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,
 238           int width, 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,
 255           int width, 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,
 274           int width, 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 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 514                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 515                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 516                 && Character.isDigit(evt.getKeyChar()))
 517         {
 518           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 519         }
 520
 521         switch (evt.getKeyCode())
 522         {
 523
 524         case 27: // escape key
 525           deselectAllSequenceMenuItem_actionPerformed(null);
 526
 527           break;
 528
 529         case KeyEvent.VK_DOWN:
 530           if (evt.isAltDown() || !viewport.cursorMode)
 531           {
 532             moveSelectedSequences(false);
 533           }
 534           if (viewport.cursorMode)
 535           {
 536             alignPanel.getSeqPanel().moveCursor(0, 1);
 537           }
 538           break;
 539
 540         case KeyEvent.VK_UP:
 541           if (evt.isAltDown() || !viewport.cursorMode)
 542           {
 543             moveSelectedSequences(true);
 544           }
 545           if (viewport.cursorMode)
 546           {
 547             alignPanel.getSeqPanel().moveCursor(0, -1);
 548           }
 549
 550           break;
 551
 552         case KeyEvent.VK_LEFT:
 553           if (evt.isAltDown() || !viewport.cursorMode)
 554           {
 555             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 556           }
 557           else
 558           {
 559             alignPanel.getSeqPanel().moveCursor(-1, 0);
 560           }
 561
 562           break;
 563
 564         case KeyEvent.VK_RIGHT:
 565           if (evt.isAltDown() || !viewport.cursorMode)
 566           {
 567             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 568           }
 569           else
 570           {
 571             alignPanel.getSeqPanel().moveCursor(1, 0);
 572           }
 573           break;
 574
 575         case KeyEvent.VK_SPACE:
 576           if (viewport.cursorMode)
 577           {
 578             alignPanel.getSeqPanel().insertGapAtCursor(
 579                     evt.isControlDown() || evt.isShiftDown()
 580                             || evt.isAltDown());
 581           }
 582           break;
 583
 584         // case KeyEvent.VK_A:
 585         // if (viewport.cursorMode)
 586         // {
 587         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 588         // //System.out.println("A");
 589         // }
 590         // break;
 591         /*
 592          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 593          * System.out.println("closing bracket"); } break;
 594          */
 595         case KeyEvent.VK_DELETE:
 596         case KeyEvent.VK_BACK_SPACE:
 597           if (!viewport.cursorMode)
 598           {
 599             cut_actionPerformed(null);
 600           }
 601           else
 602           {
 603             alignPanel.getSeqPanel().deleteGapAtCursor(
 604                     evt.isControlDown() || evt.isShiftDown()
 605                             || 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.formatMessage(
 653                   "label.keyboard_editing_mode",
 654                   new String[] { (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, viewport
 709                     .getAlignment().getSequences());
 710           }
 711           break;
 712
 713         case KeyEvent.VK_RIGHT:
 714           if (evt.isAltDown() || !viewport.cursorMode)
 715           {
 716             viewport.firePropertyChange("alignment", null, viewport
 717                     .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
 804                               .println("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.setEnabled(!nucleotide
 849             && conservationMenuItem.isSelected());
 850     showGroupConservation.setEnabled(!nucleotide);
 851
 852     showComplementMenuItem.setText(nucleotide ? MessageManager
 853             .getString("label.protein") : MessageManager
 854             .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:") ? DataSourceType.URL
1029                 : DataSourceType.FILE;
1030         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1031       }
1032       else
1033       {
1034         Rectangle bounds = this.getBounds();
1035
1036         FileLoader loader = new FileLoader();
1037         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1038                 : DataSourceType.FILE;
1039         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1040                 protocol, currentFileFormat);
1041
1042         newframe.setBounds(bounds);
1043         if (featureSettings != null && featureSettings.isShowing())
1044         {
1045           final Rectangle fspos = featureSettings.frame.getBounds();
1046           // TODO: need a 'show feature settings' function that takes bounds -
1047           // need to refactor Desktop.addFrame
1048           newframe.featureSettings_actionPerformed(null);
1049           final FeatureSettings nfs = newframe.featureSettings;
1050           SwingUtilities.invokeLater(new Runnable()
1051           {
1052             @Override
1053             public void run()
1054             {
1055               nfs.frame.setBounds(fspos);
1056             }
1057           });
1058           this.featureSettings.close();
1059           this.featureSettings = null;
1060         }
1061         this.closeMenuItem_actionPerformed(true);
1062       }
1063     }
1064   }
1065
1066   @Override
1067   public void addFromText_actionPerformed(ActionEvent e)
1068   {
1069     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1070             .getAlignPanel());
1071   }
1072
1073   @Override
1074   public void addFromURL_actionPerformed(ActionEvent e)
1075   {
1076     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1077   }
1078
1079   @Override
1080   public void save_actionPerformed(ActionEvent e)
1081   {
1082     if (fileName == null || (currentFileFormat == null)
1083             || fileName.startsWith("http"))
1084     {
1085       saveAs_actionPerformed(null);
1086     }
1087     else
1088     {
1089       saveAlignment(fileName, currentFileFormat);
1090     }
1091   }
1092
1093   /**
1094    * DOCUMENT ME!
1095    *
1096    * @param e
1097    *          DOCUMENT ME!
1098    */
1099   @Override
1100   public void saveAs_actionPerformed(ActionEvent e)
1101   {
1102     String format = currentFileFormat == null ? null : currentFileFormat
1103             .getName();
1104     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1105             Cache.getProperty("LAST_DIRECTORY"), format);
1106
1107     chooser.setFileView(new JalviewFileView());
1108     chooser.setDialogTitle(MessageManager
1109             .getString("label.save_alignment_to_file"));
1110     chooser.setToolTipText(MessageManager.getString("action.save"));
1111
1112     int value = chooser.showSaveDialog(this);
1113
1114     if (value == JalviewFileChooser.APPROVE_OPTION)
1115     {
1116       currentFileFormat = chooser.getSelectedFormat();
1117       while (currentFileFormat == null)
1118       {
1119         JvOptionPane
1120                 .showInternalMessageDialog(
1121                         Desktop.desktop,
1122                         MessageManager
1123                                 .getString("label.select_file_format_before_saving"),
1124                         MessageManager
1125                                 .getString("label.file_format_not_specified"),
1126                         JvOptionPane.WARNING_MESSAGE);
1127         currentFileFormat = chooser.getSelectedFormat();
1128         value = chooser.showSaveDialog(this);
1129         if (value != JalviewFileChooser.APPROVE_OPTION)
1130         {
1131           return;
1132         }
1133       }
1134
1135       fileName = chooser.getSelectedFile().getPath();
1136
1137       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1138
1139       Cache.setProperty("LAST_DIRECTORY", fileName);
1140       saveAlignment(fileName, currentFileFormat);
1141     }
1142   }
1143
1144   public boolean saveAlignment(String file, FileFormatI format)
1145   {
1146     boolean success = true;
1147
1148     if (FileFormat.Jalview.equals(format))
1149     {
1150       String shortName = title;
1151
1152       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1153       {
1154         shortName = shortName.substring(shortName
1155                 .lastIndexOf(java.io.File.separatorChar) + 1);
1156       }
1157
1158       success = new Jalview2XML().saveAlignment(this, file, shortName);
1159
1160       statusBar.setText(MessageManager.formatMessage(
1161               "label.successfully_saved_to_file_in_format", new Object[] {
1162                   fileName, format }));
1163
1164     }
1165     else
1166     {
1167       AlignmentExportData exportData = getAlignmentForExport(format,
1168               viewport, null);
1169       if (exportData.getSettings().isCancelled())
1170       {
1171         return false;
1172       }
1173       FormatAdapter f = new FormatAdapter(alignPanel,
1174               exportData.getSettings());
1175       String output = f.formatSequences(
1176               format,
1177               exportData.getAlignment(), // class cast exceptions will
1178               // occur in the distant future
1179               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180               f.getCacheSuffixDefault(format), viewport.getAlignment()
1181                       .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",
1198                   new Object[] { 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",
1211                       new Object[] { fileName }), MessageManager
1212               .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().forName(
1244             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
1260                               .getStartEndPostions(), viewport
1261                               .getAlignment().getHiddenColumns()));
1262       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1263               "label.alignment_output_command",
1264               new Object[] { e.getActionCommand() }), 600, 500);
1265     } catch (OutOfMemoryError oom)
1266     {
1267       new OOMWarning("Outputting alignment as " + e.getActionCommand(), 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(MessageManager
1412             .getString("label.load_jalview_annotations"));
1413     chooser.setToolTipText(MessageManager
1414             .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.formatMessage(
1514               "label.undo_command",
1515               new Object[] { 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.formatMessage(
1529               "label.redo_command",
1530               new Object[] { 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
1603                 .warn("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, originalSource
1612               .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
1643                 .warn("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, originalSource
1652               .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.get(viewport
1668               .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().getSequenceAt(
1723               alignPanel.getSeqPanel().seqCanvas.cursorY));
1724     }
1725     else if (viewport.getSelectionGroup() != null
1726             && viewport.getSelectionGroup().getSize() != viewport
1727                     .getAlignment().getHeight())
1728     {
1729       sg = viewport.getSelectionGroup().getSequences(
1730               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,
1760               size, viewport.getGapCharacter());
1761     }
1762     else
1763     {
1764       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1765               size, 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
1811               .appendSlideCommand((SlideSequencesCommand) historyList
1812                       .peek());
1813     }
1814
1815     if (!appendHistoryItem)
1816     {
1817       addHistoryItem(ssc);
1818     }
1819
1820     repaint();
1821   }
1822
1823   /**
1824    * DOCUMENT ME!
1825    *
1826    * @param e
1827    *          DOCUMENT ME!
1828    */
1829   @Override
1830   protected void copy_actionPerformed(ActionEvent e)
1831   {
1832     System.gc();
1833     if (viewport.getSelectionGroup() == null)
1834     {
1835       return;
1836     }
1837     // TODO: preserve the ordering of displayed alignment annotation in any
1838     // internal paste (particularly sequence associated annotation)
1839     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1840     String[] omitHidden = null;
1841
1842     if (viewport.hasHiddenColumns())
1843     {
1844       omitHidden = viewport.getViewAsString(true);
1845     }
1846
1847     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1848             seqs, omitHidden, null);
1849
1850     StringSelection ss = new StringSelection(output);
1851
1852     try
1853     {
1854       jalview.gui.Desktop.internalCopy = true;
1855       // Its really worth setting the clipboard contents
1856       // to empty before setting the large StringSelection!!
1857       Toolkit.getDefaultToolkit().getSystemClipboard()
1858               .setContents(new StringSelection(""), null);
1859
1860       Toolkit.getDefaultToolkit().getSystemClipboard()
1861               .setContents(ss, Desktop.instance);
1862     } catch (OutOfMemoryError er)
1863     {
1864       new OOMWarning("copying region", er);
1865       return;
1866     }
1867
1868     ArrayList<int[]> hiddenColumns = null;
1869     if (viewport.hasHiddenColumns())
1870     {
1871       hiddenColumns = new ArrayList<>();
1872       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1873       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1874       ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1875               .getHiddenColumns().getHiddenColumnsCopy();
1876       for (int[] region : hiddenRegions)
1877       {
1878         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1879         {
1880           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1881               region[1] - hiddenOffset });
1882         }
1883       }
1884     }
1885
1886     Desktop.jalviewClipboard = new Object[] { seqs,
1887         viewport.getAlignment().getDataset(), hiddenColumns };
1888     statusBar.setText(MessageManager.formatMessage(
1889             "label.copied_sequences_to_clipboard", new Object[] { Integer
1890                     .valueOf(seqs.length).toString() }));
1891   }
1892
1893   /**
1894    * DOCUMENT ME!
1895    *
1896    * @param e
1897    *          DOCUMENT ME!
1898    */
1899   @Override
1900   protected void pasteNew_actionPerformed(ActionEvent e)
1901   {
1902     paste(true);
1903   }
1904
1905   /**
1906    * DOCUMENT ME!
1907    *
1908    * @param e
1909    *          DOCUMENT ME!
1910    */
1911   @Override
1912   protected void pasteThis_actionPerformed(ActionEvent e)
1913   {
1914     paste(false);
1915   }
1916
1917   /**
1918    * Paste contents of Jalview clipboard
1919    *
1920    * @param newAlignment
1921    *          true to paste to a new alignment, otherwise add to this.
1922    */
1923   void paste(boolean newAlignment)
1924   {
1925     boolean externalPaste = true;
1926     try
1927     {
1928       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1929       Transferable contents = c.getContents(this);
1930
1931       if (contents == null)
1932       {
1933         return;
1934       }
1935
1936       String str;
1937       FileFormatI format;
1938       try
1939       {
1940         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1941         if (str.length() < 1)
1942         {
1943           return;
1944         }
1945
1946         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1947
1948       } catch (OutOfMemoryError er)
1949       {
1950         new OOMWarning("Out of memory pasting sequences!!", er);
1951         return;
1952       }
1953
1954       SequenceI[] sequences;
1955       boolean annotationAdded = false;
1956       AlignmentI alignment = null;
1957
1958       if (Desktop.jalviewClipboard != null)
1959       {
1960         // The clipboard was filled from within Jalview, we must use the
1961         // sequences
1962         // And dataset from the copied alignment
1963         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1964         // be doubly sure that we create *new* sequence objects.
1965         sequences = new SequenceI[newseq.length];
1966         for (int i = 0; i < newseq.length; i++)
1967         {
1968           sequences[i] = new Sequence(newseq[i]);
1969         }
1970         alignment = new Alignment(sequences);
1971         externalPaste = false;
1972       }
1973       else
1974       {
1975         // parse the clipboard as an alignment.
1976         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1977                 format);
1978         sequences = alignment.getSequencesArray();
1979       }
1980
1981       int alwidth = 0;
1982       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1983       int fgroup = -1;
1984
1985       if (newAlignment)
1986       {
1987
1988         if (Desktop.jalviewClipboard != null)
1989         {
1990           // dataset is inherited
1991           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1992         }
1993         else
1994         {
1995           // new dataset is constructed
1996           alignment.setDataset(null);
1997         }
1998         alwidth = alignment.getWidth() + 1;
1999       }
2000       else
2001       {
2002         AlignmentI pastedal = alignment; // preserve pasted alignment object
2003         // Add pasted sequences and dataset into existing alignment.
