src/jalview/gui/AlignFrame.java

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