util.dialogrunner.RunResponse;
  92 import jalview.viewmodel.AlignmentViewport;
  93 import jalview.viewmodel.ViewportRanges;
  94 import jalview.ws.DBRefFetcher;
  95 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  96 import jalview.ws.jws1.Discoverer;
  97 import jalview.ws.jws2.Jws2Discoverer;
  98 import jalview.ws.jws2.jabaws2.Jws2Instance;
  99 import jalview.ws.seqfetcher.DbSourceProxy;
 100
 101 import java.awt.BorderLayout;
 102 import java.awt.Color;
 103 import java.awt.Component;
 104 import java.awt.Rectangle;
 105 import java.awt.Toolkit;
 106 import java.awt.datatransfer.Clipboard;
 107 import java.awt.datatransfer.DataFlavor;
 108 import java.awt.datatransfer.StringSelection;
 109 import java.awt.datatransfer.Transferable;
 110 import java.awt.dnd.DnDConstants;
 111 import java.awt.dnd.DropTargetDragEvent;
 112 import java.awt.dnd.DropTargetDropEvent;
 113 import java.awt.dnd.DropTargetEvent;
 114 import java.awt.dnd.DropTargetListener;
 115 import java.awt.event.ActionEvent;
 116 import java.awt.event.ActionListener;
 117 import java.awt.event.FocusAdapter;
 118 import java.awt.event.FocusEvent;
 119 import java.awt.event.ItemEvent;
 120 import java.awt.event.ItemListener;
 121 import java.awt.event.KeyAdapter;
 122 import java.awt.event.KeyEvent;
 123 import java.awt.event.MouseEvent;
 124 import java.awt.print.PageFormat;
 125 import java.awt.print.PrinterJob;
 126 import java.beans.PropertyChangeEvent;
 127 import java.beans.PropertyChangeListener;
 128 import java.io.File;
 129 import java.io.FileWriter;
 130 import java.io.PrintWriter;
 131 import java.net.URL;
 132 import java.util.ArrayList;
 133 import java.util.Arrays;
 134 import java.util.Deque;
 135 import java.util.Enumeration;
 136 import java.util.Hashtable;
 137 import java.util.List;
 138 import java.util.Vector;
 139
 140 import javax.swing.JCheckBoxMenuItem;
 141 import javax.swing.JComponent;
 142 import javax.swing.JEditorPane;
 143 import javax.swing.JInternalFrame;
 144 import javax.swing.JLabel;
 145 import javax.swing.JLayeredPane;
 146 import javax.swing.JMenu;
 147 import javax.swing.JMenuItem;
 148 import javax.swing.JPanel;
 149 import javax.swing.JScrollPane;
 150 import javax.swing.SwingUtilities;
 151
 152 /**
 153  * DOCUMENT ME!
 154  *
 155  * @author $author$
 156  * @version $Revision$
 157  */
 158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 159         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener,
 160         PropertyChangeListener
 161 {
 162
 163   public static final int DEFAULT_WIDTH = 700;
 164
 165   public static final int DEFAULT_HEIGHT = 500;
 166
 167   /*
 168    * The currently displayed panel (selected tabbed view if more than one)
 169    */
 170   public AlignmentPanel alignPanel;
 171
 172   AlignViewport viewport;
 173
 174   public AlignViewControllerI avc;
 175
 176   List<AlignmentPanel> alignPanels = new ArrayList<>();
 177
 178   /**
 179    * Last format used to load or save alignments in this window
 180    */
 181   FileFormatI currentFileFormat = null;
 182
 183   /**
 184    * Current filename for this alignment
 185    */
 186   String fileName = null;
 187
 188   File fileObject;
 189
 190   /**
 191    * Creates a new AlignFrame object with specific width and height.
 192    *
 193    * @param al
 194    * @param width
 195    * @param height
 196    */
 197   public AlignFrame(AlignmentI al, int width, int height)
 198   {
 199     this(al, null, width, height);
 200   }
 201
 202   /**
 203    * Creates a new AlignFrame object with specific width, height and
 204    * sequenceSetId
 205    *
 206    * @param al
 207    * @param width
 208    * @param height
 209    * @param sequenceSetId
 210    */
 211   public AlignFrame(AlignmentI al, int width, int height,
 212           String sequenceSetId)
 213   {
 214     this(al, null, width, height, sequenceSetId);
 215   }
 216
 217   /**
 218    * Creates a new AlignFrame object with specific width, height and
 219    * sequenceSetId
 220    *
 221    * @param al
 222    * @param width
 223    * @param height
 224    * @param sequenceSetId
 225    * @param viewId
 226    */
 227   public AlignFrame(AlignmentI al, int width, int height,
 228           String sequenceSetId, String viewId)
 229   {
 230     this(al, null, width, height, sequenceSetId, viewId);
 231   }
 232
 233   /**
 234    * new alignment window with hidden columns
 235    *
 236    * @param al
 237    *          AlignmentI
 238    * @param hiddenColumns
 239    *          ColumnSelection or null
 240    * @param width
 241    *          Width of alignment frame
 242    * @param height
 243    *          height of frame.
 244    */
 245   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 246           int height)
 247   {
 248     this(al, hiddenColumns, width, height, null);
 249   }
 250
 251   /**
 252    * Create alignment frame for al with hiddenColumns, a specific width and
 253    * height, and specific sequenceId
 254    *
 255    * @param al
 256    * @param hiddenColumns
 257    * @param width
 258    * @param height
 259    * @param sequenceSetId
 260    *          (may be null)
 261    */
 262   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 263           int height, String sequenceSetId)
 264   {
 265     this(al, hiddenColumns, width, height, sequenceSetId, null);
 266   }
 267
 268   /**
 269    * Create alignment frame for al with hiddenColumns, a specific width and
 270    * height, and specific sequenceId
 271    *
 272    * @param al
 273    * @param hiddenColumns
 274    * @param width
 275    * @param height
 276    * @param sequenceSetId
 277    *          (may be null)
 278    * @param viewId
 279    *          (may be null)
 280    */
 281   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 282           int height, String sequenceSetId, String viewId)
 283   {
 284     setSize(width, height);
 285
 286     if (al.getDataset() == null)
 287     {
 288       al.setDataset(null);
 289     }
 290
 291     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 292
 293     alignPanel = new AlignmentPanel(this, viewport);
 294
 295     addAlignmentPanel(alignPanel, true);
 296     init();
 297   }
 298
 299   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 300           HiddenColumns hiddenColumns, int width, int height)
 301   {
 302     setSize(width, height);
 303
 304     if (al.getDataset() == null)
 305     {
 306       al.setDataset(null);
 307     }
 308
 309     viewport = new AlignViewport(al, hiddenColumns);
 310
 311     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 312     {
 313       viewport.hideSequence(hiddenSeqs);
 314     }
 315     alignPanel = new AlignmentPanel(this, viewport);
 316     addAlignmentPanel(alignPanel, true);
 317     init();
 318   }
 319
 320   /**
 321    * Make a new AlignFrame from existing alignmentPanels
 322    *
 323    * @param ap
 324    *          AlignmentPanel
 325    * @param av
 326    *          AlignViewport
 327    */
 328   public AlignFrame(AlignmentPanel ap)
 329   {
 330     viewport = ap.av;
 331     alignPanel = ap;
 332     addAlignmentPanel(ap, false);
 333     init();
 334   }
 335
 336   @Override
 337   public void propertyChange(PropertyChangeEvent evt)
 338   {
 339     Desktop.getDesktop().propertyChange(evt);
 340   }
 341
 342   /**
 343    * BH 2018
 344    *
 345    * @return true if we have any features
 346    */
 347   @Override
 348   protected boolean haveAlignmentFeatures()
 349   {
 350     AlignmentI alignment = getViewport().getAlignment();
 351
 352     for (int i = 0; i < alignment.getHeight(); i++)
 353     {
 354       SequenceI seq = alignment.getSequenceAt(i);
 355       for (String group : seq.getFeatures().getFeatureGroups(true))
 356       {
 357         if (group != null)
 358           return true;
 359       }
 360     }
 361     return false;
 362   }
 363
 364   /**
 365    * initalise the alignframe from the underlying viewport data and the
 366    * configurations
 367    */
 368   void init()
 369   {
 370     if (!Jalview.isHeadlessMode())
 371     {
 372       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 373     }
 374
 375     avc = new jalview.controller.AlignViewController(this, viewport,
 376             alignPanel);
 377     if (viewport.getAlignmentConservationAnnotation() == null)
 378     {
 379       // BLOSUM62Colour.setEnabled(false);
 380       conservationMenuItem.setEnabled(false);
 381       modifyConservation.setEnabled(false);
 382       // PIDColour.setEnabled(false);
 383       // abovePIDThreshold.setEnabled(false);
 384       // modifyPID.setEnabled(false);
 385     }
 386
 387     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 388             "No sort");
 389
 390     if (sortby.equals("Id"))
 391     {
 392       sortIDMenuItem_actionPerformed(null);
 393     }
 394     else if (sortby.equals("Pairwise Identity"))
 395     {
 396       sortPairwiseMenuItem_actionPerformed(null);
 397     }
 398
 399     this.alignPanel.av
 400             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 401
 402     setMenusFromViewport(viewport);
 403     buildSortByAnnotationScoresMenu();
 404     calculateTree.addActionListener(new ActionListener()
 405     {
 406
 407       @Override
 408       public void actionPerformed(ActionEvent e)
 409       {
 410         openTreePcaDialog();
 411       }
 412     });
 413     buildColourMenu();
 414
 415     if (Desktop.desktop != null)
 416     {
 417       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 418       /**
 419        * BH 2018 ignore service listeners
 420        *
 421        * @j2sNative
 422        *
 423        */
 424       {
 425         addServiceListeners();
 426       }
 427       setGUINucleotide();
 428     }
 429
 430     if (viewport.getWrapAlignment())
 431     {
 432       wrapMenuItem_actionPerformed(null);
 433     }
 434
 435     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 436     {
 437       this.overviewMenuItem_actionPerformed(null);
 438     }
 439
 440     addKeyListener();
 441
 442     final List<AlignmentPanel> selviews = new ArrayList<>();
 443     final List<AlignmentPanel> origview = new ArrayList<>();
 444     final String menuLabel = MessageManager
 445             .getString("label.copy_format_from");
 446     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 447             new ViewSetProvider()
 448             {
 449
 450               @Override
 451               public AlignmentPanel[] getAllAlignmentPanels()
 452               {
 453                 origview.clear();
 454                 origview.add(alignPanel);
 455                 // make an array of all alignment panels except for this one
 456                 List<AlignmentPanel> aps = new ArrayList<>(
 457                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 458                 aps.remove(AlignFrame.this.alignPanel);
 459                 return aps.toArray(new AlignmentPanel[aps.size()]);
 460               }
 461             }, selviews, new ItemListener()
 462             {
 463
 464               @Override
 465               public void itemStateChanged(ItemEvent e)
 466               {
 467                 if (origview.size() > 0)
 468                 {
 469                   final AlignmentPanel ap = origview.get(0);
 470
 471                   /*
 472                    * Copy the ViewStyle of the selected panel to 'this one'.
 473                    * Don't change value of 'scaleProteinAsCdna' unless copying
 474                    * from a SplitFrame.
 475                    */
 476                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 477                           .getViewStyle();
 478                   boolean fromSplitFrame = selviews.get(0)
 479                           .getAlignViewport().getCodingComplement() != null;
 480                   if (!fromSplitFrame)
 481                   {
 482                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 483                             .getViewStyle().isScaleProteinAsCdna());
 484                   }
 485                   ap.getAlignViewport().setViewStyle(vs);
 486
 487                   /*
 488                    * Also rescale ViewStyle of SplitFrame complement if there is
 489                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 490                    * the whole ViewStyle (allow cDNA protein to have different
 491                    * fonts)
 492                    */
 493                   AlignViewportI complement = ap.getAlignViewport()
 494                           .getCodingComplement();
 495                   if (complement != null && vs.isScaleProteinAsCdna())
 496                   {
 497                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 498                     ((SplitFrame) af.getSplitViewContainer())
 499                             .adjustLayout();
 500                     af.setMenusForViewport();
 501                   }
 502
 503                   ap.updateLayout();
 504                   ap.setSelected(true);
 505                   ap.alignFrame.setMenusForViewport();
 506
 507                 }
 508               }
 509             });
 510     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 511             .indexOf("devel") > -1
 512             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 513                     .indexOf("test") > -1)
 514     {
 515       formatMenu.add(vsel);
 516     }
 517     addFocusListener(new FocusAdapter()
 518     {
 519       @Override
 520       public void focusGained(FocusEvent e)
 521       {
 522         Jalview.setCurrentAlignFrame(AlignFrame.this);
 523       }
 524     });
 525
 526   }
 527
 528   /**
 529    * Change the filename and format for the alignment, and enable the 'reload'
 530    * button functionality.
 531    *
 532    * @param file
 533    *          valid filename
 534    * @param format
 535    *          format of file
 536    */
 537   public void setFileName(String file, FileFormatI format)
 538   {
 539     fileName = file;
 540     setFileFormat(format);
 541     reload.setEnabled(true);
 542   }
 543
 544   /**
 545    * JavaScript will have this, maybe others. More dependable than a file name
 546    * and maintains a reference to the actual bytes loaded.
 547    *
 548    * @param file
 549    */
 550   public void setFileObject(File file)
 551   {
 552     this.fileObject = file;
 553   }
 554
 555   /**
 556    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 557    * events
 558    */
 559   void addKeyListener()
 560   {
 561     addKeyListener(new KeyAdapter()
 562     {
 563       @Override
 564       public void keyPressed(KeyEvent evt)
 565       {
 566         if (viewport.cursorMode
 567                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 568                         && evt.getKeyCode() <= KeyEvent.VK_9)
 569                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 570                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 571                 && Character.isDigit(evt.getKeyChar()))
 572         {
 573           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 574         }
 575
 576         switch (evt.getKeyCode())
 577         {
 578
 579         case 27: // escape key
 580           deselectAllSequenceMenuItem_actionPerformed(null);
 581
 582           break;
 583
 584         case KeyEvent.VK_DOWN:
 585           if (evt.isAltDown() || !viewport.cursorMode)
 586           {
 587             moveSelectedSequences(false);
 588           }
 589           if (viewport.cursorMode)
 590           {
 591             alignPanel.getSeqPanel().moveCursor(0, 1);
 592           }
 593           break;
 594
 595         case KeyEvent.VK_UP:
 596           if (evt.isAltDown() || !viewport.cursorMode)
 597           {
 598             moveSelectedSequences(true);
 599           }
 600           if (viewport.cursorMode)
 601           {
 602             alignPanel.getSeqPanel().moveCursor(0, -1);
 603           }
 604
 605           break;
 606
 607         case KeyEvent.VK_LEFT:
 608           if (evt.isAltDown() || !viewport.cursorMode)
 609           {
 610             slideSequences(false,
 611                     alignPanel.getSeqPanel().getKeyboardNo1());
 612           }
 613           else
 614           {
 615             alignPanel.getSeqPanel().moveCursor(-1, 0);
 616           }
 617
 618           break;
 619
 620         case KeyEvent.VK_RIGHT:
 621           if (evt.isAltDown() || !viewport.cursorMode)
 622           {
 623             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 624           }
 625           else
 626           {
 627             alignPanel.getSeqPanel().moveCursor(1, 0);
 628           }
 629           break;
 630
 631         case KeyEvent.VK_SPACE:
 632           if (viewport.cursorMode)
 633           {
 634             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 635                     || evt.isShiftDown() || evt.isAltDown());
 636           }
 637           break;
 638
 639         // case KeyEvent.VK_A:
 640         // if (viewport.cursorMode)
 641         // {
 642         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 643         // //System.out.println("A");
 644         // }
 645         // break;
 646         /*
 647          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 648          * System.out.println("closing bracket"); } break;
 649          */
 650         case KeyEvent.VK_DELETE:
 651         case KeyEvent.VK_BACK_SPACE:
 652           if (!viewport.cursorMode)
 653           {
 654             cut_actionPerformed(null);
 655           }
 656           else
 657           {
 658             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 659                     || evt.isShiftDown() || evt.isAltDown());
 660           }
 661
 662           break;
 663
 664         case KeyEvent.VK_S:
 665           if (viewport.cursorMode)
 666           {
 667             alignPanel.getSeqPanel().setCursorRow();
 668           }
 669           break;
 670         case KeyEvent.VK_C:
 671           if (viewport.cursorMode && !evt.isControlDown())
 672           {
 673             alignPanel.getSeqPanel().setCursorColumn();
 674           }
 675           break;
 676         case KeyEvent.VK_P:
 677           if (viewport.cursorMode)
 678           {
 679             alignPanel.getSeqPanel().setCursorPosition();
 680           }
 681           break;
 682
 683         case KeyEvent.VK_ENTER:
 684         case KeyEvent.VK_COMMA:
 685           if (viewport.cursorMode)
 686           {
 687             alignPanel.getSeqPanel().setCursorRowAndColumn();
 688           }
 689           break;
 690
 691         case KeyEvent.VK_Q:
 692           if (viewport.cursorMode)
 693           {
 694             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 695           }
 696           break;
 697         case KeyEvent.VK_M:
 698           if (viewport.cursorMode)
 699           {
 700             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 701           }
 702           break;
 703
 704         case KeyEvent.VK_F2:
 705           viewport.cursorMode = !viewport.cursorMode;
 706           statusBar.setText(MessageManager
 707                   .formatMessage("label.keyboard_editing_mode", new String[]
 708                   { (viewport.cursorMode ? "on" : "off") }));
 709           if (viewport.cursorMode)
 710           {
 711             ViewportRanges ranges = viewport.getRanges();
 712             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 713                     .getStartRes();
 714             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 715                     .getStartSeq();
 716           }
 717           alignPanel.getSeqPanel().seqCanvas.repaint();
 718           break;
 719
 720         case KeyEvent.VK_F1:
 721           try
 722           {
 723             Help.showHelpWindow();
 724           } catch (Exception ex)
 725           {
 726             ex.printStackTrace();
 727           }
 728           break;
 729         case KeyEvent.VK_H:
 730         {
 731           boolean toggleSeqs = !evt.isControlDown();
 732           boolean toggleCols = !evt.isShiftDown();
 733           toggleHiddenRegions(toggleSeqs, toggleCols);
 734           break;
 735         }
 736         case KeyEvent.VK_B:
 737         {
 738           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 739           boolean modifyExisting = true; // always modify, don't clear
 740                                          // evt.isShiftDown();
 741           boolean invertHighlighted = evt.isAltDown();
 742           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 743                   toggleSel);
 744           break;
 745         }
 746         case KeyEvent.VK_PAGE_UP:
 747           viewport.getRanges().pageUp();
 748           break;
 749         case KeyEvent.VK_PAGE_DOWN:
 750           viewport.getRanges().pageDown();
 751           break;
 752         }
 753       }
 754
 755       @Override
 756       public void keyReleased(KeyEvent evt)
 757       {
 758         switch (evt.getKeyCode())
 759         {
 760         case KeyEvent.VK_LEFT:
 761           if (evt.isAltDown() || !viewport.cursorMode)
 762           {
 763             viewport.firePropertyChange("alignment", null,
 764                     viewport.getAlignment().getSequences());
 765           }
 766           break;
 767
 768         case KeyEvent.VK_RIGHT:
 769           if (evt.isAltDown() || !viewport.cursorMode)
 770           {
 771             viewport.firePropertyChange("alignment", null,
 772                     viewport.getAlignment().getSequences());
 773           }
 774           break;
 775         }
 776       }
 777     });
 778   }
 779
 780   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 781   {
 782     ap.alignFrame = this;
 783     avc = new jalview.controller.AlignViewController(this, viewport,
 784             alignPanel);
 785
 786     alignPanels.add(ap);
 787
 788     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 789
 790     int aSize = alignPanels.size();
 791
 792     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 793
 794     if (aSize == 1 && ap.av.viewName == null)
 795     {
 796       this.getContentPane().add(ap, BorderLayout.CENTER);
 797     }
 798     else
 799     {
 800       if (aSize == 2)
 801       {
 802         setInitialTabVisible();
 803       }
 804
 805       expandViews.setEnabled(true);
 806       gatherViews.setEnabled(true);
 807       tabbedPane.addTab(ap.av.viewName, ap);
 808
 809       ap.setVisible(false);
 810     }
 811
 812     if (newPanel)
 813     {
 814       if (ap.av.isPadGaps())
 815       {
 816         ap.av.getAlignment().padGaps();
 817       }
 818       ap.av.updateConservation(ap);
 819       ap.av.updateConsensus(ap);
 820       ap.av.updateStrucConsensus(ap);
 821     }
 822   }
 823
 824   public void setInitialTabVisible()
 825   {
 826     expandViews.setEnabled(true);
 827     gatherViews.setEnabled(true);
 828     tabbedPane.setVisible(true);
 829     AlignmentPanel first = alignPanels.get(0);
 830     tabbedPane.addTab(first.av.viewName, first);
 831     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 832   }
 833
 834   public AlignViewport getViewport()
 835   {
 836     return viewport;
 837   }
 838
 839   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 840   private void addServiceListeners()
 841   {
 842     final java.beans.PropertyChangeListener thisListener;
 843     Desktop.instance.addJalviewPropertyChangeListener("services",
 844             thisListener = new java.beans.PropertyChangeListener()
 845             {
 846               @Override
 847               public void propertyChange(PropertyChangeEvent evt)
 848               {
 849                 // // System.out.println("Discoverer property change.");
 850                 // if (evt.getPropertyName().equals("services"))
 851                 {
 852                   SwingUtilities.invokeLater(new Runnable()
 853                   {
 854
 855                     @Override
 856                     public void run()
 857                     {
 858                       System.err.println(
 859                               "Rebuild WS Menu for service change");
 860                       BuildWebServiceMenu();
 861                     }
 862
 863                   });
 864                 }
 865               }
 866             });
 867     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 868     {
 869       @Override
 870       public void internalFrameClosed(
 871               javax.swing.event.InternalFrameEvent evt)
 872       {
 873         // System.out.println("deregistering discoverer listener");
 874         Desktop.instance.removeJalviewPropertyChangeListener("services",
 875                 thisListener);
 876         closeMenuItem_actionPerformed(true);
 877       };
 878     });
 879     // Finally, build the menu once to get current service state
 880     new Thread(new Runnable()
 881     {
 882       @Override
 883       public void run()
 884       {
 885         BuildWebServiceMenu();
 886       }
 887     }).start();
 888   }
 889
 890   /**
 891    * Configure menu items that vary according to whether the alignment is
 892    * nucleotide or protein
 893    */
 894   public void setGUINucleotide()
 895   {
 896     AlignmentI al = getViewport().getAlignment();
 897     boolean nucleotide = al.isNucleotide();
 898
 899     loadVcf.setVisible(nucleotide);
 900     showTranslation.setVisible(nucleotide);
 901     showReverse.setVisible(nucleotide);
 902     showReverseComplement.setVisible(nucleotide);
 903     conservationMenuItem.setEnabled(!nucleotide);
 904     modifyConservation
 905             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 906     showGroupConservation.setEnabled(!nucleotide);
 907
 908     showComplementMenuItem
 909             .setText(nucleotide ? MessageManager.getString("label.protein")
 910                     : MessageManager.getString("label.nucleotide"));
 911   }
 912
 913   /**
 914    * set up menus for the current viewport. This may be called after any
 915    * operation that affects the data in the current view (selection changed,
 916    * etc) to update the menus to reflect the new state.