2004         alignment = viewport.getAlignment();
2005         alwidth = alignment.getWidth() + 1;
2006         // decide if we need to import sequences from an existing dataset
2007         boolean importDs = Desktop.jalviewClipboard != null
2008                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2009         // importDs==true instructs us to copy over new dataset sequences from
2010         // an existing alignment
2011         Vector newDs = (importDs) ? new Vector() : null; // used to create
2012         // minimum dataset set
2013
2014         for (int i = 0; i < sequences.length; i++)
2015         {
2016           if (importDs)
2017           {
2018             newDs.addElement(null);
2019           }
2020           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2021           // paste
2022           if (importDs && ds != null)
2023           {
2024             if (!newDs.contains(ds))
2025             {
2026               newDs.setElementAt(ds, i);
2027               ds = new Sequence(ds);
2028               // update with new dataset sequence
2029               sequences[i].setDatasetSequence(ds);
2030             }
2031             else
2032             {
2033               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2034             }
2035           }
2036           else
2037           {
2038             // copy and derive new dataset sequence
2039             sequences[i] = sequences[i].deriveSequence();
2040             alignment.getDataset().addSequence(
2041                     sequences[i].getDatasetSequence());
2042             // TODO: avoid creation of duplicate dataset sequences with a
2043             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2044           }
2045           alignment.addSequence(sequences[i]); // merges dataset
2046         }
2047         if (newDs != null)
2048         {
2049           newDs.clear(); // tidy up
2050         }
2051         if (alignment.getAlignmentAnnotation() != null)
2052         {
2053           for (AlignmentAnnotation alan : alignment
2054                   .getAlignmentAnnotation())
2055           {
2056             if (alan.graphGroup > fgroup)
2057             {
2058               fgroup = alan.graphGroup;
2059             }
2060           }
2061         }
2062         if (pastedal.getAlignmentAnnotation() != null)
2063         {
2064           // Add any annotation attached to alignment.
2065           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2066           for (int i = 0; i < alann.length; i++)
2067           {
2068             annotationAdded = true;
2069             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2070             {
2071               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2072               if (newann.graphGroup > -1)
2073               {
2074                 if (newGraphGroups.size() <= newann.graphGroup
2075                         || newGraphGroups.get(newann.graphGroup) == null)
2076                 {
2077                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2078                   {
2079                     newGraphGroups.add(q, null);
2080                   }
2081                   newGraphGroups.set(newann.graphGroup, new Integer(
2082                           ++fgroup));
2083                 }
2084                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2085                         .intValue();
2086               }
2087
2088               newann.padAnnotation(alwidth);
2089               alignment.addAnnotation(newann);
2090             }
2091           }
2092         }
2093       }
2094       if (!newAlignment)
2095       {
2096         // /////
2097         // ADD HISTORY ITEM
2098         //
2099         addHistoryItem(new EditCommand(
2100                 MessageManager.getString("label.add_sequences"),
2101                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2102       }
2103       // Add any annotations attached to sequences
2104       for (int i = 0; i < sequences.length; i++)
2105       {
2106         if (sequences[i].getAnnotation() != null)
2107         {
2108           AlignmentAnnotation newann;
2109           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2110           {
2111             annotationAdded = true;
2112             newann = sequences[i].getAnnotation()[a];
2113             newann.adjustForAlignment();
2114             newann.padAnnotation(alwidth);
2115             if (newann.graphGroup > -1)
2116             {
2117               if (newann.graphGroup > -1)
2118               {
2119                 if (newGraphGroups.size() <= newann.graphGroup
2120                         || newGraphGroups.get(newann.graphGroup) == null)
2121                 {
2122                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2123                   {
2124                     newGraphGroups.add(q, null);
2125                   }
2126                   newGraphGroups.set(newann.graphGroup, new Integer(
2127                           ++fgroup));
2128                 }
2129                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2130                         .intValue();
2131               }
2132             }
2133             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2134             // was
2135             // duplicated
2136             // earlier
2137             alignment
2138                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2139           }
2140         }
2141       }
2142       if (!newAlignment)
2143       {
2144
2145         // propagate alignment changed.
2146         vpRanges.setEndSeq(alignment.getHeight());
2147         if (annotationAdded)
2148         {
2149           // Duplicate sequence annotation in all views.
2150           AlignmentI[] alview = this.getViewAlignments();
2151           for (int i = 0; i < sequences.length; i++)
2152           {
2153             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2154             if (sann == null)
2155             {
2156               continue;
2157             }
2158             for (int avnum = 0; avnum < alview.length; avnum++)
2159             {
2160               if (alview[avnum] != alignment)
2161               {
2162                 // duplicate in a view other than the one with input focus
2163                 int avwidth = alview[avnum].getWidth() + 1;
2164                 // this relies on sann being preserved after we
2165                 // modify the sequence's annotation array for each duplication
2166                 for (int a = 0; a < sann.length; a++)
2167                 {
2168                   AlignmentAnnotation newann = new AlignmentAnnotation(
2169                           sann[a]);
2170                   sequences[i].addAlignmentAnnotation(newann);
2171                   newann.padAnnotation(avwidth);
2172                   alview[avnum].addAnnotation(newann); // annotation was
2173                   // duplicated earlier
2174                   // TODO JAL-1145 graphGroups are not updated for sequence
2175                   // annotation added to several views. This may cause
2176                   // strangeness
2177                   alview[avnum].setAnnotationIndex(newann, a);
2178                 }
2179               }
2180             }
2181           }
2182           buildSortByAnnotationScoresMenu();
2183         }
2184         viewport.firePropertyChange("alignment", null,
2185                 alignment.getSequences());
2186         if (alignPanels != null)
2187         {
2188           for (AlignmentPanel ap : alignPanels)
2189           {
2190             ap.validateAnnotationDimensions(false);
2191           }
2192         }
2193         else
2194         {
2195           alignPanel.validateAnnotationDimensions(false);
2196         }
2197
2198       }
2199       else
2200       {
2201         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2202                 DEFAULT_HEIGHT);
2203         String newtitle = new String("Copied sequences");
2204
2205         if (Desktop.jalviewClipboard != null
2206                 && Desktop.jalviewClipboard[2] != null)
2207         {
2208           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2209           for (int[] region : hc)
2210           {
2211             af.viewport.hideColumns(region[0], region[1]);
2212           }
2213         }
2214
2215         // >>>This is a fix for the moment, until a better solution is
2216         // found!!<<<
2217         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2218                 .transferSettings(
2219                         alignPanel.getSeqPanel().seqCanvas
2220                                 .getFeatureRenderer());
2221
2222         // TODO: maintain provenance of an alignment, rather than just make the
2223         // title a concatenation of operations.
2224         if (!externalPaste)
2225         {
2226           if (title.startsWith("Copied sequences"))
2227           {
2228             newtitle = title;
2229           }
2230           else
2231           {
2232             newtitle = newtitle.concat("- from " + title);
2233           }
2234         }
2235         else
2236         {
2237           newtitle = new String("Pasted sequences");
2238         }
2239
2240         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2241                 DEFAULT_HEIGHT);
2242
2243       }
2244
2245     } catch (Exception ex)
2246     {
2247       ex.printStackTrace();
2248       System.out.println("Exception whilst pasting: " + ex);
2249       // could be anything being pasted in here
2250     }
2251
2252   }
2253
2254   @Override
2255   protected void expand_newalign(ActionEvent e)
2256   {
2257     try
2258     {
2259       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2260               .getAlignment(), -1);
2261       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2262               DEFAULT_HEIGHT);
2263       String newtitle = new String("Flanking alignment");
2264
2265       if (Desktop.jalviewClipboard != null
2266               && Desktop.jalviewClipboard[2] != null)
2267       {
2268         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2269         for (int region[] : hc)
2270         {
2271           af.viewport.hideColumns(region[0], region[1]);
2272         }
2273       }
2274
2275       // >>>This is a fix for the moment, until a better solution is
2276       // found!!<<<
2277       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2278               .transferSettings(
2279                       alignPanel.getSeqPanel().seqCanvas
2280                               .getFeatureRenderer());
2281
2282       // TODO: maintain provenance of an alignment, rather than just make the
2283       // title a concatenation of operations.
2284       {
2285         if (title.startsWith("Copied sequences"))
2286         {
2287           newtitle = title;
2288         }
2289         else
2290         {
2291           newtitle = newtitle.concat("- from " + title);
2292         }
2293       }
2294
2295       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2296
2297     } catch (Exception ex)
2298     {
2299       ex.printStackTrace();
2300       System.out.println("Exception whilst pasting: " + ex);
2301       // could be anything being pasted in here
2302     } catch (OutOfMemoryError oom)
2303     {
2304       new OOMWarning("Viewing flanking region of alignment", oom);
2305     }
2306   }
2307
2308   /**
2309    * DOCUMENT ME!
2310    *
2311    * @param e
2312    *          DOCUMENT ME!
2313    */
2314   @Override
2315   protected void cut_actionPerformed(ActionEvent e)
2316   {
2317     copy_actionPerformed(null);
2318     delete_actionPerformed(null);
2319   }
2320
2321   /**
2322    * DOCUMENT ME!
2323    *
2324    * @param e
2325    *          DOCUMENT ME!
2326    */
2327   @Override
2328   protected void delete_actionPerformed(ActionEvent evt)
2329   {
2330
2331     SequenceGroup sg = viewport.getSelectionGroup();
2332     if (sg == null)
2333     {
2334       return;
2335     }
2336
2337     /*
2338      * If the cut affects all sequences, warn, remove highlighted columns
2339      */
2340     if (sg.getSize() == viewport.getAlignment().getHeight())
2341     {
2342       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2343               .getAlignment().getWidth()) ? true : false;
2344       if (isEntireAlignWidth)
2345       {
2346         int confirm = JvOptionPane.showConfirmDialog(this,
2347                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2348                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2349                 JvOptionPane.OK_CANCEL_OPTION);
2350
2351         if (confirm == JvOptionPane.CANCEL_OPTION
2352                 || confirm == JvOptionPane.CLOSED_OPTION)
2353         {
2354           return;
2355         }
2356       }
2357       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2358               sg.getEndRes() + 1);
2359     }
2360     SequenceI[] cut = sg.getSequences()
2361             .toArray(new SequenceI[sg.getSize()]);
2362
2363     addHistoryItem(new EditCommand(
2364             MessageManager.getString("label.cut_sequences"), Action.CUT,
2365             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2366             viewport.getAlignment()));
2367
2368     viewport.setSelectionGroup(null);
2369     viewport.sendSelection();
2370     viewport.getAlignment().deleteGroup(sg);
2371
2372     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2373             .getSequences());
2374     if (viewport.getAlignment().getHeight() < 1)
2375     {
2376       try
2377       {
2378         this.setClosed(true);
2379       } catch (Exception ex)
2380       {
2381       }
2382     }
2383   }
2384
2385   /**
2386    * DOCUMENT ME!
2387    *
2388    * @param e
2389    *          DOCUMENT ME!
2390    */
2391   @Override
2392   protected void deleteGroups_actionPerformed(ActionEvent e)
2393   {
2394     if (avc.deleteGroups())
2395     {
2396       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2397       alignPanel.updateAnnotation();
2398       alignPanel.paintAlignment(true);
2399     }
2400   }
2401
2402   /**
2403    * DOCUMENT ME!
2404    *
2405    * @param e
2406    *          DOCUMENT ME!
2407    */
2408   @Override
2409   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2410   {
2411     SequenceGroup sg = new SequenceGroup();
2412
2413     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2414     {
2415       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2416     }
2417
2418     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2419     viewport.setSelectionGroup(sg);
2420     viewport.sendSelection();
2421     // JAL-2034 - should delegate to
2422     // alignPanel to decide if overview needs
2423     // updating.
2424     alignPanel.paintAlignment(false);
2425     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2426   }
2427
2428   /**
2429    * DOCUMENT ME!
2430    *
2431    * @param e
2432    *          DOCUMENT ME!
2433    */
2434   @Override
2435   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2436   {
2437     if (viewport.cursorMode)
2438     {
2439       alignPanel.getSeqPanel().keyboardNo1 = null;
2440       alignPanel.getSeqPanel().keyboardNo2 = null;
2441     }
2442     viewport.setSelectionGroup(null);
2443     viewport.getColumnSelection().clear();
2444     viewport.setSelectionGroup(null);
2445     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2446     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2447     // JAL-2034 - should delegate to
2448     // alignPanel to decide if overview needs
2449     // updating.
2450     alignPanel.paintAlignment(false);
2451     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2452     viewport.sendSelection();
2453   }
2454
2455   /**
2456    * DOCUMENT ME!
2457    *
2458    * @param e
2459    *          DOCUMENT ME!
2460    */
2461   @Override
2462   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2463   {
2464     SequenceGroup sg = viewport.getSelectionGroup();
2465
2466     if (sg == null)
2467     {
2468       selectAllSequenceMenuItem_actionPerformed(null);
2469
2470       return;
2471     }
2472
2473     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2474     {
2475       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2476     }
2477     // JAL-2034 - should delegate to
2478     // alignPanel to decide if overview needs
2479     // updating.
2480
2481     alignPanel.paintAlignment(true);
2482     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2483     viewport.sendSelection();
2484   }
2485
2486   @Override
2487   public void invertColSel_actionPerformed(ActionEvent e)
2488   {
2489     viewport.invertColumnSelection();
2490     alignPanel.paintAlignment(true);
2491     viewport.sendSelection();
2492   }
2493
2494   /**
2495    * DOCUMENT ME!
2496    *
2497    * @param e
2498    *          DOCUMENT ME!
2499    */
2500   @Override
2501   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2502   {
2503     trimAlignment(true);
2504   }
2505
2506   /**
2507    * DOCUMENT ME!
2508    *
2509    * @param e
2510    *          DOCUMENT ME!
