src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenColumns;
  57 import jalview.datamodel.HiddenSequences;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileFormats;
  72 import jalview.io.FileLoader;
  73 import jalview.io.FileParse;
  74 import jalview.io.FormatAdapter;
  75 import jalview.io.HtmlSvgOutput;
  76 import jalview.io.IdentifyFile;
  77 import jalview.io.JPredFile;
  78 import jalview.io.JalviewFileChooser;
  79 import jalview.io.JalviewFileView;
  80 import jalview.io.JnetAnnotationMaker;
  81 import jalview.io.NewickFile;
  82 import jalview.io.ScoreMatrixFile;
  83 import jalview.io.TCoffeeScoreFile;
  84 import jalview.jbgui.GAlignFrame;
  85 import jalview.schemes.ColourSchemeI;
  86 import jalview.schemes.ColourSchemes;
  87 import jalview.schemes.ResidueColourScheme;
  88 import jalview.schemes.TCoffeeColourScheme;
  89 import jalview.util.MessageManager;
  90 import jalview.viewmodel.AlignmentViewport;
  91 import jalview.viewmodel.ViewportRanges;
  92 import jalview.ws.DBRefFetcher;
  93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  94 import jalview.ws.jws1.Discoverer;
  95 import jalview.ws.jws2.Jws2Discoverer;
  96 import jalview.ws.jws2.jabaws2.Jws2Instance;
  97 import jalview.ws.seqfetcher.DbSourceProxy;
  98
  99 import java.awt.BorderLayout;
 100 import java.awt.Component;
 101 import java.awt.Rectangle;
 102 import java.awt.Toolkit;
 103 import java.awt.datatransfer.Clipboard;
 104 import java.awt.datatransfer.DataFlavor;
 105 import java.awt.datatransfer.StringSelection;
 106 import java.awt.datatransfer.Transferable;
 107 import java.awt.dnd.DnDConstants;
 108 import java.awt.dnd.DropTargetDragEvent;
 109 import java.awt.dnd.DropTargetDropEvent;
 110 import java.awt.dnd.DropTargetEvent;
 111 import java.awt.dnd.DropTargetListener;
 112 import java.awt.event.ActionEvent;
 113 import java.awt.event.ActionListener;
 114 import java.awt.event.FocusAdapter;
 115 import java.awt.event.FocusEvent;
 116 import java.awt.event.ItemEvent;
 117 import java.awt.event.ItemListener;
 118 import java.awt.event.KeyAdapter;
 119 import java.awt.event.KeyEvent;
 120 import java.awt.event.MouseEvent;
 121 import java.awt.print.PageFormat;
 122 import java.awt.print.PrinterJob;
 123 import java.beans.PropertyChangeEvent;
 124 import java.io.File;
 125 import java.io.FileWriter;
 126 import java.io.PrintWriter;
 127 import java.net.URL;
 128 import java.util.ArrayList;
 129 import java.util.Arrays;
 130 import java.util.Deque;
 131 import java.util.Enumeration;
 132 import java.util.Hashtable;
 133 import java.util.List;
 134 import java.util.Vector;
 135
 136 import javax.swing.JCheckBoxMenuItem;
 137 import javax.swing.JEditorPane;
 138 import javax.swing.JInternalFrame;
 139 import javax.swing.JLayeredPane;
 140 import javax.swing.JMenu;
 141 import javax.swing.JMenuItem;
 142 import javax.swing.JScrollPane;
 143 import javax.swing.SwingUtilities;
 144
 145 /**
 146  * DOCUMENT ME!
 147  *
 148  * @author $author$
 149  * @version $Revision$
 150  */
 151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 152         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 153 {
 154
 155   public static final int DEFAULT_WIDTH = 700;
 156
 157   public static final int DEFAULT_HEIGHT = 500;
 158
 159   /*
 160    * The currently displayed panel (selected tabbed view if more than one)
 161    */
 162   public AlignmentPanel alignPanel;
 163
 164   AlignViewport viewport;
 165
 166   ViewportRanges vpRanges;
 167
 168   public AlignViewControllerI avc;
 169
 170   List<AlignmentPanel> alignPanels = new ArrayList<>();
 171
 172   /**
 173    * Last format used to load or save alignments in this window
 174    */
 175   FileFormatI currentFileFormat = null;
 176
 177   /**
 178    * Current filename for this alignment
 179    */
 180   String fileName = null;
 181
 182   /**
 183    * Creates a new AlignFrame object with specific width and height.
 184    *
 185    * @param al
 186    * @param width
 187    * @param height
 188    */
 189   public AlignFrame(AlignmentI al, int width, int height)
 190   {
 191     this(al, null, width, height);
 192   }
 193
 194   /**
 195    * Creates a new AlignFrame object with specific width, height and
 196    * sequenceSetId
 197    *
 198    * @param al
 199    * @param width
 200    * @param height
 201    * @param sequenceSetId
 202    */
 203   public AlignFrame(AlignmentI al, int width, int height,
 204           String sequenceSetId)
 205   {
 206     this(al, null, width, height, sequenceSetId);
 207   }
 208
 209   /**
 210    * Creates a new AlignFrame object with specific width, height and
 211    * sequenceSetId
 212    *
 213    * @param al
 214    * @param width
 215    * @param height
 216    * @param sequenceSetId
 217    * @param viewId
 218    */
 219   public AlignFrame(AlignmentI al, int width, int height,
 220           String sequenceSetId, String viewId)
 221   {
 222     this(al, null, width, height, sequenceSetId, viewId);
 223   }
 224
 225   /**
 226    * new alignment window with hidden columns
 227    *
 228    * @param al
 229    *          AlignmentI
 230    * @param hiddenColumns
 231    *          ColumnSelection or null
 232    * @param width
 233    *          Width of alignment frame
 234    * @param height
 235    *          height of frame.
 236    */
 237   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
 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.getIdPanel().getIdCanvas().searchResults = null;
2446     // JAL-2034 - should delegate to
2447     // alignPanel to decide if overview needs
2448     // updating.
2449     alignPanel.paintAlignment(false);
2450     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2451     viewport.sendSelection();
2452   }
2453
2454   /**
2455    * DOCUMENT ME!
2456    *
2457    * @param e
2458    *          DOCUMENT ME!
2459    */
2460   @Override
2461   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2462   {
2463     SequenceGroup sg = viewport.getSelectionGroup();
2464
2465     if (sg == null)
2466     {
2467       selectAllSequenceMenuItem_actionPerformed(null);
2468
2469       return;
2470     }
2471
2472     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2473     {
2474       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2475     }
2476     // JAL-2034 - should delegate to
2477     // alignPanel to decide if overview needs
2478     // updating.
2479
2480     alignPanel.paintAlignment(true);
2481     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2482     viewport.sendSelection();
2483   }
2484
2485   @Override
2486   public void invertColSel_actionPerformed(ActionEvent e)
2487   {
2488     viewport.invertColumnSelection();
2489     alignPanel.paintAlignment(true);
2490     viewport.sendSelection();
2491   }
2492
2493   /**
2494    * DOCUMENT ME!
2495    *
2496    * @param e
2497    *          DOCUMENT ME!
2498    */
2499   @Override
2500   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2501   {
2502     trimAlignment(true);
2503   }
2504
2505   /**
2506    * DOCUMENT ME!
2507    *
2508    * @param e
2509    *          DOCUMENT ME!
2510    */
2511   @Override
2512   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2513   {
2514     trimAlignment(false);
2515   }
2516
2517   void trimAlignment(boolean trimLeft)
2518   {
2519     ColumnSelection colSel = viewport.getColumnSelection();
2520     int column;
2521
2522     if (!colSel.isEmpty())
2523     {
2524       if (trimLeft)
2525       {
2526         column = colSel.getMin();
2527       }
2528       else
2529       {
2530         column = colSel.getMax();
2531       }
2532
2533       SequenceI[] seqs;
2534       if (viewport.getSelectionGroup() != null)
2535       {
2536         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2537                 viewport.getHiddenRepSequences());
2538       }
2539       else
2540       {
2541         seqs = viewport.getAlignment().getSequencesArray();
2542       }
2543
2544       TrimRegionCommand trimRegion;
2545       if (trimLeft)
2546       {
2547         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2548                 column, viewport.getAlignment());
2549         vpRanges.setStartRes(0);
2550       }
2551       else
2552       {
2553         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2554                 column, viewport.getAlignment());
2555       }
2556
2557       statusBar.setText(MessageManager.formatMessage(
2558               "label.removed_columns",
2559               new String[] { Integer.valueOf(trimRegion.getSize())
2560                       .toString() }));
2561
2562       addHistoryItem(trimRegion);
2563
2564       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2565       {
2566         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2567                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2568         {
2569           viewport.getAlignment().deleteGroup(sg);
2570         }
2571       }
2572
2573       viewport.firePropertyChange("alignment", null, viewport
2574               .getAlignment().getSequences());
2575     }
2576   }
2577
2578   /**
2579    * DOCUMENT ME!
2580    *
2581    * @param e
2582    *          DOCUMENT ME!
2583    */
2584   @Override
2585   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2586   {
2587     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2588
2589     SequenceI[] seqs;
2590     if (viewport.getSelectionGroup() != null)
2591     {
2592       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2593               viewport.getHiddenRepSequences());
2594       start = viewport.getSelectionGroup().getStartRes();
2595       end = viewport.getSelectionGroup().getEndRes();
2596     }
2597     else
2598     {
2599       seqs = viewport.getAlignment().getSequencesArray();
2600     }
2601
2602     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2603             "Remove Gapped Columns", seqs, start, end,
2604             viewport.getAlignment());
2605
2606     addHistoryItem(removeGapCols);
2607
2608     statusBar.setText(MessageManager.formatMessage(
2609             "label.removed_empty_columns",
2610             new Object[] { Integer.valueOf(removeGapCols.getSize())
2611                     .toString() }));
2612
2613     // This is to maintain viewport position on first residue
2614     // of first sequence
2615     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2616     int startRes = seq.findPosition(vpRanges.getStartRes());
2617     // ShiftList shifts;
2618     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2619     // edit.alColumnChanges=shifts.getInverse();
2620     // if (viewport.hasHiddenColumns)
2621     // viewport.getColumnSelection().compensateForEdits(shifts);
2622     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2623     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2624             .getSequences());
2625
2626   }
2627
2628   /**
2629    * DOCUMENT ME!
2630    *
2631    * @param e
2632    *          DOCUMENT ME!
2633    */
2634   @Override
2635   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2636   {
2637     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2638
2639     SequenceI[] seqs;
2640     if (viewport.getSelectionGroup() != null)
2641     {
2642       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2643               viewport.getHiddenRepSequences());
2644       start = viewport.getSelectionGroup().getStartRes();
2645       end = viewport.getSelectionGroup().getEndRes();
2646     }
2647     else
2648     {
2649       seqs = viewport.getAlignment().getSequencesArray();
2650     }
2651
2652     // This is to maintain viewport position on first residue
2653     // of first sequence
2654     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2655     int startRes = seq.findPosition(vpRanges.getStartRes());
2656
2657     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2658             viewport.getAlignment()));
2659
2660     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2661
2662     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2663             .getSequences());
2664
2665   }
2666
2667   /**
2668    * DOCUMENT ME!
2669    *
2670    * @param e
2671    *          DOCUMENT ME!
2672    */
2673   @Override
2674   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2675   {
2676     viewport.setPadGaps(padGapsMenuitem.isSelected());
2677     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2678             .getSequences());
2679   }
2680
2681   /**
2682    * DOCUMENT ME!
2683    *
2684    * @param e
2685    *          DOCUMENT ME!
2686    */
2687   @Override
2688   public void findMenuItem_actionPerformed(ActionEvent e)
2689   {
2690     new Finder();
2691   }
2692
2693   /**
2694    * Create a new view of the current alignment.