 917    */
 918   @Override
 919   public void setMenusForViewport()
 920   {
 921     setMenusFromViewport(viewport);
 922   }
 923
 924   /**
 925    * Need to call this method when tabs are selected for multiple views, or when
 926    * loading from Jalview2XML.java
 927    *
 928    * @param av
 929    *          AlignViewport
 930    */
 931   void setMenusFromViewport(AlignViewport av)
 932   {
 933     padGapsMenuitem.setSelected(av.isPadGaps());
 934     colourTextMenuItem.setSelected(av.isShowColourText());
 935     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 936     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 937     conservationMenuItem.setSelected(av.getConservationSelected());
 938     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 939     seqLimits.setSelected(av.getShowJVSuffix());
 940     idRightAlign.setSelected(av.isRightAlignIds());
 941     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 942     renderGapsMenuItem.setSelected(av.isRenderGaps());
 943     wrapMenuItem.setSelected(av.getWrapAlignment());
 944     scaleAbove.setVisible(av.getWrapAlignment());
 945     scaleLeft.setVisible(av.getWrapAlignment());
 946     scaleRight.setVisible(av.getWrapAlignment());
 947     annotationPanelMenuItem.setState(av.isShowAnnotation());
 948     /*
 949      * Show/hide annotations only enabled if annotation panel is shown
 950      */
 951     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 952     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 953     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 954     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 955     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 956     viewTextMenuItem.setSelected(av.getShowText());
 957     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 958     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 959     showGroupConservation.setSelected(av.isShowGroupConservation());
 960     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 961     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 962     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 963
 964     ColourMenuHelper.setColourSelected(colourMenu,
 965             av.getGlobalColourScheme());
 966
 967     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 968     hiddenMarkers.setState(av.getShowHiddenMarkers());
 969     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 970     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 971     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 972     autoCalculate.setSelected(av.autoCalculateConsensus);
 973     sortByTree.setSelected(av.sortByTree);
 974     listenToViewSelections.setSelected(av.followSelection);
 975
 976     showProducts.setEnabled(canShowProducts());
 977     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 978
 979     updateEditMenuBar();
 980   }
 981
 982   /**
 983    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 984    *
 985    * @param b
 986    */
 987   public void setGroovyEnabled(boolean b)
 988   {
 989     runGroovy.setEnabled(b);
 990   }
 991
 992   private IProgressIndicator progressBar;
 993
 994   /*
 995    * (non-Javadoc)
 996    *
 997    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 998    */
 999   @Override
1000   public void setProgressBar(String message, long id)
1001   {
1002     progressBar.setProgressBar(message, id);
1003   }
1004
1005   @Override
1006   public void registerHandler(final long id,
1007           final IProgressIndicatorHandler handler)
1008   {
1009     progressBar.registerHandler(id, handler);
1010   }
1011
1012   /**
1013    *
1014    * @return true if any progress bars are still active
1015    */
1016   @Override
1017   public boolean operationInProgress()
1018   {
1019     return progressBar.operationInProgress();
1020   }
1021
1022   @Override
1023   public void setStatus(String text)
1024   {
1025     statusBar.setText(text);
1026   }
1027
1028   /*
1029    * Added so Castor Mapping file can obtain Jalview Version
1030    */
1031   public String getVersion()
1032   {
1033     return jalview.bin.Cache.getProperty("VERSION");
1034   }
1035
1036   public FeatureRenderer getFeatureRenderer()
1037   {
1038     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1039   }
1040
1041   @Override
1042   public void fetchSequence_actionPerformed(ActionEvent e)
1043   {
1044     new jalview.gui.SequenceFetcher(this);
1045   }
1046
1047   @Override
1048   public void addFromFile_actionPerformed(ActionEvent e)
1049   {
1050     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1051   }
1052
1053   @Override
1054   public void reload_actionPerformed(ActionEvent e)
1055   {
1056     if (fileName != null)
1057     {
1058       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1059       // originating file's format
1060       // TODO: work out how to recover feature settings for correct view(s) when
1061       // file is reloaded.
1062       if (FileFormat.Jalview.equals(currentFileFormat))
1063       {
1064         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1065         for (int i = 0; i < frames.length; i++)
1066         {
1067           if (frames[i] instanceof AlignFrame && frames[i] != this
1068                   && ((AlignFrame) frames[i]).fileName != null
1069                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1070           {
1071             try
1072             {
1073               frames[i].setSelected(true);
1074               Desktop.instance.closeAssociatedWindows();
1075             } catch (java.beans.PropertyVetoException ex)
1076             {
1077             }
1078           }
1079
1080         }
1081         Desktop.instance.closeAssociatedWindows();
1082
1083         FileLoader loader = new FileLoader();
1084         DataSourceType protocol = fileName.startsWith("http:")
1085                 ? DataSourceType.URL
1086                 : DataSourceType.FILE;
1087         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1088       }
1089       else
1090       {
1091         Rectangle bounds = this.getBounds();
1092
1093         FileLoader loader = new FileLoader();
1094
1095         AlignFrame newframe = null;
1096
1097         if (fileObject == null)
1098         {
1099
1100           DataSourceType protocol = (fileName.startsWith("http:")
1101                   ? DataSourceType.URL
1102                   : DataSourceType.FILE);
1103           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1104                   currentFileFormat);
1105         }
1106         else
1107         {
1108           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1109                   DataSourceType.FILE, currentFileFormat);
1110         }
1111
1112         newframe.setBounds(bounds);
1113         if (featureSettings != null && featureSettings.isShowing())
1114         {
1115           final Rectangle fspos = featureSettings.frame.getBounds();
1116           // TODO: need a 'show feature settings' function that takes bounds -
1117           // need to refactor Desktop.addFrame
1118           newframe.featureSettings_actionPerformed(null);
1119           final FeatureSettings nfs = newframe.featureSettings;
1120           SwingUtilities.invokeLater(new Runnable()
1121           {
1122             @Override
1123             public void run()
1124             {
1125               nfs.frame.setBounds(fspos);
1126             }
1127           });
1128           this.featureSettings.close();
1129           this.featureSettings = null;
1130         }
1131         this.closeMenuItem_actionPerformed(true);
1132       }
1133     }
1134   }
1135
1136   @Override
1137   public void addFromText_actionPerformed(ActionEvent e)
1138   {
1139     Desktop.instance
1140             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1141   }
1142
1143   @Override
1144   public void addFromURL_actionPerformed(ActionEvent e)
1145   {
1146     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1147   }
1148
1149   @Override
1150   public void save_actionPerformed(ActionEvent e)
1151   {
1152     if (fileName == null || (currentFileFormat == null)
1153             || fileName.startsWith("http"))
1154     {
1155       saveAs_actionPerformed();
1156     }
1157     else
1158     {
1159       saveAlignment(fileName, currentFileFormat);
1160     }
1161   }
1162
1163   /**
1164    * Saves the alignment to a file with a name chosen by the user, if necessary
1165    * warning if a file would be overwritten
1166    */
1167   @Override
1168   public void saveAs_actionPerformed()
1169   {
1170     String format = currentFileFormat == null ? null
1171             : currentFileFormat.getName();
1172     JalviewFileChooser chooser = JalviewFileChooser
1173             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1174
1175     chooser.setFileView(new JalviewFileView());
1176     chooser.setDialogTitle(
1177             MessageManager.getString("label.save_alignment_to_file"));
1178     chooser.setToolTipText(MessageManager.getString("action.save"));
1179
1180     int value = chooser.showSaveDialog(this);
1181
1182     if (value == JalviewFileChooser.APPROVE_OPTION)
1183     {
1184       currentFileFormat = chooser.getSelectedFormat();
1185       while (currentFileFormat == null)
1186       {
1187         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1188                 MessageManager.getString(
1189                         "label.select_file_format_before_saving"),
1190                 MessageManager.getString("label.file_format_not_specified"),
1191                 JvOptionPane.WARNING_MESSAGE);
1192         currentFileFormat = chooser.getSelectedFormat();
1193         value = chooser.showSaveDialog(this);
1194         if (value != JalviewFileChooser.APPROVE_OPTION)
1195         {
1196           return;
1197         }
1198       }
1199
1200       fileName = chooser.getSelectedFile().getPath();
1201
1202       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1203       Cache.setProperty("LAST_DIRECTORY", fileName);
1204       saveAlignment(fileName, currentFileFormat);
1205     }
1206   }
1207
1208   private boolean lastSaveSuccessful = false;
1209
1210   private FileFormatI lastFormatSaved;
1211
1212   private String lastFilenameSaved;
1213
1214   /**
1215    * Raise a dialog or status message for the last call to saveAlignment.
1216    *
1217    * @return true if last call to saveAlignment(file, format) was successful.
1218    */
1219   public boolean isSaveAlignmentSuccessful()
1220   {
1221
1222     if (!lastSaveSuccessful)
1223     {
1224       JvOptionPane.showInternalMessageDialog(this, MessageManager
1225               .formatMessage("label.couldnt_save_file", new Object[]
1226               { lastFilenameSaved }),
1227               MessageManager.getString("label.error_saving_file"),
1228               JvOptionPane.WARNING_MESSAGE);
1229     }
1230     else
1231     {
1232
1233       statusBar.setText(MessageManager.formatMessage(
1234               "label.successfully_saved_to_file_in_format", new Object[]
1235               { lastFilenameSaved, lastFormatSaved }));
1236
1237     }
1238     return lastSaveSuccessful;
1239   }
1240
1241   public void saveAlignment(String file, FileFormatI format)
1242   {
1243     lastSaveSuccessful = false;
1244     lastFilenameSaved = file;
1245     lastFormatSaved = format;
1246     AlignFrame us = this;
1247     if (FileFormat.Jalview.equals(format))
1248     {
1249       String shortName = title;
1250
1251       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1252       {
1253         shortName = shortName.substring(
1254                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1255       }
1256
1257       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1258               shortName);
1259     }
1260     else
1261     {
1262       AlignExportSettingI settings = getAlignmentForExport(format,
1263               alignPanel, null);
1264       settings.addActionListener(new ActionListener()
1265       {
1266         @Override
1267         public void actionPerformed(ActionEvent e)
1268         {
1269
1270           if (settings.isCancelled())
1271           {
1272             lastSaveSuccessful = false;
1273             return;
1274           }
1275           AlignmentExportData exportData = settings.getAlignExportData();
1276           FormatAdapter f = new FormatAdapter(alignPanel,
1277                   exportData.getSettings());
1278           String output = f.formatSequences(format,
1279                   exportData.getAlignment(), // class
1280                                              // cast
1281                                              // exceptions
1282                                              // will
1283                   // occur in the distant future
1284                   exportData.getOmitHidden(),
1285                   exportData.getStartEndPostions(),
1286                   f.getCacheSuffixDefault(format),
1287                   viewport.getAlignment().getHiddenColumns());
1288
1289           if (output == null)
1290           {
1291             lastSaveSuccessful = false;
1292           }
1293           else
1294           {
1295             try
1296             {
1297               PrintWriter out = new PrintWriter(new FileWriter(file));
1298
1299               out.print(output);
1300               out.close();
1301               us.setTitle(file);
1302               statusBar.setText(MessageManager.formatMessage(
1303                       "label.successfully_saved_to_file_in_format",
1304                       new Object[]
1305                       { fileName, format.getName() }));
1306             } catch (Exception ex)
1307             {
1308               lastSaveSuccessful = false;
1309               ex.printStackTrace();
1310             }
1311           }
1312         }
1313       });
1314
1315       settings.doShowSettings();
1316     }
1317   }
1318
1319   /**
1320    * DOCUMENT ME!
1321    *
1322    * @param e
1323    *          DOCUMENT ME!
1324    */
1325   @Override
1326   protected void outputText_actionPerformed(ActionEvent e)
1327   {
1328     FileFormatI fileFormat = FileFormats.getInstance()
1329             .forName(e.getActionCommand());
1330     AlignExportSettingI settings = getAlignmentForExport(fileFormat,
1331             alignPanel, null);
1332     settings.addActionListener(new ActionListener()
1333     {
1334       @Override
1335       public void actionPerformed(ActionEvent e)
1336       {
1337         if (settings.isCancelled())
1338         {
1339           return;
1340         }
1341         AlignmentExportData exportData = settings.getAlignExportData();
1342         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1343         cap.setForInput(null);
1344         try
1345         {
1346           FileFormatI format = fileFormat;
1347           cap.setText(new FormatAdapter(alignPanel, settings)
1348                   .formatSequences(format, exportData.getAlignment(),
1349                           exportData.getOmitHidden(),
1350                           exportData.getStartEndPostions(),
1351                           viewport.getAlignment().getHiddenColumns()));
1352           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1353                   "label.alignment_output_command", new Object[]
1354                   { fileFormat.getName() }), 600, 500);
1355         } catch (OutOfMemoryError oom)
1356         {
1357           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1358                   oom);
1359           cap.dispose();
1360         }
1361         // TODO Auto-generated method stub
1362
1363       }
1364     });
1365     settings.doShowSettings();
1366   }
1367
1368   public static AlignExportSettingI getAlignmentForExport(
1369           FileFormatI format, AlignmentPanel alignPanel,
1370           AlignExportSettingBeanI exportSettings)
1371   {
1372
1373     return new AlignExportSettings(alignPanel, format, exportSettings);
1374   }
1375
1376   /**
1377    * DOCUMENT ME!
1378    *
1379    * @param e
1380    *          DOCUMENT ME!
1381    */
1382   @Override
1383   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1384   {
1385     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1386     htmlSVG.exportHTML(null);
1387   }
1388
1389   @Override
1390   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1391   {
1392     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1393     bjs.exportHTML(null);
1394   }
1395
1396   public void createImageMap(File file, String image)
1397   {
1398     alignPanel.makePNGImageMap(file, image);
1399   }
1400
1401   /**
1402    * DOCUMENT ME!
1403    *
1404    * @param e
1405    *          DOCUMENT ME!
1406    */
1407   @Override
1408   public void createPNG(File f)
1409   {
1410     alignPanel.makePNG(f);
1411   }
1412
1413   /**
1414    * DOCUMENT ME!
1415    *
1416    * @param e
1417    *          DOCUMENT ME!
1418    */
1419   @Override
1420   public void createEPS(File f)
1421   {
1422     alignPanel.makeEPS(f);
1423   }
1424
1425   @Override
1426   public void createSVG(File f)
1427   {
1428     alignPanel.makeSVG(f);
1429   }
1430
1431   @Override
1432   public void pageSetup_actionPerformed(ActionEvent e)
1433   {
1434     PrinterJob printJob = PrinterJob.getPrinterJob();
1435     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1436   }
1437
1438   /**
1439    * DOCUMENT ME!
1440    *
1441    * @param e
1442    *          DOCUMENT ME!
1443    */
1444   @Override
1445   public void printMenuItem_actionPerformed(ActionEvent e)
1446   {
1447     // Putting in a thread avoids Swing painting problems
1448     PrintThread thread = new PrintThread(alignPanel);
1449     thread.start();
1450   }
1451
1452   @Override
1453   public void exportFeatures_actionPerformed(ActionEvent e)
1454   {
1455     new AnnotationExporter(alignPanel).exportFeatures();
1456   }
1457
1458   @Override
1459   public void exportAnnotations_actionPerformed(ActionEvent e)
1460   {
1461     new AnnotationExporter(alignPanel).exportAnnotations();
1462   }
1463
1464   @Override
1465   public void associatedData_actionPerformed(ActionEvent e)
1466   {
1467     final JalviewFileChooser chooser = new JalviewFileChooser(
1468             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1469     chooser.setFileView(new JalviewFileView());
1470     chooser.setDialogTitle(
1471             MessageManager.getString("label.load_jalview_annotations"));
1472     chooser.setToolTipText(
1473             MessageManager.getString("label.load_jalview_annotations"));
1474     chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
1475     {
1476
1477       @Override
1478       public void run()
1479       {
1480         String choice = chooser.getSelectedFile().getPath();
1481         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1482         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1483       }
1484
1485     });
1486
1487     chooser.openDialog(this);
1488   }
1489
1490   /**
1491    * Close the current view or all views in the alignment frame. If the frame
1492    * only contains one view then the alignment will be removed from memory.