2511    */
2512   @Override
2513   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2514   {
2515     trimAlignment(false);
2516   }
2517
2518   void trimAlignment(boolean trimLeft)
2519   {
2520     ColumnSelection colSel = viewport.getColumnSelection();
2521     int column;
2522
2523     if (!colSel.isEmpty())
2524     {
2525       if (trimLeft)
2526       {
2527         column = colSel.getMin();
2528       }
2529       else
2530       {
2531         column = colSel.getMax();
2532       }
2533
2534       SequenceI[] seqs;
2535       if (viewport.getSelectionGroup() != null)
2536       {
2537         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2538                 viewport.getHiddenRepSequences());
2539       }
2540       else
2541       {
2542         seqs = viewport.getAlignment().getSequencesArray();
2543       }
2544
2545       TrimRegionCommand trimRegion;
2546       if (trimLeft)
2547       {
2548         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2549                 column, viewport.getAlignment());
2550         vpRanges.setStartRes(0);
2551       }
2552       else
2553       {
2554         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2555                 column, viewport.getAlignment());
2556       }
2557
2558       statusBar.setText(MessageManager.formatMessage(
2559               "label.removed_columns",
2560               new String[] { Integer.valueOf(trimRegion.getSize())
2561                       .toString() }));
2562
2563       addHistoryItem(trimRegion);
2564
2565       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2566       {
2567         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2568                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2569         {
2570           viewport.getAlignment().deleteGroup(sg);
2571         }
2572       }
2573
2574       viewport.firePropertyChange("alignment", null, viewport
2575               .getAlignment().getSequences());
2576     }
2577   }
2578
2579   /**
2580    * DOCUMENT ME!
2581    *
2582    * @param e
2583    *          DOCUMENT ME!
2584    */
2585   @Override
2586   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2587   {
2588     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2589
2590     SequenceI[] seqs;
2591     if (viewport.getSelectionGroup() != null)
2592     {
2593       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2594               viewport.getHiddenRepSequences());
2595       start = viewport.getSelectionGroup().getStartRes();
2596       end = viewport.getSelectionGroup().getEndRes();
2597     }
2598     else
2599     {
2600       seqs = viewport.getAlignment().getSequencesArray();
2601     }
2602
2603     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2604             "Remove Gapped Columns", seqs, start, end,
2605             viewport.getAlignment());
2606
2607     addHistoryItem(removeGapCols);
2608
2609     statusBar.setText(MessageManager.formatMessage(
2610             "label.removed_empty_columns",
2611             new Object[] { Integer.valueOf(removeGapCols.getSize())
2612                     .toString() }));
2613
2614     // This is to maintain viewport position on first residue
2615     // of first sequence
2616     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2617     int startRes = seq.findPosition(vpRanges.getStartRes());
2618     // ShiftList shifts;
2619     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2620     // edit.alColumnChanges=shifts.getInverse();
2621     // if (viewport.hasHiddenColumns)
2622     // viewport.getColumnSelection().compensateForEdits(shifts);
2623     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2624     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2625             .getSequences());
2626
2627   }
2628
2629   /**
2630    * DOCUMENT ME!
2631    *
2632    * @param e
2633    *          DOCUMENT ME!
2634    */
2635   @Override
2636   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2637   {
2638     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2639
2640     SequenceI[] seqs;
2641     if (viewport.getSelectionGroup() != null)
2642     {
2643       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2644               viewport.getHiddenRepSequences());
2645       start = viewport.getSelectionGroup().getStartRes();
2646       end = viewport.getSelectionGroup().getEndRes();
2647     }
2648     else
2649     {
2650       seqs = viewport.getAlignment().getSequencesArray();
2651     }
2652
2653     // This is to maintain viewport position on first residue
2654     // of first sequence
2655     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2656     int startRes = seq.findPosition(vpRanges.getStartRes());
2657
2658     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2659             viewport.getAlignment()));
2660
2661     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2662
2663     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2664             .getSequences());
2665
2666   }
2667
2668   /**
2669    * DOCUMENT ME!
2670    *
2671    * @param e
2672    *          DOCUMENT ME!
2673    */
2674   @Override
2675   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2676   {
2677     viewport.setPadGaps(padGapsMenuitem.isSelected());
2678     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2679             .getSequences());
2680   }
2681
2682   /**
2683    * DOCUMENT ME!
2684    *
2685    * @param e
2686    *          DOCUMENT ME!
2687    */
2688   @Override
2689   public void findMenuItem_actionPerformed(ActionEvent e)
2690   {
2691     new Finder();
2692   }
2693
2694   /**
2695    * Create a new view of the current alignment.
2696    */
2697   @Override
2698   public void newView_actionPerformed(ActionEvent e)
2699   {
2700     newView(null, true);
2701   }
2702
2703   /**
2704    * Creates and shows a new view of the current alignment.
2705    *
2706    * @param viewTitle
2707    *          title of newly created view; if null, one will be generated
2708    * @param copyAnnotation
2709    *          if true then duplicate all annnotation, groups and settings
2710    * @return new alignment panel, already displayed.
2711    */
2712   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2713   {
2714     /*
2715      * Create a new AlignmentPanel (with its own, new Viewport)
2716      */
2717     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2718             true);
2719     if (!copyAnnotation)
2720     {
2721       /*
2722        * remove all groups and annotation except for the automatic stuff
2723        */
2724       newap.av.getAlignment().deleteAllGroups();
2725       newap.av.getAlignment().deleteAllAnnotations(false);
2726     }
2727
2728     newap.av.setGatherViewsHere(false);
2729
2730     if (viewport.viewName == null)
2731     {
2732       viewport.viewName = MessageManager
2733               .getString("label.view_name_original");
2734     }
2735
2736     /*
2737      * Views share the same edits undo and redo stacks
2738      */
2739     newap.av.setHistoryList(viewport.getHistoryList());
2740     newap.av.setRedoList(viewport.getRedoList());
2741
2742     /*
2743      * Views share the same mappings; need to deregister any new mappings
2744      * created by copyAlignPanel, and register the new reference to the shared
2745      * mappings
2746      */
2747     newap.av.replaceMappings(viewport.getAlignment());
2748
2749     /*
2750      * start up cDNA consensus (if applicable) now mappings are in place
2751      */
2752     if (newap.av.initComplementConsensus())
2753     {
2754       newap.refresh(true); // adjust layout of annotations
2755     }
2756
2757     newap.av.viewName = getNewViewName(viewTitle);
2758
2759     addAlignmentPanel(newap, true);
2760     newap.alignmentChanged();
2761
2762     if (alignPanels.size() == 2)
2763     {
2764       viewport.setGatherViewsHere(true);
2765     }
2766     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2767     return newap;
2768   }
2769
2770   /**
2771    * Make a new name for the view, ensuring it is unique within the current
2772    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2773    * these now use viewId. Unique view names are still desirable for usability.)
2774    *
2775    * @param viewTitle
2776    * @return
2777    */
2778   protected String getNewViewName(String viewTitle)
2779   {
2780     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2781     boolean addFirstIndex = false;
2782     if (viewTitle == null || viewTitle.trim().length() == 0)
2783     {
2784       viewTitle = MessageManager.getString("action.view");
2785       addFirstIndex = true;
2786     }
2787     else
2788     {
2789       index = 1;// we count from 1 if given a specific name
2790     }
2791     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2792
2793     List<Component> comps = PaintRefresher.components.get(viewport
2794             .getSequenceSetId());
2795
2796     List<String> existingNames = getExistingViewNames(comps);
2797
2798     while (existingNames.contains(newViewName))
2799     {
2800       newViewName = viewTitle + " " + (++index);
2801     }
2802     return newViewName;
2803   }
2804
2805   /**
2806    * Returns a list of distinct view names found in the given list of
2807    * components. View names are held on the viewport of an AlignmentPanel.
2808    *
2809    * @param comps
2810    * @return
2811    */
2812   protected List<String> getExistingViewNames(List<Component> comps)
2813   {
2814     List<String> existingNames = new ArrayList<>();
2815     for (Component comp : comps)
2816     {
2817       if (comp instanceof AlignmentPanel)
2818       {
2819         AlignmentPanel ap = (AlignmentPanel) comp;
2820         if (!existingNames.contains(ap.av.viewName))
2821         {
2822           existingNames.add(ap.av.viewName);
2823         }
2824       }
2825     }
2826     return existingNames;
2827   }
2828
2829   /**
2830    * Explode tabbed views into separate windows.
2831    */
2832   @Override
2833   public void expandViews_actionPerformed(ActionEvent e)
2834   {
2835     Desktop.explodeViews(this);
2836   }
2837
2838   /**
2839    * Gather views in separate windows back into a tabbed presentation.
2840    */
2841   @Override
2842   public void gatherViews_actionPerformed(ActionEvent e)
2843   {
2844     Desktop.instance.gatherViews(this);
2845   }
2846
2847   /**
2848    * DOCUMENT ME!
2849    *
2850    * @param e
2851    *          DOCUMENT ME!
2852    */
2853   @Override
2854   public void font_actionPerformed(ActionEvent e)
2855   {
2856     new FontChooser(alignPanel);
2857   }
2858
2859   /**
2860    * DOCUMENT ME!
2861    *
2862    * @param e
2863    *          DOCUMENT ME!
2864    */
2865   @Override
2866   protected void seqLimit_actionPerformed(ActionEvent e)
2867   {
2868     viewport.setShowJVSuffix(seqLimits.isSelected());
2869
2870     alignPanel.getIdPanel().getIdCanvas()
2871             .setPreferredSize(alignPanel.calculateIdWidth());
2872     alignPanel.paintAlignment(true);
2873   }
2874
2875   @Override
2876   public void idRightAlign_actionPerformed(ActionEvent e)
2877   {
2878     viewport.setRightAlignIds(idRightAlign.isSelected());
2879     alignPanel.paintAlignment(true);
2880   }
2881
2882   @Override
2883   public void centreColumnLabels_actionPerformed(ActionEvent e)
2884   {
2885     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2886     alignPanel.paintAlignment(true);
2887   }
2888
2889   /*
2890    * (non-Javadoc)
2891    *
2892    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2893    */
2894   @Override
2895   protected void followHighlight_actionPerformed()
2896   {
2897     /*
2898      * Set the 'follow' flag on the Viewport (and scroll to position if now
2899      * true).
2900      */
2901     final boolean state = this.followHighlightMenuItem.getState();
2902     viewport.setFollowHighlight(state);
2903     if (state)
2904     {
2905       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2906     }
2907   }
2908
2909   /**
2910    * DOCUMENT ME!
2911    *
2912    * @param e
2913    *          DOCUMENT ME!
2914    */
2915   @Override
2916   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2917   {
2918     viewport.setColourText(colourTextMenuItem.isSelected());
2919     alignPanel.paintAlignment(true);
2920   }
2921
2922   /**
2923    * DOCUMENT ME!
2924    *
2925    * @param e
2926    *          DOCUMENT ME!
2927    */
2928   @Override
2929   public void wrapMenuItem_actionPerformed(ActionEvent e)
2930   {
2931     scaleAbove.setVisible(wrapMenuItem.isSelected());
2932     scaleLeft.setVisible(wrapMenuItem.isSelected());
2933     scaleRight.setVisible(wrapMenuItem.isSelected());
2934     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2935     alignPanel.updateLayout();
2936   }
2937
2938   @Override
2939   public void showAllSeqs_actionPerformed(ActionEvent e)
2940   {
2941     viewport.showAllHiddenSeqs();
2942   }
2943
2944   @Override
2945   public void showAllColumns_actionPerformed(ActionEvent e)
2946   {
2947     viewport.showAllHiddenColumns();
2948     repaint();
2949     viewport.sendSelection();
2950   }
2951
2952   @Override
2953   public void hideSelSequences_actionPerformed(ActionEvent e)
2954   {
2955     viewport.hideAllSelectedSeqs();
2956     // alignPanel.paintAlignment(true);
2957   }
2958
2959   /**
2960    * called by key handler and the hide all/show all menu items
2961    *
2962    * @param toggleSeqs
2963    * @param toggleCols
2964    */
2965   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2966   {
2967
2968     boolean hide = false;
2969     SequenceGroup sg = viewport.getSelectionGroup();
2970     if (!toggleSeqs && !toggleCols)
2971     {
2972       // Hide everything by the current selection - this is a hack - we do the
2973       // invert and then hide
2974       // first check that there will be visible columns after the invert.
2975       if (viewport.hasSelectedColumns()
2976               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2977                       .getEndRes()))
2978       {
2979         // now invert the sequence set, if required - empty selection implies
2980         // that no hiding is required.
2981         if (sg != null)
2982         {
2983           invertSequenceMenuItem_actionPerformed(null);
2984           sg = viewport.getSelectionGroup();
2985           toggleSeqs = true;
2986
2987         }
2988         viewport.expandColSelection(sg, true);
2989         // finally invert the column selection and get the new sequence
2990         // selection.
2991         invertColSel_actionPerformed(null);
2992         toggleCols = true;
2993       }
2994     }
2995
2996     if (toggleSeqs)
2997     {
2998       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2999       {
3000         hideSelSequences_actionPerformed(null);
3001         hide = true;
3002       }
3003       else if (!(toggleCols && viewport.hasSelectedColumns()))
3004       {
3005         showAllSeqs_actionPerformed(null);
3006       }
3007     }
3008
3009     if (toggleCols)
3010     {
3011       if (viewport.hasSelectedColumns())
3012       {
3013         hideSelColumns_actionPerformed(null);
3014         if (!toggleSeqs)
3015         {
3016           viewport.setSelectionGroup(sg);
3017         }
3018       }
3019       else if (!hide)
3020       {
3021         showAllColumns_actionPerformed(null);
3022       }
3023     }
3024   }
3025
3026   /*
3027    * (non-Javadoc)
3028    *
3029    * @see
3030    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3031    * event.ActionEvent)
3032    */
3033   @Override
3034   public void hideAllButSelection_actionPerformed(ActionEvent e)
3035   {
3036     toggleHiddenRegions(false, false);
3037     viewport.sendSelection();
3038   }
3039
3040   /*
3041    * (non-Javadoc)
3042    *
3043    * @see
3044    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3045    * .ActionEvent)
3046    */
3047   @Override
3048   public void hideAllSelection_actionPerformed(ActionEvent e)
3049   {
3050     SequenceGroup sg = viewport.getSelectionGroup();
3051     viewport.expandColSelection(sg, false);
3052     viewport.hideAllSelectedSeqs();
3053     viewport.hideSelectedColumns();
3054     alignPanel.paintAlignment(true);
3055     viewport.sendSelection();
3056   }
3057
3058   /*
3059    * (non-Javadoc)
3060    *
3061    * @see
3062    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3063    * ActionEvent)
3064    */
3065   @Override
3066   public void showAllhidden_actionPerformed(ActionEvent e)
3067   {
3068     viewport.showAllHiddenColumns();
3069     viewport.showAllHiddenSeqs();
3070     alignPanel.paintAlignment(true);
3071     viewport.sendSelection();
3072   }
3073
3074   @Override
3075   public void hideSelColumns_actionPerformed(ActionEvent e)
3076   {
3077     viewport.hideSelectedColumns();
3078     alignPanel.paintAlignment(true);
3079     viewport.sendSelection();
3080   }
3081
3082   @Override
3083   public void hiddenMarkers_actionPerformed(ActionEvent e)
3084   {
3085     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3086     repaint();
3087   }
3088
3089   /**
3090    * DOCUMENT ME!