2695    */
2696   @Override
2697   public void newView_actionPerformed(ActionEvent e)
2698   {
2699     newView(null, true);
2700   }
2701
2702   /**
2703    * Creates and shows a new view of the current alignment.
2704    *
2705    * @param viewTitle
2706    *          title of newly created view; if null, one will be generated
2707    * @param copyAnnotation
2708    *          if true then duplicate all annnotation, groups and settings
2709    * @return new alignment panel, already displayed.
2710    */
2711   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2712   {
2713     /*
2714      * Create a new AlignmentPanel (with its own, new Viewport)
2715      */
2716     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2717             true);
2718     if (!copyAnnotation)
2719     {
2720       /*
2721        * remove all groups and annotation except for the automatic stuff
2722        */
2723       newap.av.getAlignment().deleteAllGroups();
2724       newap.av.getAlignment().deleteAllAnnotations(false);
2725     }
2726
2727     newap.av.setGatherViewsHere(false);
2728
2729     if (viewport.viewName == null)
2730     {
2731       viewport.viewName = MessageManager
2732               .getString("label.view_name_original");
2733     }
2734
2735     /*
2736      * Views share the same edits undo and redo stacks
2737      */
2738     newap.av.setHistoryList(viewport.getHistoryList());
2739     newap.av.setRedoList(viewport.getRedoList());
2740
2741     /*
2742      * Views share the same mappings; need to deregister any new mappings
2743      * created by copyAlignPanel, and register the new reference to the shared
2744      * mappings
2745      */
2746     newap.av.replaceMappings(viewport.getAlignment());
2747
2748     /*
2749      * start up cDNA consensus (if applicable) now mappings are in place
2750      */
2751     if (newap.av.initComplementConsensus())
2752     {
2753       newap.refresh(true); // adjust layout of annotations
2754     }
2755
2756     newap.av.viewName = getNewViewName(viewTitle);
2757
2758     addAlignmentPanel(newap, true);
2759     newap.alignmentChanged();
2760
2761     if (alignPanels.size() == 2)
2762     {
2763       viewport.setGatherViewsHere(true);
2764     }
2765     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2766     return newap;
2767   }
2768
2769   /**
2770    * Make a new name for the view, ensuring it is unique within the current
2771    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2772    * these now use viewId. Unique view names are still desirable for usability.)
2773    *
2774    * @param viewTitle
2775    * @return
2776    */
2777   protected String getNewViewName(String viewTitle)
2778   {
2779     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2780     boolean addFirstIndex = false;
2781     if (viewTitle == null || viewTitle.trim().length() == 0)
2782     {
2783       viewTitle = MessageManager.getString("action.view");
2784       addFirstIndex = true;
2785     }
2786     else
2787     {
2788       index = 1;// we count from 1 if given a specific name
2789     }
2790     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2791
2792     List<Component> comps = PaintRefresher.components.get(viewport
2793             .getSequenceSetId());
2794
2795     List<String> existingNames = getExistingViewNames(comps);
2796
2797     while (existingNames.contains(newViewName))
2798     {
2799       newViewName = viewTitle + " " + (++index);
2800     }
2801     return newViewName;
2802   }
2803
2804   /**
2805    * Returns a list of distinct view names found in the given list of
2806    * components. View names are held on the viewport of an AlignmentPanel.
2807    *
2808    * @param comps
2809    * @return
2810    */
2811   protected List<String> getExistingViewNames(List<Component> comps)
2812   {
2813     List<String> existingNames = new ArrayList<>();
2814     for (Component comp : comps)
2815     {
2816       if (comp instanceof AlignmentPanel)
2817       {
2818         AlignmentPanel ap = (AlignmentPanel) comp;
2819         if (!existingNames.contains(ap.av.viewName))
2820         {
2821           existingNames.add(ap.av.viewName);
2822         }
2823       }
2824     }
2825     return existingNames;
2826   }
2827
2828   /**
2829    * Explode tabbed views into separate windows.
2830    */
2831   @Override
2832   public void expandViews_actionPerformed(ActionEvent e)
2833   {
2834     Desktop.explodeViews(this);
2835   }
2836
2837   /**
2838    * Gather views in separate windows back into a tabbed presentation.
2839    */
2840   @Override
2841   public void gatherViews_actionPerformed(ActionEvent e)
2842   {
2843     Desktop.instance.gatherViews(this);
2844   }
2845
2846   /**
2847    * DOCUMENT ME!
2848    *
2849    * @param e
2850    *          DOCUMENT ME!
2851    */
2852   @Override
2853   public void font_actionPerformed(ActionEvent e)
2854   {
2855     new FontChooser(alignPanel);
2856   }
2857
2858   /**
2859    * DOCUMENT ME!
2860    *
2861    * @param e
2862    *          DOCUMENT ME!
2863    */
2864   @Override
2865   protected void seqLimit_actionPerformed(ActionEvent e)
2866   {
2867     viewport.setShowJVSuffix(seqLimits.isSelected());
2868
2869     alignPanel.getIdPanel().getIdCanvas()
2870             .setPreferredSize(alignPanel.calculateIdWidth());
2871     alignPanel.paintAlignment(true);
2872   }
2873
2874   @Override
2875   public void idRightAlign_actionPerformed(ActionEvent e)
2876   {
2877     viewport.setRightAlignIds(idRightAlign.isSelected());
2878     alignPanel.paintAlignment(true);
2879   }
2880
2881   @Override
2882   public void centreColumnLabels_actionPerformed(ActionEvent e)
2883   {
2884     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2885     alignPanel.paintAlignment(true);
2886   }
2887
2888   /*
2889    * (non-Javadoc)
2890    *
2891    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2892    */
2893   @Override
2894   protected void followHighlight_actionPerformed()
2895   {
2896     /*
2897      * Set the 'follow' flag on the Viewport (and scroll to position if now
2898      * true).
2899      */
2900     final boolean state = this.followHighlightMenuItem.getState();
2901     viewport.setFollowHighlight(state);
2902     if (state)
2903     {
2904       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2905     }
2906   }
2907
2908   /**
2909    * DOCUMENT ME!
2910    *
2911    * @param e
2912    *          DOCUMENT ME!
2913    */
2914   @Override
2915   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2916   {
2917     viewport.setColourText(colourTextMenuItem.isSelected());
2918     alignPanel.paintAlignment(true);
2919   }
2920
2921   /**
2922    * DOCUMENT ME!
2923    *
2924    * @param e
2925    *          DOCUMENT ME!
2926    */
2927   @Override
2928   public void wrapMenuItem_actionPerformed(ActionEvent e)
2929   {
2930     scaleAbove.setVisible(wrapMenuItem.isSelected());
2931     scaleLeft.setVisible(wrapMenuItem.isSelected());
2932     scaleRight.setVisible(wrapMenuItem.isSelected());
2933     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2934     alignPanel.updateLayout();
2935   }
2936
2937   @Override
2938   public void showAllSeqs_actionPerformed(ActionEvent e)
2939   {
2940     viewport.showAllHiddenSeqs();
2941   }
2942
2943   @Override
2944   public void showAllColumns_actionPerformed(ActionEvent e)
2945   {
2946     viewport.showAllHiddenColumns();
2947     alignPanel.paintAlignment(true);
2948     viewport.sendSelection();
2949   }
2950
2951   @Override
2952   public void hideSelSequences_actionPerformed(ActionEvent e)
2953   {
2954     viewport.hideAllSelectedSeqs();
2955   }
2956
2957   /**
2958    * called by key handler and the hide all/show all menu items
2959    *
2960    * @param toggleSeqs
2961    * @param toggleCols
2962    */
2963   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2964   {
2965
2966     boolean hide = false;
2967     SequenceGroup sg = viewport.getSelectionGroup();
2968     if (!toggleSeqs && !toggleCols)
2969     {
2970       // Hide everything by the current selection - this is a hack - we do the
2971       // invert and then hide
2972       // first check that there will be visible columns after the invert.
2973       if (viewport.hasSelectedColumns()
2974               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2975                       .getEndRes()))
2976       {
2977         // now invert the sequence set, if required - empty selection implies
2978         // that no hiding is required.
2979         if (sg != null)
2980         {
2981           invertSequenceMenuItem_actionPerformed(null);
2982           sg = viewport.getSelectionGroup();
2983           toggleSeqs = true;
2984
2985         }
2986         viewport.expandColSelection(sg, true);
2987         // finally invert the column selection and get the new sequence
2988         // selection.
2989         invertColSel_actionPerformed(null);
2990         toggleCols = true;
2991       }
2992     }
2993
2994     if (toggleSeqs)
2995     {
2996       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2997       {
2998         hideSelSequences_actionPerformed(null);
2999         hide = true;
3000       }
3001       else if (!(toggleCols && viewport.hasSelectedColumns()))
3002       {
3003         showAllSeqs_actionPerformed(null);
3004       }
3005     }
3006
3007     if (toggleCols)
3008     {
3009       if (viewport.hasSelectedColumns())
3010       {
3011         hideSelColumns_actionPerformed(null);
3012         if (!toggleSeqs)
3013         {
3014           viewport.setSelectionGroup(sg);
3015         }
3016       }
3017       else if (!hide)
3018       {
3019         showAllColumns_actionPerformed(null);
3020       }
3021     }
3022   }
3023
3024   /*
3025    * (non-Javadoc)
3026    *
3027    * @see
3028    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3029    * event.ActionEvent)
3030    */
3031   @Override
3032   public void hideAllButSelection_actionPerformed(ActionEvent e)
3033   {
3034     toggleHiddenRegions(false, false);
3035     viewport.sendSelection();
3036   }
3037
3038   /*
3039    * (non-Javadoc)
3040    *
3041    * @see
3042    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3043    * .ActionEvent)
3044    */
3045   @Override
3046   public void hideAllSelection_actionPerformed(ActionEvent e)
3047   {
3048     SequenceGroup sg = viewport.getSelectionGroup();
3049     viewport.expandColSelection(sg, false);
3050     viewport.hideAllSelectedSeqs();
3051     viewport.hideSelectedColumns();
3052     alignPanel.paintAlignment(true);
3053     viewport.sendSelection();
3054   }
3055
3056   /*
3057    * (non-Javadoc)
3058    *
3059    * @see
3060    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3061    * ActionEvent)
3062    */
3063   @Override
3064   public void showAllhidden_actionPerformed(ActionEvent e)
3065   {
3066     viewport.showAllHiddenColumns();
3067     viewport.showAllHiddenSeqs();
3068     alignPanel.paintAlignment(true);
3069     viewport.sendSelection();
3070   }
3071
3072   @Override
3073   public void hideSelColumns_actionPerformed(ActionEvent e)
3074   {
3075     viewport.hideSelectedColumns();
3076     alignPanel.paintAlignment(true);
3077     viewport.sendSelection();
3078   }
3079
3080   @Override
3081   public void hiddenMarkers_actionPerformed(ActionEvent e)
3082   {
3083     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3084     repaint();
3085   }
3086
3087   /**
3088    * DOCUMENT ME!
3089    *
3090    * @param e
3091    *          DOCUMENT ME!
3092    */
3093   @Override
3094   protected void scaleAbove_actionPerformed(ActionEvent e)
3095   {
3096     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3097     alignPanel.paintAlignment(true);
3098   }
3099
3100   /**
3101    * DOCUMENT ME!
3102    *
3103    * @param e
3104    *          DOCUMENT ME!
3105    */
3106   @Override
3107   protected void scaleLeft_actionPerformed(ActionEvent e)
3108   {
3109     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3110     alignPanel.paintAlignment(true);
3111   }
3112
3113   /**
3114    * DOCUMENT ME!
3115    *
3116    * @param e
3117    *          DOCUMENT ME!