1493    *
1494    * @param closeAllTabs
1495    */
1496   @Override
1497   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1498   {
1499     if (alignPanels != null && alignPanels.size() < 2)
1500     {
1501       closeAllTabs = true;
1502     }
1503
1504     try
1505     {
1506       if (alignPanels != null)
1507       {
1508         if (closeAllTabs)
1509         {
1510           if (this.isClosed())
1511           {
1512             // really close all the windows - otherwise wait till
1513             // setClosed(true) is called
1514             for (int i = 0; i < alignPanels.size(); i++)
1515             {
1516               AlignmentPanel ap = alignPanels.get(i);
1517               ap.closePanel();
1518             }
1519           }
1520         }
1521         else
1522         {
1523           closeView(alignPanel);
1524         }
1525       }
1526
1527       if (closeAllTabs)
1528       {
1529         /*
1530          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1531          * be called recursively, with the frame now in 'closed' state
1532          */
1533         this.setClosed(true);
1534       }
1535     } catch (Exception ex)
1536     {
1537       ex.printStackTrace();
1538     }
1539   }
1540
1541   /**
1542    * Close the specified panel and close up tabs appropriately.
1543    *
1544    * @param panelToClose
1545    */
1546   public void closeView(AlignmentPanel panelToClose)
1547   {
1548     int index = tabbedPane.getSelectedIndex();
1549     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1550     alignPanels.remove(panelToClose);
1551     panelToClose.closePanel();
1552     panelToClose = null;
1553
1554     tabbedPane.removeTabAt(closedindex);
1555     tabbedPane.validate();
1556
1557     if (index > closedindex || index == tabbedPane.getTabCount())
1558     {
1559       // modify currently selected tab index if necessary.
1560       index--;
1561     }
1562
1563     this.tabSelectionChanged(index);
1564   }
1565
1566   /**
1567    * DOCUMENT ME!
1568    */
1569   void updateEditMenuBar()
1570   {
1571
1572     if (viewport.getHistoryList().size() > 0)
1573     {
1574       undoMenuItem.setEnabled(true);
1575       CommandI command = viewport.getHistoryList().peek();
1576       undoMenuItem.setText(MessageManager
1577               .formatMessage("label.undo_command", new Object[]
1578               { command.getDescription() }));
1579     }
1580     else
1581     {
1582       undoMenuItem.setEnabled(false);
1583       undoMenuItem.setText(MessageManager.getString("action.undo"));
1584     }
1585
1586     if (viewport.getRedoList().size() > 0)
1587     {
1588       redoMenuItem.setEnabled(true);
1589
1590       CommandI command = viewport.getRedoList().peek();
1591       redoMenuItem.setText(MessageManager
1592               .formatMessage("label.redo_command", new Object[]
1593               { command.getDescription() }));
1594     }
1595     else
1596     {
1597       redoMenuItem.setEnabled(false);
1598       redoMenuItem.setText(MessageManager.getString("action.redo"));
1599     }
1600   }
1601
1602   @Override
1603   public void addHistoryItem(CommandI command)
1604   {
1605     if (command.getSize() > 0)
1606     {
1607       viewport.addToHistoryList(command);
1608       viewport.clearRedoList();
1609       updateEditMenuBar();
1610       viewport.updateHiddenColumns();
1611       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1612       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1613       // viewport.getColumnSelection()
1614       // .getHiddenColumns().size() > 0);
1615     }
1616   }
1617
1618   /**
1619    *
1620    * @return alignment objects for all views
1621    */
1622   AlignmentI[] getViewAlignments()
1623   {
1624     if (alignPanels != null)
1625     {
1626       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1627       int i = 0;
1628       for (AlignmentPanel ap : alignPanels)
1629       {
1630         als[i++] = ap.av.getAlignment();
1631       }
1632       return als;
1633     }
1634     if (viewport != null)
1635     {
1636       return new AlignmentI[] { viewport.getAlignment() };
1637     }
1638     return null;
1639   }
1640
1641   /**
1642    * DOCUMENT ME!
1643    *
1644    * @param e
1645    *          DOCUMENT ME!
1646    */
1647   @Override
1648   protected void undoMenuItem_actionPerformed(ActionEvent e)
1649   {
1650     if (viewport.getHistoryList().isEmpty())
1651     {
1652       return;
1653     }
1654     CommandI command = viewport.getHistoryList().pop();
1655     viewport.addToRedoList(command);
1656     command.undoCommand(getViewAlignments());
1657
1658     AlignmentViewport originalSource = getOriginatingSource(command);
1659     updateEditMenuBar();
1660
1661     if (originalSource != null)
1662     {
1663       if (originalSource != viewport)
1664       {
1665         Cache.log.warn(
1666                 "Implementation worry: mismatch of viewport origin for undo");
1667       }
1668       originalSource.updateHiddenColumns();
1669       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1670       // null
1671       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1672       // viewport.getColumnSelection()
1673       // .getHiddenColumns().size() > 0);
1674       originalSource.firePropertyChange("alignment", null,
1675               originalSource.getAlignment().getSequences());
1676     }
1677   }
1678
1679   /**
1680    * DOCUMENT ME!
1681    *
1682    * @param e
1683    *          DOCUMENT ME!
1684    */
1685   @Override
1686   protected void redoMenuItem_actionPerformed(ActionEvent e)
1687   {
1688     if (viewport.getRedoList().size() < 1)
1689     {
1690       return;
1691     }
1692
1693     CommandI command = viewport.getRedoList().pop();
1694     viewport.addToHistoryList(command);
1695     command.doCommand(getViewAlignments());
1696
1697     AlignmentViewport originalSource = getOriginatingSource(command);
1698     updateEditMenuBar();
1699
1700     if (originalSource != null)
1701     {
1702
1703       if (originalSource != viewport)
1704       {
1705         Cache.log.warn(
1706                 "Implementation worry: mismatch of viewport origin for redo");
1707       }
1708       originalSource.updateHiddenColumns();
1709       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1710       // null
1711       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1712       // viewport.getColumnSelection()
1713       // .getHiddenColumns().size() > 0);
1714       originalSource.firePropertyChange("alignment", null,
1715               originalSource.getAlignment().getSequences());
1716     }
1717   }
1718
1719   AlignmentViewport getOriginatingSource(CommandI command)
1720   {
1721     AlignmentViewport originalSource = null;
1722     // For sequence removal and addition, we need to fire
1723     // the property change event FROM the viewport where the
1724     // original alignment was altered
1725     AlignmentI al = null;
1726     if (command instanceof EditCommand)
1727     {
1728       EditCommand editCommand = (EditCommand) command;
1729       al = editCommand.getAlignment();
1730       List<Component> comps = PaintRefresher.components
1731               .get(viewport.getSequenceSetId());
1732
1733       for (Component comp : comps)
1734       {
1735         if (comp instanceof AlignmentPanel)
1736         {
1737           if (al == ((AlignmentPanel) comp).av.getAlignment())
1738           {
1739             originalSource = ((AlignmentPanel) comp).av;
1740             break;
1741           }
1742         }
1743       }
1744     }
1745
1746     if (originalSource == null)
1747     {
1748       // The original view is closed, we must validate
1749       // the current view against the closed view first
1750       if (al != null)
1751       {
1752         PaintRefresher.validateSequences(al, viewport.getAlignment());
1753       }
1754
1755       originalSource = viewport;
1756     }
1757
1758     return originalSource;
1759   }
1760
1761   /**
1762    * DOCUMENT ME!
1763    *
1764    * @param up
1765    *          DOCUMENT ME!
1766    */
1767   public void moveSelectedSequences(boolean up)
1768   {
1769     SequenceGroup sg = viewport.getSelectionGroup();
1770
1771     if (sg == null)
1772     {
1773       return;
1774     }
1775     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1776             viewport.getHiddenRepSequences(), up);
1777     alignPanel.paintAlignment(true, false);
1778   }
1779
1780   synchronized void slideSequences(boolean right, int size)
1781   {
1782     List<SequenceI> sg = new ArrayList<>();
1783     if (viewport.cursorMode)
1784     {
1785       sg.add(viewport.getAlignment()
1786               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1787     }
1788     else if (viewport.getSelectionGroup() != null
1789             && viewport.getSelectionGroup().getSize() != viewport
1790                     .getAlignment().getHeight())
1791     {
1792       sg = viewport.getSelectionGroup()
1793               .getSequences(viewport.getHiddenRepSequences());
1794     }
1795
1796     if (sg.size() < 1)
1797     {
1798       return;
1799     }
1800
1801     List<SequenceI> invertGroup = new ArrayList<>();
1802
1803     for (SequenceI seq : viewport.getAlignment().getSequences())
1804     {
1805       if (!sg.contains(seq))
1806       {
1807         invertGroup.add(seq);
1808       }
1809     }
1810
1811     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1812
1813     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1814     for (int i = 0; i < invertGroup.size(); i++)
1815     {
1816       seqs2[i] = invertGroup.get(i);
1817     }
1818
1819     SlideSequencesCommand ssc;
1820     if (right)
1821     {
1822       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1823               viewport.getGapCharacter());
1824     }
1825     else
1826     {
1827       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1828               viewport.getGapCharacter());
1829     }
1830
1831     int groupAdjustment = 0;
1832     if (ssc.getGapsInsertedBegin() && right)
1833     {
1834       if (viewport.cursorMode)
1835       {
1836         alignPanel.getSeqPanel().moveCursor(size, 0);
1837       }
1838       else
1839       {
1840         groupAdjustment = size;
1841       }
1842     }
1843     else if (!ssc.getGapsInsertedBegin() && !right)
1844     {
1845       if (viewport.cursorMode)
1846       {
1847         alignPanel.getSeqPanel().moveCursor(-size, 0);
1848       }
1849       else
1850       {
1851         groupAdjustment = -size;
1852       }
1853     }
1854
1855     if (groupAdjustment != 0)
1856     {
1857       viewport.getSelectionGroup().setStartRes(
1858               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1859       viewport.getSelectionGroup().setEndRes(
1860               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1861     }
1862
1863     /*
1864      * just extend the last slide command if compatible; but not if in
1865      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1866      */
1867     boolean appendHistoryItem = false;
1868     Deque<CommandI> historyList = viewport.getHistoryList();
1869     boolean inSplitFrame = getSplitViewContainer() != null;
1870     if (!inSplitFrame && historyList != null && historyList.size() > 0
1871             && historyList.peek() instanceof SlideSequencesCommand)
1872     {
1873       appendHistoryItem = ssc.appendSlideCommand(
1874               (SlideSequencesCommand) historyList.peek());
1875     }
1876
1877     if (!appendHistoryItem)
1878     {
1879       addHistoryItem(ssc);
1880     }
1881
1882     repaint();
1883   }
1884
1885   /**
1886    * DOCUMENT ME!
1887    *
1888    * @param e
1889    *          DOCUMENT ME!
1890    */
1891   @Override
1892   protected void copy_actionPerformed(ActionEvent e)
1893   {
1894     if (viewport.getSelectionGroup() == null)
1895     {
1896       return;
1897     }
1898     // TODO: preserve the ordering of displayed alignment annotation in any
1899     // internal paste (particularly sequence associated annotation)
1900     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1901     String[] omitHidden = null;
1902
1903     if (viewport.hasHiddenColumns())
1904     {
1905       omitHidden = viewport.getViewAsString(true);
1906     }
1907
1908     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1909             seqs, omitHidden, null);
1910
1911     StringSelection ss = new StringSelection(output);
1912
1913     try
1914     {
1915       jalview.gui.Desktop.internalCopy = true;
1916       // Its really worth setting the clipboard contents
1917       // to empty before setting the large StringSelection!!
1918       Toolkit.getDefaultToolkit().getSystemClipboard()
1919               .setContents(new StringSelection(""), null);
1920
1921       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1922               Desktop.instance);
1923     } catch (OutOfMemoryError er)
1924     {
1925       new OOMWarning("copying region", er);
1926       return;
1927     }
1928
1929     HiddenColumns hiddenColumns = null;
1930     if (viewport.hasHiddenColumns())
1931     {
1932       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1933       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1934
1935       // create new HiddenColumns object with copy of hidden regions
1936       // between startRes and endRes, offset by startRes
1937       hiddenColumns = new HiddenColumns(
1938               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1939               hiddenCutoff, hiddenOffset);
1940     }
1941
1942     Desktop.jalviewClipboard = new Object[] { seqs,
1943         viewport.getAlignment().getDataset(), hiddenColumns };
1944     statusBar.setText(MessageManager.formatMessage(
1945             "label.copied_sequences_to_clipboard", new Object[]
1946             { Integer.valueOf(seqs.length).toString() }));
1947   }
1948
1949   /**
1950    * DOCUMENT ME!
1951    *
1952    * @param e
1953    *          DOCUMENT ME!
1954    */
1955   @Override
1956   protected void pasteNew_actionPerformed(ActionEvent e)
1957   {
1958     paste(true);
1959   }
1960
1961   /**
1962    * DOCUMENT ME!
1963    *
1964    * @param e
1965    *          DOCUMENT ME!
1966    */
1967   @Override
1968   protected void pasteThis_actionPerformed(ActionEvent e)
1969   {
1970     paste(false);
1971   }
1972
1973   /**
1974    * Paste contents of Jalview clipboard
1975    *
1976    * @param newAlignment
1977    *          true to paste to a new alignment, otherwise add to this.
1978    */
1979   void paste(boolean newAlignment)
1980   {
1981     boolean externalPaste = true;
1982     try
1983     {
1984       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1985       Transferable contents = c.getContents(this);
1986
1987       if (contents == null)
1988       {
1989         return;
1990       }
1991
1992       String str;
1993       FileFormatI format;
1994       try
1995       {
1996         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1997         if (str.length() < 1)
1998         {
1999           return;
2000         }
2001
2002         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2003
2004       } catch (OutOfMemoryError er)
2005       {
2006         new OOMWarning("Out of memory pasting sequences!!", er);
2007         return;
2008       }
2009
2010       SequenceI[] sequences;
2011       boolean annotationAdded = false;
2012       AlignmentI alignment = null;
2013
2014       if (Desktop.jalviewClipboard != null)
2015       {
2016         // The clipboard was filled from within Jalview, we must use the
2017         // sequences
2018         // And dataset from the copied alignment
2019         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2020         // be doubly sure that we create *new* sequence objects.
2021         sequences = new SequenceI[newseq.length];
2022         for (int i = 0; i < newseq.length; i++)
2023         {
2024           sequences[i] = new Sequence(newseq[i]);
2025         }
2026         alignment = new Alignment(sequences);
2027         externalPaste = false;
2028       }
2029       else
2030       {
2031         // parse the clipboard as an alignment.
2032         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2033                 format);
2034         sequences = alignment.getSequencesArray();
2035       }
2036
2037       int alwidth = 0;
2038       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2039       int fgroup = -1;
2040
2041       if (newAlignment)
2042       {
2043
2044         if (Desktop.jalviewClipboard != null)
2045         {
2046           // dataset is inherited
2047           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2048         }
2049         else
2050         {
2051           // new dataset is constructed
2052           alignment.setDataset(null);
2053         }
2054         alwidth = alignment.getWidth() + 1;
2055       }
2056       else
2057       {
2058         AlignmentI pastedal = alignment; // preserve pasted alignment object
2059         // Add pasted sequences and dataset into existing alignment.
2060         alignment = viewport.getAlignment();
2061         alwidth = alignment.getWidth() + 1;
2062         // decide if we need to import sequences from an existing dataset
2063         boolean importDs = Desktop.jalviewClipboard != null
2064                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2065         // importDs==true instructs us to copy over new dataset sequences from
2066         // an existing alignment
2067         Vector newDs = (importDs) ? new Vector() : null; // used to create
2068         // minimum dataset set
2069
2070         for (int i = 0; i < sequences.length; i++)
2071         {
2072           if (importDs)
2073           {
2074             newDs.addElement(null);
2075           }
2076           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2077           // paste
2078           if (importDs && ds != null)
2079           {
2080             if (!newDs.contains(ds))
2081             {
2082               newDs.setElementAt(ds, i);
2083               ds = new Sequence(ds);
2084               // update with new dataset sequence
2085               sequences[i].setDatasetSequence(ds);
2086             }
2087             else
2088             {
2089               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2090             }
2091           }
2092           else
2093           {
2094             // copy and derive new dataset sequence
2095             sequences[i] = sequences[i].deriveSequence();
2096             alignment.getDataset()
2097                     .addSequence(sequences[i].getDatasetSequence());
2098             // TODO: avoid creation of duplicate dataset sequences with a
2099             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2100           }
2101           alignment.addSequence(sequences[i]); // merges dataset
2102         }
2103         if (newDs != null)
2104         {
2105           newDs.clear(); // tidy up
2106         }
2107         if (alignment.getAlignmentAnnotation() != null)
2108         {
2109           for (AlignmentAnnotation alan : alignment
2110                   .getAlignmentAnnotation())
2111           {
2112             if (alan.graphGroup > fgroup)
2113             {
2114               fgroup = alan.graphGroup;
2115             }
2116           }
2117         }
2118         if (pastedal.getAlignmentAnnotation() != null)
2119         {
2120           // Add any annotation attached to alignment.
2121           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2122           for (int i = 0; i < alann.length; i++)
2123           {
2124             annotationAdded = true;
2125             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2126             {
2127               AlignmentAnnotation newann = new AlignmentAnnotation(
2128                       alann[i]);
2129               if (newann.graphGroup > -1)
2130               {
2131                 if (newGraphGroups.size() <= newann.graphGroup
2132                         || newGraphGroups.get(newann.graphGroup) == null)
2133                 {
2134                   for (int q = newGraphGroups
2135                           .size(); q <= newann.graphGroup; q++)
2136                   {
2137                     newGraphGroups.add(q, null);
2138                   }
2139                   newGraphGroups.set(newann.graphGroup,
2140                           new Integer(++fgroup));
2141                 }
2142                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2143                         .intValue();
2144               }
2145
2146               newann.padAnnotation(alwidth);
2147               alignment.addAnnotation(newann);
2148             }
2149           }
2150         }
2151       }
2152       if (!newAlignment)
2153       {
2154         // /////
2155         // ADD HISTORY ITEM
2156         //
2157         addHistoryItem(new EditCommand(
2158                 MessageManager.getString("label.add_sequences"),
2159                 Action.PASTE, sequences, 0, alignment.getWidth(),
2160                 alignment));
2161       }
2162       // Add any annotations attached to sequences
2163       for (int i = 0; i < sequences.length; i++)
2164       {
2165         if (sequences[i].getAnnotation() != null)
2166         {
2167           AlignmentAnnotation newann;
2168           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2169           {
2170             annotationAdded = true;
2171             newann = sequences[i].getAnnotation()[a];
2172             newann.adjustForAlignment();
2173             newann.padAnnotation(alwidth);
2174             if (newann.graphGroup > -1)
2175             {
2176               if (newann.graphGroup > -1)
2177               {
2178                 if (newGraphGroups.size() <= newann.graphGroup
2179                         || newGraphGroups.get(newann.graphGroup) == null)
2180                 {
2181                   for (int q = newGraphGroups
2182                           .size(); q <= newann.graphGroup; q++)
2183                   {
2184                     newGraphGroups.add(q, null);
2185                   }
2186                   newGraphGroups.set(newann.graphGroup,
2187                           new Integer(++fgroup));
2188                 }
2189                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2190                         .intValue();
2191               }
2192             }
2193             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2194             // was
2195             // duplicated
2196             // earlier
2197             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2198                     a);
2199           }
2200         }
2201       }
2202       if (!newAlignment)
2203       {
2204
2205         // propagate alignment changed.
2206         viewport.getRanges().setEndSeq(alignment.getHeight());
2207         if (annotationAdded)
2208         {
2209           // Duplicate sequence annotation in all views.