3091    *
3092    * @param e
3093    *          DOCUMENT ME!
3094    */
3095   @Override
3096   protected void scaleAbove_actionPerformed(ActionEvent e)
3097   {
3098     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3099     alignPanel.paintAlignment(true);
3100   }
3101
3102   /**
3103    * DOCUMENT ME!
3104    *
3105    * @param e
3106    *          DOCUMENT ME!
3107    */
3108   @Override
3109   protected void scaleLeft_actionPerformed(ActionEvent e)
3110   {
3111     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3112     alignPanel.paintAlignment(true);
3113   }
3114
3115   /**
3116    * DOCUMENT ME!
3117    *
3118    * @param e
3119    *          DOCUMENT ME!
3120    */
3121   @Override
3122   protected void scaleRight_actionPerformed(ActionEvent e)
3123   {
3124     viewport.setScaleRightWrapped(scaleRight.isSelected());
3125     alignPanel.paintAlignment(true);
3126   }
3127
3128   /**
3129    * DOCUMENT ME!
3130    *
3131    * @param e
3132    *          DOCUMENT ME!
3133    */
3134   @Override
3135   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3136   {
3137     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3138     alignPanel.paintAlignment(true);
3139   }
3140
3141   /**
3142    * DOCUMENT ME!
3143    *
3144    * @param e
3145    *          DOCUMENT ME!
3146    */
3147   @Override
3148   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3149   {
3150     viewport.setShowText(viewTextMenuItem.isSelected());
3151     alignPanel.paintAlignment(true);
3152   }
3153
3154   /**
3155    * DOCUMENT ME!
3156    *
3157    * @param e
3158    *          DOCUMENT ME!
3159    */
3160   @Override
3161   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3162   {
3163     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3164     alignPanel.paintAlignment(true);
3165   }
3166
3167   public FeatureSettings featureSettings;
3168
3169   @Override
3170   public FeatureSettingsControllerI getFeatureSettingsUI()
3171   {
3172     return featureSettings;
3173   }
3174
3175   @Override
3176   public void featureSettings_actionPerformed(ActionEvent e)
3177   {
3178     if (featureSettings != null)
3179     {
3180       featureSettings.close();
3181       featureSettings = null;
3182     }
3183     if (!showSeqFeatures.isSelected())
3184     {
3185       // make sure features are actually displayed
3186       showSeqFeatures.setSelected(true);
3187       showSeqFeatures_actionPerformed(null);
3188     }
3189     featureSettings = new FeatureSettings(this);
3190   }
3191
3192   /**
3193    * Set or clear 'Show Sequence Features'
3194    *
3195    * @param evt
3196    *          DOCUMENT ME!
3197    */
3198   @Override
3199   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3200   {
3201     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3202     alignPanel.paintAlignment(true);
3203   }
3204
3205   /**
3206    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3207    * the annotations panel as a whole.
3208    *
3209    * The options to show/hide all annotations should be enabled when the panel
3210    * is shown, and disabled when the panel is hidden.
3211    *
3212    * @param e
3213    */
3214   @Override
3215   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3216   {
3217     final boolean setVisible = annotationPanelMenuItem.isSelected();
3218     viewport.setShowAnnotation(setVisible);
3219     this.showAllSeqAnnotations.setEnabled(setVisible);
3220     this.hideAllSeqAnnotations.setEnabled(setVisible);
3221     this.showAllAlAnnotations.setEnabled(setVisible);
3222     this.hideAllAlAnnotations.setEnabled(setVisible);
3223     alignPanel.updateLayout();
3224   }
3225
3226   @Override
3227   public void alignmentProperties()
3228   {
3229     JEditorPane editPane = new JEditorPane("text/html", "");
3230     editPane.setEditable(false);
3231     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3232             .formatAsHtml();
3233     editPane.setText(MessageManager.formatMessage("label.html_content",
3234             new Object[] { contents.toString() }));
3235     JInternalFrame frame = new JInternalFrame();
3236     frame.getContentPane().add(new JScrollPane(editPane));
3237
3238     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3239             "label.alignment_properties", new Object[] { getTitle() }),
3240             500, 400);
3241   }
3242
3243   /**
3244    * DOCUMENT ME!
3245    *
3246    * @param e
3247    *          DOCUMENT ME!
3248    */
3249   @Override
3250   public void overviewMenuItem_actionPerformed(ActionEvent e)
3251   {
3252     if (alignPanel.overviewPanel != null)
3253     {
3254       return;
3255     }
3256
3257     JInternalFrame frame = new JInternalFrame();
3258     final OverviewPanel overview = new OverviewPanel(alignPanel);
3259     frame.setContentPane(overview);
3260     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3261             "label.overview_params", new Object[] { this.getTitle() }),
3262             true, frame.getWidth(), frame.getHeight(), true, true);
3263     frame.pack();
3264     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3265     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3266     {
3267       @Override
3268       public void internalFrameClosed(
3269               javax.swing.event.InternalFrameEvent evt)
3270       {
3271         overview.dispose();
3272         alignPanel.setOverviewPanel(null);
3273       };
3274     });
3275
3276     alignPanel.setOverviewPanel(overview);
3277   }
3278
3279   @Override
3280   public void textColour_actionPerformed()
3281   {
3282     new TextColourChooser().chooseColour(alignPanel, null);
3283   }
3284
3285   /*
3286    * public void covariationColour_actionPerformed() {
3287    * changeColour(new
3288    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3289    * ()[0])); }
3290    */
3291   @Override
3292   public void annotationColour_actionPerformed()
3293   {
3294     new AnnotationColourChooser(viewport, alignPanel);
3295   }
3296
3297   @Override
3298   public void annotationColumn_actionPerformed(ActionEvent e)
3299   {
3300     new AnnotationColumnChooser(viewport, alignPanel);
3301   }
3302
3303   /**
3304    * Action on the user checking or unchecking the option to apply the selected
3305    * colour scheme to all groups. If unchecked, groups may have their own
3306    * independent colour schemes.
3307    *
3308    * @param selected
3309    */
3310   @Override
3311   public void applyToAllGroups_actionPerformed(boolean selected)
3312   {
3313     viewport.setColourAppliesToAllGroups(selected);
3314   }
3315
3316   /**
3317    * Action on user selecting a colour from the colour menu
3318    *
3319    * @param name
3320    *          the name (not the menu item label!) of the colour scheme
3321    */
3322   @Override
3323   public void changeColour_actionPerformed(String name)
3324   {
3325     /*
3326      * 'User Defined' opens a panel to configure or load a
3327      * user-defined colour scheme
3328      */
3329     if (ResidueColourScheme.USER_DEFINED.equals(name))
3330     {
3331       new UserDefinedColours(alignPanel);
3332       return;
3333     }
3334
3335     /*
3336      * otherwise set the chosen colour scheme (or null for 'None')
3337      */
3338     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3339             viewport.getAlignment(), viewport.getHiddenRepSequences());
3340     changeColour(cs);
3341   }
3342
3343   /**
3344    * Actions on setting or changing the alignment colour scheme
3345    *
3346    * @param cs
3347    */
3348   @Override
3349   public void changeColour(ColourSchemeI cs)
3350   {
3351     // TODO: pull up to controller method
3352     ColourMenuHelper.setColourSelected(colourMenu, cs);
3353
3354     viewport.setGlobalColourScheme(cs);
3355
3356     alignPanel.paintAlignment(true);
3357   }
3358
3359   /**
3360    * Show the PID threshold slider panel
3361    */
3362   @Override
3363   protected void modifyPID_actionPerformed()
3364   {
3365     SliderPanel.setPIDSliderSource(alignPanel,
3366             viewport.getResidueShading(), alignPanel.getViewName());
3367     SliderPanel.showPIDSlider();
3368   }
3369
3370   /**
3371    * Show the Conservation slider panel
3372    */
3373   @Override
3374   protected void modifyConservation_actionPerformed()
3375   {
3376     SliderPanel.setConservationSlider(alignPanel,
3377             viewport.getResidueShading(), alignPanel.getViewName());
3378     SliderPanel.showConservationSlider();
3379   }
3380
3381   /**
3382    * Action on selecting or deselecting (Colour) By Conservation
3383    */
3384   @Override
3385   public void conservationMenuItem_actionPerformed(boolean selected)
3386   {
3387     modifyConservation.setEnabled(selected);
3388     viewport.setConservationSelected(selected);
3389     viewport.getResidueShading().setConservationApplied(selected);
3390
3391     changeColour(viewport.getGlobalColourScheme());
3392     if (selected)
3393     {
3394       modifyConservation_actionPerformed();
3395     }
3396     else
3397     {
3398       SliderPanel.hideConservationSlider();
3399     }
3400   }
3401
3402   /**
3403    * Action on selecting or deselecting (Colour) Above PID Threshold
3404    */
3405   @Override
3406   public void abovePIDThreshold_actionPerformed(boolean selected)
3407   {
3408     modifyPID.setEnabled(selected);
3409     viewport.setAbovePIDThreshold(selected);
3410     if (!selected)
3411     {
3412       viewport.getResidueShading().setThreshold(0,
3413               viewport.isIgnoreGapsConsensus());
3414     }
3415
3416     changeColour(viewport.getGlobalColourScheme());
3417     if (selected)
3418     {
3419       modifyPID_actionPerformed();
3420     }
3421     else
3422     {
3423       SliderPanel.hidePIDSlider();
3424     }
3425   }
3426
3427   /**
3428    * DOCUMENT ME!
3429    *
3430    * @param e
3431    *          DOCUMENT ME!
3432    */
3433   @Override
3434   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3435   {
3436     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3437     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3438             .getAlignment().getSequenceAt(0));
3439     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3440             viewport.getAlignment()));
3441     alignPanel.paintAlignment(true);
3442   }
3443
3444   /**
3445    * DOCUMENT ME!
3446    *
3447    * @param e
3448    *          DOCUMENT ME!
3449    */
3450   @Override
3451   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3452   {
3453     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3454     AlignmentSorter.sortByID(viewport.getAlignment());
3455     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3456             viewport.getAlignment()));
3457     alignPanel.paintAlignment(true);
3458   }
3459
3460   /**
3461    * DOCUMENT ME!
3462    *
3463    * @param e
3464    *          DOCUMENT ME!
3465    */
3466   @Override
3467   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3468   {
3469     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470     AlignmentSorter.sortByLength(viewport.getAlignment());
3471     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3472             viewport.getAlignment()));
3473     alignPanel.paintAlignment(true);
3474   }
3475
3476   /**
3477    * DOCUMENT ME!
3478    *
3479    * @param e
3480    *          DOCUMENT ME!
3481    */
3482   @Override
3483   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3484   {
3485     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3486     AlignmentSorter.sortByGroup(viewport.getAlignment());
3487     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3488             viewport.getAlignment()));
3489
3490     alignPanel.paintAlignment(true);
3491   }
3492
3493   /**
3494    * DOCUMENT ME!
3495    *
3496    * @param e
3497    *          DOCUMENT ME!
3498    */
3499   @Override
3500   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3501   {
3502     new RedundancyPanel(alignPanel, this);
3503   }
3504
3505   /**
3506    * DOCUMENT ME!
3507    *
3508    * @param e
3509    *          DOCUMENT ME!
3510    */
3511   @Override
3512   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3513   {
3514     if ((viewport.getSelectionGroup() == null)
3515             || (viewport.getSelectionGroup().getSize() < 2))
3516     {
3517       JvOptionPane.showInternalMessageDialog(this, MessageManager
3518               .getString("label.you_must_select_least_two_sequences"),
3519               MessageManager.getString("label.invalid_selection"),
3520               JvOptionPane.WARNING_MESSAGE);
3521     }
3522     else
3523     {
3524       JInternalFrame frame = new JInternalFrame();
3525       frame.setContentPane(new PairwiseAlignPanel(viewport));
3526       Desktop.addInternalFrame(frame,
3527               MessageManager.getString("action.pairwise_alignment"), 600,
3528               500);
3529     }
3530   }
3531
3532   @Override
3533   public void autoCalculate_actionPerformed(ActionEvent e)
3534   {
3535     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3536     if (viewport.autoCalculateConsensus)
3537     {
3538       viewport.firePropertyChange("alignment", null, viewport
3539               .getAlignment().getSequences());
3540     }
3541   }
3542
3543   @Override
3544   public void sortByTreeOption_actionPerformed(ActionEvent e)
3545   {
3546     viewport.sortByTree = sortByTree.isSelected();
3547   }
3548
3549   @Override
3550   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3551   {
3552     viewport.followSelection = listenToViewSelections.isSelected();
3553   }
3554
3555   /**
3556    * Constructs a tree panel and adds it to the desktop
3557    *
3558    * @param type
3559    *          tree type (NJ or AV)
3560    * @param modelName
3561    *          name of score model used to compute the tree
3562    * @param options
3563    *          parameters for the distance or similarity calculation
3564    */
3565   void newTreePanel(String type, String modelName, SimilarityParamsI options)
3566   {
3567     String frameTitle = "";
3568     TreePanel tp;
3569
3570     boolean onSelection = false;
3571     if (viewport.getSelectionGroup() != null
3572             && viewport.getSelectionGroup().getSize() > 0)
3573     {
3574       SequenceGroup sg = viewport.getSelectionGroup();
3575
3576       /* Decide if the selection is a column region */
3577       for (SequenceI _s : sg.getSequences())
3578       {
3579         if (_s.getLength() < sg.getEndRes())
3580         {
3581           JvOptionPane
3582                   .showMessageDialog(
3583                           Desktop.desktop,
3584                           MessageManager
3585                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3586                           MessageManager
3587                                   .getString("label.sequences_selection_not_aligned"),
3588                           JvOptionPane.WARNING_MESSAGE);
3589
3590           return;
3591         }
3592       }
3593       onSelection = true;
3594     }
3595     else
3596     {
3597       if (viewport.getAlignment().getHeight() < 2)
3598       {
3599         return;
3600       }
3601     }
3602
3603     tp = new TreePanel(alignPanel, type, modelName, options);
3604     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3605
3606     frameTitle += " from ";
3607
3608     if (viewport.viewName != null)
3609     {
3610       frameTitle += viewport.viewName + " of ";
3611     }
3612
3613     frameTitle += this.title;
3614
3615     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3616   }
3617
3618   /**
3619    * DOCUMENT ME!