3118    */
3119   @Override
3120   protected void scaleRight_actionPerformed(ActionEvent e)
3121   {
3122     viewport.setScaleRightWrapped(scaleRight.isSelected());
3123     alignPanel.paintAlignment(true);
3124   }
3125
3126   /**
3127    * DOCUMENT ME!
3128    *
3129    * @param e
3130    *          DOCUMENT ME!
3131    */
3132   @Override
3133   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3134   {
3135     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3136     alignPanel.paintAlignment(true);
3137   }
3138
3139   /**
3140    * DOCUMENT ME!
3141    *
3142    * @param e
3143    *          DOCUMENT ME!
3144    */
3145   @Override
3146   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3147   {
3148     viewport.setShowText(viewTextMenuItem.isSelected());
3149     alignPanel.paintAlignment(true);
3150   }
3151
3152   /**
3153    * DOCUMENT ME!
3154    *
3155    * @param e
3156    *          DOCUMENT ME!
3157    */
3158   @Override
3159   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3160   {
3161     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3162     alignPanel.paintAlignment(true);
3163   }
3164
3165   public FeatureSettings featureSettings;
3166
3167   @Override
3168   public FeatureSettingsControllerI getFeatureSettingsUI()
3169   {
3170     return featureSettings;
3171   }
3172
3173   @Override
3174   public void featureSettings_actionPerformed(ActionEvent e)
3175   {
3176     if (featureSettings != null)
3177     {
3178       featureSettings.close();
3179       featureSettings = null;
3180     }
3181     if (!showSeqFeatures.isSelected())
3182     {
3183       // make sure features are actually displayed
3184       showSeqFeatures.setSelected(true);
3185       showSeqFeatures_actionPerformed(null);
3186     }
3187     featureSettings = new FeatureSettings(this);
3188   }
3189
3190   /**
3191    * Set or clear 'Show Sequence Features'
3192    *
3193    * @param evt
3194    *          DOCUMENT ME!
3195    */
3196   @Override
3197   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3198   {
3199     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3200     alignPanel.paintAlignment(true);
3201   }
3202
3203   /**
3204    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3205    * the annotations panel as a whole.
3206    *
3207    * The options to show/hide all annotations should be enabled when the panel
3208    * is shown, and disabled when the panel is hidden.
3209    *
3210    * @param e
3211    */
3212   @Override
3213   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3214   {
3215     final boolean setVisible = annotationPanelMenuItem.isSelected();
3216     viewport.setShowAnnotation(setVisible);
3217     this.showAllSeqAnnotations.setEnabled(setVisible);
3218     this.hideAllSeqAnnotations.setEnabled(setVisible);
3219     this.showAllAlAnnotations.setEnabled(setVisible);
3220     this.hideAllAlAnnotations.setEnabled(setVisible);
3221     alignPanel.updateLayout();
3222   }
3223
3224   @Override
3225   public void alignmentProperties()
3226   {
3227     JEditorPane editPane = new JEditorPane("text/html", "");
3228     editPane.setEditable(false);
3229     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3230             .formatAsHtml();
3231     editPane.setText(MessageManager.formatMessage("label.html_content",
3232             new Object[] { contents.toString() }));
3233     JInternalFrame frame = new JInternalFrame();
3234     frame.getContentPane().add(new JScrollPane(editPane));
3235
3236     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3237             "label.alignment_properties", new Object[] { getTitle() }),
3238             500, 400);
3239   }
3240
3241   /**
3242    * DOCUMENT ME!
3243    *
3244    * @param e
3245    *          DOCUMENT ME!
3246    */
3247   @Override
3248   public void overviewMenuItem_actionPerformed(ActionEvent e)
3249   {
3250     if (alignPanel.overviewPanel != null)
3251     {
3252       return;
3253     }
3254
3255     JInternalFrame frame = new JInternalFrame();
3256     final OverviewPanel overview = new OverviewPanel(alignPanel);
3257     frame.setContentPane(overview);
3258     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3259             "label.overview_params", new Object[] { this.getTitle() }),
3260             true, frame.getWidth(), frame.getHeight(), true, true);
3261     frame.pack();
3262     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3263     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3264     {
3265       @Override
3266       public void internalFrameClosed(
3267               javax.swing.event.InternalFrameEvent evt)
3268       {
3269         overview.dispose();
3270         alignPanel.setOverviewPanel(null);
3271       };
3272     });
3273
3274     alignPanel.setOverviewPanel(overview);
3275   }
3276
3277   @Override
3278   public void textColour_actionPerformed()
3279   {
3280     new TextColourChooser().chooseColour(alignPanel, null);
3281   }
3282
3283   /*
3284    * public void covariationColour_actionPerformed() {
3285    * changeColour(new
3286    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3287    * ()[0])); }
3288    */
3289   @Override
3290   public void annotationColour_actionPerformed()
3291   {
3292     new AnnotationColourChooser(viewport, alignPanel);
3293   }
3294
3295   @Override
3296   public void annotationColumn_actionPerformed(ActionEvent e)
3297   {
3298     new AnnotationColumnChooser(viewport, alignPanel);
3299   }
3300
3301   /**
3302    * Action on the user checking or unchecking the option to apply the selected
3303    * colour scheme to all groups. If unchecked, groups may have their own
3304    * independent colour schemes.
3305    *
3306    * @param selected
3307    */
3308   @Override
3309   public void applyToAllGroups_actionPerformed(boolean selected)
3310   {
3311     viewport.setColourAppliesToAllGroups(selected);
3312   }
3313
3314   /**
3315    * Action on user selecting a colour from the colour menu
3316    *
3317    * @param name
3318    *          the name (not the menu item label!) of the colour scheme
3319    */
3320   @Override
3321   public void changeColour_actionPerformed(String name)
3322   {
3323     /*
3324      * 'User Defined' opens a panel to configure or load a
3325      * user-defined colour scheme
3326      */
3327     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3328     {
3329       new UserDefinedColours(alignPanel);
3330       return;
3331     }
3332
3333     /*
3334      * otherwise set the chosen colour scheme (or null for 'None')
3335      */
3336     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3337             viewport.getAlignment(), viewport.getHiddenRepSequences());
3338     changeColour(cs);
3339   }
3340
3341   /**
3342    * Actions on setting or changing the alignment colour scheme
3343    *
3344    * @param cs
3345    */
3346   @Override
3347   public void changeColour(ColourSchemeI cs)
3348   {
3349     // TODO: pull up to controller method
3350     ColourMenuHelper.setColourSelected(colourMenu, cs);
3351
3352     viewport.setGlobalColourScheme(cs);
3353
3354     alignPanel.paintAlignment(true);
3355   }
3356
3357   /**
3358    * Show the PID threshold slider panel
3359    */
3360   @Override
3361   protected void modifyPID_actionPerformed()
3362   {
3363     SliderPanel.setPIDSliderSource(alignPanel,
3364             viewport.getResidueShading(), alignPanel.getViewName());
3365     SliderPanel.showPIDSlider();
3366   }
3367
3368   /**
3369    * Show the Conservation slider panel
3370    */
3371   @Override
3372   protected void modifyConservation_actionPerformed()
3373   {
3374     SliderPanel.setConservationSlider(alignPanel,
3375             viewport.getResidueShading(), alignPanel.getViewName());
3376     SliderPanel.showConservationSlider();
3377   }
3378
3379   /**
3380    * Action on selecting or deselecting (Colour) By Conservation
3381    */
3382   @Override
3383   public void conservationMenuItem_actionPerformed(boolean selected)
3384   {
3385     modifyConservation.setEnabled(selected);
3386     viewport.setConservationSelected(selected);
3387     viewport.getResidueShading().setConservationApplied(selected);
3388
3389     changeColour(viewport.getGlobalColourScheme());
3390     if (selected)
3391     {
3392       modifyConservation_actionPerformed();
3393     }
3394     else
3395     {
3396       SliderPanel.hideConservationSlider();
3397     }
3398   }
3399
3400   /**
3401    * Action on selecting or deselecting (Colour) Above PID Threshold
3402    */
3403   @Override
3404   public void abovePIDThreshold_actionPerformed(boolean selected)
3405   {
3406     modifyPID.setEnabled(selected);
3407     viewport.setAbovePIDThreshold(selected);
3408     if (!selected)
3409     {
3410       viewport.getResidueShading().setThreshold(0,
3411               viewport.isIgnoreGapsConsensus());
3412     }
3413
3414     changeColour(viewport.getGlobalColourScheme());
3415     if (selected)
3416     {
3417       modifyPID_actionPerformed();
3418     }
3419     else
3420     {
3421       SliderPanel.hidePIDSlider();
3422     }
3423   }
3424
3425   /**
3426    * DOCUMENT ME!
3427    *
3428    * @param e
3429    *          DOCUMENT ME!
3430    */
3431   @Override
3432   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3433   {
3434     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3435     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3436             .getAlignment().getSequenceAt(0));
3437     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3438             viewport.getAlignment()));
3439     alignPanel.paintAlignment(true);
3440   }
3441
3442   /**
3443    * DOCUMENT ME!
3444    *
3445    * @param e
3446    *          DOCUMENT ME!
3447    */
3448   @Override
3449   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3450   {
3451     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3452     AlignmentSorter.sortByID(viewport.getAlignment());
3453     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3454             viewport.getAlignment()));
3455     alignPanel.paintAlignment(true);
3456   }
3457
3458   /**
3459    * DOCUMENT ME!
3460    *
3461    * @param e
3462    *          DOCUMENT ME!
3463    */
3464   @Override
3465   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3466   {
3467     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3468     AlignmentSorter.sortByLength(viewport.getAlignment());
3469     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3470             viewport.getAlignment()));
3471     alignPanel.paintAlignment(true);
3472   }
3473
3474   /**
3475    * DOCUMENT ME!
3476    *
3477    * @param e
3478    *          DOCUMENT ME!
3479    */
3480   @Override
3481   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3482   {
3483     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3484     AlignmentSorter.sortByGroup(viewport.getAlignment());
3485     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3486             viewport.getAlignment()));
3487
3488     alignPanel.paintAlignment(true);
3489   }
3490
3491   /**
3492    * DOCUMENT ME!
3493    *
3494    * @param e
3495    *          DOCUMENT ME!
3496    */
3497   @Override
3498   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3499   {
3500     new RedundancyPanel(alignPanel, this);
3501   }
3502
3503   /**
3504    * DOCUMENT ME!
3505    *
3506    * @param e
3507    *          DOCUMENT ME!
