src/jalview/gui/AlignFrame.java

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