2210           AlignmentI[] alview = this.getViewAlignments();
2211           for (int i = 0; i < sequences.length; i++)
2212           {
2213             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2214             if (sann == null)
2215             {
2216               continue;
2217             }
2218             for (int avnum = 0; avnum < alview.length; avnum++)
2219             {
2220               if (alview[avnum] != alignment)
2221               {
2222                 // duplicate in a view other than the one with input focus
2223                 int avwidth = alview[avnum].getWidth() + 1;
2224                 // this relies on sann being preserved after we
2225                 // modify the sequence's annotation array for each duplication
2226                 for (int a = 0; a < sann.length; a++)
2227                 {
2228                   AlignmentAnnotation newann = new AlignmentAnnotation(
2229                           sann[a]);
2230                   sequences[i].addAlignmentAnnotation(newann);
2231                   newann.padAnnotation(avwidth);
2232                   alview[avnum].addAnnotation(newann); // annotation was
2233                   // duplicated earlier
2234                   // TODO JAL-1145 graphGroups are not updated for sequence
2235                   // annotation added to several views. This may cause
2236                   // strangeness
2237                   alview[avnum].setAnnotationIndex(newann, a);
2238                 }
2239               }
2240             }
2241           }
2242           buildSortByAnnotationScoresMenu();
2243         }
2244         viewport.firePropertyChange("alignment", null,
2245                 alignment.getSequences());
2246         if (alignPanels != null)
2247         {
2248           for (AlignmentPanel ap : alignPanels)
2249           {
2250             ap.validateAnnotationDimensions(false);
2251           }
2252         }
2253         else
2254         {
2255           alignPanel.validateAnnotationDimensions(false);
2256         }
2257
2258       }
2259       else
2260       {
2261         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2262                 DEFAULT_HEIGHT);
2263         String newtitle = new String("Copied sequences");
2264
2265         if (Desktop.jalviewClipboard != null
2266                 && Desktop.jalviewClipboard[2] != null)
2267         {
2268           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2269           af.viewport.setHiddenColumns(hc);
2270         }
2271
2272         // >>>This is a fix for the moment, until a better solution is
2273         // found!!<<<
2274         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2275                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2276                         .getFeatureRenderer());
2277
2278         // TODO: maintain provenance of an alignment, rather than just make the
2279         // title a concatenation of operations.
2280         if (!externalPaste)
2281         {
2282           if (title.startsWith("Copied sequences"))
2283           {
2284             newtitle = title;
2285           }
2286           else
2287           {
2288             newtitle = newtitle.concat("- from " + title);
2289           }
2290         }
2291         else
2292         {
2293           newtitle = new String("Pasted sequences");
2294         }
2295
2296         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2297                 DEFAULT_HEIGHT);
2298
2299       }
2300
2301     } catch (Exception ex)
2302     {
2303       ex.printStackTrace();
2304       System.out.println("Exception whilst pasting: " + ex);
2305       // could be anything being pasted in here
2306     }
2307
2308   }
2309
2310   @Override
2311   protected void expand_newalign(ActionEvent e)
2312   {
2313     try
2314     {
2315       AlignmentI alignment = AlignmentUtils
2316               .expandContext(getViewport().getAlignment(), -1);
2317       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2318               DEFAULT_HEIGHT);
2319       String newtitle = new String("Flanking alignment");
2320
2321       if (Desktop.jalviewClipboard != null
2322               && Desktop.jalviewClipboard[2] != null)
2323       {
2324         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2325         af.viewport.setHiddenColumns(hc);
2326       }
2327
2328       // >>>This is a fix for the moment, until a better solution is
2329       // found!!<<<
2330       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2331               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2332                       .getFeatureRenderer());
2333
2334       // TODO: maintain provenance of an alignment, rather than just make the
2335       // title a concatenation of operations.
2336       {
2337         if (title.startsWith("Copied sequences"))
2338         {
2339           newtitle = title;
2340         }
2341         else
2342         {
2343           newtitle = newtitle.concat("- from " + title);
2344         }
2345       }
2346
2347       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2348
2349     } catch (Exception ex)
2350     {
2351       ex.printStackTrace();
2352       System.out.println("Exception whilst pasting: " + ex);
2353       // could be anything being pasted in here
2354     } catch (OutOfMemoryError oom)
2355     {
2356       new OOMWarning("Viewing flanking region of alignment", oom);
2357     }
2358   }
2359
2360   /**
2361    * DOCUMENT ME!
2362    *
2363    * @param e
2364    *          DOCUMENT ME!
2365    */
2366   @Override
2367   protected void cut_actionPerformed(ActionEvent e)
2368   {
2369     copy_actionPerformed(null);
2370     delete_actionPerformed(null);
2371   }
2372
2373   /**
2374    * DOCUMENT ME!
2375    *
2376    * @param e
2377    *          DOCUMENT ME!
2378    */
2379   @Override
2380   protected void delete_actionPerformed(ActionEvent evt)
2381   {
2382
2383     SequenceGroup sg = viewport.getSelectionGroup();
2384     if (sg == null)
2385     {
2386       return;
2387     }
2388
2389     /*
2390      * If the cut affects all sequences, warn, remove highlighted columns
2391      */
2392     if (sg.getSize() == viewport.getAlignment().getHeight())
2393     {
2394       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2395               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2396       if (isEntireAlignWidth)
2397       {
2398         int confirm = JvOptionPane.showConfirmDialog(this,
2399                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2400                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2401                 JvOptionPane.OK_CANCEL_OPTION);
2402
2403         if (confirm == JvOptionPane.CANCEL_OPTION
2404                 || confirm == JvOptionPane.CLOSED_OPTION)
2405         {
2406           return;
2407         }
2408       }
2409       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2410               sg.getEndRes() + 1);
2411     }
2412     SequenceI[] cut = sg.getSequences()
2413             .toArray(new SequenceI[sg.getSize()]);
2414
2415     addHistoryItem(new EditCommand(
2416             MessageManager.getString("label.cut_sequences"), Action.CUT,
2417             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2418             viewport.getAlignment()));
2419
2420     viewport.setSelectionGroup(null);
2421     viewport.sendSelection();
2422     viewport.getAlignment().deleteGroup(sg);
2423
2424     viewport.firePropertyChange("alignment", null,
2425             viewport.getAlignment().getSequences());
2426     if (viewport.getAlignment().getHeight() < 1)
2427     {
2428       try
2429       {
2430         this.setClosed(true);
2431       } catch (Exception ex)
2432       {
2433       }
2434     }
2435   }
2436
2437   /**
2438    * DOCUMENT ME!
2439    *
2440    * @param e
2441    *          DOCUMENT ME!
2442    */
2443   @Override
2444   protected void deleteGroups_actionPerformed(ActionEvent e)
2445   {
2446     if (avc.deleteGroups())
2447     {
2448       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2449       alignPanel.updateAnnotation();
2450       alignPanel.paintAlignment(true, true);
2451     }
2452   }
2453
2454   /**
2455    * DOCUMENT ME!
2456    *
2457    * @param e
2458    *          DOCUMENT ME!
2459    */
2460   @Override
2461   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2462   {
2463     SequenceGroup sg = new SequenceGroup();
2464
2465     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2466     {
2467       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2468     }
2469
2470     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2471     viewport.setSelectionGroup(sg);
2472     viewport.sendSelection();
2473     // JAL-2034 - should delegate to
2474     // alignPanel to decide if overview needs
2475     // updating.
2476     alignPanel.paintAlignment(false, false);
2477     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2478   }
2479
2480   /**
2481    * DOCUMENT ME!
2482    *
2483    * @param e
2484    *          DOCUMENT ME!
2485    */
2486   @Override
2487   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2488   {
2489     if (viewport.cursorMode)
2490     {
2491       alignPanel.getSeqPanel().keyboardNo1 = null;
2492       alignPanel.getSeqPanel().keyboardNo2 = null;
2493     }
2494     viewport.setSelectionGroup(null);
2495     viewport.getColumnSelection().clear();
2496     viewport.setSelectionGroup(null);
2497     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2498     // JAL-2034 - should delegate to
2499     // alignPanel to decide if overview needs
2500     // updating.
2501     alignPanel.paintAlignment(false, false);
2502     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2503     viewport.sendSelection();
2504   }
2505
2506   /**
2507    * DOCUMENT ME!
2508    *
2509    * @param e
2510    *          DOCUMENT ME!
2511    */
2512   @Override
2513   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2514   {
2515     SequenceGroup sg = viewport.getSelectionGroup();
2516
2517     if (sg == null)
2518     {
2519       selectAllSequenceMenuItem_actionPerformed(null);
2520
2521       return;
2522     }
2523
2524     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2525     {
2526       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2527     }
2528     // JAL-2034 - should delegate to
2529     // alignPanel to decide if overview needs
2530     // updating.
2531
2532     alignPanel.paintAlignment(true, false);
2533     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2534     viewport.sendSelection();
2535   }
2536
2537   @Override
2538   public void invertColSel_actionPerformed(ActionEvent e)
2539   {
2540     viewport.invertColumnSelection();
2541     alignPanel.paintAlignment(true, false);
2542     viewport.sendSelection();
2543   }
2544
2545   /**
2546    * DOCUMENT ME!
2547    *
2548    * @param e
2549    *          DOCUMENT ME!
2550    */
2551   @Override
2552   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2553   {
2554     trimAlignment(true);
2555   }
2556
2557   /**
2558    * DOCUMENT ME!
2559    *
2560    * @param e
2561    *          DOCUMENT ME!
2562    */
2563   @Override
2564   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2565   {
2566     trimAlignment(false);
2567   }
2568
2569   void trimAlignment(boolean trimLeft)
2570   {
2571     ColumnSelection colSel = viewport.getColumnSelection();
2572     int column;
2573
2574     if (!colSel.isEmpty())
2575     {
2576       if (trimLeft)
2577       {
2578         column = colSel.getMin();
2579       }
2580       else
2581       {
2582         column = colSel.getMax();
2583       }
2584
2585       SequenceI[] seqs;
2586       if (viewport.getSelectionGroup() != null)
2587       {
2588         seqs = viewport.getSelectionGroup()
2589                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2590       }
2591       else
2592       {
2593         seqs = viewport.getAlignment().getSequencesArray();
2594       }
2595
2596       TrimRegionCommand trimRegion;
2597       if (trimLeft)
2598       {
2599         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2600                 column, viewport.getAlignment());
2601         viewport.getRanges().setStartRes(0);
2602       }
2603       else
2604       {
2605         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2606                 column, viewport.getAlignment());
2607       }
2608
2609       statusBar.setText(MessageManager
2610               .formatMessage("label.removed_columns", new String[]
2611               { Integer.valueOf(trimRegion.getSize()).toString() }));
2612
2613       addHistoryItem(trimRegion);
2614
2615       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2616       {
2617         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2618                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2619         {
2620           viewport.getAlignment().deleteGroup(sg);
2621         }
2622       }
2623
2624       viewport.firePropertyChange("alignment", null,
2625               viewport.getAlignment().getSequences());
2626     }
2627   }
2628
2629   /**
2630    * DOCUMENT ME!
2631    *
2632    * @param e
2633    *          DOCUMENT ME!
2634    */
2635   @Override
2636   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2637   {
2638     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2639
2640     SequenceI[] seqs;
2641     if (viewport.getSelectionGroup() != null)
2642     {
2643       seqs = viewport.getSelectionGroup()
2644               .getSequencesAsArray(viewport.getHiddenRepSequences());
2645       start = viewport.getSelectionGroup().getStartRes();
2646       end = viewport.getSelectionGroup().getEndRes();
2647     }
2648     else
2649     {
2650       seqs = viewport.getAlignment().getSequencesArray();
2651     }
2652
2653     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2654             "Remove Gapped Columns", seqs, start, end,
2655             viewport.getAlignment());
2656
2657     addHistoryItem(removeGapCols);
2658
2659     statusBar.setText(MessageManager
2660             .formatMessage("label.removed_empty_columns", new Object[]
2661             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2662
2663     // This is to maintain viewport position on first residue
2664     // of first sequence
2665     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2666     ViewportRanges ranges = viewport.getRanges();
2667     int startRes = seq.findPosition(ranges.getStartRes());
2668     // ShiftList shifts;
2669     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2670     // edit.alColumnChanges=shifts.getInverse();
2671     // if (viewport.hasHiddenColumns)
2672     // viewport.getColumnSelection().compensateForEdits(shifts);
2673     ranges.setStartRes(seq.findIndex(startRes) - 1);
2674     viewport.firePropertyChange("alignment", null,
2675             viewport.getAlignment().getSequences());
2676
2677   }
2678
2679   /**
2680    * DOCUMENT ME!
2681    *
2682    * @param e
2683    *          DOCUMENT ME!
2684    */
2685   @Override
2686   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2687   {
2688     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2689
2690     SequenceI[] seqs;
2691     if (viewport.getSelectionGroup() != null)
2692     {
2693       seqs = viewport.getSelectionGroup()
2694               .getSequencesAsArray(viewport.getHiddenRepSequences());
2695       start = viewport.getSelectionGroup().getStartRes();
2696       end = viewport.getSelectionGroup().getEndRes();
2697     }
2698     else
2699     {
2700       seqs = viewport.getAlignment().getSequencesArray();
2701     }
2702
2703     // This is to maintain viewport position on first residue
2704     // of first sequence
2705     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2706     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2707
2708     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2709             viewport.getAlignment()));
2710
2711     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2712
2713     viewport.firePropertyChange("alignment", null,
2714             viewport.getAlignment().getSequences());
2715
2716   }
2717
2718   /**
2719    * DOCUMENT ME!
2720    *
2721    * @param e
2722    *          DOCUMENT ME!
2723    */
2724   @Override
2725   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2726   {
2727     viewport.setPadGaps(padGapsMenuitem.isSelected());
2728     viewport.firePropertyChange("alignment", null,
2729             viewport.getAlignment().getSequences());
2730   }
2731
2732   /**
2733    * DOCUMENT ME!
2734    *
2735    * @param e
2736    *          DOCUMENT ME!
2737    */
2738   @Override
2739   public void findMenuItem_actionPerformed(ActionEvent e)
2740   {
2741     new Finder();
2742   }
2743
2744   /**
2745    * Create a new view of the current alignment.
2746    */
2747   @Override
2748   public void newView_actionPerformed(ActionEvent e)
2749   {
2750     newView(null, true);
2751   }
2752
2753   /**
2754    * Creates and shows a new view of the current alignment.
2755    *
2756    * @param viewTitle
2757    *          title of newly created view; if null, one will be generated
2758    * @param copyAnnotation
2759    *          if true then duplicate all annnotation, groups and settings
2760    * @return new alignment panel, already displayed.
2761    */
2762   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2763   {
2764     /*
2765      * Create a new AlignmentPanel (with its own, new Viewport)
2766      */
2767     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2768     if (!copyAnnotation)
2769     {
2770       /*
2771        * remove all groups and annotation except for the automatic stuff
2772        */
2773       newap.av.getAlignment().deleteAllGroups();
2774       newap.av.getAlignment().deleteAllAnnotations(false);
2775     }
2776
2777     newap.av.setGatherViewsHere(false);
2778
2779     if (viewport.viewName == null)
2780     {
2781       viewport.viewName = MessageManager
2782               .getString("label.view_name_original");
2783     }
2784
2785     /*
2786      * Views share the same edits undo and redo stacks
2787      */
2788     newap.av.setHistoryList(viewport.getHistoryList());
2789     newap.av.setRedoList(viewport.getRedoList());
2790
2791     /*
2792      * Views share the same mappings; need to deregister any new mappings
2793      * created by copyAlignPanel, and register the new reference to the shared
2794      * mappings
2795      */
2796     newap.av.replaceMappings(viewport.getAlignment());
2797
2798     /*
2799      * start up cDNA consensus (if applicable) now mappings are in place
2800      */
2801     if (newap.av.initComplementConsensus())
2802     {
2803       newap.refresh(true); // adjust layout of annotations
2804     }
2805
2806     newap.av.viewName = getNewViewName(viewTitle);
2807
2808     addAlignmentPanel(newap, true);
2809     newap.alignmentChanged();
2810
2811     if (alignPanels.size() == 2)
2812     {
2813       viewport.setGatherViewsHere(true);
2814     }
2815     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2816     return newap;
2817   }
2818
2819   /**
2820    * Make a new name for the view, ensuring it is unique within the current
2821    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2822    * these now use viewId. Unique view names are still desirable for usability.)
2823    *
2824    * @param viewTitle
2825    * @return
2826    */
2827   protected String getNewViewName(String viewTitle)
2828   {
2829     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2830     boolean addFirstIndex = false;
2831     if (viewTitle == null || viewTitle.trim().length() == 0)
2832     {
2833       viewTitle = MessageManager.getString("action.view");
2834       addFirstIndex = true;
2835     }
2836     else
2837     {
2838       index = 1;// we count from 1 if given a specific name
2839     }
2840     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2841
2842     List<Component> comps = PaintRefresher.components
2843             .get(viewport.getSequenceSetId());
2844
2845     List<String> existingNames = getExistingViewNames(comps);
2846
2847     while (existingNames.contains(newViewName))
2848     {
2849       newViewName = viewTitle + " " + (++index);
2850     }
2851     return newViewName;
2852   }
2853
2854   /**
2855    * Returns a list of distinct view names found in the given list of
2856    * components. View names are held on the viewport of an AlignmentPanel.
2857    *
2858    * @param comps
2859    * @return
2860    */
2861   protected List<String> getExistingViewNames(List<Component> comps)
2862   {
2863     List<String> existingNames = new ArrayList<>();
2864     for (Component comp : comps)
2865     {
2866       if (comp instanceof AlignmentPanel)
2867       {
2868         AlignmentPanel ap = (AlignmentPanel) comp;
2869         if (!existingNames.contains(ap.av.viewName))
2870         {
2871           existingNames.add(ap.av.viewName);
2872         }
2873       }
2874     }
2875     return existingNames;
2876   }
2877
2878   /**
2879    * Explode tabbed views into separate windows.
2880    */
2881   @Override
2882   public void expandViews_actionPerformed(ActionEvent e)
2883   {
2884     Desktop.explodeViews(this);
2885   }
2886
2887   /**
2888    * Gather views in separate windows back into a tabbed presentation.
2889    */
2890   @Override
2891   public void gatherViews_actionPerformed(ActionEvent e)
2892   {
2893     Desktop.instance.gatherViews(this);
2894   }
2895
2896   /**
2897    * DOCUMENT ME!
2898    *
2899    * @param e
2900    *          DOCUMENT ME!
2901    */
2902   @Override
2903   public void font_actionPerformed(ActionEvent e)
2904   {
2905     new FontChooser(alignPanel);
2906   }
2907
2908   /**
2909    * DOCUMENT ME!
2910    *
2911    * @param e
2912    *          DOCUMENT ME!
2913    */
2914   @Override
2915   protected void seqLimit_actionPerformed(ActionEvent e)
2916   {
2917     viewport.setShowJVSuffix(seqLimits.isSelected());
2918
2919     alignPanel.getIdPanel().getIdCanvas()
2920             .setPreferredSize(alignPanel.calculateIdWidth());
2921     alignPanel.paintAlignment(true, false);
2922   }
2923
2924   @Override
2925   public void idRightAlign_actionPerformed(ActionEvent e)
2926   {
2927     viewport.setRightAlignIds(idRightAlign.isSelected());
2928     alignPanel.paintAlignment(false, false);
2929   }
2930
2931   @Override
2932   public void centreColumnLabels_actionPerformed(ActionEvent e)
2933   {
2934     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2935     alignPanel.paintAlignment(false, false);
2936   }
2937
2938   /*
2939    * (non-Javadoc)
2940    *
2941    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2942    */
2943   @Override
2944   protected void followHighlight_actionPerformed()
2945   {
2946     /*
2947      * Set the 'follow' flag on the Viewport (and scroll to position if now
2948      * true).