3508    */
3509   @Override
3510   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3511   {
3512     if ((viewport.getSelectionGroup() == null)
3513             || (viewport.getSelectionGroup().getSize() < 2))
3514     {
3515       JvOptionPane.showInternalMessageDialog(this, MessageManager
3516               .getString("label.you_must_select_least_two_sequences"),
3517               MessageManager.getString("label.invalid_selection"),
3518               JvOptionPane.WARNING_MESSAGE);
3519     }
3520     else
3521     {
3522       JInternalFrame frame = new JInternalFrame();
3523       frame.setContentPane(new PairwiseAlignPanel(viewport));
3524       Desktop.addInternalFrame(frame,
3525               MessageManager.getString("action.pairwise_alignment"), 600,
3526               500);
3527     }
3528   }
3529
3530   @Override
3531   public void autoCalculate_actionPerformed(ActionEvent e)
3532   {
3533     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3534     if (viewport.autoCalculateConsensus)
3535     {
3536       viewport.firePropertyChange("alignment", null, viewport
3537               .getAlignment().getSequences());
3538     }
3539   }
3540
3541   @Override
3542   public void sortByTreeOption_actionPerformed(ActionEvent e)
3543   {
3544     viewport.sortByTree = sortByTree.isSelected();
3545   }
3546
3547   @Override
3548   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3549   {
3550     viewport.followSelection = listenToViewSelections.isSelected();
3551   }
3552
3553   /**
3554    * Constructs a tree panel and adds it to the desktop
3555    *
3556    * @param type
3557    *          tree type (NJ or AV)
3558    * @param modelName
3559    *          name of score model used to compute the tree
3560    * @param options
3561    *          parameters for the distance or similarity calculation
3562    */
3563   void newTreePanel(String type, String modelName, SimilarityParamsI options)
3564   {
3565     String frameTitle = "";
3566     TreePanel tp;
3567
3568     boolean onSelection = false;
3569     if (viewport.getSelectionGroup() != null
3570             && viewport.getSelectionGroup().getSize() > 0)
3571     {
3572       SequenceGroup sg = viewport.getSelectionGroup();
3573
3574       /* Decide if the selection is a column region */
3575       for (SequenceI _s : sg.getSequences())
3576       {
3577         if (_s.getLength() < sg.getEndRes())
3578         {
3579           JvOptionPane
3580                   .showMessageDialog(
3581                           Desktop.desktop,
3582                           MessageManager
3583                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3584                           MessageManager
3585                                   .getString("label.sequences_selection_not_aligned"),
3586                           JvOptionPane.WARNING_MESSAGE);
3587
3588           return;
3589         }
3590       }
3591       onSelection = true;
3592     }
3593     else
3594     {
3595       if (viewport.getAlignment().getHeight() < 2)
3596       {
3597         return;
3598       }
3599     }
3600
3601     tp = new TreePanel(alignPanel, type, modelName, options);
3602     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3603
3604     frameTitle += " from ";
3605
3606     if (viewport.viewName != null)
3607     {
3608       frameTitle += viewport.viewName + " of ";
3609     }
3610
3611     frameTitle += this.title;
3612
3613     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3614   }
3615
3616   /**
3617    * DOCUMENT ME!
3618    *
3619    * @param title
3620    *          DOCUMENT ME!
3621    * @param order
3622    *          DOCUMENT ME!
3623    */
3624   public void addSortByOrderMenuItem(String title,
3625           final AlignmentOrder order)
3626   {
3627     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3628             "action.by_title_param", new Object[] { title }));
3629     sort.add(item);
3630     item.addActionListener(new java.awt.event.ActionListener()
3631     {
3632       @Override
3633       public void actionPerformed(ActionEvent e)
3634       {
3635         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3636
3637         // TODO: JBPNote - have to map order entries to curent SequenceI
3638         // pointers
3639         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3640
3641         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3642                 .getAlignment()));
3643
3644         alignPanel.paintAlignment(true);
3645       }
3646     });
3647   }
3648
3649   /**
3650    * Add a new sort by annotation score menu item
3651    *
3652    * @param sort
3653    *          the menu to add the option to
3654    * @param scoreLabel
3655    *          the label used to retrieve scores for each sequence on the
3656    *          alignment
3657    */
3658   public void addSortByAnnotScoreMenuItem(JMenu sort,
3659           final String scoreLabel)
3660   {
3661     final JMenuItem item = new JMenuItem(scoreLabel);
3662     sort.add(item);
3663     item.addActionListener(new java.awt.event.ActionListener()
3664     {
3665       @Override
3666       public void actionPerformed(ActionEvent e)
3667       {
3668         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3669         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3670                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3671         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3672                 viewport.getAlignment()));
3673         alignPanel.paintAlignment(true);
3674       }
3675     });
3676   }
3677
3678   /**
3679    * last hash for alignment's annotation array - used to minimise cost of
3680    * rebuild.
3681    */
3682   protected int _annotationScoreVectorHash;
3683
3684   /**
3685    * search the alignment and rebuild the sort by annotation score submenu the
3686    * last alignment annotation vector hash is stored to minimize cost of
3687    * rebuilding in subsequence calls.
3688    *
3689    */
3690   @Override
3691   public void buildSortByAnnotationScoresMenu()
3692   {
3693     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3694     {
3695       return;
3696     }
3697
3698     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3699     {
3700       sortByAnnotScore.removeAll();
3701       // almost certainly a quicker way to do this - but we keep it simple
3702       Hashtable scoreSorts = new Hashtable();
3703       AlignmentAnnotation aann[];
3704       for (SequenceI sqa : viewport.getAlignment().getSequences())
3705       {
3706         aann = sqa.getAnnotation();
3707         for (int i = 0; aann != null && i < aann.length; i++)
3708         {
3709           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3710           {
3711             scoreSorts.put(aann[i].label, aann[i].label);
3712           }
3713         }
3714       }
3715       Enumeration labels = scoreSorts.keys();
3716       while (labels.hasMoreElements())
3717       {
3718         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3719                 (String) labels.nextElement());
3720       }
3721       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3722       scoreSorts.clear();
3723
3724       _annotationScoreVectorHash = viewport.getAlignment()
3725               .getAlignmentAnnotation().hashCode();
3726     }
3727   }
3728
3729   /**
3730    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3731    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3732    * call. Listeners are added to remove the menu item when the treePanel is
3733    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3734    * modified.
3735    */
3736   @Override
3737   public void buildTreeSortMenu()
3738   {
3739     sortByTreeMenu.removeAll();
3740
3741     List<Component> comps = PaintRefresher.components.get(viewport
3742             .getSequenceSetId());
3743     List<TreePanel> treePanels = new ArrayList<>();
3744     for (Component comp : comps)
3745     {
3746       if (comp instanceof TreePanel)
3747       {
3748         treePanels.add((TreePanel) comp);
3749       }
3750     }
3751
3752     if (treePanels.size() < 1)
3753     {
3754       sortByTreeMenu.setVisible(false);
3755       return;
3756     }
3757
3758     sortByTreeMenu.setVisible(true);
3759
3760     for (final TreePanel tp : treePanels)
3761     {
3762       final JMenuItem item = new JMenuItem(tp.getTitle());
3763       item.addActionListener(new java.awt.event.ActionListener()
3764       {
3765         @Override
3766         public void actionPerformed(ActionEvent e)
3767         {
3768           tp.sortByTree_actionPerformed();
3769           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3770
3771         }
3772       });
3773
3774       sortByTreeMenu.add(item);
3775     }
3776   }
3777
3778   public boolean sortBy(AlignmentOrder alorder, String undoname)
3779   {
3780     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3781     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3782     if (undoname != null)
3783     {
3784       addHistoryItem(new OrderCommand(undoname, oldOrder,
3785               viewport.getAlignment()));
3786     }
3787     alignPanel.paintAlignment(true);
3788     return true;
3789   }
3790
3791   /**
3792    * Work out whether the whole set of sequences or just the selected set will
3793    * be submitted for multiple alignment.
3794    *
3795    */
3796   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3797   {
3798     // Now, check we have enough sequences
3799     AlignmentView msa = null;
3800
3801     if ((viewport.getSelectionGroup() != null)
3802             && (viewport.getSelectionGroup().getSize() > 1))
3803     {
3804       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3805       // some common interface!
3806       /*
3807        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3808        * SequenceI[sz = seqs.getSize(false)];
3809        *
3810        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3811        * seqs.getSequenceAt(i); }
3812        */
3813       msa = viewport.getAlignmentView(true);
3814     }
3815     else if (viewport.getSelectionGroup() != null
3816             && viewport.getSelectionGroup().getSize() == 1)
3817     {
3818       int option = JvOptionPane.showConfirmDialog(this,
3819               MessageManager.getString("warn.oneseq_msainput_selection"),
3820               MessageManager.getString("label.invalid_selection"),
3821               JvOptionPane.OK_CANCEL_OPTION);
3822       if (option == JvOptionPane.OK_OPTION)
3823       {
3824         msa = viewport.getAlignmentView(false);
3825       }
3826     }
3827     else
3828     {
3829       msa = viewport.getAlignmentView(false);
3830     }
3831     return msa;
3832   }
3833
3834   /**
3835    * Decides what is submitted to a secondary structure prediction service: the
3836    * first sequence in the alignment, or in the current selection, or, if the
3837    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3838    * region or the whole alignment. (where the first sequence in the set is the
3839    * one that the prediction will be for).
3840    */
3841   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3842   {
3843     AlignmentView seqs = null;
3844
3845     if ((viewport.getSelectionGroup() != null)
3846             && (viewport.getSelectionGroup().getSize() > 0))
3847     {
3848       seqs = viewport.getAlignmentView(true);
3849     }
3850     else
3851     {
3852       seqs = viewport.getAlignmentView(false);
3853     }
3854     // limit sequences - JBPNote in future - could spawn multiple prediction
3855     // jobs
3856     // TODO: viewport.getAlignment().isAligned is a global state - the local
3857     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3858     if (!viewport.getAlignment().isAligned(false))
3859     {
3860       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3861       // TODO: if seqs.getSequences().length>1 then should really have warned
3862       // user!
3863
3864     }
3865     return seqs;
3866   }
3867
3868   /**
3869    * DOCUMENT ME!
3870    *
3871    * @param e
3872    *          DOCUMENT ME!
3873    */
3874   @Override
3875   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3876   {
3877     // Pick the tree file
3878     JalviewFileChooser chooser = new JalviewFileChooser(
3879             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3880     chooser.setFileView(new JalviewFileView());
3881     chooser.setDialogTitle(MessageManager
3882             .getString("label.select_newick_like_tree_file"));
3883     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3884
3885     int value = chooser.showOpenDialog(null);
3886
3887     if (value == JalviewFileChooser.APPROVE_OPTION)
3888     {
3889       String filePath = chooser.getSelectedFile().getPath();
3890       Cache.setProperty("LAST_DIRECTORY", filePath);
3891       NewickFile fin = null;
3892       try
3893       {
3894         fin = new NewickFile(filePath, DataSourceType.FILE);
3895         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3896       } catch (Exception ex)
3897       {
3898         JvOptionPane
3899                 .showMessageDialog(
3900                         Desktop.desktop,
3901                         ex.getMessage(),
3902                         MessageManager
3903                                 .getString("label.problem_reading_tree_file"),
3904                         JvOptionPane.WARNING_MESSAGE);
3905         ex.printStackTrace();
3906       }
3907       if (fin != null && fin.hasWarningMessage())
3908       {
3909         JvOptionPane.showMessageDialog(Desktop.desktop, fin
3910                 .getWarningMessage(), MessageManager
3911                 .getString("label.possible_problem_with_tree_file"),
3912                 JvOptionPane.WARNING_MESSAGE);
3913       }
3914     }
3915   }
3916
3917   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3918   {
3919     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3920   }
3921
3922   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3923           int h, int x, int y)
3924   {
3925     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3926   }
3927
3928   /**
3929    * Add a treeviewer for the tree extracted from a Newick file object to the
3930    * current alignment view
3931    *
3932    * @param nf
3933    *          the tree
3934    * @param title
3935    *          tree viewer title
3936    * @param input
3937    *          Associated alignment input data (or null)
3938    * @param w
3939    *          width
3940    * @param h
3941    *          height
3942    * @param x
3943    *          position
3944    * @param y
3945    *          position
3946    * @return TreePanel handle
3947    */
3948   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3949           AlignmentView input, int w, int h, int x, int y)
3950   {
3951     TreePanel tp = null;
3952
3953     try
3954     {
3955       nf.parse();
3956
3957       if (nf.getTree() != null)
3958       {
3959         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3960
3961         tp.setSize(w, h);
3962
3963         if (x > 0 && y > 0)
3964         {
3965           tp.setLocation(x, y);
3966         }
3967
3968         Desktop.addInternalFrame(tp, treeTitle, w, h);
3969       }
3970     } catch (Exception ex)
3971     {
3972       ex.printStackTrace();
3973     }
3974
3975     return tp;
3976   }
3977
3978   private boolean buildingMenu = false;
3979
3980   /**
3981    * Generates menu items and listener event actions for web service clients
3982    *
3983    */
3984   public void BuildWebServiceMenu()
3985   {
3986     while (buildingMenu)
3987     {
3988       try
3989       {
3990         System.err.println("Waiting for building menu to finish.");
3991         Thread.sleep(10);
3992       } catch (Exception e)
3993       {
3994       }
3995     }
3996     final AlignFrame me = this;
3997     buildingMenu = true;
3998     new Thread(new Runnable()
3999     {
4000       @Override
4001       public void run()
4002       {
4003         final List<JMenuItem> legacyItems = new ArrayList<>();
4004         try
4005         {
4006           // System.err.println("Building ws menu again "
4007           // + Thread.currentThread());
4008           // TODO: add support for context dependent disabling of services based
4009           // on
4010           // alignment and current selection
4011           // TODO: add additional serviceHandle parameter to specify abstract
4012           // handler
4013           // class independently of AbstractName
4014           // TODO: add in rediscovery GUI function to restart discoverer
4015           // TODO: group services by location as well as function and/or
4016           // introduce
4017           // object broker mechanism.
