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