3620    *
3621    * @param title
3622    *          DOCUMENT ME!
3623    * @param order
3624    *          DOCUMENT ME!
3625    */
3626   public void addSortByOrderMenuItem(String title,
3627           final AlignmentOrder order)
3628   {
3629     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3630             "action.by_title_param", new Object[] { title }));
3631     sort.add(item);
3632     item.addActionListener(new java.awt.event.ActionListener()
3633     {
3634       @Override
3635       public void actionPerformed(ActionEvent e)
3636       {
3637         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3638
3639         // TODO: JBPNote - have to map order entries to curent SequenceI
3640         // pointers
3641         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3642
3643         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3644                 .getAlignment()));
3645
3646         alignPanel.paintAlignment(true);
3647       }
3648     });
3649   }
3650
3651   /**
3652    * Add a new sort by annotation score menu item
3653    *
3654    * @param sort
3655    *          the menu to add the option to
3656    * @param scoreLabel
3657    *          the label used to retrieve scores for each sequence on the
3658    *          alignment
3659    */
3660   public void addSortByAnnotScoreMenuItem(JMenu sort,
3661           final String scoreLabel)
3662   {
3663     final JMenuItem item = new JMenuItem(scoreLabel);
3664     sort.add(item);
3665     item.addActionListener(new java.awt.event.ActionListener()
3666     {
3667       @Override
3668       public void actionPerformed(ActionEvent e)
3669       {
3670         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3671         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3672                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3673         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3674                 viewport.getAlignment()));
3675         alignPanel.paintAlignment(true);
3676       }
3677     });
3678   }
3679
3680   /**
3681    * last hash for alignment's annotation array - used to minimise cost of
3682    * rebuild.
3683    */
3684   protected int _annotationScoreVectorHash;
3685
3686   /**
3687    * search the alignment and rebuild the sort by annotation score submenu the
3688    * last alignment annotation vector hash is stored to minimize cost of
3689    * rebuilding in subsequence calls.
3690    *
3691    */
3692   @Override
3693   public void buildSortByAnnotationScoresMenu()
3694   {
3695     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3696     {
3697       return;
3698     }
3699
3700     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3701     {
3702       sortByAnnotScore.removeAll();
3703       // almost certainly a quicker way to do this - but we keep it simple
3704       Hashtable scoreSorts = new Hashtable();
3705       AlignmentAnnotation aann[];
3706       for (SequenceI sqa : viewport.getAlignment().getSequences())
3707       {
3708         aann = sqa.getAnnotation();
3709         for (int i = 0; aann != null && i < aann.length; i++)
3710         {
3711           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3712           {
3713             scoreSorts.put(aann[i].label, aann[i].label);
3714           }
3715         }
3716       }
3717       Enumeration labels = scoreSorts.keys();
3718       while (labels.hasMoreElements())
3719       {
3720         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3721                 (String) labels.nextElement());
3722       }
3723       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3724       scoreSorts.clear();
3725
3726       _annotationScoreVectorHash = viewport.getAlignment()
3727               .getAlignmentAnnotation().hashCode();
3728     }
3729   }
3730
3731   /**
3732    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3733    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3734    * call. Listeners are added to remove the menu item when the treePanel is
3735    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3736    * modified.
3737    */
3738   @Override
3739   public void buildTreeSortMenu()
3740   {
3741     sortByTreeMenu.removeAll();
3742
3743     List<Component> comps = PaintRefresher.components.get(viewport
3744             .getSequenceSetId());
3745     List<TreePanel> treePanels = new ArrayList<>();
3746     for (Component comp : comps)
3747     {
3748       if (comp instanceof TreePanel)
3749       {
3750         treePanels.add((TreePanel) comp);
3751       }
3752     }
3753
3754     if (treePanels.size() < 1)
3755     {
3756       sortByTreeMenu.setVisible(false);
3757       return;
3758     }
3759
3760     sortByTreeMenu.setVisible(true);
3761
3762     for (final TreePanel tp : treePanels)
3763     {
3764       final JMenuItem item = new JMenuItem(tp.getTitle());
3765       item.addActionListener(new java.awt.event.ActionListener()
3766       {
3767         @Override
3768         public void actionPerformed(ActionEvent e)
3769         {
3770           tp.sortByTree_actionPerformed();
3771           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3772
3773         }
3774       });
3775
3776       sortByTreeMenu.add(item);
3777     }
3778   }
3779
3780   public boolean sortBy(AlignmentOrder alorder, String undoname)
3781   {
3782     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3783     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3784     if (undoname != null)
3785     {
3786       addHistoryItem(new OrderCommand(undoname, oldOrder,
3787               viewport.getAlignment()));
3788     }
3789     alignPanel.paintAlignment(true);
3790     return true;
3791   }
3792
3793   /**
3794    * Work out whether the whole set of sequences or just the selected set will
3795    * be submitted for multiple alignment.
3796    *
3797    */
3798   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3799   {
3800     // Now, check we have enough sequences
3801     AlignmentView msa = null;
3802
3803     if ((viewport.getSelectionGroup() != null)
3804             && (viewport.getSelectionGroup().getSize() > 1))
3805     {
3806       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3807       // some common interface!
3808       /*
3809        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3810        * SequenceI[sz = seqs.getSize(false)];
3811        *
3812        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3813        * seqs.getSequenceAt(i); }
3814        */
3815       msa = viewport.getAlignmentView(true);
3816     }
3817     else if (viewport.getSelectionGroup() != null
3818             && viewport.getSelectionGroup().getSize() == 1)
3819     {
3820       int option = JvOptionPane.showConfirmDialog(this,
3821               MessageManager.getString("warn.oneseq_msainput_selection"),
3822               MessageManager.getString("label.invalid_selection"),
3823               JvOptionPane.OK_CANCEL_OPTION);
3824       if (option == JvOptionPane.OK_OPTION)
3825       {
3826         msa = viewport.getAlignmentView(false);
3827       }
3828     }
3829     else
3830     {
3831       msa = viewport.getAlignmentView(false);
3832     }
3833     return msa;
3834   }
3835
3836   /**
3837    * Decides what is submitted to a secondary structure prediction service: the
3838    * first sequence in the alignment, or in the current selection, or, if the
3839    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3840    * region or the whole alignment. (where the first sequence in the set is the
3841    * one that the prediction will be for).
3842    */
3843   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3844   {
3845     AlignmentView seqs = null;
3846
3847     if ((viewport.getSelectionGroup() != null)
3848             && (viewport.getSelectionGroup().getSize() > 0))
3849     {
3850       seqs = viewport.getAlignmentView(true);
3851     }
3852     else
3853     {
3854       seqs = viewport.getAlignmentView(false);
3855     }
3856     // limit sequences - JBPNote in future - could spawn multiple prediction
3857     // jobs
3858     // TODO: viewport.getAlignment().isAligned is a global state - the local
3859     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3860     if (!viewport.getAlignment().isAligned(false))
3861     {
3862       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3863       // TODO: if seqs.getSequences().length>1 then should really have warned
3864       // user!
3865
3866     }
3867     return seqs;
3868   }
3869
3870   /**
3871    * DOCUMENT ME!
3872    *
3873    * @param e
3874    *          DOCUMENT ME!
3875    */
3876   @Override
3877   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3878   {
3879     // Pick the tree file
3880     JalviewFileChooser chooser = new JalviewFileChooser(
3881             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3882     chooser.setFileView(new JalviewFileView());
3883     chooser.setDialogTitle(MessageManager
3884             .getString("label.select_newick_like_tree_file"));
3885     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3886
3887     int value = chooser.showOpenDialog(null);
3888
3889     if (value == JalviewFileChooser.APPROVE_OPTION)
3890     {
3891       String filePath = chooser.getSelectedFile().getPath();
3892       Cache.setProperty("LAST_DIRECTORY", filePath);
3893       NewickFile fin = null;
3894       try
3895       {
3896         fin = new NewickFile(filePath, DataSourceType.FILE);
3897         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3898       } catch (Exception ex)
3899       {
3900         JvOptionPane
3901                 .showMessageDialog(
3902                         Desktop.desktop,
3903                         ex.getMessage(),
3904                         MessageManager
3905                                 .getString("label.problem_reading_tree_file"),
3906                         JvOptionPane.WARNING_MESSAGE);
3907         ex.printStackTrace();
3908       }
3909       if (fin != null && fin.hasWarningMessage())
3910       {
3911         JvOptionPane.showMessageDialog(Desktop.desktop, fin
3912                 .getWarningMessage(), MessageManager
3913                 .getString("label.possible_problem_with_tree_file"),
3914                 JvOptionPane.WARNING_MESSAGE);
3915       }
3916     }
3917   }
3918
3919   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3920   {
3921     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3922   }
3923
3924   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3925           int h, int x, int y)
3926   {
3927     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3928   }
3929
3930   /**
3931    * Add a treeviewer for the tree extracted from a Newick file object to the
3932    * current alignment view
3933    *
3934    * @param nf
3935    *          the tree
3936    * @param title
3937    *          tree viewer title
3938    * @param input
3939    *          Associated alignment input data (or null)
3940    * @param w
3941    *          width
3942    * @param h
3943    *          height
3944    * @param x
3945    *          position
3946    * @param y
3947    *          position
3948    * @return TreePanel handle
3949    */
3950   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3951           AlignmentView input, int w, int h, int x, int y)
3952   {
3953     TreePanel tp = null;
3954
3955     try
3956     {
3957       nf.parse();
3958
3959       if (nf.getTree() != null)
3960       {
3961         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3962
3963         tp.setSize(w, h);
3964
3965         if (x > 0 && y > 0)
3966         {
3967           tp.setLocation(x, y);
3968         }
3969
3970         Desktop.addInternalFrame(tp, treeTitle, w, h);
3971       }
3972     } catch (Exception ex)
3973     {
3974       ex.printStackTrace();
3975     }
3976
3977     return tp;
3978   }
3979
3980   private boolean buildingMenu = false;
3981
3982   /**
3983    * Generates menu items and listener event actions for web service clients
3984    *
3985    */
3986   public void BuildWebServiceMenu()
3987   {
3988     while (buildingMenu)
3989     {
3990       try
3991       {
3992         System.err.println("Waiting for building menu to finish.");
3993         Thread.sleep(10);
3994       } catch (Exception e)
3995       {
3996       }
3997     }
3998     final AlignFrame me = this;
3999     buildingMenu = true;
4000     new Thread(new Runnable()
4001     {
4002       @Override
4003       public void run()
4004       {
4005         final List<JMenuItem> legacyItems = new ArrayList<>();
4006         try
4007         {
4008           // System.err.println("Building ws menu again "
4009           // + Thread.currentThread());
4010           // TODO: add support for context dependent disabling of services based
4011           // on
4012           // alignment and current selection
4013           // TODO: add additional serviceHandle parameter to specify abstract
4014           // handler
4015           // class independently of AbstractName
4016           // TODO: add in rediscovery GUI function to restart discoverer
4017           // TODO: group services by location as well as function and/or
4018           // introduce
4019           // object broker mechanism.
4020           final Vector<JMenu> wsmenu = new Vector<>();
4021           final IProgressIndicator af = me;
4022
4023           /*
4024            * do not i18n these strings - they are hard-coded in class
4025            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4026            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4027            */
4028           final JMenu msawsmenu = new JMenu("Alignment");
4029           final JMenu secstrmenu = new JMenu(
4030                   "Secondary Structure Prediction");
4031           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4032           final JMenu analymenu = new JMenu("Analysis");
4033           final JMenu dismenu = new JMenu("Protein Disorder");
4034           // JAL-940 - only show secondary structure prediction services from
4035           // the legacy server
4036           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4037               // &&
4038           Discoverer.services != null && (Discoverer.services.size() > 0))
4039           {
4040             // TODO: refactor to allow list of AbstractName/Handler bindings to
4041             // be
4042             // stored or retrieved from elsewhere
4043             // No MSAWS used any more:
4044             // Vector msaws = null; // (Vector)
4045             // Discoverer.services.get("MsaWS");
4046             Vector secstrpr = (Vector) Discoverer.services
4047                     .get("SecStrPred");
4048             if (secstrpr != null)
4049             {
4050               // Add any secondary structure prediction services
4051               for (int i = 0, j = secstrpr.size(); i < j; i++)
4052               {
4053                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4054                         .get(i);
4055                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4056                         .getServiceClient(sh);
4057                 int p = secstrmenu.getItemCount();
4058                 impl.attachWSMenuEntry(secstrmenu, me);
4059                 int q = secstrmenu.getItemCount();
4060                 for (int litm = p; litm < q; litm++)
4061                 {
4062                   legacyItems.add(secstrmenu.getItem(litm));
4063                 }
4064               }
4065             }
4066           }
4067
4068           // Add all submenus in the order they should appear on the web
4069           // services menu
4070           wsmenu.add(msawsmenu);
4071           wsmenu.add(secstrmenu);
4072           wsmenu.add(dismenu);
4073           wsmenu.add(analymenu);
4074           // No search services yet
4075           // wsmenu.add(seqsrchmenu);
4076
4077           javax.swing.SwingUtilities.invokeLater(new Runnable()
4078           {
4079             @Override
4080             public void run()
4081             {
4082               try
4083               {
4084                 webService.removeAll();
4085                 // first, add discovered services onto the webservices menu
4086                 if (wsmenu.size() > 0)
4087                 {
4088                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4089                   {
4090                     webService.add(wsmenu.get(i));
4091                   }
4092                 }
4093                 else
4094                 {
4095                   webService.add(me.webServiceNoServices);
4096                 }
4097                 // TODO: move into separate menu builder class.