4018           final Vector<JMenu> wsmenu = new Vector<>();
4019           final IProgressIndicator af = me;
4020
4021           /*
4022            * do not i18n these strings - they are hard-coded in class
4023            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4024            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4025            */
4026           final JMenu msawsmenu = new JMenu("Alignment");
4027           final JMenu secstrmenu = new JMenu(
4028                   "Secondary Structure Prediction");
4029           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4030           final JMenu analymenu = new JMenu("Analysis");
4031           final JMenu dismenu = new JMenu("Protein Disorder");
4032           // JAL-940 - only show secondary structure prediction services from
4033           // the legacy server
4034           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4035               // &&
4036           Discoverer.services != null && (Discoverer.services.size() > 0))
4037           {
4038             // TODO: refactor to allow list of AbstractName/Handler bindings to
4039             // be
4040             // stored or retrieved from elsewhere
4041             // No MSAWS used any more:
4042             // Vector msaws = null; // (Vector)
4043             // Discoverer.services.get("MsaWS");
4044             Vector secstrpr = (Vector) Discoverer.services
4045                     .get("SecStrPred");
4046             if (secstrpr != null)
4047             {
4048               // Add any secondary structure prediction services
4049               for (int i = 0, j = secstrpr.size(); i < j; i++)
4050               {
4051                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4052                         .get(i);
4053                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4054                         .getServiceClient(sh);
4055                 int p = secstrmenu.getItemCount();
4056                 impl.attachWSMenuEntry(secstrmenu, me);
4057                 int q = secstrmenu.getItemCount();
4058                 for (int litm = p; litm < q; litm++)
4059                 {
4060                   legacyItems.add(secstrmenu.getItem(litm));
4061                 }
4062               }
4063             }
4064           }
4065
4066           // Add all submenus in the order they should appear on the web
4067           // services menu
4068           wsmenu.add(msawsmenu);
4069           wsmenu.add(secstrmenu);
4070           wsmenu.add(dismenu);
4071           wsmenu.add(analymenu);
4072           // No search services yet
4073           // wsmenu.add(seqsrchmenu);
4074
4075           javax.swing.SwingUtilities.invokeLater(new Runnable()
4076           {
4077             @Override
4078             public void run()
4079             {
4080               try
4081               {
4082                 webService.removeAll();
4083                 // first, add discovered services onto the webservices menu
4084                 if (wsmenu.size() > 0)
4085                 {
4086                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4087                   {
4088                     webService.add(wsmenu.get(i));
4089                   }
4090                 }
4091                 else
4092                 {
4093                   webService.add(me.webServiceNoServices);
4094                 }
4095                 // TODO: move into separate menu builder class.
4096                 boolean new_sspred = false;
4097                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4098                 {
4099                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4100                   if (jws2servs != null)
4101                   {
4102                     if (jws2servs.hasServices())
4103                     {
4104                       jws2servs.attachWSMenuEntry(webService, me);
4105                       for (Jws2Instance sv : jws2servs.getServices())
4106                       {
4107                         if (sv.description.toLowerCase().contains("jpred"))
4108                         {
4109                           for (JMenuItem jmi : legacyItems)
4110                           {
4111                             jmi.setVisible(false);
4112                           }
4113                         }
4114                       }
4115
4116                     }
4117                     if (jws2servs.isRunning())
4118                     {
4119                       JMenuItem tm = new JMenuItem(
4120                               "Still discovering JABA Services");
4121                       tm.setEnabled(false);
4122                       webService.add(tm);
4123                     }
4124                   }
4125                 }
4126                 build_urlServiceMenu(me.webService);
4127                 build_fetchdbmenu(webService);
4128                 for (JMenu item : wsmenu)
4129                 {
4130                   if (item.getItemCount() == 0)
4131                   {
4132                     item.setEnabled(false);
4133                   }
4134                   else
4135                   {
4136                     item.setEnabled(true);
4137                   }
4138                 }
4139               } catch (Exception e)
4140               {
4141                 Cache.log
4142                         .debug("Exception during web service menu building process.",
4143                                 e);
4144               }
4145             }
4146           });
4147         } catch (Exception e)
4148         {
4149         }
4150         buildingMenu = false;
4151       }
4152     }).start();
4153
4154   }
4155
4156   /**
4157    * construct any groupURL type service menu entries.
4158    *
4159    * @param webService
4160    */
4161   private void build_urlServiceMenu(JMenu webService)
4162   {
4163     // TODO: remove this code when 2.7 is released
4164     // DEBUG - alignmentView
4165     /*
4166      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4167      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4168      *
4169      * @Override public void actionPerformed(ActionEvent e) {
4170      * jalview.datamodel.AlignmentView
4171      * .testSelectionViews(af.viewport.getAlignment(),
4172      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4173      *
4174      * }); webService.add(testAlView);
4175      */
4176     // TODO: refactor to RestClient discoverer and merge menu entries for
4177     // rest-style services with other types of analysis/calculation service
4178     // SHmmr test client - still being implemented.
4179     // DEBUG - alignmentView
4180
4181     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4182             .getRestClients())
4183     {
4184       client.attachWSMenuEntry(
4185               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4186               this);
4187     }
4188   }
4189
4190   /**
4191    * Searches the alignment sequences for xRefs and builds the Show
4192    * Cross-References menu (formerly called Show Products), with database
4193    * sources for which cross-references are found (protein sources for a
4194    * nucleotide alignment and vice versa)
4195    *
4196    * @return true if Show Cross-references menu should be enabled
4197    */
4198   public boolean canShowProducts()
4199   {
4200     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4201     AlignmentI dataset = viewport.getAlignment().getDataset();
4202
4203     showProducts.removeAll();
4204     final boolean dna = viewport.getAlignment().isNucleotide();
4205
4206     if (seqs == null || seqs.length == 0)
4207     {
4208       // nothing to see here.
4209       return false;
4210     }
4211
4212     boolean showp = false;
4213     try
4214     {
4215       List<String> ptypes = new CrossRef(seqs, dataset)
4216               .findXrefSourcesForSequences(dna);
4217
4218       for (final String source : ptypes)
4219       {
4220         showp = true;
4221         final AlignFrame af = this;
4222         JMenuItem xtype = new JMenuItem(source);
4223         xtype.addActionListener(new ActionListener()
4224         {
4225           @Override
4226           public void actionPerformed(ActionEvent e)
4227           {
4228             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4229           }
4230         });
4231         showProducts.add(xtype);
4232       }
4233       showProducts.setVisible(showp);
4234       showProducts.setEnabled(showp);
4235     } catch (Exception e)
4236     {
4237       Cache.log
4238               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4239                       e);
4240       return false;
4241     }
4242     return showp;
4243   }
4244
4245   /**
4246    * Finds and displays cross-references for the selected sequences (protein
4247    * products for nucleotide sequences, dna coding sequences for peptides).
4248    *
4249    * @param sel
4250    *          the sequences to show cross-references for
4251    * @param dna
4252    *          true if from a nucleotide alignment (so showing proteins)
4253    * @param source
4254    *          the database to show cross-references for
4255    */
4256   protected void showProductsFor(final SequenceI[] sel,
4257           final boolean _odna, final String source)
4258   {
4259     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4260             .start();
4261   }
4262
4263   /**
4264    * Construct and display a new frame containing the translation of this
4265    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4266    */
4267   @Override
4268   public void showTranslation_actionPerformed(ActionEvent e)
4269   {
4270     AlignmentI al = null;
4271     try
4272     {
4273       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4274
4275       al = dna.translateCdna();
4276     } catch (Exception ex)
4277     {
4278       jalview.bin.Cache.log.error(
4279               "Exception during translation. Please report this !", ex);
4280       final String msg = MessageManager
4281               .getString("label.error_when_translating_sequences_submit_bug_report");
4282       final String errorTitle = MessageManager
4283               .getString("label.implementation_error")
4284               + MessageManager.getString("label.translation_failed");
4285       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4286               JvOptionPane.ERROR_MESSAGE);
4287       return;
4288     }
4289     if (al == null || al.getHeight() == 0)
4290     {
4291       final String msg = MessageManager
4292               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4293       final String errorTitle = MessageManager
4294               .getString("label.translation_failed");
4295       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4296               JvOptionPane.WARNING_MESSAGE);
4297     }
4298     else
4299     {
4300       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4301       af.setFileFormat(this.currentFileFormat);
4302       final String newTitle = MessageManager.formatMessage(
4303               "label.translation_of_params",
4304               new Object[] { this.getTitle() });
4305       af.setTitle(newTitle);
4306       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4307       {
4308         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4309         viewport.openSplitFrame(af, new Alignment(seqs));
4310       }
4311       else
4312       {
4313         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4314                 DEFAULT_HEIGHT);
4315       }
4316     }
4317   }
4318
4319   /**
4320    * Set the file format
4321    *
4322    * @param format
4323    */
4324   public void setFileFormat(FileFormatI format)
4325   {
4326     this.currentFileFormat = format;
4327   }
4328
4329   /**
4330    * Try to load a features file onto the alignment.
4331    *
4332    * @param file
4333    *          contents or path to retrieve file
4334    * @param sourceType
4335    *          access mode of file (see jalview.io.AlignFile)
4336    * @return true if features file was parsed correctly.