2949      */
2950     final boolean state = this.followHighlightMenuItem.getState();
2951     viewport.setFollowHighlight(state);
2952     if (state)
2953     {
2954       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2955     }
2956   }
2957
2958   /**
2959    * DOCUMENT ME!
2960    *
2961    * @param e
2962    *          DOCUMENT ME!
2963    */
2964   @Override
2965   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2966   {
2967     viewport.setColourText(colourTextMenuItem.isSelected());
2968     alignPanel.paintAlignment(false, false);
2969   }
2970
2971   /**
2972    * DOCUMENT ME!
2973    *
2974    * @param e
2975    *          DOCUMENT ME!
2976    */
2977   @Override
2978   public void wrapMenuItem_actionPerformed(ActionEvent e)
2979   {
2980     scaleAbove.setVisible(wrapMenuItem.isSelected());
2981     scaleLeft.setVisible(wrapMenuItem.isSelected());
2982     scaleRight.setVisible(wrapMenuItem.isSelected());
2983     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2984     alignPanel.updateLayout();
2985   }
2986
2987   @Override
2988   public void showAllSeqs_actionPerformed(ActionEvent e)
2989   {
2990     viewport.showAllHiddenSeqs();
2991   }
2992
2993   @Override
2994   public void showAllColumns_actionPerformed(ActionEvent e)
2995   {
2996     viewport.showAllHiddenColumns();
2997     alignPanel.paintAlignment(true, true);
2998     viewport.sendSelection();
2999   }
3000
3001   @Override
3002   public void hideSelSequences_actionPerformed(ActionEvent e)
3003   {
3004     viewport.hideAllSelectedSeqs();
3005   }
3006
3007   /**
3008    * called by key handler and the hide all/show all menu items
3009    *
3010    * @param toggleSeqs
3011    * @param toggleCols
3012    */
3013   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3014   {
3015
3016     boolean hide = false;
3017     SequenceGroup sg = viewport.getSelectionGroup();
3018     if (!toggleSeqs && !toggleCols)
3019     {
3020       // Hide everything by the current selection - this is a hack - we do the
3021       // invert and then hide
3022       // first check that there will be visible columns after the invert.
3023       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3024               && sg.getStartRes() <= sg.getEndRes()))
3025       {
3026         // now invert the sequence set, if required - empty selection implies
3027         // that no hiding is required.
3028         if (sg != null)
3029         {
3030           invertSequenceMenuItem_actionPerformed(null);
3031           sg = viewport.getSelectionGroup();
3032           toggleSeqs = true;
3033
3034         }
3035         viewport.expandColSelection(sg, true);
3036         // finally invert the column selection and get the new sequence
3037         // selection.
3038         invertColSel_actionPerformed(null);
3039         toggleCols = true;
3040       }
3041     }
3042
3043     if (toggleSeqs)
3044     {
3045       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3046       {
3047         hideSelSequences_actionPerformed(null);
3048         hide = true;
3049       }
3050       else if (!(toggleCols && viewport.hasSelectedColumns()))
3051       {
3052         showAllSeqs_actionPerformed(null);
3053       }
3054     }
3055
3056     if (toggleCols)
3057     {
3058       if (viewport.hasSelectedColumns())
3059       {
3060         hideSelColumns_actionPerformed(null);
3061         if (!toggleSeqs)
3062         {
3063           viewport.setSelectionGroup(sg);
3064         }
3065       }
3066       else if (!hide)
3067       {
3068         showAllColumns_actionPerformed(null);
3069       }
3070     }
3071   }
3072
3073   /*
3074    * (non-Javadoc)
3075    *
3076    * @see
3077    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3078    * event.ActionEvent)
3079    */
3080   @Override
3081   public void hideAllButSelection_actionPerformed(ActionEvent e)
3082   {
3083     toggleHiddenRegions(false, false);
3084     viewport.sendSelection();
3085   }
3086
3087   /*
3088    * (non-Javadoc)
3089    *
3090    * @see
3091    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3092    * .ActionEvent)
3093    */
3094   @Override
3095   public void hideAllSelection_actionPerformed(ActionEvent e)
3096   {
3097     SequenceGroup sg = viewport.getSelectionGroup();
3098     viewport.expandColSelection(sg, false);
3099     viewport.hideAllSelectedSeqs();
3100     viewport.hideSelectedColumns();
3101     alignPanel.paintAlignment(true, true);
3102     viewport.sendSelection();
3103   }
3104
3105   /*
3106    * (non-Javadoc)
3107    *
3108    * @see
3109    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3110    * ActionEvent)
3111    */
3112   @Override
3113   public void showAllhidden_actionPerformed(ActionEvent e)
3114   {
3115     viewport.showAllHiddenColumns();
3116     viewport.showAllHiddenSeqs();
3117     alignPanel.paintAlignment(true, true);
3118     viewport.sendSelection();
3119   }
3120
3121   @Override
3122   public void hideSelColumns_actionPerformed(ActionEvent e)
3123   {
3124     viewport.hideSelectedColumns();
3125     alignPanel.paintAlignment(true, true);
3126     viewport.sendSelection();
3127   }
3128
3129   @Override
3130   public void hiddenMarkers_actionPerformed(ActionEvent e)
3131   {
3132     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3133     repaint();
3134   }
3135
3136   /**
3137    * DOCUMENT ME!
3138    *
3139    * @param e
3140    *          DOCUMENT ME!
3141    */
3142   @Override
3143   protected void scaleAbove_actionPerformed(ActionEvent e)
3144   {
3145     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3146     // TODO: do we actually need to update overview for scale above change ?
3147     alignPanel.paintAlignment(true, false);
3148   }
3149
3150   /**
3151    * DOCUMENT ME!
3152    *
3153    * @param e
3154    *          DOCUMENT ME!
3155    */
3156   @Override
3157   protected void scaleLeft_actionPerformed(ActionEvent e)
3158   {
3159     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3160     alignPanel.paintAlignment(true, false);
3161   }
3162
3163   /**
3164    * DOCUMENT ME!
3165    *
3166    * @param e
3167    *          DOCUMENT ME!
3168    */
3169   @Override
3170   protected void scaleRight_actionPerformed(ActionEvent e)
3171   {
3172     viewport.setScaleRightWrapped(scaleRight.isSelected());
3173     alignPanel.paintAlignment(true, false);
3174   }
3175
3176   /**
3177    * DOCUMENT ME!
3178    *
3179    * @param e
3180    *          DOCUMENT ME!
3181    */
3182   @Override
3183   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3184   {
3185     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3186     alignPanel.paintAlignment(false, false);
3187   }
3188
3189   /**
3190    * DOCUMENT ME!
3191    *
3192    * @param e
3193    *          DOCUMENT ME!
3194    */
3195   @Override
3196   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3197   {
3198     viewport.setShowText(viewTextMenuItem.isSelected());
3199     alignPanel.paintAlignment(false, false);
3200   }
3201
3202   /**
3203    * DOCUMENT ME!
3204    *
3205    * @param e
3206    *          DOCUMENT ME!
3207    */
3208   @Override
3209   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3210   {
3211     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3212     alignPanel.paintAlignment(false, false);
3213   }
3214
3215   public FeatureSettings featureSettings;
3216
3217   @Override
3218   public FeatureSettingsControllerI getFeatureSettingsUI()
3219   {
3220     return featureSettings;
3221   }
3222
3223   @Override
3224   public void featureSettings_actionPerformed(ActionEvent e)
3225   {
3226     if (featureSettings != null)
3227     {
3228       featureSettings.close();
3229       featureSettings = null;
3230     }
3231     if (!showSeqFeatures.isSelected())
3232     {
3233       // make sure features are actually displayed
3234       showSeqFeatures.setSelected(true);
3235       showSeqFeatures_actionPerformed(null);
3236     }
3237     featureSettings = new FeatureSettings(this);
3238   }
3239
3240   /**
3241    * Set or clear 'Show Sequence Features'
3242    *
3243    * @param evt
3244    *          DOCUMENT ME!
3245    */
3246   @Override
3247   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3248   {
3249     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3250     alignPanel.paintAlignment(true, true);
3251   }
3252
3253   /**
3254    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3255    * the annotations panel as a whole.
3256    *
3257    * The options to show/hide all annotations should be enabled when the panel
3258    * is shown, and disabled when the panel is hidden.
3259    *
3260    * @param e
3261    */
3262   @Override
3263   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3264   {
3265     final boolean setVisible = annotationPanelMenuItem.isSelected();
3266     viewport.setShowAnnotation(setVisible);
3267     this.showAllSeqAnnotations.setEnabled(setVisible);
3268     this.hideAllSeqAnnotations.setEnabled(setVisible);
3269     this.showAllAlAnnotations.setEnabled(setVisible);
3270     this.hideAllAlAnnotations.setEnabled(setVisible);
3271     alignPanel.updateLayout();
3272   }
3273
3274   @Override
3275   public void alignmentProperties()
3276   {
3277     JComponent pane;
3278     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3279
3280             .formatAsHtml();
3281     String content = MessageManager.formatMessage("label.html_content",
3282             new Object[]
3283             { contents.toString() });
3284     contents = null;
3285
3286     if (/** @j2sNative true || */
3287     false)
3288     {
3289       JLabel textLabel = new JLabel();
3290       textLabel.setText(content);
3291       textLabel.setBackground(Color.WHITE);
3292
3293       pane = new JPanel(new BorderLayout());
3294       ((JPanel) pane).setOpaque(true);
3295       ((JPanel) pane).add(textLabel, BorderLayout.CENTER);
3296     }
3297     else
3298     {
3299       JEditorPane editPane = new JEditorPane("text/html", "");
3300       editPane.setEditable(false);
3301       editPane.setText(content);
3302       pane = editPane;
3303     }
3304
3305     JInternalFrame frame = new JInternalFrame();
3306
3307     frame.getContentPane().add(new JScrollPane(pane));
3308
3309     Desktop.addInternalFrame(frame, MessageManager
3310             .formatMessage("label.alignment_properties", new Object[]
3311             { getTitle() }), 500, 400);
3312   }
3313
3314   /**
3315    * DOCUMENT ME!
3316    *
3317    * @param e
3318    *          DOCUMENT ME!
3319    */
3320   @Override
3321   public void overviewMenuItem_actionPerformed(ActionEvent e)
3322   {
3323     if (alignPanel.overviewPanel != null)
3324     {
3325       return;
3326     }
3327
3328     JInternalFrame frame = new JInternalFrame();
3329     final OverviewPanel overview = new OverviewPanel(alignPanel);
3330     frame.setContentPane(overview);
3331     Desktop.addInternalFrame(frame, MessageManager
3332             .formatMessage("label.overview_params", new Object[]
3333             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3334             true, true);
3335     frame.pack();
3336     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3337     frame.addInternalFrameListener(
3338             new javax.swing.event.InternalFrameAdapter()
3339             {
3340               @Override
3341               public void internalFrameClosed(
3342                       javax.swing.event.InternalFrameEvent evt)
3343               {
3344                 overview.dispose();
3345                 alignPanel.setOverviewPanel(null);
3346               };
3347             });
3348     if (getKeyListeners().length > 0)
3349     {
3350       frame.addKeyListener(getKeyListeners()[0]);
3351     }
3352
3353     alignPanel.setOverviewPanel(overview);
3354   }
3355
3356   @Override
3357   public void textColour_actionPerformed()
3358   {
3359     new TextColourChooser().chooseColour(alignPanel, null);
3360   }
3361
3362   /*
3363    * public void covariationColour_actionPerformed() {
3364    * changeColour(new
3365    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3366    * ()[0])); }
3367    */
3368   @Override
3369   public void annotationColour_actionPerformed()
3370   {
3371     new AnnotationColourChooser(viewport, alignPanel);
3372   }
3373
3374   @Override
3375   public void annotationColumn_actionPerformed(ActionEvent e)
3376   {
3377     new AnnotationColumnChooser(viewport, alignPanel);
3378   }
3379
3380   /**
3381    * Action on the user checking or unchecking the option to apply the selected
3382    * colour scheme to all groups. If unchecked, groups may have their own
3383    * independent colour schemes.
3384    *
3385    * @param selected
3386    */
3387   @Override
3388   public void applyToAllGroups_actionPerformed(boolean selected)
3389   {
3390     viewport.setColourAppliesToAllGroups(selected);
3391   }
3392
3393   /**
3394    * Action on user selecting a colour from the colour menu
3395    *
3396    * @param name
3397    *          the name (not the menu item label!) of the colour scheme
3398    */
3399   @Override
3400   public void changeColour_actionPerformed(String name)
3401   {
3402     /*
3403      * 'User Defined' opens a panel to configure or load a
3404      * user-defined colour scheme
3405      */
3406     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3407     {
3408       new UserDefinedColours(alignPanel);
3409       return;
3410     }
3411
3412     /*
3413      * otherwise set the chosen colour scheme (or null for 'None')
3414      */
3415     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3416             viewport.getAlignment(), viewport.getHiddenRepSequences());
3417     changeColour(cs);
3418   }
3419
3420   /**
3421    * Actions on setting or changing the alignment colour scheme
3422    *
3423    * @param cs
3424    */
3425   @Override
3426   public void changeColour(ColourSchemeI cs)
3427   {
3428     // TODO: pull up to controller method
3429     ColourMenuHelper.setColourSelected(colourMenu, cs);
3430
3431     viewport.setGlobalColourScheme(cs);
3432
3433     alignPanel.paintAlignment(true, true);
3434   }
3435
3436   /**
3437    * Show the PID threshold slider panel
3438    */
3439   @Override
3440   protected void modifyPID_actionPerformed()
3441   {
3442     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3443             alignPanel.getViewName());
3444     SliderPanel.showPIDSlider();
3445   }
3446
3447   /**
3448    * Show the Conservation slider panel
3449    */
3450   @Override
3451   protected void modifyConservation_actionPerformed()
3452   {
3453     SliderPanel.setConservationSlider(alignPanel,
3454             viewport.getResidueShading(), alignPanel.getViewName());
3455     SliderPanel.showConservationSlider();
3456   }
3457
3458   /**
3459    * Action on selecting or deselecting (Colour) By Conservation
3460    */
3461   @Override
3462   public void conservationMenuItem_actionPerformed(boolean selected)
3463   {
3464     modifyConservation.setEnabled(selected);
3465     viewport.setConservationSelected(selected);
3466     viewport.getResidueShading().setConservationApplied(selected);
3467
3468     changeColour(viewport.getGlobalColourScheme());
3469     if (selected)
3470     {
3471       modifyConservation_actionPerformed();
3472     }
3473     else
3474     {
3475       SliderPanel.hideConservationSlider();
3476     }
3477   }
3478
3479   /**
3480    * Action on selecting or deselecting (Colour) Above PID Threshold
3481    */
3482   @Override
3483   public void abovePIDThreshold_actionPerformed(boolean selected)
3484   {
3485     modifyPID.setEnabled(selected);
3486     viewport.setAbovePIDThreshold(selected);
3487     if (!selected)
3488     {
3489       viewport.getResidueShading().setThreshold(0,
3490               viewport.isIgnoreGapsConsensus());
3491     }
3492
3493     changeColour(viewport.getGlobalColourScheme());
3494     if (selected)
3495     {
3496       modifyPID_actionPerformed();
3497     }
3498     else
3499     {
3500       SliderPanel.hidePIDSlider();
3501     }
3502   }
3503
3504   /**
3505    * DOCUMENT ME!
3506    *
3507    * @param e
3508    *          DOCUMENT ME!
3509    */
3510   @Override
3511   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3512   {
3513     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3514     AlignmentSorter.sortByPID(viewport.getAlignment(),
3515             viewport.getAlignment().getSequenceAt(0));
3516     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3517             viewport.getAlignment()));
3518     alignPanel.paintAlignment(true, false);
3519   }
3520
3521   /**
3522    * DOCUMENT ME!
3523    *
3524    * @param e
3525    *          DOCUMENT ME!
3526    */
3527   @Override
3528   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3529   {
3530     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3531     AlignmentSorter.sortByID(viewport.getAlignment());
3532     addHistoryItem(
3533             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3534     alignPanel.paintAlignment(true, false);
3535   }
3536
3537   /**
3538    * DOCUMENT ME!
3539    *
3540    * @param e
3541    *          DOCUMENT ME!
3542    */
3543   @Override
3544   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3545   {
3546     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3547     AlignmentSorter.sortByLength(viewport.getAlignment());
3548     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3549             viewport.getAlignment()));
3550     alignPanel.paintAlignment(true, false);
3551   }
3552
3553   /**
3554    * DOCUMENT ME!
3555    *
3556    * @param e
3557    *          DOCUMENT ME!
3558    */
3559   @Override
3560   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3561   {
3562     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3563     AlignmentSorter.sortByGroup(viewport.getAlignment());
3564     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3565             viewport.getAlignment()));
3566
3567     alignPanel.paintAlignment(true, false);
3568   }
3569
3570   /**
3571    * DOCUMENT ME!
3572    *
3573    * @param e
3574    *          DOCUMENT ME!
3575    */
3576   @Override
3577   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3578   {
3579     new RedundancyPanel(alignPanel, this);
3580   }
3581
3582   /**
3583    * DOCUMENT ME!
3584    *
3585    * @param e
3586    *          DOCUMENT ME!
3587    */
3588   @Override
3589   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3590   {
3591     if ((viewport.getSelectionGroup() == null)
3592             || (viewport.getSelectionGroup().getSize() < 2))
3593     {
3594       JvOptionPane.showInternalMessageDialog(this,
3595               MessageManager.getString(
3596                       "label.you_must_select_least_two_sequences"),
3597               MessageManager.getString("label.invalid_selection"),
3598               JvOptionPane.WARNING_MESSAGE);
3599     }
3600     else
3601     {
3602       JInternalFrame frame = new JInternalFrame();
3603       frame.setContentPane(new PairwiseAlignPanel(viewport));
3604       Desktop.addInternalFrame(frame,
3605               MessageManager.getString("action.pairwise_alignment"), 600,
3606               500);
3607     }
3608   }
3609
3610   @Override
3611   public void autoCalculate_actionPerformed(ActionEvent e)
3612   {
3613     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3614     if (viewport.autoCalculateConsensus)
3615     {
3616       viewport.firePropertyChange("alignment", null,
3617               viewport.getAlignment().getSequences());
3618     }
3619   }
3620
3621   @Override
3622   public void sortByTreeOption_actionPerformed(ActionEvent e)
3623   {
3624     viewport.sortByTree = sortByTree.isSelected();
3625   }
3626
3627   @Override
3628   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3629   {
3630     viewport.followSelection = listenToViewSelections.isSelected();
3631   }
3632
3633   /**
3634    * Constructs a tree panel and adds it to the desktop
3635    *
3636    * @param type
3637    *          tree type (NJ or AV)
3638    * @param modelName
3639    *          name of score model used to compute the tree
3640    * @param options
3641    *          parameters for the distance or similarity calculation
3642    */
3643   void newTreePanel(String type, String modelName,
3644           SimilarityParamsI options)
3645   {
3646     String frameTitle = "";
3647     TreePanel tp;
3648
3649     boolean onSelection = false;
3650     if (viewport.getSelectionGroup() != null
3651             && viewport.getSelectionGroup().getSize() > 0)
3652     {
3653       SequenceGroup sg = viewport.getSelectionGroup();
3654
3655       /* Decide if the selection is a column region */
3656       for (SequenceI _s : sg.getSequences())
3657       {
3658         if (_s.getLength() < sg.getEndRes())
3659         {
3660           JvOptionPane.showMessageDialog(Desktop.desktop,
3661                   MessageManager.getString(
3662                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3663                   MessageManager.getString(
3664                           "label.sequences_selection_not_aligned"),
3665                   JvOptionPane.WARNING_MESSAGE);
3666
3667           return;
3668         }
3669       }
3670       onSelection = true;
3671     }
3672     else
3673     {
3674       if (viewport.getAlignment().getHeight() < 2)
3675       {
3676         return;
3677       }
3678     }
3679
3680     tp = new TreePanel(alignPanel, type, modelName, options);
3681     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3682
3683     frameTitle += " from ";
3684
3685     if (viewport.viewName != null)
3686     {
3687       frameTitle += viewport.viewName + " of ";
3688     }
3689
3690     frameTitle += this.title;
3691
3692     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3693   }
3694
3695   /**
3696    * DOCUMENT ME!