4098                 boolean new_sspred = false;
4099                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4100                 {
4101                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4102                   if (jws2servs != null)
4103                   {
4104                     if (jws2servs.hasServices())
4105                     {
4106                       jws2servs.attachWSMenuEntry(webService, me);
4107                       for (Jws2Instance sv : jws2servs.getServices())
4108                       {
4109                         if (sv.description.toLowerCase().contains("jpred"))
4110                         {
4111                           for (JMenuItem jmi : legacyItems)
4112                           {
4113                             jmi.setVisible(false);
4114                           }
4115                         }
4116                       }
4117
4118                     }
4119                     if (jws2servs.isRunning())
4120                     {
4121                       JMenuItem tm = new JMenuItem(
4122                               "Still discovering JABA Services");
4123                       tm.setEnabled(false);
4124                       webService.add(tm);
4125                     }
4126                   }
4127                 }
4128                 build_urlServiceMenu(me.webService);
4129                 build_fetchdbmenu(webService);
4130                 for (JMenu item : wsmenu)
4131                 {
4132                   if (item.getItemCount() == 0)
4133                   {
4134                     item.setEnabled(false);
4135                   }
4136                   else
4137                   {
4138                     item.setEnabled(true);
4139                   }
4140                 }
4141               } catch (Exception e)
4142               {
4143                 Cache.log
4144                         .debug("Exception during web service menu building process.",
4145                                 e);
4146               }
4147             }
4148           });
4149         } catch (Exception e)
4150         {
4151         }
4152         buildingMenu = false;
4153       }
4154     }).start();
4155
4156   }
4157
4158   /**
4159    * construct any groupURL type service menu entries.
4160    *
4161    * @param webService
4162    */
4163   private void build_urlServiceMenu(JMenu webService)
4164   {
4165     // TODO: remove this code when 2.7 is released
4166     // DEBUG - alignmentView
4167     /*
4168      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4169      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4170      *
4171      * @Override public void actionPerformed(ActionEvent e) {
4172      * jalview.datamodel.AlignmentView
4173      * .testSelectionViews(af.viewport.getAlignment(),
4174      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4175      *
4176      * }); webService.add(testAlView);
4177      */
4178     // TODO: refactor to RestClient discoverer and merge menu entries for
4179     // rest-style services with other types of analysis/calculation service
4180     // SHmmr test client - still being implemented.
4181     // DEBUG - alignmentView
4182
4183     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4184             .getRestClients())
4185     {
4186       client.attachWSMenuEntry(
4187               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4188               this);
4189     }
4190   }
4191
4192   /**
4193    * Searches the alignment sequences for xRefs and builds the Show
4194    * Cross-References menu (formerly called Show Products), with database
4195    * sources for which cross-references are found (protein sources for a
4196    * nucleotide alignment and vice versa)
4197    *
4198    * @return true if Show Cross-references menu should be enabled
4199    */
4200   public boolean canShowProducts()
4201   {
4202     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4203     AlignmentI dataset = viewport.getAlignment().getDataset();
4204
4205     showProducts.removeAll();
4206     final boolean dna = viewport.getAlignment().isNucleotide();
4207
4208     if (seqs == null || seqs.length == 0)
4209     {
4210       // nothing to see here.
4211       return false;
4212     }
4213
4214     boolean showp = false;
4215     try
4216     {
4217       List<String> ptypes = new CrossRef(seqs, dataset)
4218               .findXrefSourcesForSequences(dna);
4219
4220       for (final String source : ptypes)
4221       {
4222         showp = true;
4223         final AlignFrame af = this;
4224         JMenuItem xtype = new JMenuItem(source);
4225         xtype.addActionListener(new ActionListener()
4226         {
4227           @Override
4228           public void actionPerformed(ActionEvent e)
4229           {
4230             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4231           }
4232         });
4233         showProducts.add(xtype);
4234       }
4235       showProducts.setVisible(showp);
4236       showProducts.setEnabled(showp);
4237     } catch (Exception e)
4238     {
4239       Cache.log
4240               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4241                       e);
4242       return false;
4243     }
4244     return showp;
4245   }
4246
4247   /**
4248    * Finds and displays cross-references for the selected sequences (protein
4249    * products for nucleotide sequences, dna coding sequences for peptides).
4250    *
4251    * @param sel
4252    *          the sequences to show cross-references for
4253    * @param dna
4254    *          true if from a nucleotide alignment (so showing proteins)
4255    * @param source
4256    *          the database to show cross-references for
4257    */
4258   protected void showProductsFor(final SequenceI[] sel,
4259           final boolean _odna, final String source)
4260   {
4261     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4262             .start();
4263   }
4264
4265   /**
4266    * Construct and display a new frame containing the translation of this
4267    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4268    */
4269   @Override
4270   public void showTranslation_actionPerformed(ActionEvent e)
4271   {
4272     AlignmentI al = null;
4273     try
4274     {
4275       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4276
4277       al = dna.translateCdna();
4278     } catch (Exception ex)
4279     {
4280       jalview.bin.Cache.log.error(
4281               "Exception during translation. Please report this !", ex);
4282       final String msg = MessageManager
4283               .getString("label.error_when_translating_sequences_submit_bug_report");
4284       final String errorTitle = MessageManager
4285               .getString("label.implementation_error")
4286               + MessageManager.getString("label.translation_failed");
4287       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4288               JvOptionPane.ERROR_MESSAGE);
4289       return;
4290     }
4291     if (al == null || al.getHeight() == 0)
4292     {
4293       final String msg = MessageManager
4294               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4295       final String errorTitle = MessageManager
4296               .getString("label.translation_failed");
4297       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4298               JvOptionPane.WARNING_MESSAGE);
4299     }
4300     else
4301     {
4302       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4303       af.setFileFormat(this.currentFileFormat);
4304       final String newTitle = MessageManager.formatMessage(
4305               "label.translation_of_params",
4306               new Object[] { this.getTitle() });
4307       af.setTitle(newTitle);
4308       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4309       {
4310         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4311         viewport.openSplitFrame(af, new Alignment(seqs));
4312       }
4313       else
4314       {
4315         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4316                 DEFAULT_HEIGHT);
4317       }
4318     }
4319   }
4320
4321   /**
4322    * Set the file format
4323    *
4324    * @param format
4325    */
4326   public void setFileFormat(FileFormatI format)
4327   {
4328     this.currentFileFormat = format;
4329   }
4330
4331   /**
4332    * Try to load a features file onto the alignment.
4333    *
4334    * @param file
4335    *          contents or path to retrieve file
4336    * @param sourceType
4337    *          access mode of file (see jalview.io.AlignFile)
4338    * @return true if features file was parsed correctly.
4339    */
4340   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4341   {
4342     return avc.parseFeaturesFile(file, sourceType,
4343             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4344
4345   }
4346
4347   @Override
4348   public void refreshFeatureUI(boolean enableIfNecessary)
4349   {
4350     // note - currently this is only still here rather than in the controller
4351     // because of the featureSettings hard reference that is yet to be
4352     // abstracted
4353     if (enableIfNecessary)
4354     {
4355       viewport.setShowSequenceFeatures(true);
4356       showSeqFeatures.setSelected(true);
4357     }
4358
4359   }
4360
4361   @Override
4362   public void dragEnter(DropTargetDragEvent evt)
4363   {
4364   }
4365
4366   @Override
4367   public void dragExit(DropTargetEvent evt)
4368   {
4369   }
4370
4371   @Override
4372   public void dragOver(DropTargetDragEvent evt)
4373   {
4374   }
4375
4376   @Override
4377   public void dropActionChanged(DropTargetDragEvent evt)
4378   {
4379   }
4380
4381   @Override
4382   public void drop(DropTargetDropEvent evt)
4383   {
4384     // JAL-1552 - acceptDrop required before getTransferable call for
4385     // Java's Transferable for native dnd
4386     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4387     Transferable t = evt.getTransferable();
4388     List<String> files = new ArrayList<>();
4389     List<DataSourceType> protocols = new ArrayList<>();
4390
4391     try
4392     {
4393       Desktop.transferFromDropTarget(files, protocols, evt, t);
4394     } catch (Exception e)
4395     {
4396       e.printStackTrace();
4397     }
4398     if (files != null)
4399     {
4400       try
4401       {
4402         // check to see if any of these files have names matching sequences in
4403         // the alignment
4404         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4405                 .getAlignment().getSequencesArray());
4406         /**
4407          * Object[] { String,SequenceI}
4408          */
4409         ArrayList<Object[]> filesmatched = new ArrayList<>();
4410         ArrayList<String> filesnotmatched = new ArrayList<>();
4411         for (int i = 0; i < files.size(); i++)
4412         {
4413           String file = files.get(i).toString();
4414           String pdbfn = "";
4415           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4416           if (protocol == DataSourceType.FILE)
4417           {
4418             File fl = new File(file);
4419             pdbfn = fl.getName();
4420           }
4421           else if (protocol == DataSourceType.URL)
4422           {
4423             URL url = new URL(file);
4424             pdbfn = url.getFile();
4425           }
4426           if (pdbfn.length() > 0)
4427           {
4428             // attempt to find a match in the alignment
4429             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4430             int l = 0, c = pdbfn.indexOf(".");
4431             while (mtch == null && c != -1)
4432             {
4433               do
4434               {
4435                 l = c;
4436               } while ((c = pdbfn.indexOf(".", l)) > l);
4437               if (l > -1)
4438               {
4439                 pdbfn = pdbfn.substring(0, l);
4440               }
4441               mtch = idm.findAllIdMatches(pdbfn);
4442             }
4443             if (mtch != null)
4444             {
4445               FileFormatI type = null;
4446               try
4447               {
4448                 type = new IdentifyFile().identify(file, protocol);
4449               } catch (Exception ex)
4450               {
4451                 type = null;
4452               }
4453               if (type != null && type.isStructureFile())
4454               {
4455                 filesmatched.add(new Object[] { file, protocol, mtch });
4456                 continue;
4457               }
4458             }
4459             // File wasn't named like one of the sequences or wasn't a PDB file.
4460             filesnotmatched.add(file);
4461           }
4462         }
4463         int assocfiles = 0;
4464         if (filesmatched.size() > 0)
4465         {
4466           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4467                   || JvOptionPane
4468                           .showConfirmDialog(
4469                                   this,
4470                                   MessageManager
4471                                           .formatMessage(
4472                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4473                                                   new Object[] { Integer
4474                                                           .valueOf(
4475                                                                   filesmatched
4476                                                                           .size())
4477                                                           .toString() }),
4478                                   MessageManager
4479                                           .getString("label.automatically_associate_structure_files_by_name"),
4480                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4481
4482           {
4483             for (Object[] fm : filesmatched)
4484             {
4485               // try and associate
4486               // TODO: may want to set a standard ID naming formalism for
4487               // associating PDB files which have no IDs.
4488               for (SequenceI toassoc : (SequenceI[]) fm[2])
4489               {
4490                 PDBEntry pe = new AssociatePdbFileWithSeq()
4491                         .associatePdbWithSeq((String) fm[0],
4492                                 (DataSourceType) fm[1], toassoc, false,
4493                                 Desktop.instance);
4494                 if (pe != null)
4495                 {
4496                   System.err.println("Associated file : "
4497                           + ((String) fm[0]) + " with "
4498                           + toassoc.getDisplayId(true));
4499                   assocfiles++;
4500                 }
4501               }
4502               alignPanel.paintAlignment(true);
4503             }
4504           }
4505         }
4506         if (filesnotmatched.size() > 0)
4507         {
4508           if (assocfiles > 0
4509                   && (Cache.getDefault(
4510                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4511                           .showConfirmDialog(
4512                                   this,
4513                                   "<html>"
4514                                           + MessageManager
4515                                                   .formatMessage(
4516                                                           "label.ignore_unmatched_dropped_files_info",
4517                                                           new Object[] { Integer
4518                                                                   .valueOf(
4519                                                                           filesnotmatched
4520                                                                                   .size())
4521                                                                   .toString() })
4522                                           + "</html>",
4523                                   MessageManager
4524                                           .getString("label.ignore_unmatched_dropped_files"),
4525                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4526           {
4527             return;
4528           }
4529           for (String fn : filesnotmatched)
4530           {
4531             loadJalviewDataFile(fn, null, null, null);
4532           }
4533
4534         }
4535       } catch (Exception ex)
4536       {
4537         ex.printStackTrace();
4538       }
4539     }
4540   }
4541
4542   /**
4543    * Attempt to load a "dropped" file or URL string, by testing in turn for
4544    * <ul>
4545    * <li>an Annotation file</li>
4546    * <li>a JNet file</li>
4547    * <li>a features file</li>
4548    * <li>else try to interpret as an alignment file</li>
4549    * </ul>
4550    *
4551    * @param file
4552    *          either a filename or a URL string.
4553    */
4554   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4555           FileFormatI format, SequenceI assocSeq)
4556   {
4557     try
4558     {
4559       if (sourceType == null)
4560       {
4561         sourceType = FormatAdapter.checkProtocol(file);
4562       }
4563       // if the file isn't identified, or not positively identified as some
4564       // other filetype (PFAM is default unidentified alignment file type) then
4565       // try to parse as annotation.