4337    */
4338   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4339   {
4340     return avc.parseFeaturesFile(file, sourceType,
4341             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4342
4343   }
4344
4345   @Override
4346   public void refreshFeatureUI(boolean enableIfNecessary)
4347   {
4348     // note - currently this is only still here rather than in the controller
4349     // because of the featureSettings hard reference that is yet to be
4350     // abstracted
4351     if (enableIfNecessary)
4352     {
4353       viewport.setShowSequenceFeatures(true);
4354       showSeqFeatures.setSelected(true);
4355     }
4356
4357   }
4358
4359   @Override
4360   public void dragEnter(DropTargetDragEvent evt)
4361   {
4362   }
4363
4364   @Override
4365   public void dragExit(DropTargetEvent evt)
4366   {
4367   }
4368
4369   @Override
4370   public void dragOver(DropTargetDragEvent evt)
4371   {
4372   }
4373
4374   @Override
4375   public void dropActionChanged(DropTargetDragEvent evt)
4376   {
4377   }
4378
4379   @Override
4380   public void drop(DropTargetDropEvent evt)
4381   {
4382     // JAL-1552 - acceptDrop required before getTransferable call for
4383     // Java's Transferable for native dnd
4384     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4385     Transferable t = evt.getTransferable();
4386     List<String> files = new ArrayList<>();
4387     List<DataSourceType> protocols = new ArrayList<>();
4388
4389     try
4390     {
4391       Desktop.transferFromDropTarget(files, protocols, evt, t);
4392     } catch (Exception e)
4393     {
4394       e.printStackTrace();
4395     }
4396     if (files != null)
4397     {
4398       try
4399       {
4400         // check to see if any of these files have names matching sequences in
4401         // the alignment
4402         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4403                 .getAlignment().getSequencesArray());
4404         /**
4405          * Object[] { String,SequenceI}
4406          */
4407         ArrayList<Object[]> filesmatched = new ArrayList<>();
4408         ArrayList<String> filesnotmatched = new ArrayList<>();
4409         for (int i = 0; i < files.size(); i++)
4410         {
4411           String file = files.get(i).toString();
4412           String pdbfn = "";
4413           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4414           if (protocol == DataSourceType.FILE)
4415           {
4416             File fl = new File(file);
4417             pdbfn = fl.getName();
4418           }
4419           else if (protocol == DataSourceType.URL)
4420           {
4421             URL url = new URL(file);
4422             pdbfn = url.getFile();
4423           }
4424           if (pdbfn.length() > 0)
4425           {
4426             // attempt to find a match in the alignment
4427             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4428             int l = 0, c = pdbfn.indexOf(".");
4429             while (mtch == null && c != -1)
4430             {
4431               do
4432               {
4433                 l = c;
4434               } while ((c = pdbfn.indexOf(".", l)) > l);
4435               if (l > -1)
4436               {
4437                 pdbfn = pdbfn.substring(0, l);
4438               }
4439               mtch = idm.findAllIdMatches(pdbfn);
4440             }
4441             if (mtch != null)
4442             {
4443               FileFormatI type = null;
4444               try
4445               {
4446                 type = new IdentifyFile().identify(file, protocol);
4447               } catch (Exception ex)
4448               {
4449                 type = null;
4450               }
4451               if (type != null && type.isStructureFile())
4452               {
4453                 filesmatched.add(new Object[] { file, protocol, mtch });
4454                 continue;
4455               }
4456             }
4457             // File wasn't named like one of the sequences or wasn't a PDB file.
4458             filesnotmatched.add(file);
4459           }
4460         }
4461         int assocfiles = 0;
4462         if (filesmatched.size() > 0)
4463         {
4464           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4465                   || JvOptionPane
4466                           .showConfirmDialog(
4467                                   this,
4468                                   MessageManager
4469                                           .formatMessage(
4470                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4471                                                   new Object[] { Integer
4472                                                           .valueOf(
4473                                                                   filesmatched
4474                                                                           .size())
4475                                                           .toString() }),
4476                                   MessageManager
4477                                           .getString("label.automatically_associate_structure_files_by_name"),
4478                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4479
4480           {
4481             for (Object[] fm : filesmatched)
4482             {
4483               // try and associate
4484               // TODO: may want to set a standard ID naming formalism for
4485               // associating PDB files which have no IDs.
4486               for (SequenceI toassoc : (SequenceI[]) fm[2])
4487               {
4488                 PDBEntry pe = new AssociatePdbFileWithSeq()
4489                         .associatePdbWithSeq((String) fm[0],
4490                                 (DataSourceType) fm[1], toassoc, false,
4491                                 Desktop.instance);
4492                 if (pe != null)
4493                 {
4494                   System.err.println("Associated file : "
4495                           + ((String) fm[0]) + " with "
4496                           + toassoc.getDisplayId(true));
4497                   assocfiles++;
4498                 }
4499               }
4500               alignPanel.paintAlignment(true);
4501             }
4502           }
4503         }
4504         if (filesnotmatched.size() > 0)
4505         {
4506           if (assocfiles > 0
4507                   && (Cache.getDefault(
4508                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4509                           .showConfirmDialog(
4510                                   this,
4511                                   "<html>"
4512                                           + MessageManager
4513                                                   .formatMessage(
4514                                                           "label.ignore_unmatched_dropped_files_info",
4515                                                           new Object[] { Integer
4516                                                                   .valueOf(
4517                                                                           filesnotmatched
4518                                                                                   .size())
4519                                                                   .toString() })
4520                                           + "</html>",
4521                                   MessageManager
4522                                           .getString("label.ignore_unmatched_dropped_files"),
4523                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4524           {
4525             return;
4526           }
4527           for (String fn : filesnotmatched)
4528           {
4529             loadJalviewDataFile(fn, null, null, null);
4530           }
4531
4532         }
4533       } catch (Exception ex)
4534       {
4535         ex.printStackTrace();
4536       }
4537     }
4538   }
4539
4540   /**
4541    * Attempt to load a "dropped" file or URL string, by testing in turn for
4542    * <ul>
4543    * <li>an Annotation file</li>
4544    * <li>a JNet file</li>
4545    * <li>a features file</li>
4546    * <li>else try to interpret as an alignment file</li>
4547    * </ul>
4548    *
4549    * @param file
4550    *          either a filename or a URL string.
4551    */
4552   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4553           FileFormatI format, SequenceI assocSeq)
4554   {
4555     try
4556     {
4557       if (sourceType == null)
4558       {
4559         sourceType = FormatAdapter.checkProtocol(file);
4560       }
4561       // if the file isn't identified, or not positively identified as some
4562       // other filetype (PFAM is default unidentified alignment file type) then
4563       // try to parse as annotation.
4564       boolean isAnnotation = (format == null || FileFormat.Pfam
4565               .equals(format)) ? new AnnotationFile()
4566               .annotateAlignmentView(viewport, file, sourceType) : false;
4567
4568       if (!isAnnotation)
4569       {
4570         // first see if its a T-COFFEE score file
4571         TCoffeeScoreFile tcf = null;
4572         try
4573         {
4574           tcf = new TCoffeeScoreFile(file, sourceType);
4575           if (tcf.isValid())
4576           {
4577             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4578             {
4579               buildColourMenu();
4580               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4581               isAnnotation = true;
4582               statusBar
4583                       .setText(MessageManager
4584                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4585             }
4586             else
4587             {
4588               // some problem - if no warning its probable that the ID matching
4589               // process didn't work
4590               JvOptionPane
4591                       .showMessageDialog(
4592                               Desktop.desktop,
4593                               tcf.getWarningMessage() == null ? MessageManager
4594                                       .getString("label.check_file_matches_sequence_ids_alignment")
4595                                       : tcf.getWarningMessage(),
4596                               MessageManager
4597                                       .getString("label.problem_reading_tcoffee_score_file"),
4598                               JvOptionPane.WARNING_MESSAGE);
4599             }
4600           }
4601           else
4602           {
4603             tcf = null;
4604           }
4605         } catch (Exception x)
4606         {
4607           Cache.log
4608                   .debug("Exception when processing data source as T-COFFEE score file",
4609                           x);
4610           tcf = null;
4611         }
4612         if (tcf == null)
4613         {
4614           // try to see if its a JNet 'concise' style annotation file *before*
4615           // we
4616           // try to parse it as a features file
4617           if (format == null)
4618           {
4619             format = new IdentifyFile().identify(file, sourceType);
4620           }
4621           if (FileFormat.ScoreMatrix == format)
4622           {
4623             ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4624                     sourceType));
4625             sm.parse();
4626             // todo: i18n this message
4627             statusBar
4628                     .setText(MessageManager.formatMessage(
4629                             "label.successfully_loaded_matrix",
4630                             sm.getMatrixName()));
4631           }
4632           else if (FileFormat.Jnet.equals(format))
4633           {
4634             JPredFile predictions = new JPredFile(file, sourceType);
4635             new JnetAnnotationMaker();
4636             JnetAnnotationMaker.add_annotation(predictions,
4637                     viewport.getAlignment(), 0, false);
4638             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4639             viewport.getAlignment().setSeqrep(repseq);
4640             HiddenColumns cs = new HiddenColumns();
4641             cs.hideInsertionsFor(repseq);
4642             viewport.getAlignment().setHiddenColumns(cs);
4643             isAnnotation = true;
4644           }
4645           // else if (IdentifyFile.FeaturesFile.equals(format))
4646           else if (FileFormat.Features.equals(format))
4647           {
4648             if (parseFeaturesFile(file, sourceType))
4649             {
4650               alignPanel.paintAlignment(true);
4651             }
4652           }
4653           else
4654           {
4655             new FileLoader().LoadFile(viewport, file, sourceType, format);
4656           }
4657         }
4658       }
4659       if (isAnnotation)
4660       {
4661
4662         alignPanel.adjustAnnotationHeight();
4663         viewport.updateSequenceIdColours();
4664         buildSortByAnnotationScoresMenu();
4665         alignPanel.paintAlignment(true);
4666       }
4667     } catch (Exception ex)
4668     {
4669       ex.printStackTrace();
4670     } catch (OutOfMemoryError oom)
4671     {
4672       try
4673       {
4674         System.gc();
4675       } catch (Exception x)
4676       {
4677       }
4678       new OOMWarning(
4679               "loading data "
4680                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4681                               : "using " + sourceType + " from " + file)
4682                               : ".")
4683                       + (format != null ? "(parsing as '" + format
4684                               + "' file)" : ""), oom, Desktop.desktop);
4685     }
4686   }
4687
4688   /**
4689    * Method invoked by the ChangeListener on the tabbed pane, in other words
4690    * when a different tabbed pane is selected by the user or programmatically.
4691    */
4692   @Override
4693   public void tabSelectionChanged(int index)
4694   {
4695     if (index > -1)
4696     {
4697       alignPanel = alignPanels.get(index);
4698       viewport = alignPanel.av;
4699       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4700       setMenusFromViewport(viewport);
4701     }
4702
4703     /*
4704      * 'focus' any colour slider that is open to the selected viewport
4705      */
4706     if (viewport.getConservationSelected())
4707     {
4708       SliderPanel.setConservationSlider(alignPanel,
4709               viewport.getResidueShading(), alignPanel.getViewName());
4710     }
4711     else
4712     {
4713       SliderPanel.hideConservationSlider();
4714     }
4715     if (viewport.getAbovePIDThreshold())
4716     {
4717       SliderPanel.setPIDSliderSource(alignPanel,
4718               viewport.getResidueShading(), alignPanel.getViewName());
4719     }
4720     else
4721     {
4722       SliderPanel.hidePIDSlider();
4723     }
4724
4725     /*
4726      * If there is a frame linked to this one in a SplitPane, switch it to the
4727      * same view tab index. No infinite recursion of calls should happen, since
4728      * tabSelectionChanged() should not get invoked on setting the selected
4729      * index to an unchanged value. Guard against setting an invalid index
4730      * before the new view peer tab has been created.
4731      */
4732     final AlignViewportI peer = viewport.getCodingComplement();
4733     if (peer != null)
4734     {
4735       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4736       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4737       {
4738         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4739       }
4740     }
4741   }
4742
4743   /**
4744    * On right mouse click on view tab, prompt for and set new view name.
4745    */
4746   @Override
4747   public void tabbedPane_mousePressed(MouseEvent e)
4748   {
4749     if (e.isPopupTrigger())
4750     {
4751       String msg = MessageManager.getString("label.enter_view_name");
4752       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4753               JvOptionPane.QUESTION_MESSAGE);
4754
4755       if (reply != null)
4756       {
4757         viewport.viewName = reply;
4758         // TODO warn if reply is in getExistingViewNames()?
4759         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4760       }
4761     }
4762   }
4763
4764   public AlignViewport getCurrentView()
4765   {
4766     return viewport;
4767   }
4768
4769   /**
4770    * Open the dialog for regex description parsing.