3697    *
3698    * @param title
3699    *          DOCUMENT ME!
3700    * @param order
3701    *          DOCUMENT ME!
3702    */
3703   public void addSortByOrderMenuItem(String title,
3704           final AlignmentOrder order)
3705   {
3706     final JMenuItem item = new JMenuItem(MessageManager
3707             .formatMessage("action.by_title_param", new Object[]
3708             { title }));
3709     sort.add(item);
3710     item.addActionListener(new java.awt.event.ActionListener()
3711     {
3712       @Override
3713       public void actionPerformed(ActionEvent e)
3714       {
3715         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3716
3717         // TODO: JBPNote - have to map order entries to curent SequenceI
3718         // pointers
3719         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3720
3721         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3722                 viewport.getAlignment()));
3723
3724         alignPanel.paintAlignment(true, false);
3725       }
3726     });
3727   }
3728
3729   /**
3730    * Add a new sort by annotation score menu item
3731    *
3732    * @param sort
3733    *          the menu to add the option to
3734    * @param scoreLabel
3735    *          the label used to retrieve scores for each sequence on the
3736    *          alignment
3737    */
3738   public void addSortByAnnotScoreMenuItem(JMenu sort,
3739           final String scoreLabel)
3740   {
3741     final JMenuItem item = new JMenuItem(scoreLabel);
3742     sort.add(item);
3743     item.addActionListener(new java.awt.event.ActionListener()
3744     {
3745       @Override
3746       public void actionPerformed(ActionEvent e)
3747       {
3748         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3749         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3750                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3751         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3752                 viewport.getAlignment()));
3753         alignPanel.paintAlignment(true, false);
3754       }
3755     });
3756   }
3757
3758   /**
3759    * last hash for alignment's annotation array - used to minimise cost of
3760    * rebuild.
3761    */
3762   protected int _annotationScoreVectorHash;
3763
3764   /**
3765    * search the alignment and rebuild the sort by annotation score submenu the
3766    * last alignment annotation vector hash is stored to minimize cost of
3767    * rebuilding in subsequence calls.
3768    *
3769    */
3770   @Override
3771   public void buildSortByAnnotationScoresMenu()
3772   {
3773     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3774     {
3775       return;
3776     }
3777
3778     if (viewport.getAlignment().getAlignmentAnnotation()
3779             .hashCode() != _annotationScoreVectorHash)
3780     {
3781       sortByAnnotScore.removeAll();
3782       // almost certainly a quicker way to do this - but we keep it simple
3783       Hashtable scoreSorts = new Hashtable();
3784       AlignmentAnnotation aann[];
3785       for (SequenceI sqa : viewport.getAlignment().getSequences())
3786       {
3787         aann = sqa.getAnnotation();
3788         for (int i = 0; aann != null && i < aann.length; i++)
3789         {
3790           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3791           {
3792             scoreSorts.put(aann[i].label, aann[i].label);
3793           }
3794         }
3795       }
3796       Enumeration labels = scoreSorts.keys();
3797       while (labels.hasMoreElements())
3798       {
3799         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3800                 (String) labels.nextElement());
3801       }
3802       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3803       scoreSorts.clear();
3804
3805       _annotationScoreVectorHash = viewport.getAlignment()
3806               .getAlignmentAnnotation().hashCode();
3807     }
3808   }
3809
3810   /**
3811    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3812    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3813    * call. Listeners are added to remove the menu item when the treePanel is
3814    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3815    * modified.
3816    */
3817   @Override
3818   public void buildTreeSortMenu()
3819   {
3820     sortByTreeMenu.removeAll();
3821
3822     List<Component> comps = PaintRefresher.components
3823             .get(viewport.getSequenceSetId());
3824     List<TreePanel> treePanels = new ArrayList<>();
3825     for (Component comp : comps)
3826     {
3827       if (comp instanceof TreePanel)
3828       {
3829         treePanels.add((TreePanel) comp);
3830       }
3831     }
3832
3833     if (treePanels.size() < 1)
3834     {
3835       sortByTreeMenu.setVisible(false);
3836       return;
3837     }
3838
3839     sortByTreeMenu.setVisible(true);
3840
3841     for (final TreePanel tp : treePanels)
3842     {
3843       final JMenuItem item = new JMenuItem(tp.getTitle());
3844       item.addActionListener(new java.awt.event.ActionListener()
3845       {
3846         @Override
3847         public void actionPerformed(ActionEvent e)
3848         {
3849           tp.sortByTree_actionPerformed();
3850           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3851
3852         }
3853       });
3854
3855       sortByTreeMenu.add(item);
3856     }
3857   }
3858
3859   public boolean sortBy(AlignmentOrder alorder, String undoname)
3860   {
3861     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3862     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3863     if (undoname != null)
3864     {
3865       addHistoryItem(new OrderCommand(undoname, oldOrder,
3866               viewport.getAlignment()));
3867     }
3868     alignPanel.paintAlignment(true, false);
3869     return true;
3870   }
3871
3872   /**
3873    * Work out whether the whole set of sequences or just the selected set will
3874    * be submitted for multiple alignment.
3875    *
3876    */
3877   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3878   {
3879     // Now, check we have enough sequences
3880     AlignmentView msa = null;
3881
3882     if ((viewport.getSelectionGroup() != null)
3883             && (viewport.getSelectionGroup().getSize() > 1))
3884     {
3885       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3886       // some common interface!
3887       /*
3888        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3889        * SequenceI[sz = seqs.getSize(false)];
3890        *
3891        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3892        * seqs.getSequenceAt(i); }
3893        */
3894       msa = viewport.getAlignmentView(true);
3895     }
3896     else if (viewport.getSelectionGroup() != null
3897             && viewport.getSelectionGroup().getSize() == 1)
3898     {
3899       int option = JvOptionPane.showConfirmDialog(this,
3900               MessageManager.getString("warn.oneseq_msainput_selection"),
3901               MessageManager.getString("label.invalid_selection"),
3902               JvOptionPane.OK_CANCEL_OPTION);
3903       if (option == JvOptionPane.OK_OPTION)
3904       {
3905         msa = viewport.getAlignmentView(false);
3906       }
3907     }
3908     else
3909     {
3910       msa = viewport.getAlignmentView(false);
3911     }
3912     return msa;
3913   }
3914
3915   /**
3916    * Decides what is submitted to a secondary structure prediction service: the
3917    * first sequence in the alignment, or in the current selection, or, if the
3918    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3919    * region or the whole alignment. (where the first sequence in the set is the
3920    * one that the prediction will be for).
3921    */
3922   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3923   {
3924     AlignmentView seqs = null;
3925
3926     if ((viewport.getSelectionGroup() != null)
3927             && (viewport.getSelectionGroup().getSize() > 0))
3928     {
3929       seqs = viewport.getAlignmentView(true);
3930     }
3931     else
3932     {
3933       seqs = viewport.getAlignmentView(false);
3934     }
3935     // limit sequences - JBPNote in future - could spawn multiple prediction
3936     // jobs
3937     // TODO: viewport.getAlignment().isAligned is a global state - the local
3938     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3939     if (!viewport.getAlignment().isAligned(false))
3940     {
3941       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3942       // TODO: if seqs.getSequences().length>1 then should really have warned
3943       // user!
3944
3945     }
3946     return seqs;
3947   }
3948
3949   /**
3950    * DOCUMENT ME!
3951    *
3952    * @param e
3953    *          DOCUMENT ME!
3954    */
3955   @Override
3956   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3957   {
3958     // Pick the tree file
3959     JalviewFileChooser chooser = new JalviewFileChooser(
3960             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3961     chooser.setFileView(new JalviewFileView());
3962     chooser.setDialogTitle(
3963             MessageManager.getString("label.select_newick_like_tree_file"));
3964     chooser.setToolTipText(
3965             MessageManager.getString("label.load_tree_file"));
3966
3967     chooser.response(new jalview.util.dialogrunner.RunResponse(
3968             JalviewFileChooser.APPROVE_OPTION)
3969     {
3970       @Override
3971       public void run()
3972       {
3973         String filePath = chooser.getSelectedFile().getPath();
3974         Cache.setProperty("LAST_DIRECTORY", filePath);
3975         NewickFile fin = null;
3976         try
3977         {
3978           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
3979                   DataSourceType.FILE));
3980           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3981         } catch (Exception ex)
3982         {
3983           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3984                   MessageManager
3985                           .getString("label.problem_reading_tree_file"),
3986                   JvOptionPane.WARNING_MESSAGE);
3987           ex.printStackTrace();
3988         }
3989         if (fin != null && fin.hasWarningMessage())
3990         {
3991           JvOptionPane.showMessageDialog(Desktop.desktop,
3992                   fin.getWarningMessage(),
3993                   MessageManager.getString(
3994                           "label.possible_problem_with_tree_file"),
3995                   JvOptionPane.WARNING_MESSAGE);
3996         }
3997       }
3998     }).openDialog(this);
3999   }
4000
4001   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4002   {
4003     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4004   }
4005
4006   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4007           int h, int x, int y)
4008   {
4009     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4010   }
4011
4012   /**
4013    * Add a treeviewer for the tree extracted from a Newick file object to the
4014    * current alignment view
4015    *
4016    * @param nf
4017    *          the tree
4018    * @param title
4019    *          tree viewer title
4020    * @param input
4021    *          Associated alignment input data (or null)
4022    * @param w
4023    *          width
4024    * @param h
4025    *          height
4026    * @param x
4027    *          position
4028    * @param y
4029    *          position
4030    * @return TreePanel handle
4031    */
4032   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4033           AlignmentView input, int w, int h, int x, int y)
4034   {
4035     TreePanel tp = null;
4036
4037     try
4038     {
4039       nf.parse();
4040
4041       if (nf.getTree() != null)
4042       {
4043         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4044
4045         tp.setSize(w, h);
4046
4047         if (x > 0 && y > 0)
4048         {
4049           tp.setLocation(x, y);
4050         }
4051
4052         Desktop.addInternalFrame(tp, treeTitle, w, h);
4053       }
4054     } catch (Exception ex)
4055     {
4056       ex.printStackTrace();
4057     }
4058
4059     return tp;
4060   }
4061
4062   private boolean buildingMenu = false;
4063
4064   /**
4065    * Generates menu items and listener event actions for web service clients
4066    *
4067    */
4068   public void BuildWebServiceMenu()
4069   {
4070     while (buildingMenu)
4071     {
4072       try
4073       {
4074         System.err.println("Waiting for building menu to finish.");
4075         Thread.sleep(10);
4076       } catch (Exception e)
4077       {
4078       }
4079     }
4080     final AlignFrame me = this;
4081     buildingMenu = true;
4082     new Thread(new Runnable()
4083     {
4084       @Override
4085       public void run()
4086       {
4087         final List<JMenuItem> legacyItems = new ArrayList<>();
4088         try
4089         {
4090           // System.err.println("Building ws menu again "
4091           // + Thread.currentThread());
4092           // TODO: add support for context dependent disabling of services based
4093           // on
4094           // alignment and current selection
4095           // TODO: add additional serviceHandle parameter to specify abstract
4096           // handler
4097           // class independently of AbstractName
4098           // TODO: add in rediscovery GUI function to restart discoverer
4099           // TODO: group services by location as well as function and/or
4100           // introduce
4101           // object broker mechanism.
4102           final Vector<JMenu> wsmenu = new Vector<>();
4103           final IProgressIndicator af = me;
4104
4105           /*
4106            * do not i18n these strings - they are hard-coded in class
4107            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4108            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4109            */
4110           final JMenu msawsmenu = new JMenu("Alignment");
4111           final JMenu secstrmenu = new JMenu(
4112                   "Secondary Structure Prediction");
4113           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4114           final JMenu analymenu = new JMenu("Analysis");
4115           final JMenu dismenu = new JMenu("Protein Disorder");
4116           // JAL-940 - only show secondary structure prediction services from
4117           // the legacy server
4118           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4119               // &&
4120           Discoverer.services != null && (Discoverer.services.size() > 0))
4121           {
4122             // TODO: refactor to allow list of AbstractName/Handler bindings to
4123             // be
4124             // stored or retrieved from elsewhere
4125             // No MSAWS used any more:
4126             // Vector msaws = null; // (Vector)
4127             // Discoverer.services.get("MsaWS");
4128             Vector secstrpr = (Vector) Discoverer.services
4129                     .get("SecStrPred");
4130             if (secstrpr != null)
4131             {
4132               // Add any secondary structure prediction services
4133               for (int i = 0, j = secstrpr.size(); i < j; i++)
4134               {
4135                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4136                         .get(i);
4137                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4138                         .getServiceClient(sh);
4139                 int p = secstrmenu.getItemCount();
4140                 impl.attachWSMenuEntry(secstrmenu, me);
4141                 int q = secstrmenu.getItemCount();
4142                 for (int litm = p; litm < q; litm++)
4143                 {
4144                   legacyItems.add(secstrmenu.getItem(litm));
4145                 }
4146               }
4147             }
4148           }
4149
4150           // Add all submenus in the order they should appear on the web
4151           // services menu
4152           wsmenu.add(msawsmenu);
4153           wsmenu.add(secstrmenu);
4154           wsmenu.add(dismenu);
4155           wsmenu.add(analymenu);
4156           // No search services yet
4157           // wsmenu.add(seqsrchmenu);
4158
4159           javax.swing.SwingUtilities.invokeLater(new Runnable()
4160           {
4161             @Override
4162             public void run()
4163             {
4164               try
4165               {
4166                 webService.removeAll();
4167                 // first, add discovered services onto the webservices menu
4168                 if (wsmenu.size() > 0)
4169                 {
4170                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4171                   {
4172                     webService.add(wsmenu.get(i));
4173                   }
4174                 }
4175                 else
4176                 {
4177                   webService.add(me.webServiceNoServices);
4178                 }
4179                 // TODO: move into separate menu builder class.
4180                 boolean new_sspred = false;
4181                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4182                 {
4183                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4184                   if (jws2servs != null)
4185                   {
4186                     if (jws2servs.hasServices())
4187                     {
4188                       jws2servs.attachWSMenuEntry(webService, me);
4189                       for (Jws2Instance sv : jws2servs.getServices())
4190                       {
4191                         if (sv.description.toLowerCase().contains("jpred"))
4192                         {
4193                           for (JMenuItem jmi : legacyItems)
4194                           {
4195                             jmi.setVisible(false);
4196                           }
4197                         }
4198                       }
4199
4200                     }
4201                     if (jws2servs.isRunning())
4202                     {
4203                       JMenuItem tm = new JMenuItem(
4204                               "Still discovering JABA Services");
4205                       tm.setEnabled(false);
4206                       webService.add(tm);
4207                     }
4208                   }
4209                 }
4210                 build_urlServiceMenu(me.webService);
4211                 build_fetchdbmenu(webService);
4212                 for (JMenu item : wsmenu)
4213                 {
4214                   if (item.getItemCount() == 0)
4215                   {
4216                     item.setEnabled(false);
4217                   }
4218                   else
4219                   {
4220                     item.setEnabled(true);
4221                   }
4222                 }
4223               } catch (Exception e)
4224               {
4225                 Cache.log.debug(
4226                         "Exception during web service menu building process.",
4227                         e);
4228               }
4229             }
4230           });
4231         } catch (Exception e)
4232         {
4233         }
4234         buildingMenu = false;
4235       }
4236     }).start();
4237
4238   }
4239
4240   /**
4241    * construct any groupURL type service menu entries.
4242    *
4243    * @param webService
4244    */
4245   private void build_urlServiceMenu(JMenu webService)
4246   {
4247     // TODO: remove this code when 2.7 is released
4248     // DEBUG - alignmentView
4249     /*
4250      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4251      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4252      *
4253      * @Override public void actionPerformed(ActionEvent e) {
4254      * jalview.datamodel.AlignmentView
4255      * .testSelectionViews(af.viewport.getAlignment(),
4256      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4257      *
4258      * }); webService.add(testAlView);
4259      */
4260     // TODO: refactor to RestClient discoverer and merge menu entries for
4261     // rest-style services with other types of analysis/calculation service
4262     // SHmmr test client - still being implemented.
4263     // DEBUG - alignmentView
4264
4265     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4266             .getRestClients())
4267     {
4268       client.attachWSMenuEntry(
4269               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4270               this);
4271     }
4272   }
4273
4274   /**
4275    * Searches the alignment sequences for xRefs and builds the Show
4276    * Cross-References menu (formerly called Show Products), with database
4277    * sources for which cross-references are found (protein sources for a
4278    * nucleotide alignment and vice versa)
4279    *
4280    * @return true if Show Cross-references menu should be enabled
4281    */
4282   public boolean canShowProducts()
4283   {
4284     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4285     AlignmentI dataset = viewport.getAlignment().getDataset();
4286
4287     showProducts.removeAll();
4288     final boolean dna = viewport.getAlignment().isNucleotide();
4289
4290     if (seqs == null || seqs.length == 0)
4291     {
4292       // nothing to see here.
4293       return false;
4294     }
4295
4296     boolean showp = false;
4297     try
4298     {
4299       List<String> ptypes = new CrossRef(seqs, dataset)
4300               .findXrefSourcesForSequences(dna);
4301
4302       for (final String source : ptypes)
4303       {
4304         showp = true;
4305         final AlignFrame af = this;
4306         JMenuItem xtype = new JMenuItem(source);
4307         xtype.addActionListener(new ActionListener()
4308         {
4309           @Override
4310           public void actionPerformed(ActionEvent e)
4311           {
4312             showProductsFor(af.viewport.getSequenceSelection(), dna,
4313                     source);
4314           }
4315         });
4316         showProducts.add(xtype);
4317       }
4318       showProducts.setVisible(showp);
4319       showProducts.setEnabled(showp);
4320     } catch (Exception e)
4321     {
4322       Cache.log.warn(
4323               "canShowProducts threw an exception - please report to help@jalview.org",
4324               e);
4325       return false;
4326     }
4327     return showp;
4328   }
4329
4330   /**
4331    * Finds and displays cross-references for the selected sequences (protein
4332    * products for nucleotide sequences, dna coding sequences for peptides).