4566       boolean isAnnotation = (format == null || FileFormat.Pfam
4567               .equals(format)) ? new AnnotationFile()
4568               .annotateAlignmentView(viewport, file, sourceType) : false;
4569
4570       if (!isAnnotation)
4571       {
4572         // first see if its a T-COFFEE score file
4573         TCoffeeScoreFile tcf = null;
4574         try
4575         {
4576           tcf = new TCoffeeScoreFile(file, sourceType);
4577           if (tcf.isValid())
4578           {
4579             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4580             {
4581               buildColourMenu();
4582               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4583               isAnnotation = true;
4584               statusBar
4585                       .setText(MessageManager
4586                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4587             }
4588             else
4589             {
4590               // some problem - if no warning its probable that the ID matching
4591               // process didn't work
4592               JvOptionPane
4593                       .showMessageDialog(
4594                               Desktop.desktop,
4595                               tcf.getWarningMessage() == null ? MessageManager
4596                                       .getString("label.check_file_matches_sequence_ids_alignment")
4597                                       : tcf.getWarningMessage(),
4598                               MessageManager
4599                                       .getString("label.problem_reading_tcoffee_score_file"),
4600                               JvOptionPane.WARNING_MESSAGE);
4601             }
4602           }
4603           else
4604           {
4605             tcf = null;
4606           }
4607         } catch (Exception x)
4608         {
4609           Cache.log
4610                   .debug("Exception when processing data source as T-COFFEE score file",
4611                           x);
4612           tcf = null;
4613         }
4614         if (tcf == null)
4615         {
4616           // try to see if its a JNet 'concise' style annotation file *before*
4617           // we
4618           // try to parse it as a features file
4619           if (format == null)
4620           {
4621             format = new IdentifyFile().identify(file, sourceType);
4622           }
4623           if (FileFormat.ScoreMatrix == format)
4624           {
4625             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4626                     sourceType));
4627             sm.parse();
4628             // todo: i18n this message
4629             statusBar
4630                     .setText(MessageManager.formatMessage(
4631                             "label.successfully_loaded_matrix",
4632                             sm.getMatrixName()));
4633           }
4634           else if (FileFormat.Jnet.equals(format))
4635           {
4636             JPredFile predictions = new JPredFile(file, sourceType);
4637             new JnetAnnotationMaker();
4638             JnetAnnotationMaker.add_annotation(predictions,
4639                     viewport.getAlignment(), 0, false);
4640             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4641             viewport.getAlignment().setSeqrep(repseq);
4642             HiddenColumns cs = new HiddenColumns();
4643             cs.hideInsertionsFor(repseq);
4644             viewport.getAlignment().setHiddenColumns(cs);
4645             isAnnotation = true;
4646           }
4647           // else if (IdentifyFile.FeaturesFile.equals(format))
4648           else if (FileFormat.Features.equals(format))
4649           {
4650             if (parseFeaturesFile(file, sourceType))
4651             {
4652               alignPanel.paintAlignment(true);
4653             }
4654           }
4655           else
4656           {
4657             new FileLoader().LoadFile(viewport, file, sourceType, format);
4658           }
4659         }
4660       }
4661       if (isAnnotation)
4662       {
4663
4664         alignPanel.adjustAnnotationHeight();
4665         viewport.updateSequenceIdColours();
4666         buildSortByAnnotationScoresMenu();
4667         alignPanel.paintAlignment(true);
4668       }
4669     } catch (Exception ex)
4670     {
4671       ex.printStackTrace();
4672     } catch (OutOfMemoryError oom)
4673     {
4674       try
4675       {
4676         System.gc();
4677       } catch (Exception x)
4678       {
4679       }
4680       new OOMWarning(
4681               "loading data "
4682                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4683                               : "using " + sourceType + " from " + file)
4684                               : ".")
4685                       + (format != null ? "(parsing as '" + format
4686                               + "' file)" : ""), oom, Desktop.desktop);
4687     }
4688   }
4689
4690   /**
4691    * Method invoked by the ChangeListener on the tabbed pane, in other words
4692    * when a different tabbed pane is selected by the user or programmatically.
4693    */
4694   @Override
4695   public void tabSelectionChanged(int index)
4696   {
4697     if (index > -1)
4698     {
4699       alignPanel = alignPanels.get(index);
4700       viewport = alignPanel.av;
4701       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4702       setMenusFromViewport(viewport);
4703     }
4704
4705     /*
4706      * 'focus' any colour slider that is open to the selected viewport
4707      */
4708     if (viewport.getConservationSelected())
4709     {
4710       SliderPanel.setConservationSlider(alignPanel,
4711               viewport.getResidueShading(), alignPanel.getViewName());
4712     }
4713     else
4714     {
4715       SliderPanel.hideConservationSlider();
4716     }
4717     if (viewport.getAbovePIDThreshold())
4718     {
4719       SliderPanel.setPIDSliderSource(alignPanel,
4720               viewport.getResidueShading(), alignPanel.getViewName());
4721     }
4722     else
4723     {
4724       SliderPanel.hidePIDSlider();
4725     }
4726
4727     /*
4728      * If there is a frame linked to this one in a SplitPane, switch it to the
4729      * same view tab index. No infinite recursion of calls should happen, since
4730      * tabSelectionChanged() should not get invoked on setting the selected
4731      * index to an unchanged value. Guard against setting an invalid index
4732      * before the new view peer tab has been created.
4733      */
4734     final AlignViewportI peer = viewport.getCodingComplement();
4735     if (peer != null)
4736     {
4737       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4738       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4739       {
4740         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4741       }
4742     }
4743   }
4744
4745   /**
4746    * On right mouse click on view tab, prompt for and set new view name.
4747    */
4748   @Override
4749   public void tabbedPane_mousePressed(MouseEvent e)
4750   {
4751     if (e.isPopupTrigger())
4752     {
4753       String msg = MessageManager.getString("label.enter_view_name");
4754       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4755               JvOptionPane.QUESTION_MESSAGE);
4756
4757       if (reply != null)
4758       {
4759         viewport.viewName = reply;
4760         // TODO warn if reply is in getExistingViewNames()?
4761         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4762       }
4763     }
4764   }
4765
4766   public AlignViewport getCurrentView()
4767   {
4768     return viewport;
4769   }
4770
4771   /**
4772    * Open the dialog for regex description parsing.
4773    */
4774   @Override
4775   protected void extractScores_actionPerformed(ActionEvent e)
4776   {
4777     ParseProperties pp = new jalview.analysis.ParseProperties(
4778             viewport.getAlignment());
4779     // TODO: verify regex and introduce GUI dialog for version 2.5
4780     // if (pp.getScoresFromDescription("col", "score column ",
4781     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4782     // true)>0)
4783     if (pp.getScoresFromDescription("description column",
4784             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4785     {
4786       buildSortByAnnotationScoresMenu();
4787     }
4788   }
4789
4790   /*
4791    * (non-Javadoc)
4792    *
4793    * @see
4794    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4795    * )
4796    */
4797   @Override
4798   protected void showDbRefs_actionPerformed(ActionEvent e)
4799   {
4800     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4801   }
4802
4803   /*
4804    * (non-Javadoc)
4805    *
4806    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4807    * ActionEvent)
4808    */
4809   @Override
4810   protected void showNpFeats_actionPerformed(ActionEvent e)
4811   {
4812     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4813   }
4814
4815   /**
4816    * find the viewport amongst the tabs in this alignment frame and close that
4817    * tab
4818    *
4819    * @param av
4820    */
4821   public boolean closeView(AlignViewportI av)
4822   {
4823     if (viewport == av)
4824     {
4825       this.closeMenuItem_actionPerformed(false);
4826       return true;
4827     }
4828     Component[] comp = tabbedPane.getComponents();
4829     for (int i = 0; comp != null && i < comp.length; i++)
4830     {
4831       if (comp[i] instanceof AlignmentPanel)
4832       {
4833         if (((AlignmentPanel) comp[i]).av == av)
4834         {
4835           // close the view.
4836           closeView((AlignmentPanel) comp[i]);
4837           return true;
4838         }
4839       }
4840     }
4841     return false;
4842   }
4843
4844   protected void build_fetchdbmenu(JMenu webService)
4845   {
4846     // Temporary hack - DBRef Fetcher always top level ws entry.
4847     // TODO We probably want to store a sequence database checklist in
4848     // preferences and have checkboxes.. rather than individual sources selected
4849     // here
4850     final JMenu rfetch = new JMenu(
4851             MessageManager.getString("action.fetch_db_references"));
4852     rfetch.setToolTipText(MessageManager
4853             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4854     webService.add(rfetch);
4855
4856     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4857             MessageManager.getString("option.trim_retrieved_seqs"));
4858     trimrs.setToolTipText(MessageManager
4859             .getString("label.trim_retrieved_sequences"));
4860     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4861     trimrs.addActionListener(new ActionListener()
4862     {
4863       @Override
4864       public void actionPerformed(ActionEvent e)
4865       {
4866         trimrs.setSelected(trimrs.isSelected());
4867         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4868                 Boolean.valueOf(trimrs.isSelected()).toString());
4869       };
4870     });
4871     rfetch.add(trimrs);
4872     JMenuItem fetchr = new JMenuItem(
4873             MessageManager.getString("label.standard_databases"));
4874     fetchr.setToolTipText(MessageManager
4875             .getString("label.fetch_embl_uniprot"));
4876     fetchr.addActionListener(new ActionListener()
4877     {
4878
4879       @Override
4880       public void actionPerformed(ActionEvent e)
4881       {
4882         new Thread(new Runnable()
4883         {
4884           @Override
4885           public void run()
4886           {
4887             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4888                     .getAlignment().isNucleotide();
4889             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4890                     .getSequenceSelection(), alignPanel.alignFrame, null,
4891                     alignPanel.alignFrame.featureSettings, isNucleotide);
4892             dbRefFetcher.addListener(new FetchFinishedListenerI()
4893             {
4894               @Override
4895               public void finished()
4896               {
4897                 AlignFrame.this.setMenusForViewport();
4898               }
4899             });
4900             dbRefFetcher.fetchDBRefs(false);
4901           }
4902         }).start();
4903
4904       }
4905
4906     });
4907     rfetch.add(fetchr);
4908     final AlignFrame me = this;
4909     new Thread(new Runnable()
4910     {
4911       @Override
4912       public void run()
4913       {
4914         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4915                 .getSequenceFetcherSingleton(me);
4916         javax.swing.SwingUtilities.invokeLater(new Runnable()
4917         {
4918           @Override
4919           public void run()
4920           {
4921             String[] dbclasses = sf.getOrderedSupportedSources();
4922             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4923             // jalview.util.QuickSort.sort(otherdb, otherdb);
4924             List<DbSourceProxy> otherdb;
4925             JMenu dfetch = new JMenu();
4926             JMenu ifetch = new JMenu();
4927             JMenuItem fetchr = null;
4928             int comp = 0, icomp = 0, mcomp = 15;
4929             String mname = null;
4930             int dbi = 0;
4931             for (String dbclass : dbclasses)
4932             {
4933               otherdb = sf.getSourceProxy(dbclass);
4934               // add a single entry for this class, or submenu allowing 'fetch
4935               // all' or pick one
4936               if (otherdb == null || otherdb.size() < 1)
4937               {
4938                 continue;
4939               }
4940               // List<DbSourceProxy> dbs=otherdb;
4941               // otherdb=new ArrayList<DbSourceProxy>();
4942               // for (DbSourceProxy db:dbs)
4943               // {
4944               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4945               // }
4946               if (mname == null)
4947               {
4948                 mname = "From " + dbclass;
4949               }
4950               if (otherdb.size() == 1)
4951               {
4952                 final DbSourceProxy[] dassource = otherdb
4953                         .toArray(new DbSourceProxy[0]);
4954                 DbSourceProxy src = otherdb.get(0);
4955                 fetchr = new JMenuItem(src.getDbSource());
4956                 fetchr.addActionListener(new ActionListener()
4957                 {
4958
4959                   @Override
4960                   public void actionPerformed(ActionEvent e)
4961                   {
4962                     new Thread(new Runnable()
4963                     {
4964
4965                       @Override
4966                       public void run()
4967                       {
4968                         boolean isNucleotide = alignPanel.alignFrame
4969                                 .getViewport().getAlignment()
4970                                 .isNucleotide();
4971                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4972                                 alignPanel.av.getSequenceSelection(),
4973                                 alignPanel.alignFrame, dassource,
4974                                 alignPanel.alignFrame.featureSettings,
4975                                 isNucleotide);
4976                         dbRefFetcher
4977                                 .addListener(new FetchFinishedListenerI()
4978                                 {
4979                                   @Override
4980                                   public void finished()
4981                                   {
4982                                     AlignFrame.this.setMenusForViewport();
4983                                   }
4984                                 });
4985                         dbRefFetcher.fetchDBRefs(false);
4986                       }
4987                     }).start();
4988                   }
4989
4990                 });
4991                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
4992                         MessageManager.formatMessage(
4993                                 "label.fetch_retrieve_from",
4994                                 new Object[] { src.getDbName() })));
4995                 dfetch.add(fetchr);
4996                 comp++;
4997               }
4998               else
4999               {
5000                 final DbSourceProxy[] dassource = otherdb
5001                         .toArray(new DbSourceProxy[0]);
5002                 // fetch all entry
5003                 DbSourceProxy src = otherdb.get(0);
5004                 fetchr = new JMenuItem(MessageManager.formatMessage(
5005                         "label.fetch_all_param",
5006                         new Object[] { src.getDbSource() }));
5007                 fetchr.addActionListener(new ActionListener()
5008                 {
5009                   @Override
5010                   public void actionPerformed(ActionEvent e)
5011                   {
5012                     new Thread(new Runnable()
5013                     {
5014
5015                       @Override
5016                       public void run()
5017                       {
5018                         boolean isNucleotide = alignPanel.alignFrame
5019                                 .getViewport().getAlignment()
5020                                 .isNucleotide();
5021                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5022                                 alignPanel.av.getSequenceSelection(),
5023                                 alignPanel.alignFrame, dassource,
5024                                 alignPanel.alignFrame.featureSettings,
5025                                 isNucleotide);
5026                         dbRefFetcher
5027                                 .addListener(new FetchFinishedListenerI()
5028                                 {
5029                                   @Override
5030                                   public void finished()
5031                                   {
5032                                     AlignFrame.this.setMenusForViewport();
5033                                   }
5034                                 });
5035                         dbRefFetcher.fetchDBRefs(false);
5036                       }
5037                     }).start();
5038                   }
5039                 });
5040
5041                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5042                         MessageManager.formatMessage(
5043                                 "label.fetch_retrieve_from_all_sources",
5044                                 new Object[] {
5045                                     Integer.valueOf(otherdb.size())
5046                                             .toString(), src.getDbSource(),
5047                                     src.getDbName() })));
5048                 dfetch.add(fetchr);
5049                 comp++;
5050                 // and then build the rest of the individual menus
5051                 ifetch = new JMenu(MessageManager.formatMessage(
5052                         "label.source_from_db_source",
5053                         new Object[] { src.getDbSource() }));
5054                 icomp = 0;
5055                 String imname = null;
5056                 int i = 0;
5057                 for (DbSourceProxy sproxy : otherdb)
5058                 {
5059                   String dbname = sproxy.getDbName();
5060                   String sname = dbname.length() > 5 ? dbname.substring(0,
5061                           5) + "..." : dbname;
5062                   String msname = dbname.length() > 10 ? dbname.substring(
5063                           0, 10) + "..." : dbname;
5064                   if (imname == null)
5065                   {
5066                     imname = MessageManager.formatMessage(
5067                             "label.from_msname", new Object[] { sname });
5068                   }
5069                   fetchr = new JMenuItem(msname);
5070                   final DbSourceProxy[] dassrc = { sproxy };
5071                   fetchr.addActionListener(new ActionListener()
5072                   {
5073
5074                     @Override
5075                     public void actionPerformed(ActionEvent e)
5076                     {
5077                       new Thread(new Runnable()
5078                       {
5079
5080                         @Override
5081                         public void run()
5082                         {
5083                           boolean isNucleotide = alignPanel.alignFrame
5084                                   .getViewport().getAlignment()
5085                                   .isNucleotide();
5086                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5087                                   alignPanel.av.getSequenceSelection(),
5088                                   alignPanel.alignFrame, dassrc,
5089                                   alignPanel.alignFrame.featureSettings,
5090                                   isNucleotide);
5091                           dbRefFetcher
5092                                   .addListener(new FetchFinishedListenerI()
5093                                   {
5094                                     @Override
5095                                     public void finished()
5096                                     {
5097                                       AlignFrame.this.setMenusForViewport();
5098                                     }
5099                                   });
5100                           dbRefFetcher.fetchDBRefs(false);
5101                         }
5102                       }).start();
5103                     }
5104
5105                   });
5106                   fetchr.setToolTipText("<html>"
5107                           + MessageManager.formatMessage(
5108                                   "label.fetch_retrieve_from", new Object[]
5109                                   { dbname }));
5110                   ifetch.add(fetchr);
5111                   ++i;
5112                   if (++icomp >= mcomp || i == (otherdb.size()))
5113                   {
5114                     ifetch.setText(MessageManager.formatMessage(
5115                             "label.source_to_target", imname, sname));
5116                     dfetch.add(ifetch);
5117                     ifetch = new JMenu();
5118                     imname = null;
5119                     icomp = 0;
5120                     comp++;
5121                   }
5122                 }
5123               }
5124               ++dbi;
5125               if (comp >= mcomp || dbi >= (dbclasses.length))
5126               {
5127                 dfetch.setText(MessageManager.formatMessage(
5128                         "label.source_to_target", mname, dbclass));
5129                 rfetch.add(dfetch);
5130                 dfetch = new JMenu();
5131                 mname = null;
5132                 comp = 0;
5133               }
5134             }
5135           }
5136         });
5137       }
5138     }).start();
5139
5140   }
5141
5142   /**
5143    * Left justify the whole alignment.