4771    */
4772   @Override
4773   protected void extractScores_actionPerformed(ActionEvent e)
4774   {
4775     ParseProperties pp = new jalview.analysis.ParseProperties(
4776             viewport.getAlignment());
4777     // TODO: verify regex and introduce GUI dialog for version 2.5
4778     // if (pp.getScoresFromDescription("col", "score column ",
4779     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4780     // true)>0)
4781     if (pp.getScoresFromDescription("description column",
4782             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4783     {
4784       buildSortByAnnotationScoresMenu();
4785     }
4786   }
4787
4788   /*
4789    * (non-Javadoc)
4790    *
4791    * @see
4792    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4793    * )
4794    */
4795   @Override
4796   protected void showDbRefs_actionPerformed(ActionEvent e)
4797   {
4798     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4799   }
4800
4801   /*
4802    * (non-Javadoc)
4803    *
4804    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4805    * ActionEvent)
4806    */
4807   @Override
4808   protected void showNpFeats_actionPerformed(ActionEvent e)
4809   {
4810     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4811   }
4812
4813   /**
4814    * find the viewport amongst the tabs in this alignment frame and close that
4815    * tab
4816    *
4817    * @param av
4818    */
4819   public boolean closeView(AlignViewportI av)
4820   {
4821     if (viewport == av)
4822     {
4823       this.closeMenuItem_actionPerformed(false);
4824       return true;
4825     }
4826     Component[] comp = tabbedPane.getComponents();
4827     for (int i = 0; comp != null && i < comp.length; i++)
4828     {
4829       if (comp[i] instanceof AlignmentPanel)
4830       {
4831         if (((AlignmentPanel) comp[i]).av == av)
4832         {
4833           // close the view.
4834           closeView((AlignmentPanel) comp[i]);
4835           return true;
4836         }
4837       }
4838     }
4839     return false;
4840   }
4841
4842   protected void build_fetchdbmenu(JMenu webService)
4843   {
4844     // Temporary hack - DBRef Fetcher always top level ws entry.
4845     // TODO We probably want to store a sequence database checklist in
4846     // preferences and have checkboxes.. rather than individual sources selected
4847     // here
4848     final JMenu rfetch = new JMenu(
4849             MessageManager.getString("action.fetch_db_references"));
4850     rfetch.setToolTipText(MessageManager
4851             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4852     webService.add(rfetch);
4853
4854     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4855             MessageManager.getString("option.trim_retrieved_seqs"));
4856     trimrs.setToolTipText(MessageManager
4857             .getString("label.trim_retrieved_sequences"));
4858     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4859     trimrs.addActionListener(new ActionListener()
4860     {
4861       @Override
4862       public void actionPerformed(ActionEvent e)
4863       {
4864         trimrs.setSelected(trimrs.isSelected());
4865         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4866                 Boolean.valueOf(trimrs.isSelected()).toString());
4867       };
4868     });
4869     rfetch.add(trimrs);
4870     JMenuItem fetchr = new JMenuItem(
4871             MessageManager.getString("label.standard_databases"));
4872     fetchr.setToolTipText(MessageManager
4873             .getString("label.fetch_embl_uniprot"));
4874     fetchr.addActionListener(new ActionListener()
4875     {
4876
4877       @Override
4878       public void actionPerformed(ActionEvent e)
4879       {
4880         new Thread(new Runnable()
4881         {
4882           @Override
4883           public void run()
4884           {
4885             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4886                     .getAlignment().isNucleotide();
4887             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4888                     .getSequenceSelection(), alignPanel.alignFrame, null,
4889                     alignPanel.alignFrame.featureSettings, isNucleotide);
4890             dbRefFetcher.addListener(new FetchFinishedListenerI()
4891             {
4892               @Override
4893               public void finished()
4894               {
4895                 AlignFrame.this.setMenusForViewport();
4896               }
4897             });
4898             dbRefFetcher.fetchDBRefs(false);
4899           }
4900         }).start();
4901
4902       }
4903
4904     });
4905     rfetch.add(fetchr);
4906     final AlignFrame me = this;
4907     new Thread(new Runnable()
4908     {
4909       @Override
4910       public void run()
4911       {
4912         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4913                 .getSequenceFetcherSingleton(me);
4914         javax.swing.SwingUtilities.invokeLater(new Runnable()
4915         {
4916           @Override
4917           public void run()
4918           {
4919             String[] dbclasses = sf.getOrderedSupportedSources();
4920             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4921             // jalview.util.QuickSort.sort(otherdb, otherdb);
4922             List<DbSourceProxy> otherdb;
4923             JMenu dfetch = new JMenu();
4924             JMenu ifetch = new JMenu();
4925             JMenuItem fetchr = null;
4926             int comp = 0, icomp = 0, mcomp = 15;
4927             String mname = null;
4928             int dbi = 0;
4929             for (String dbclass : dbclasses)
4930             {
4931               otherdb = sf.getSourceProxy(dbclass);
4932               // add a single entry for this class, or submenu allowing 'fetch
4933               // all' or pick one
4934               if (otherdb == null || otherdb.size() < 1)
4935               {
4936                 continue;
4937               }
4938               // List<DbSourceProxy> dbs=otherdb;
4939               // otherdb=new ArrayList<DbSourceProxy>();
4940               // for (DbSourceProxy db:dbs)
4941               // {
4942               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4943               // }
4944               if (mname == null)
4945               {
4946                 mname = "From " + dbclass;
4947               }
4948               if (otherdb.size() == 1)
4949               {
4950                 final DbSourceProxy[] dassource = otherdb
4951                         .toArray(new DbSourceProxy[0]);
4952                 DbSourceProxy src = otherdb.get(0);
4953                 fetchr = new JMenuItem(src.getDbSource());
4954                 fetchr.addActionListener(new ActionListener()
4955                 {
4956
4957                   @Override
4958                   public void actionPerformed(ActionEvent e)
4959                   {
4960                     new Thread(new Runnable()
4961                     {
4962
4963                       @Override
4964                       public void run()
4965                       {
4966                         boolean isNucleotide = alignPanel.alignFrame
4967                                 .getViewport().getAlignment()
4968                                 .isNucleotide();
4969                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4970                                 alignPanel.av.getSequenceSelection(),
4971                                 alignPanel.alignFrame, dassource,
4972                                 alignPanel.alignFrame.featureSettings,
4973                                 isNucleotide);
4974                         dbRefFetcher
4975                                 .addListener(new FetchFinishedListenerI()
4976                                 {
4977                                   @Override
4978                                   public void finished()
4979                                   {
4980                                     AlignFrame.this.setMenusForViewport();
4981                                   }
4982                                 });
4983                         dbRefFetcher.fetchDBRefs(false);
4984                       }
4985                     }).start();
4986                   }
4987
4988                 });
4989                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
4990                         MessageManager.formatMessage(
4991                                 "label.fetch_retrieve_from",
4992                                 new Object[] { src.getDbName() })));
4993                 dfetch.add(fetchr);
4994                 comp++;
4995               }
4996               else
4997               {
4998                 final DbSourceProxy[] dassource = otherdb
4999                         .toArray(new DbSourceProxy[0]);
5000                 // fetch all entry
5001                 DbSourceProxy src = otherdb.get(0);
5002                 fetchr = new JMenuItem(MessageManager.formatMessage(
5003                         "label.fetch_all_param",
5004                         new Object[] { src.getDbSource() }));
5005                 fetchr.addActionListener(new ActionListener()
5006                 {
5007                   @Override
5008                   public void actionPerformed(ActionEvent e)
5009                   {
5010                     new Thread(new Runnable()
5011                     {
5012
5013                       @Override
5014                       public void run()
5015                       {
5016                         boolean isNucleotide = alignPanel.alignFrame
5017                                 .getViewport().getAlignment()
5018                                 .isNucleotide();
5019                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5020                                 alignPanel.av.getSequenceSelection(),
5021                                 alignPanel.alignFrame, dassource,
5022                                 alignPanel.alignFrame.featureSettings,
5023                                 isNucleotide);
5024                         dbRefFetcher
5025                                 .addListener(new FetchFinishedListenerI()
5026                                 {
5027                                   @Override
5028                                   public void finished()
5029                                   {
5030                                     AlignFrame.this.setMenusForViewport();
5031                                   }
5032                                 });
5033                         dbRefFetcher.fetchDBRefs(false);
5034                       }
5035                     }).start();
5036                   }
5037                 });
5038
5039                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5040                         MessageManager.formatMessage(
5041                                 "label.fetch_retrieve_from_all_sources",
5042                                 new Object[] {
5043                                     Integer.valueOf(otherdb.size())
5044                                             .toString(), src.getDbSource(),
5045                                     src.getDbName() })));
5046                 dfetch.add(fetchr);
5047                 comp++;
5048                 // and then build the rest of the individual menus
5049                 ifetch = new JMenu(MessageManager.formatMessage(
5050                         "label.source_from_db_source",
5051                         new Object[] { src.getDbSource() }));
5052                 icomp = 0;
5053                 String imname = null;
5054                 int i = 0;
5055                 for (DbSourceProxy sproxy : otherdb)
5056                 {
5057                   String dbname = sproxy.getDbName();
5058                   String sname = dbname.length() > 5 ? dbname.substring(0,
5059                           5) + "..." : dbname;
5060                   String msname = dbname.length() > 10 ? dbname.substring(
5061                           0, 10) + "..." : dbname;
5062                   if (imname == null)
5063                   {
5064                     imname = MessageManager.formatMessage(
5065                             "label.from_msname", new Object[] { sname });
5066                   }
5067                   fetchr = new JMenuItem(msname);
5068                   final DbSourceProxy[] dassrc = { sproxy };
5069                   fetchr.addActionListener(new ActionListener()
5070                   {
5071
5072                     @Override
5073                     public void actionPerformed(ActionEvent e)
5074                     {
5075                       new Thread(new Runnable()
5076                       {
5077
5078                         @Override
5079                         public void run()
5080                         {
5081                           boolean isNucleotide = alignPanel.alignFrame
5082                                   .getViewport().getAlignment()
5083                                   .isNucleotide();
5084                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5085                                   alignPanel.av.getSequenceSelection(),
5086                                   alignPanel.alignFrame, dassrc,
5087                                   alignPanel.alignFrame.featureSettings,
5088                                   isNucleotide);
5089                           dbRefFetcher
5090                                   .addListener(new FetchFinishedListenerI()
5091                                   {
5092                                     @Override
5093                                     public void finished()
5094                                     {
5095                                       AlignFrame.this.setMenusForViewport();
5096                                     }
5097                                   });
5098                           dbRefFetcher.fetchDBRefs(false);
5099                         }
5100                       }).start();
5101                     }
5102
5103                   });
5104                   fetchr.setToolTipText("<html>"
5105                           + MessageManager.formatMessage(
5106                                   "label.fetch_retrieve_from", new Object[]
5107                                   { dbname }));
5108                   ifetch.add(fetchr);
5109                   ++i;
5110                   if (++icomp >= mcomp || i == (otherdb.size()))
5111                   {
5112                     ifetch.setText(MessageManager.formatMessage(
5113                             "label.source_to_target", imname, sname));
5114                     dfetch.add(ifetch);
5115                     ifetch = new JMenu();
5116                     imname = null;
5117                     icomp = 0;
5118                     comp++;
5119                   }
5120                 }
5121               }
5122               ++dbi;
5123               if (comp >= mcomp || dbi >= (dbclasses.length))
5124               {
5125                 dfetch.setText(MessageManager.formatMessage(
5126                         "label.source_to_target", mname, dbclass));
5127                 rfetch.add(dfetch);
5128                 dfetch = new JMenu();
5129                 mname = null;
5130                 comp = 0;
5131               }
5132             }
5133           }
5134         });
5135       }
5136     }).start();
5137
5138   }
5139
5140   /**
5141    * Left justify the whole alignment.
5142    */
5143   @Override
5144   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5145   {
5146     AlignmentI al = viewport.getAlignment();
5147     al.justify(false);
5148     viewport.firePropertyChange("alignment", null, al);
5149   }
5150
5151   /**
5152    * Right justify the whole alignment.