4333    *
4334    * @param sel
4335    *          the sequences to show cross-references for
4336    * @param dna
4337    *          true if from a nucleotide alignment (so showing proteins)
4338    * @param source
4339    *          the database to show cross-references for
4340    */
4341   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4342           final String source)
4343   {
4344     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4345             .start();
4346   }
4347
4348   /**
4349    * Construct and display a new frame containing the translation of this
4350    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4351    */
4352   @Override
4353   public void showTranslation_actionPerformed(ActionEvent e)
4354   {
4355     AlignmentI al = null;
4356     try
4357     {
4358       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4359
4360       al = dna.translateCdna();
4361     } catch (Exception ex)
4362     {
4363       jalview.bin.Cache.log.error(
4364               "Exception during translation. Please report this !", ex);
4365       final String msg = MessageManager.getString(
4366               "label.error_when_translating_sequences_submit_bug_report");
4367       final String errorTitle = MessageManager
4368               .getString("label.implementation_error")
4369               + MessageManager.getString("label.translation_failed");
4370       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4371               JvOptionPane.ERROR_MESSAGE);
4372       return;
4373     }
4374     if (al == null || al.getHeight() == 0)
4375     {
4376       final String msg = MessageManager.getString(
4377               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4378       final String errorTitle = MessageManager
4379               .getString("label.translation_failed");
4380       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4381               JvOptionPane.WARNING_MESSAGE);
4382     }
4383     else
4384     {
4385       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4386       af.setFileFormat(this.currentFileFormat);
4387       final String newTitle = MessageManager
4388               .formatMessage("label.translation_of_params", new Object[]
4389               { this.getTitle() });
4390       af.setTitle(newTitle);
4391       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4392       {
4393         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4394         viewport.openSplitFrame(af, new Alignment(seqs));
4395       }
4396       else
4397       {
4398         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4399                 DEFAULT_HEIGHT);
4400       }
4401     }
4402   }
4403
4404   /**
4405    * Set the file format
4406    *
4407    * @param format
4408    */
4409   public void setFileFormat(FileFormatI format)
4410   {
4411     this.currentFileFormat = format;
4412   }
4413
4414   /**
4415    * Try to load a features file onto the alignment.
4416    *
4417    * @param file
4418    *          contents or path to retrieve file or a File object
4419    * @param sourceType
4420    *          access mode of file (see jalview.io.AlignFile)
4421    * @return true if features file was parsed correctly.
4422    */
4423   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4424   {
4425     // BH 2018
4426     return avc.parseFeaturesFile(file, sourceType,
4427             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4428
4429   }
4430
4431   @Override
4432   public void refreshFeatureUI(boolean enableIfNecessary)
4433   {
4434     // note - currently this is only still here rather than in the controller
4435     // because of the featureSettings hard reference that is yet to be
4436     // abstracted
4437     if (enableIfNecessary)
4438     {
4439       viewport.setShowSequenceFeatures(true);
4440       showSeqFeatures.setSelected(true);
4441     }
4442
4443   }
4444
4445   @Override
4446   public void dragEnter(DropTargetDragEvent evt)
4447   {
4448   }
4449
4450   @Override
4451   public void dragExit(DropTargetEvent evt)
4452   {
4453   }
4454
4455   @Override
4456   public void dragOver(DropTargetDragEvent evt)
4457   {
4458   }
4459
4460   @Override
4461   public void dropActionChanged(DropTargetDragEvent evt)
4462   {
4463   }
4464
4465   @Override
4466   public void drop(DropTargetDropEvent evt)
4467   {
4468     // JAL-1552 - acceptDrop required before getTransferable call for
4469     // Java's Transferable for native dnd
4470     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4471     Transferable t = evt.getTransferable();
4472
4473     final AlignFrame thisaf = this;
4474     final List<Object> files = new ArrayList<>();
4475     List<DataSourceType> protocols = new ArrayList<>();
4476
4477     try
4478     {
4479       Desktop.transferFromDropTarget(files, protocols, evt, t);
4480     } catch (Exception e)
4481     {
4482       e.printStackTrace();
4483     }
4484     if (files != null)
4485     {
4486       new Thread(new Runnable()
4487       {
4488         @Override
4489         public void run()
4490         {
4491           try
4492           {
4493             // check to see if any of these files have names matching sequences
4494             // in
4495             // the alignment
4496             SequenceIdMatcher idm = new SequenceIdMatcher(
4497                     viewport.getAlignment().getSequencesArray());
4498             /**
4499              * Object[] { String,SequenceI}
4500              */
4501             ArrayList<Object[]> filesmatched = new ArrayList<>();
4502             ArrayList<Object> filesnotmatched = new ArrayList<>();
4503             for (int i = 0; i < files.size(); i++)
4504             {
4505               // BH 2018
4506               Object file = files.get(i);
4507               String fileName = file.toString();
4508               String pdbfn = "";
4509               DataSourceType protocol = (file instanceof File
4510                       ? DataSourceType.FILE
4511                       : FormatAdapter.checkProtocol(fileName));
4512               if (protocol == DataSourceType.FILE)
4513               {
4514                 File fl = (file instanceof File ? (File) file
4515                         : new File(fileName));
4516                 pdbfn = fl.getName();
4517               }
4518               else if (protocol == DataSourceType.URL)
4519               {
4520                 URL url = new URL(fileName);
4521                 pdbfn = url.getFile();
4522               }
4523               if (pdbfn.length() > 0)
4524               {
4525                 // attempt to find a match in the alignment
4526                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4527                 int l = 0, c = pdbfn.indexOf(".");
4528                 while (mtch == null && c != -1)
4529                 {
4530                   do
4531                   {
4532                     l = c;
4533                   } while ((c = pdbfn.indexOf(".", l)) > l);
4534                   if (l > -1)
4535                   {
4536                     pdbfn = pdbfn.substring(0, l);
4537                   }
4538                   mtch = idm.findAllIdMatches(pdbfn);
4539                 }
4540                 if (mtch != null)
4541                 {
4542                   FileFormatI type;
4543                   try
4544                   {
4545                     type = new IdentifyFile().identify(file, protocol);
4546                   } catch (Exception ex)
4547                   {
4548                     type = null;
4549                   }
4550                   if (type != null && type.isStructureFile())
4551                   {
4552                     filesmatched.add(new Object[] { file, protocol, mtch });
4553                     continue;
4554                   }
4555                 }
4556                 // File wasn't named like one of the sequences or wasn't a PDB
4557                 // file.
4558                 filesnotmatched.add(file);
4559               }
4560             }
4561             int assocfiles = 0;
4562             if (filesmatched.size() > 0)
4563             {
4564               boolean autoAssociate = Cache
4565                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4566               if (!autoAssociate)
4567               {
4568                 String msg = MessageManager.formatMessage(
4569                         "label.automatically_associate_structure_files_with_sequences_same_name",
4570                         new Object[]
4571                         { Integer.valueOf(filesmatched.size())
4572                                 .toString() });
4573                 String ttl = MessageManager.getString(
4574                         "label.automatically_associate_structure_files_by_name");
4575                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4576                         ttl, JvOptionPane.YES_NO_OPTION);
4577                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4578               }
4579               if (autoAssociate)
4580               {
4581                 for (Object[] fm : filesmatched)
4582                 {
4583                   // try and associate
4584                   // TODO: may want to set a standard ID naming formalism for
4585                   // associating PDB files which have no IDs.
4586                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4587                   {
4588                     PDBEntry pe = new AssociatePdbFileWithSeq()
4589                             .associatePdbWithSeq((String) fm[0],
4590                                     (DataSourceType) fm[1], toassoc, false,
4591                                     Desktop.instance);
4592                     if (pe != null)
4593                     {
4594                       System.err.println("Associated file : "
4595                               + ((String) fm[0]) + " with "
4596                               + toassoc.getDisplayId(true));
4597                       assocfiles++;
4598                     }
4599                   }
4600                   // TODO: do we need to update overview ? only if features are
4601                   // shown I guess
4602                   alignPanel.paintAlignment(true, false);
4603                 }
4604               }
4605               else
4606               {
4607                 /*
4608                  * add declined structures as sequences
4609                  */
4610                 for (Object[] o : filesmatched)
4611                 {
4612                   filesnotmatched.add(o[0]);
4613                 }
4614               }
4615             }
4616             if (filesnotmatched.size() > 0)
4617             {
4618               if (assocfiles > 0 && (Cache.getDefault(
4619                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4620                       || JvOptionPane.showConfirmDialog(thisaf,
4621                               "<html>" + MessageManager.formatMessage(
4622                                       "label.ignore_unmatched_dropped_files_info",
4623                                       new Object[]
4624                                       { Integer.valueOf(
4625                                               filesnotmatched.size())
4626                                               .toString() })
4627                                       + "</html>",
4628                               MessageManager.getString(
4629                                       "label.ignore_unmatched_dropped_files"),
4630                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4631               {
4632                 return;
4633               }
4634               for (Object fn : filesnotmatched)
4635               {
4636                 loadJalviewDataFile(fn, null, null, null);
4637               }
4638
4639             }
4640           } catch (Exception ex)
4641           {
4642             ex.printStackTrace();
4643           }
4644         }
4645       }).start();
4646     }
4647   }
4648
4649   /**
4650    * Attempt to load a "dropped" file or URL string, by testing in turn for
4651    * <ul>
4652    * <li>an Annotation file</li>
4653    * <li>a JNet file</li>
4654    * <li>a features file</li>
4655    * <li>else try to interpret as an alignment file</li>
4656    * </ul>
4657    *
4658    * @param file
4659    *          either a filename or a URL string.
4660    */
4661   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4662           FileFormatI format, SequenceI assocSeq)
4663   {
4664     // BH 2018 was String file
4665     try
4666     {
4667       if (sourceType == null)
4668       {
4669         sourceType = FormatAdapter.checkProtocol(file);
4670       }
4671       // if the file isn't identified, or not positively identified as some
4672       // other filetype (PFAM is default unidentified alignment file type) then
4673       // try to parse as annotation.
4674       boolean isAnnotation = (format == null
4675               || FileFormat.Pfam.equals(format))
4676                       ? new AnnotationFile().annotateAlignmentView(viewport,
4677                               file, sourceType)
4678                       : false;
4679
4680       if (!isAnnotation)
4681       {
4682         // first see if its a T-COFFEE score file
4683         TCoffeeScoreFile tcf = null;
4684         try
4685         {
4686           tcf = new TCoffeeScoreFile(file, sourceType);
4687           if (tcf.isValid())
4688           {
4689             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4690             {
4691               buildColourMenu();
4692               changeColour(
4693                       new TCoffeeColourScheme(viewport.getAlignment()));
4694               isAnnotation = true;
4695               statusBar.setText(MessageManager.getString(
4696                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4697             }
4698             else
4699             {
4700               // some problem - if no warning its probable that the ID matching
4701               // process didn't work
4702               JvOptionPane.showMessageDialog(Desktop.desktop,
4703                       tcf.getWarningMessage() == null
4704                               ? MessageManager.getString(
4705                                       "label.check_file_matches_sequence_ids_alignment")
4706                               : tcf.getWarningMessage(),
4707                       MessageManager.getString(
4708                               "label.problem_reading_tcoffee_score_file"),
4709                       JvOptionPane.WARNING_MESSAGE);
4710             }
4711           }
4712           else
4713           {
4714             tcf = null;
4715           }
4716         } catch (Exception x)
4717         {
4718           Cache.log.debug(
4719                   "Exception when processing data source as T-COFFEE score file",
4720                   x);
4721           tcf = null;
4722         }
4723         if (tcf == null)
4724         {
4725           // try to see if its a JNet 'concise' style annotation file *before*
4726           // we
4727           // try to parse it as a features file
4728           if (format == null)
4729           {
4730             format = new IdentifyFile().identify(file, sourceType);
4731           }
4732           if (FileFormat.ScoreMatrix == format)
4733           {
4734             ScoreMatrixFile sm = new ScoreMatrixFile(
4735                     new FileParse(file, sourceType));
4736             sm.parse();
4737             // todo: i18n this message
4738             statusBar.setText(MessageManager.formatMessage(
4739                     "label.successfully_loaded_matrix",
4740                     sm.getMatrixName()));
4741           }
4742           else if (FileFormat.Jnet.equals(format))
4743           {
4744             JPredFile predictions = new JPredFile(file, sourceType);
4745             new JnetAnnotationMaker();
4746             JnetAnnotationMaker.add_annotation(predictions,
4747                     viewport.getAlignment(), 0, false);
4748             viewport.getAlignment().setupJPredAlignment();
4749             isAnnotation = true;
4750           }
4751           // else if (IdentifyFile.FeaturesFile.equals(format))
4752           else if (FileFormat.Features.equals(format))
4753           {
4754             if (parseFeaturesFile(file, sourceType))
4755             {
4756               alignPanel.paintAlignment(true, true);
4757             }
4758           }
4759           else
4760           {
4761             new FileLoader().LoadFile(viewport, file, sourceType, format);
4762           }
4763         }
4764       }
4765       if (isAnnotation)
4766       {
4767
4768         alignPanel.adjustAnnotationHeight();
4769         viewport.updateSequenceIdColours();
4770         buildSortByAnnotationScoresMenu();
4771         alignPanel.paintAlignment(true, true);
4772       }
4773     } catch (Exception ex)
4774     {
4775       ex.printStackTrace();
4776     } catch (OutOfMemoryError oom)
4777     {
4778       try
4779       {
4780         System.gc();
4781       } catch (Exception x)
4782       {
4783       }
4784       new OOMWarning(
4785               "loading data "
4786                       + (sourceType != null
4787                               ? (sourceType == DataSourceType.PASTE
4788                                       ? "from clipboard."
4789                                       : "using " + sourceType + " from "
4790                                               + file)
4791                               : ".")
4792                       + (format != null
4793                               ? "(parsing as '" + format + "' file)"
4794                               : ""),
4795               oom, Desktop.desktop);
4796     }
4797   }
4798
4799   /**
4800    * Method invoked by the ChangeListener on the tabbed pane, in other words
4801    * when a different tabbed pane is selected by the user or programmatically.
4802    */
4803   @Override
4804   public void tabSelectionChanged(int index)
4805   {
4806     if (index > -1)
4807     {
4808       alignPanel = alignPanels.get(index);
4809       viewport = alignPanel.av;
4810       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4811       setMenusFromViewport(viewport);
4812     }
4813
4814     /*
4815      * 'focus' any colour slider that is open to the selected viewport
4816      */
4817     if (viewport.getConservationSelected())
4818     {
4819       SliderPanel.setConservationSlider(alignPanel,
4820               viewport.getResidueShading(), alignPanel.getViewName());
4821     }
4822     else
4823     {
4824       SliderPanel.hideConservationSlider();
4825     }
4826     if (viewport.getAbovePIDThreshold())
4827     {
4828       SliderPanel.setPIDSliderSource(alignPanel,
4829               viewport.getResidueShading(), alignPanel.getViewName());
4830     }
4831     else
4832     {
4833       SliderPanel.hidePIDSlider();
4834     }
4835
4836     /*
4837      * If there is a frame linked to this one in a SplitPane, switch it to the
4838      * same view tab index. No infinite recursion of calls should happen, since
4839      * tabSelectionChanged() should not get invoked on setting the selected
4840      * index to an unchanged value. Guard against setting an invalid index
4841      * before the new view peer tab has been created.
4842      */
4843     final AlignViewportI peer = viewport.getCodingComplement();
4844     if (peer != null)
4845     {
4846       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4847               .getAlignPanel().alignFrame;
4848       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4849       {
4850         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4851       }
4852     }
4853   }
4854
4855   /**
4856    * On right mouse click on view tab, prompt for and set new view name.
4857    */
4858   @Override
4859   public void tabbedPane_mousePressed(MouseEvent e)
4860   {
4861     if (e.isPopupTrigger())
4862     {
4863       String msg = MessageManager.getString("label.enter_view_name");
4864       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4865               JvOptionPane.QUESTION_MESSAGE);
4866
4867       if (reply != null)
4868       {
4869         viewport.viewName = reply;
4870         // TODO warn if reply is in getExistingViewNames()?
4871         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4872       }
4873     }
4874   }
4875
4876   public AlignViewport getCurrentView()
4877   {
4878     return viewport;
4879   }
4880
4881   /**
4882    * Open the dialog for regex description parsing.
4883    */
4884   @Override
4885   protected void extractScores_actionPerformed(ActionEvent e)
4886   {
4887     ParseProperties pp = new jalview.analysis.ParseProperties(
4888             viewport.getAlignment());
4889     // TODO: verify regex and introduce GUI dialog for version 2.5
4890     // if (pp.getScoresFromDescription("col", "score column ",
4891     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4892     // true)>0)
4893     if (pp.getScoresFromDescription("description column",
4894             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4895     {
4896       buildSortByAnnotationScoresMenu();
4897     }
4898   }
4899
4900   /*
4901    * (non-Javadoc)
4902    *
4903    * @see
4904    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4905    * )
4906    */
4907   @Override
4908   protected void showDbRefs_actionPerformed(ActionEvent e)
4909   {
4910     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4911   }
4912
4913   /*
4914    * (non-Javadoc)
4915    *
4916    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4917    * ActionEvent)
4918    */
4919   @Override
4920   protected void showNpFeats_actionPerformed(ActionEvent e)
4921   {
4922     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4923   }
4924
4925   /**
4926    * find the viewport amongst the tabs in this alignment frame and close that
4927    * tab
4928    *
4929    * @param av
4930    */
4931   public boolean closeView(AlignViewportI av)
4932   {
4933     if (viewport == av)
4934     {
4935       this.closeMenuItem_actionPerformed(false);
4936       return true;
4937     }
4938     Component[] comp = tabbedPane.getComponents();
4939     for (int i = 0; comp != null && i < comp.length; i++)
4940     {
4941       if (comp[i] instanceof AlignmentPanel)
4942       {
4943         if (((AlignmentPanel) comp[i]).av == av)
4944         {
4945           // close the view.
4946           closeView((AlignmentPanel) comp[i]);
4947           return true;
4948         }
4949       }
4950     }
4951     return false;
4952   }
4953
4954   protected void build_fetchdbmenu(JMenu webService)
4955   {
4956     // Temporary hack - DBRef Fetcher always top level ws entry.