5144    */
5145   @Override
5146   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5147   {
5148     AlignmentI al = viewport.getAlignment();
5149     al.justify(false);
5150     viewport.firePropertyChange("alignment", null, al);
5151   }
5152
5153   /**
5154    * Right justify the whole alignment.
5155    */
5156   @Override
5157   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5158   {
5159     AlignmentI al = viewport.getAlignment();
5160     al.justify(true);
5161     viewport.firePropertyChange("alignment", null, al);
5162   }
5163
5164   @Override
5165   public void setShowSeqFeatures(boolean b)
5166   {
5167     showSeqFeatures.setSelected(b);
5168     viewport.setShowSequenceFeatures(b);
5169   }
5170
5171   /*
5172    * (non-Javadoc)
5173    *
5174    * @see
5175    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5176    * awt.event.ActionEvent)
5177    */
5178   @Override
5179   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5180   {
5181     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5182     alignPanel.paintAlignment(true);
5183   }
5184
5185   /*
5186    * (non-Javadoc)
5187    *
5188    * @see
5189    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5190    * .ActionEvent)
5191    */
5192   @Override
5193   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5194   {
5195     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5196     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5197
5198   }
5199
5200   /*
5201    * (non-Javadoc)
5202    *
5203    * @see
5204    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5205    * .event.ActionEvent)
5206    */
5207   @Override
5208   protected void showGroupConservation_actionPerformed(ActionEvent e)
5209   {
5210     viewport.setShowGroupConservation(showGroupConservation.getState());
5211     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5212   }
5213
5214   /*
5215    * (non-Javadoc)
5216    *
5217    * @see
5218    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5219    * .event.ActionEvent)
5220    */
5221   @Override
5222   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5223   {
5224     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5225     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5226   }
5227
5228   /*
5229    * (non-Javadoc)
5230    *
5231    * @see
5232    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5233    * .event.ActionEvent)
5234    */
5235   @Override
5236   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5237   {
5238     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5239     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5240   }
5241
5242   @Override
5243   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5244   {
5245     showSequenceLogo.setState(true);
5246     viewport.setShowSequenceLogo(true);
5247     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5248     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5249   }
5250
5251   @Override
5252   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5253   {
5254     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5255   }
5256
5257   /*
5258    * (non-Javadoc)
5259    *
5260    * @see
5261    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5262    * .event.ActionEvent)
5263    */
5264   @Override
5265   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5266   {
5267     if (avc.makeGroupsFromSelection())
5268     {
5269       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5270       alignPanel.updateAnnotation();
5271       alignPanel.paintAlignment(true);
5272     }
5273   }
5274
5275   public void clearAlignmentSeqRep()
5276   {
5277     // TODO refactor alignmentseqrep to controller
5278     if (viewport.getAlignment().hasSeqrep())
5279     {
5280       viewport.getAlignment().setSeqrep(null);
5281       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5282       alignPanel.updateAnnotation();
5283       alignPanel.paintAlignment(true);
5284     }
5285   }
5286
5287   @Override
5288   protected void createGroup_actionPerformed(ActionEvent e)
5289   {
5290     if (avc.createGroup())
5291     {
5292       alignPanel.alignmentChanged();
5293     }
5294   }
5295
5296   @Override
5297   protected void unGroup_actionPerformed(ActionEvent e)
5298   {
5299     if (avc.unGroup())
5300     {
5301       alignPanel.alignmentChanged();
5302     }
5303   }
5304
5305   /**
5306    * make the given alignmentPanel the currently selected tab
5307    *
5308    * @param alignmentPanel
5309    */
5310   public void setDisplayedView(AlignmentPanel alignmentPanel)
5311   {
5312     if (!viewport.getSequenceSetId().equals(
5313             alignmentPanel.av.getSequenceSetId()))
5314     {
5315       throw new Error(
5316               MessageManager
5317                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5318     }
5319     if (tabbedPane != null
5320             && tabbedPane.getTabCount() > 0
5321             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5322                     .getSelectedIndex())
5323     {
5324       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5325     }
5326   }
5327
5328   /**
5329    * Action on selection of menu options to Show or Hide annotations.
5330    *
5331    * @param visible
5332    * @param forSequences
5333    *          update sequence-related annotations
5334    * @param forAlignment
5335    *          update non-sequence-related annotations
5336    */
5337   @Override
5338   protected void setAnnotationsVisibility(boolean visible,
5339           boolean forSequences, boolean forAlignment)
5340   {
5341     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5342             .getAlignmentAnnotation();
5343     if (anns == null)
5344     {
5345       return;
5346     }
5347     for (AlignmentAnnotation aa : anns)
5348     {
5349       /*
5350        * don't display non-positional annotations on an alignment
5351        */
5352       if (aa.annotations == null)
5353       {
5354         continue;
5355       }
5356       boolean apply = (aa.sequenceRef == null && forAlignment)
5357               || (aa.sequenceRef != null && forSequences);
5358       if (apply)
5359       {
5360         aa.visible = visible;
5361       }
5362     }
5363     alignPanel.validateAnnotationDimensions(true);
5364     alignPanel.alignmentChanged();
5365   }
5366
5367   /**
5368    * Store selected annotation sort order for the view and repaint.
5369    */
5370   @Override
5371   protected void sortAnnotations_actionPerformed()
5372   {
5373     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5374     this.alignPanel.av
5375             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5376     alignPanel.paintAlignment(true);
5377   }
5378
5379   /**
5380    *
5381    * @return alignment panels in this alignment frame
5382    */
5383   public List<? extends AlignmentViewPanel> getAlignPanels()
5384   {
5385     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5386   }
5387
5388   /**
5389    * Open a new alignment window, with the cDNA associated with this (protein)
5390    * alignment, aligned as is the protein.
5391    */
5392   protected void viewAsCdna_actionPerformed()
5393   {
5394     // TODO no longer a menu action - refactor as required
5395     final AlignmentI alignment = getViewport().getAlignment();
5396     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5397     if (mappings == null)
5398     {
5399       return;
5400     }
5401     List<SequenceI> cdnaSeqs = new ArrayList<>();
5402     for (SequenceI aaSeq : alignment.getSequences())
5403     {
5404       for (AlignedCodonFrame acf : mappings)
5405       {
5406         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5407         if (dnaSeq != null)
5408         {
5409           /*
5410            * There is a cDNA mapping for this protein sequence - add to new
5411            * alignment. It will share the same dataset sequence as other mapped
5412            * cDNA (no new mappings need to be created).
5413            */
5414           final Sequence newSeq = new Sequence(dnaSeq);
5415           newSeq.setDatasetSequence(dnaSeq);
5416           cdnaSeqs.add(newSeq);
5417         }
5418       }
5419     }
5420     if (cdnaSeqs.size() == 0)
5421     {
5422       // show a warning dialog no mapped cDNA
5423       return;
5424     }
5425     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5426             .size()]));
5427     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5428             AlignFrame.DEFAULT_HEIGHT);
5429     cdna.alignAs(alignment);
5430     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5431             + this.title;
5432     Desktop.addInternalFrame(alignFrame, newtitle,
5433             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5434   }
5435
5436   /**
5437    * Set visibility of dna/protein complement view (available when shown in a
5438    * split frame).
5439    *
5440    * @param show
5441    */
5442   @Override
5443   protected void showComplement_actionPerformed(boolean show)
5444   {
5445     SplitContainerI sf = getSplitViewContainer();
5446     if (sf != null)
5447     {
5448       sf.setComplementVisible(this, show);
5449     }
5450   }
5451
5452   /**
5453    * Generate the reverse (optionally complemented) of the selected sequences,
5454    * and add them to the alignment
5455    */
5456   @Override
5457   protected void showReverse_actionPerformed(boolean complement)
5458   {
5459     AlignmentI al = null;
5460     try
5461     {
5462       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5463       al = dna.reverseCdna(complement);
5464       viewport.addAlignment(al, "");
5465       addHistoryItem(new EditCommand(
5466               MessageManager.getString("label.add_sequences"),
5467               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5468               viewport.getAlignment()));
5469     } catch (Exception ex)
5470     {
5471       System.err.println(ex.getMessage());
5472       return;
5473     }
5474   }
5475
5476   /**
5477    * Try to run a script in the Groovy console, having first ensured that this
5478    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5479    * be targeted at this alignment.
5480    */
5481   @Override
5482   protected void runGroovy_actionPerformed()
5483   {
5484     Jalview.setCurrentAlignFrame(this);
5485     groovy.ui.Console console = Desktop.getGroovyConsole();
5486     if (console != null)
5487     {
5488       try
5489       {
5490         console.runScript();
5491       } catch (Exception ex)
5492       {
5493         System.err.println((ex.toString()));
5494         JvOptionPane
5495                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5496                         .getString("label.couldnt_run_groovy_script"),
5497                         MessageManager
5498                                 .getString("label.groovy_support_failed"),
5499                         JvOptionPane.ERROR_MESSAGE);
5500       }
5501     }
5502     else
5503     {
5504       System.err.println("Can't run Groovy script as console not found");
5505     }
5506   }
5507
5508   /**
5509    * Hides columns containing (or not containing) a specified feature, provided
5510    * that would not leave all columns hidden
5511    *
5512    * @param featureType
5513    * @param columnsContaining
5514    * @return
5515    */
5516   public boolean hideFeatureColumns(String featureType,
5517           boolean columnsContaining)
5518   {
5519     boolean notForHiding = avc.markColumnsContainingFeatures(
5520             columnsContaining, false, false, featureType);
5521     if (notForHiding)
5522     {
5523       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5524               false, featureType))
5525       {
5526         getViewport().hideSelectedColumns();
5527         return true;
5528       }
5529     }
5530     return false;
5531   }
5532
5533   @Override
5534   protected void selectHighlightedColumns_actionPerformed(
5535           ActionEvent actionEvent)
5536   {
5537     // include key modifier check in case user selects from menu
5538     avc.markHighlightedColumns(
5539             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5540             true,
5541             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5542   }
5543
5544   /**
5545    * Rebuilds the Colour menu, including any user-defined colours which have
5546    * been loaded either on startup or during the session
5547    */
5548   public void buildColourMenu()
5549   {
5550     colourMenu.removeAll();
5551
5552     colourMenu.add(applyToAllGroups);
5553     colourMenu.add(textColour);
5554     colourMenu.addSeparator();
5555
5556     ColourMenuHelper.addMenuItems(colourMenu, this,
5557             viewport.getAlignment(), false);
5558
5559     colourMenu.addSeparator();
5560     colourMenu.add(conservationMenuItem);
5561     colourMenu.add(modifyConservation);
5562     colourMenu.add(abovePIDThreshold);
5563     colourMenu.add(modifyPID);
5564     colourMenu.add(annotationColour);
5565
5566     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5567     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5568   }
5569
5570   /**
5571    * Open a dialog (if not already open) that allows the user to select and
5572    * calculate PCA or Tree analysis
5573    */
5574   protected void openTreePcaDialog()
5575   {
5576     if (alignPanel.getCalculationDialog() == null)
5577     {
5578       new CalculationChooser(AlignFrame.this);
5579     }
5580   }
5581 }
5582
5583 class PrintThread extends Thread
5584 {
5585   AlignmentPanel ap;
5586
5587   public PrintThread(AlignmentPanel ap)
5588   {
5589     this.ap = ap;
5590   }
5591
5592   static PageFormat pf;
5593
5594   @Override
5595   public void run()
5596   {
5597     PrinterJob printJob = PrinterJob.getPrinterJob();
5598
5599     if (pf != null)
5600     {
5601       printJob.setPrintable(ap, pf);
5602     }
5603     else
5604     {
5605       printJob.setPrintable(ap);
5606     }
5607
5608     if (printJob.printDialog())
5609     {
5610       try
5611       {
5612         printJob.print();
5613       } catch (Exception PrintException)
5614       {
5615         PrintException.printStackTrace();
5616       }
5617     }
5618   }
5619 }