5153    */
5154   @Override
5155   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5156   {
5157     AlignmentI al = viewport.getAlignment();
5158     al.justify(true);
5159     viewport.firePropertyChange("alignment", null, al);
5160   }
5161
5162   @Override
5163   public void setShowSeqFeatures(boolean b)
5164   {
5165     showSeqFeatures.setSelected(b);
5166     viewport.setShowSequenceFeatures(b);
5167   }
5168
5169   /*
5170    * (non-Javadoc)
5171    *
5172    * @see
5173    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5174    * awt.event.ActionEvent)
5175    */
5176   @Override
5177   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5178   {
5179     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5180     alignPanel.paintAlignment(true);
5181   }
5182
5183   /*
5184    * (non-Javadoc)
5185    *
5186    * @see
5187    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5188    * .ActionEvent)
5189    */
5190   @Override
5191   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5192   {
5193     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5194     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5195
5196   }
5197
5198   /*
5199    * (non-Javadoc)
5200    *
5201    * @see
5202    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5203    * .event.ActionEvent)
5204    */
5205   @Override
5206   protected void showGroupConservation_actionPerformed(ActionEvent e)
5207   {
5208     viewport.setShowGroupConservation(showGroupConservation.getState());
5209     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5210   }
5211
5212   /*
5213    * (non-Javadoc)
5214    *
5215    * @see
5216    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5217    * .event.ActionEvent)
5218    */
5219   @Override
5220   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5221   {
5222     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5223     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5224   }
5225
5226   /*
5227    * (non-Javadoc)
5228    *
5229    * @see
5230    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5231    * .event.ActionEvent)
5232    */
5233   @Override
5234   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5235   {
5236     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5237     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5238   }
5239
5240   @Override
5241   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5242   {
5243     showSequenceLogo.setState(true);
5244     viewport.setShowSequenceLogo(true);
5245     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5246     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5247   }
5248
5249   @Override
5250   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5251   {
5252     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5253   }
5254
5255   /*
5256    * (non-Javadoc)
5257    *
5258    * @see
5259    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5260    * .event.ActionEvent)
5261    */
5262   @Override
5263   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5264   {
5265     if (avc.makeGroupsFromSelection())
5266     {
5267       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5268       alignPanel.updateAnnotation();
5269       alignPanel.paintAlignment(true);
5270     }
5271   }
5272
5273   public void clearAlignmentSeqRep()
5274   {
5275     // TODO refactor alignmentseqrep to controller
5276     if (viewport.getAlignment().hasSeqrep())
5277     {
5278       viewport.getAlignment().setSeqrep(null);
5279       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5280       alignPanel.updateAnnotation();
5281       alignPanel.paintAlignment(true);
5282     }
5283   }
5284
5285   @Override
5286   protected void createGroup_actionPerformed(ActionEvent e)
5287   {
5288     if (avc.createGroup())
5289     {
5290       alignPanel.alignmentChanged();
5291     }
5292   }
5293
5294   @Override
5295   protected void unGroup_actionPerformed(ActionEvent e)
5296   {
5297     if (avc.unGroup())
5298     {
5299       alignPanel.alignmentChanged();
5300     }
5301   }
5302
5303   /**
5304    * make the given alignmentPanel the currently selected tab
5305    *
5306    * @param alignmentPanel
5307    */
5308   public void setDisplayedView(AlignmentPanel alignmentPanel)
5309   {
5310     if (!viewport.getSequenceSetId().equals(
5311             alignmentPanel.av.getSequenceSetId()))
5312     {
5313       throw new Error(
5314               MessageManager
5315                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5316     }
5317     if (tabbedPane != null
5318             && tabbedPane.getTabCount() > 0
5319             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5320                     .getSelectedIndex())
5321     {
5322       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5323     }
5324   }
5325
5326   /**
5327    * Action on selection of menu options to Show or Hide annotations.
5328    *
5329    * @param visible
5330    * @param forSequences
5331    *          update sequence-related annotations
5332    * @param forAlignment
5333    *          update non-sequence-related annotations
5334    */
5335   @Override
5336   protected void setAnnotationsVisibility(boolean visible,
5337           boolean forSequences, boolean forAlignment)
5338   {
5339     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5340             .getAlignmentAnnotation();
5341     if (anns == null)
5342     {
5343       return;
5344     }
5345     for (AlignmentAnnotation aa : anns)
5346     {
5347       /*
5348        * don't display non-positional annotations on an alignment
5349        */
5350       if (aa.annotations == null)
5351       {
5352         continue;
5353       }
5354       boolean apply = (aa.sequenceRef == null && forAlignment)
5355               || (aa.sequenceRef != null && forSequences);
5356       if (apply)
5357       {
5358         aa.visible = visible;
5359       }
5360     }
5361     alignPanel.validateAnnotationDimensions(true);
5362     alignPanel.alignmentChanged();
5363   }
5364
5365   /**
5366    * Store selected annotation sort order for the view and repaint.
5367    */
5368   @Override
5369   protected void sortAnnotations_actionPerformed()
5370   {
5371     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5372     this.alignPanel.av
5373             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5374     alignPanel.paintAlignment(true);
5375   }
5376
5377   /**
5378    *
5379    * @return alignment panels in this alignment frame
5380    */
5381   public List<? extends AlignmentViewPanel> getAlignPanels()
5382   {
5383     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5384   }
5385
5386   /**
5387    * Open a new alignment window, with the cDNA associated with this (protein)
5388    * alignment, aligned as is the protein.
5389    */
5390   protected void viewAsCdna_actionPerformed()
5391   {
5392     // TODO no longer a menu action - refactor as required
5393     final AlignmentI alignment = getViewport().getAlignment();
5394     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5395     if (mappings == null)
5396     {
5397       return;
5398     }
5399     List<SequenceI> cdnaSeqs = new ArrayList<>();
5400     for (SequenceI aaSeq : alignment.getSequences())
5401     {
5402       for (AlignedCodonFrame acf : mappings)
5403       {
5404         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5405         if (dnaSeq != null)
5406         {
5407           /*
5408            * There is a cDNA mapping for this protein sequence - add to new
5409            * alignment. It will share the same dataset sequence as other mapped
5410            * cDNA (no new mappings need to be created).
5411            */
5412           final Sequence newSeq = new Sequence(dnaSeq);
5413           newSeq.setDatasetSequence(dnaSeq);
5414           cdnaSeqs.add(newSeq);
5415         }
5416       }
5417     }
5418     if (cdnaSeqs.size() == 0)
5419     {
5420       // show a warning dialog no mapped cDNA
5421       return;
5422     }
5423     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5424             .size()]));
5425     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5426             AlignFrame.DEFAULT_HEIGHT);
5427     cdna.alignAs(alignment);
5428     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5429             + this.title;
5430     Desktop.addInternalFrame(alignFrame, newtitle,
5431             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5432   }
5433
5434   /**
5435    * Set visibility of dna/protein complement view (available when shown in a
5436    * split frame).
5437    *
5438    * @param show
5439    */
5440   @Override
5441   protected void showComplement_actionPerformed(boolean show)
5442   {
5443     SplitContainerI sf = getSplitViewContainer();
5444     if (sf != null)
5445     {
5446       sf.setComplementVisible(this, show);
5447     }
5448   }
5449
5450   /**
5451    * Generate the reverse (optionally complemented) of the selected sequences,
5452    * and add them to the alignment
5453    */
5454   @Override
5455   protected void showReverse_actionPerformed(boolean complement)
5456   {
5457     AlignmentI al = null;
5458     try
5459     {
5460       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5461       al = dna.reverseCdna(complement);
5462       viewport.addAlignment(al, "");
5463       addHistoryItem(new EditCommand(
5464               MessageManager.getString("label.add_sequences"),
5465               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5466               viewport.getAlignment()));
5467     } catch (Exception ex)
5468     {
5469       System.err.println(ex.getMessage());
5470       return;
5471     }
5472   }
5473
5474   /**
5475    * Try to run a script in the Groovy console, having first ensured that this
5476    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5477    * be targeted at this alignment.
5478    */
5479   @Override
5480   protected void runGroovy_actionPerformed()
5481   {
5482     Jalview.setCurrentAlignFrame(this);
5483     groovy.ui.Console console = Desktop.getGroovyConsole();
5484     if (console != null)
5485     {
5486       try
5487       {
5488         console.runScript();
5489       } catch (Exception ex)
5490       {
5491         System.err.println((ex.toString()));
5492         JvOptionPane
5493                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5494                         .getString("label.couldnt_run_groovy_script"),
5495                         MessageManager
5496                                 .getString("label.groovy_support_failed"),
5497                         JvOptionPane.ERROR_MESSAGE);
5498       }
5499     }
5500     else
5501     {
5502       System.err.println("Can't run Groovy script as console not found");
5503     }
5504   }
5505
5506   /**
5507    * Hides columns containing (or not containing) a specified feature, provided
5508    * that would not leave all columns hidden
5509    *
5510    * @param featureType
5511    * @param columnsContaining
5512    * @return
5513    */
5514   public boolean hideFeatureColumns(String featureType,
5515           boolean columnsContaining)
5516   {
5517     boolean notForHiding = avc.markColumnsContainingFeatures(
5518             columnsContaining, false, false, featureType);
5519     if (notForHiding)
5520     {
5521       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5522               false, featureType))
5523       {
5524         getViewport().hideSelectedColumns();
5525         return true;
5526       }
5527     }
5528     return false;
5529   }
5530
5531   @Override
5532   protected void selectHighlightedColumns_actionPerformed(
5533           ActionEvent actionEvent)
5534   {
5535     // include key modifier check in case user selects from menu
5536     avc.markHighlightedColumns(
5537             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5538             true,
5539             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5540   }
5541
5542   /**
5543    * Rebuilds the Colour menu, including any user-defined colours which have
5544    * been loaded either on startup or during the session
5545    */
5546   public void buildColourMenu()
5547   {
5548     colourMenu.removeAll();
5549
5550     colourMenu.add(applyToAllGroups);
5551     colourMenu.add(textColour);
5552     colourMenu.addSeparator();
5553
5554     ColourMenuHelper.addMenuItems(colourMenu, this,
5555             viewport.getAlignment(), false);
5556
5557     colourMenu.addSeparator();
5558     colourMenu.add(conservationMenuItem);
5559     colourMenu.add(modifyConservation);
5560     colourMenu.add(abovePIDThreshold);
5561     colourMenu.add(modifyPID);
5562     colourMenu.add(annotationColour);
5563
5564     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5565     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5566   }
5567
5568   /**
5569    * Open a dialog (if not already open) that allows the user to select and
5570    * calculate PCA or Tree analysis
5571    */
5572   protected void openTreePcaDialog()
5573   {
5574     if (alignPanel.getCalculationDialog() == null)
5575     {
5576       new CalculationChooser(AlignFrame.this);
5577     }
5578   }
5579 }
5580
5581 class PrintThread extends Thread
5582 {
5583   AlignmentPanel ap;
5584
5585   public PrintThread(AlignmentPanel ap)
5586   {
5587     this.ap = ap;
5588   }
5589
5590   static PageFormat pf;
5591
5592   @Override
5593   public void run()
5594   {
5595     PrinterJob printJob = PrinterJob.getPrinterJob();
5596
5597     if (pf != null)
5598     {
5599       printJob.setPrintable(ap, pf);
5600     }
5601     else
5602     {
5603       printJob.setPrintable(ap);
5604     }
5605
5606     if (printJob.printDialog())
5607     {
5608       try
5609       {
5610         printJob.print();
5611       } catch (Exception PrintException)
5612       {
5613         PrintException.printStackTrace();
5614       }
5615     }
5616   }
5617 }