4957     // TODO We probably want to store a sequence database checklist in
4958     // preferences and have checkboxes.. rather than individual sources selected
4959     // here
4960     final JMenu rfetch = new JMenu(
4961             MessageManager.getString("action.fetch_db_references"));
4962     rfetch.setToolTipText(MessageManager.getString(
4963             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4964     webService.add(rfetch);
4965
4966     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4967             MessageManager.getString("option.trim_retrieved_seqs"));
4968     trimrs.setToolTipText(
4969             MessageManager.getString("label.trim_retrieved_sequences"));
4970     trimrs.setSelected(
4971             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4972     trimrs.addActionListener(new ActionListener()
4973     {
4974       @Override
4975       public void actionPerformed(ActionEvent e)
4976       {
4977         trimrs.setSelected(trimrs.isSelected());
4978         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4979                 Boolean.valueOf(trimrs.isSelected()).toString());
4980       };
4981     });
4982     rfetch.add(trimrs);
4983     JMenuItem fetchr = new JMenuItem(
4984             MessageManager.getString("label.standard_databases"));
4985     fetchr.setToolTipText(
4986             MessageManager.getString("label.fetch_embl_uniprot"));
4987     fetchr.addActionListener(new ActionListener()
4988     {
4989
4990       @Override
4991       public void actionPerformed(ActionEvent e)
4992       {
4993         new Thread(new Runnable()
4994         {
4995           @Override
4996           public void run()
4997           {
4998             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4999                     .getAlignment().isNucleotide();
5000             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5001                     alignPanel.av.getSequenceSelection(),
5002                     alignPanel.alignFrame, null,
5003                     alignPanel.alignFrame.featureSettings, isNucleotide);
5004             dbRefFetcher.addListener(new FetchFinishedListenerI()
5005             {
5006               @Override
5007               public void finished()
5008               {
5009                 AlignFrame.this.setMenusForViewport();
5010               }
5011             });
5012             dbRefFetcher.fetchDBRefs(false);
5013           }
5014         }).start();
5015
5016       }
5017
5018     });
5019     rfetch.add(fetchr);
5020     final AlignFrame me = this;
5021     new Thread(new Runnable()
5022     {
5023       @Override
5024       public void run()
5025       {
5026         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5027                 .getSequenceFetcherSingleton(me);
5028         javax.swing.SwingUtilities.invokeLater(new Runnable()
5029         {
5030           @Override
5031           public void run()
5032           {
5033             String[] dbclasses = sf.getOrderedSupportedSources();
5034             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5035             // jalview.util.QuickSort.sort(otherdb, otherdb);
5036             List<DbSourceProxy> otherdb;
5037             JMenu dfetch = new JMenu();
5038             JMenu ifetch = new JMenu();
5039             JMenuItem fetchr = null;
5040             int comp = 0, icomp = 0, mcomp = 15;
5041             String mname = null;
5042             int dbi = 0;
5043             for (String dbclass : dbclasses)
5044             {
5045               otherdb = sf.getSourceProxy(dbclass);
5046               // add a single entry for this class, or submenu allowing 'fetch
5047               // all' or pick one
5048               if (otherdb == null || otherdb.size() < 1)
5049               {
5050                 continue;
5051               }
5052               // List<DbSourceProxy> dbs=otherdb;
5053               // otherdb=new ArrayList<DbSourceProxy>();
5054               // for (DbSourceProxy db:dbs)
5055               // {
5056               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5057               // }
5058               if (mname == null)
5059               {
5060                 mname = "From " + dbclass;
5061               }
5062               if (otherdb.size() == 1)
5063               {
5064                 final DbSourceProxy[] dassource = otherdb
5065                         .toArray(new DbSourceProxy[0]);
5066                 DbSourceProxy src = otherdb.get(0);
5067                 fetchr = new JMenuItem(src.getDbSource());
5068                 fetchr.addActionListener(new ActionListener()
5069                 {
5070
5071                   @Override
5072                   public void actionPerformed(ActionEvent e)
5073                   {
5074                     new Thread(new Runnable()
5075                     {
5076
5077                       @Override
5078                       public void run()
5079                       {
5080                         boolean isNucleotide = alignPanel.alignFrame
5081                                 .getViewport().getAlignment()
5082                                 .isNucleotide();
5083                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5084                                 alignPanel.av.getSequenceSelection(),
5085                                 alignPanel.alignFrame, dassource,
5086                                 alignPanel.alignFrame.featureSettings,
5087                                 isNucleotide);
5088                         dbRefFetcher
5089                                 .addListener(new FetchFinishedListenerI()
5090                                 {
5091                                   @Override
5092                                   public void finished()
5093                                   {
5094                                     AlignFrame.this.setMenusForViewport();
5095                                   }
5096                                 });
5097                         dbRefFetcher.fetchDBRefs(false);
5098                       }
5099                     }).start();
5100                   }
5101
5102                 });
5103                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5104                         MessageManager.formatMessage(
5105                                 "label.fetch_retrieve_from", new Object[]
5106                                 { src.getDbName() })));
5107                 dfetch.add(fetchr);
5108                 comp++;
5109               }
5110               else
5111               {
5112                 final DbSourceProxy[] dassource = otherdb
5113                         .toArray(new DbSourceProxy[0]);
5114                 // fetch all entry
5115                 DbSourceProxy src = otherdb.get(0);
5116                 fetchr = new JMenuItem(MessageManager
5117                         .formatMessage("label.fetch_all_param", new Object[]
5118                         { src.getDbSource() }));
5119                 fetchr.addActionListener(new ActionListener()
5120                 {
5121                   @Override
5122                   public void actionPerformed(ActionEvent e)
5123                   {
5124                     new Thread(new Runnable()
5125                     {
5126
5127                       @Override
5128                       public void run()
5129                       {
5130                         boolean isNucleotide = alignPanel.alignFrame
5131                                 .getViewport().getAlignment()
5132                                 .isNucleotide();
5133                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5134                                 alignPanel.av.getSequenceSelection(),
5135                                 alignPanel.alignFrame, dassource,
5136                                 alignPanel.alignFrame.featureSettings,
5137                                 isNucleotide);
5138                         dbRefFetcher
5139                                 .addListener(new FetchFinishedListenerI()
5140                                 {
5141                                   @Override
5142                                   public void finished()
5143                                   {
5144                                     AlignFrame.this.setMenusForViewport();
5145                                   }
5146                                 });
5147                         dbRefFetcher.fetchDBRefs(false);
5148                       }
5149                     }).start();
5150                   }
5151                 });
5152
5153                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5154                         MessageManager.formatMessage(
5155                                 "label.fetch_retrieve_from_all_sources",
5156                                 new Object[]
5157                                 { Integer.valueOf(otherdb.size())
5158                                         .toString(),
5159                                     src.getDbSource(), src.getDbName() })));
5160                 dfetch.add(fetchr);
5161                 comp++;
5162                 // and then build the rest of the individual menus
5163                 ifetch = new JMenu(MessageManager.formatMessage(
5164                         "label.source_from_db_source", new Object[]
5165                         { src.getDbSource() }));
5166                 icomp = 0;
5167                 String imname = null;
5168                 int i = 0;
5169                 for (DbSourceProxy sproxy : otherdb)
5170                 {
5171                   String dbname = sproxy.getDbName();
5172                   String sname = dbname.length() > 5
5173                           ? dbname.substring(0, 5) + "..."
5174                           : dbname;
5175                   String msname = dbname.length() > 10
5176                           ? dbname.substring(0, 10) + "..."
5177                           : dbname;
5178                   if (imname == null)
5179                   {
5180                     imname = MessageManager
5181                             .formatMessage("label.from_msname", new Object[]
5182                             { sname });
5183                   }
5184                   fetchr = new JMenuItem(msname);
5185                   final DbSourceProxy[] dassrc = { sproxy };
5186                   fetchr.addActionListener(new ActionListener()
5187                   {
5188
5189                     @Override
5190                     public void actionPerformed(ActionEvent e)
5191                     {
5192                       new Thread(new Runnable()
5193                       {
5194
5195                         @Override
5196                         public void run()
5197                         {
5198                           boolean isNucleotide = alignPanel.alignFrame
5199                                   .getViewport().getAlignment()
5200                                   .isNucleotide();
5201                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5202                                   alignPanel.av.getSequenceSelection(),
5203                                   alignPanel.alignFrame, dassrc,
5204                                   alignPanel.alignFrame.featureSettings,
5205                                   isNucleotide);
5206                           dbRefFetcher
5207                                   .addListener(new FetchFinishedListenerI()
5208                                   {
5209                                     @Override
5210                                     public void finished()
5211                                     {
5212                                       AlignFrame.this.setMenusForViewport();
5213                                     }
5214                                   });
5215                           dbRefFetcher.fetchDBRefs(false);
5216                         }
5217                       }).start();
5218                     }
5219
5220                   });
5221                   fetchr.setToolTipText(
5222                           "<html>" + MessageManager.formatMessage(
5223                                   "label.fetch_retrieve_from", new Object[]
5224                                   { dbname }));
5225                   ifetch.add(fetchr);
5226                   ++i;
5227                   if (++icomp >= mcomp || i == (otherdb.size()))
5228                   {
5229                     ifetch.setText(MessageManager.formatMessage(
5230                             "label.source_to_target", imname, sname));
5231                     dfetch.add(ifetch);
5232                     ifetch = new JMenu();
5233                     imname = null;
5234                     icomp = 0;
5235                     comp++;
5236                   }
5237                 }
5238               }
5239               ++dbi;
5240               if (comp >= mcomp || dbi >= (dbclasses.length))
5241               {
5242                 dfetch.setText(MessageManager.formatMessage(
5243                         "label.source_to_target", mname, dbclass));
5244                 rfetch.add(dfetch);
5245                 dfetch = new JMenu();
5246                 mname = null;
5247                 comp = 0;
5248               }
5249             }
5250           }
5251         });
5252       }
5253     }).start();
5254
5255   }
5256
5257   /**
5258    * Left justify the whole alignment.
5259    */
5260   @Override
5261   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5262   {
5263     AlignmentI al = viewport.getAlignment();
5264     al.justify(false);
5265     viewport.firePropertyChange("alignment", null, al);
5266   }
5267
5268   /**
5269    * Right justify the whole alignment.
5270    */
5271   @Override
5272   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5273   {
5274     AlignmentI al = viewport.getAlignment();
5275     al.justify(true);
5276     viewport.firePropertyChange("alignment", null, al);
5277   }
5278
5279   @Override
5280   public void setShowSeqFeatures(boolean b)
5281   {
5282     showSeqFeatures.setSelected(b);
5283     viewport.setShowSequenceFeatures(b);
5284   }
5285
5286   /*
5287    * (non-Javadoc)
5288    *
5289    * @see
5290    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5291    * awt.event.ActionEvent)
5292    */
5293   @Override
5294   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5295   {
5296     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5297     alignPanel.paintAlignment(false, false);
5298   }
5299
5300   /*
5301    * (non-Javadoc)
5302    *
5303    * @see
5304    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5305    * .ActionEvent)
5306    */
5307   @Override
5308   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5309   {
5310     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5311     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5312
5313   }
5314
5315   /*
5316    * (non-Javadoc)
5317    *
5318    * @see
5319    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5320    * .event.ActionEvent)
5321    */
5322   @Override
5323   protected void showGroupConservation_actionPerformed(ActionEvent e)
5324   {
5325     viewport.setShowGroupConservation(showGroupConservation.getState());
5326     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5327   }
5328
5329   /*
5330    * (non-Javadoc)
5331    *
5332    * @see
5333    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5334    * .event.ActionEvent)
5335    */
5336   @Override
5337   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5338   {
5339     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5340     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5341   }
5342
5343   /*
5344    * (non-Javadoc)
5345    *
5346    * @see
5347    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5348    * .event.ActionEvent)
5349    */
5350   @Override
5351   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5352   {
5353     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5354     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5355   }
5356
5357   @Override
5358   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5359   {
5360     showSequenceLogo.setState(true);
5361     viewport.setShowSequenceLogo(true);
5362     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5363     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5364   }
5365
5366   @Override
5367   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5368   {
5369     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5370   }
5371
5372   /*
5373    * (non-Javadoc)
5374    *
5375    * @see
5376    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5377    * .event.ActionEvent)
5378    */
5379   @Override
5380   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5381   {
5382     if (avc.makeGroupsFromSelection())
5383     {
5384       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5385       alignPanel.updateAnnotation();
5386       alignPanel.paintAlignment(true, true);
5387     }
5388   }
5389
5390   public void clearAlignmentSeqRep()
5391   {
5392     // TODO refactor alignmentseqrep to controller
5393     if (viewport.getAlignment().hasSeqrep())
5394     {
5395       viewport.getAlignment().setSeqrep(null);
5396       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5397       alignPanel.updateAnnotation();
5398       alignPanel.paintAlignment(true, true);
5399     }
5400   }
5401
5402   @Override
5403   protected void createGroup_actionPerformed(ActionEvent e)
5404   {
5405     if (avc.createGroup())
5406     {
5407       alignPanel.alignmentChanged();
5408     }
5409   }
5410
5411   @Override
5412   protected void unGroup_actionPerformed(ActionEvent e)
5413   {
5414     if (avc.unGroup())
5415     {
5416       alignPanel.alignmentChanged();
5417     }
5418   }
5419
5420   /**
5421    * make the given alignmentPanel the currently selected tab
5422    *
5423    * @param alignmentPanel
5424    */
5425   public void setDisplayedView(AlignmentPanel alignmentPanel)
5426   {
5427     if (!viewport.getSequenceSetId()
5428             .equals(alignmentPanel.av.getSequenceSetId()))
5429     {
5430       throw new Error(MessageManager.getString(
5431               "error.implementation_error_cannot_show_view_alignment_frame"));
5432     }
5433     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5434             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5435     {
5436       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5437     }
5438   }
5439
5440   /**
5441    * Action on selection of menu options to Show or Hide annotations.
5442    *
5443    * @param visible
5444    * @param forSequences
5445    *          update sequence-related annotations
5446    * @param forAlignment
5447    *          update non-sequence-related annotations
5448    */
5449   @Override
5450   protected void setAnnotationsVisibility(boolean visible,
5451           boolean forSequences, boolean forAlignment)
5452   {
5453     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5454             .getAlignmentAnnotation();
5455     if (anns == null)
5456     {
5457       return;
5458     }
5459     for (AlignmentAnnotation aa : anns)
5460     {
5461       /*
5462        * don't display non-positional annotations on an alignment
5463        */
5464       if (aa.annotations == null)
5465       {
5466         continue;
5467       }
5468       boolean apply = (aa.sequenceRef == null && forAlignment)
5469               || (aa.sequenceRef != null && forSequences);
5470       if (apply)
5471       {
5472         aa.visible = visible;
5473       }
5474     }
5475     alignPanel.validateAnnotationDimensions(true);
5476     alignPanel.alignmentChanged();
5477   }
5478
5479   /**
5480    * Store selected annotation sort order for the view and repaint.
5481    */
5482   @Override
5483   protected void sortAnnotations_actionPerformed()
5484   {
5485     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5486     this.alignPanel.av
5487             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5488     alignPanel.paintAlignment(false, false);
5489   }
5490
5491   /**
5492    *
5493    * @return alignment panels in this alignment frame
5494    */
5495   public List<? extends AlignmentViewPanel> getAlignPanels()
5496   {
5497     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5498   }
5499
5500   /**
5501    * Open a new alignment window, with the cDNA associated with this (protein)
5502    * alignment, aligned as is the protein.
5503    */
5504   protected void viewAsCdna_actionPerformed()
5505   {
5506     // TODO no longer a menu action - refactor as required
5507     final AlignmentI alignment = getViewport().getAlignment();
5508     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5509     if (mappings == null)
5510     {
5511       return;
5512     }
5513     List<SequenceI> cdnaSeqs = new ArrayList<>();
5514     for (SequenceI aaSeq : alignment.getSequences())
5515     {
5516       for (AlignedCodonFrame acf : mappings)
5517       {
5518         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5519         if (dnaSeq != null)
5520         {
5521           /*
5522            * There is a cDNA mapping for this protein sequence - add to new
5523            * alignment. It will share the same dataset sequence as other mapped
5524            * cDNA (no new mappings need to be created).
5525            */
5526           final Sequence newSeq = new Sequence(dnaSeq);
5527           newSeq.setDatasetSequence(dnaSeq);
5528           cdnaSeqs.add(newSeq);
5529         }
5530       }
5531     }
5532     if (cdnaSeqs.size() == 0)
5533     {
5534       // show a warning dialog no mapped cDNA
5535       return;
5536     }
5537     AlignmentI cdna = new Alignment(
5538             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5539     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5540             AlignFrame.DEFAULT_HEIGHT);
5541     cdna.alignAs(alignment);
5542     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5543             + this.title;
5544     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5545             AlignFrame.DEFAULT_HEIGHT);
5546   }
5547
5548   /**
5549    * Set visibility of dna/protein complement view (available when shown in a
5550    * split frame).
5551    *
5552    * @param show
5553    */
5554   @Override
5555   protected void showComplement_actionPerformed(boolean show)
5556   {
5557     SplitContainerI sf = getSplitViewContainer();
5558     if (sf != null)
5559     {
5560       sf.setComplementVisible(this, show);
5561     }
5562   }
5563
5564   /**
5565    * Generate the reverse (optionally complemented) of the selected sequences,
5566    * and add them to the alignment
5567    */
5568   @Override
5569   protected void showReverse_actionPerformed(boolean complement)
5570   {
5571     AlignmentI al = null;
5572     try
5573     {
5574       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5575       al = dna.reverseCdna(complement);
5576       viewport.addAlignment(al, "");
5577       addHistoryItem(new EditCommand(
5578               MessageManager.getString("label.add_sequences"), Action.PASTE,
5579               al.getSequencesArray(), 0, al.getWidth(),
5580               viewport.getAlignment()));
5581     } catch (Exception ex)
5582     {
5583       System.err.println(ex.getMessage());
5584       return;
5585     }
5586   }
5587
5588   /**
5589    * Try to run a script in the Groovy console, having first ensured that this
5590    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5591    * be targeted at this alignment.
5592    */
5593   @Override
5594   protected void runGroovy_actionPerformed()
5595   {
5596     Jalview.setCurrentAlignFrame(this);
5597     groovy.ui.Console console = Desktop.getGroovyConsole();
5598     if (console != null)
5599     {
5600       try
5601       {
5602         console.runScript();
5603       } catch (Exception ex)
5604       {
5605         System.err.println((ex.toString()));
5606         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5607                 MessageManager.getString("label.couldnt_run_groovy_script"),
5608                 MessageManager.getString("label.groovy_support_failed"),
5609                 JvOptionPane.ERROR_MESSAGE);
5610       }
5611     }
5612     else
5613     {
5614       System.err.println("Can't run Groovy script as console not found");
5615     }
5616   }
5617
5618   /**
5619    * Hides columns containing (or not containing) a specified feature, provided
5620    * that would not leave all columns hidden
5621    *
5622    * @param featureType
5623    * @param columnsContaining
5624    * @return
5625    */
5626   public boolean hideFeatureColumns(String featureType,
5627           boolean columnsContaining)
5628   {
5629     boolean notForHiding = avc.markColumnsContainingFeatures(
5630             columnsContaining, false, false, featureType);
5631     if (notForHiding)
5632     {
5633       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5634               false, featureType))
5635       {
5636         getViewport().hideSelectedColumns();
5637         return true;
5638       }
5639     }
5640     return false;
5641   }
5642
5643   @Override
5644   protected void selectHighlightedColumns_actionPerformed(
5645           ActionEvent actionEvent)
5646   {
5647     // include key modifier check in case user selects from menu
5648     avc.markHighlightedColumns(
5649             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5650             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5651                     | ActionEvent.CTRL_MASK)) != 0);
5652   }
5653
5654   /**
5655    * Rebuilds the Colour menu, including any user-defined colours which have
5656    * been loaded either on startup or during the session
5657    */
5658   public void buildColourMenu()
5659   {
5660     colourMenu.removeAll();
5661
5662     colourMenu.add(applyToAllGroups);
5663     colourMenu.add(textColour);
5664     colourMenu.addSeparator();
5665
5666     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5667             false);
5668
5669     colourMenu.addSeparator();
5670     colourMenu.add(conservationMenuItem);
5671     colourMenu.add(modifyConservation);
5672     colourMenu.add(abovePIDThreshold);
5673     colourMenu.add(modifyPID);
5674     colourMenu.add(annotationColour);
5675
5676     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5677     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5678   }
5679
5680   /**
5681    * Open a dialog (if not already open) that allows the user to select and
5682    * calculate PCA or Tree analysis
5683    */
5684   protected void openTreePcaDialog()
5685   {
5686     if (alignPanel.getCalculationDialog() == null)
5687     {
5688       new CalculationChooser(AlignFrame.this);
5689     }
5690   }
5691
5692   @Override
5693   protected void loadVcf_actionPerformed()
5694   {
5695     JalviewFileChooser chooser = new JalviewFileChooser(
5696             Cache.getProperty("LAST_DIRECTORY"));
5697     chooser.setFileView(new JalviewFileView());
5698     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5699     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5700     final AlignFrame us = this;
5701     chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
5702     {
5703       @Override
5704       public void run()
5705       {
5706
5707         {
5708           String choice = chooser.getSelectedFile().getPath();
5709           Cache.setProperty("LAST_DIRECTORY", choice);
5710           SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5711           new VCFLoader(choice).loadVCF(seqs, us);
5712         }
5713
5714       };
5715     }).openDialog(null);
5716
5717   }
5718
5719 }
5720
5721 class PrintThread extends Thread
5722 {
5723   AlignmentPanel ap;
5724
5725   public PrintThread(AlignmentPanel ap)
5726   {
5727     this.ap = ap;
5728   }
5729
5730   static PageFormat pf;
5731
5732   @Override
5733   public void run()
5734   {
5735     PrinterJob printJob = PrinterJob.getPrinterJob();
5736
5737     if (pf != null)
5738     {
5739       printJob.setPrintable(ap, pf);
5740     }
5741     else
5742     {
5743       printJob.setPrintable(ap);
5744     }
5745
5746     if (printJob.printDialog())
5747     {
5748       try
5749       {
5750         printJob.print();
5751       } catch (Exception PrintException)
5752       {
5753         PrintException.printStackTrace();
5754       }
5755     }
5756   }
5757 }