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 java.awt.BorderLayout;
  24 import java.awt.Component;
  25 import java.awt.Rectangle;
  26 import java.awt.Toolkit;
  27 import java.awt.datatransfer.Clipboard;
  28 import java.awt.datatransfer.DataFlavor;
  29 import java.awt.datatransfer.StringSelection;
  30 import java.awt.datatransfer.Transferable;
  31 import java.awt.dnd.DnDConstants;
  32 import java.awt.dnd.DropTargetDragEvent;
  33 import java.awt.dnd.DropTargetDropEvent;
  34 import java.awt.dnd.DropTargetEvent;
  35 import java.awt.dnd.DropTargetListener;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.FocusAdapter;
  39 import java.awt.event.FocusEvent;
  40 import java.awt.event.ItemEvent;
  41 import java.awt.event.ItemListener;
  42 import java.awt.event.KeyAdapter;
  43 import java.awt.event.KeyEvent;
  44 import java.awt.event.MouseEvent;
  45 import java.awt.print.PageFormat;
  46 import java.awt.print.PrinterJob;
  47 import java.beans.PropertyChangeEvent;
  48 import java.io.File;
  49 import java.io.FileWriter;
  50 import java.io.IOException;
  51 import java.io.PrintWriter;
  52 import java.net.URL;
  53 import java.util.ArrayList;
  54 import java.util.Arrays;
  55 import java.util.Deque;
  56 import java.util.Enumeration;
  57 import java.util.Hashtable;
  58 import java.util.List;
  59 import java.util.Vector;
  60
  61 import javax.swing.ButtonGroup;
  62 import javax.swing.JCheckBoxMenuItem;
  63 import javax.swing.JEditorPane;
  64 import javax.swing.JInternalFrame;
  65 import javax.swing.JLayeredPane;
  66 import javax.swing.JMenu;
  67 import javax.swing.JMenuItem;
  68 import javax.swing.JScrollPane;
  69 import javax.swing.SwingUtilities;
  70
  71 import jalview.analysis.AlignmentSorter;
  72 import jalview.analysis.AlignmentUtils;
  73 import jalview.analysis.CrossRef;
  74 import jalview.analysis.Dna;
  75 import jalview.analysis.GeneticCodeI;
  76 import jalview.analysis.ParseProperties;
  77 import jalview.analysis.SequenceIdMatcher;
  78 import jalview.api.AlignExportSettingI;
  79 import jalview.api.AlignViewControllerGuiI;
  80 import jalview.api.AlignViewControllerI;
  81 import jalview.api.AlignViewportI;
  82 import jalview.api.AlignmentViewPanel;
  83 import jalview.api.FeatureSettingsControllerI;
  84 import jalview.api.FeatureSettingsModelI;
  85 import jalview.api.SplitContainerI;
  86 import jalview.api.ViewStyleI;
  87 import jalview.api.analysis.SimilarityParamsI;
  88 import jalview.bin.Cache;
  89 import jalview.bin.Jalview;
  90 import jalview.commands.CommandI;
  91 import jalview.commands.EditCommand;
  92 import jalview.commands.EditCommand.Action;
  93 import jalview.commands.OrderCommand;
  94 import jalview.commands.RemoveGapColCommand;
  95 import jalview.commands.RemoveGapsCommand;
  96 import jalview.commands.SlideSequencesCommand;
  97 import jalview.commands.TrimRegionCommand;
  98 import jalview.datamodel.AlignedCodonFrame;
  99 import jalview.datamodel.Alignment;
 100 import jalview.datamodel.AlignmentAnnotation;
 101 import jalview.datamodel.AlignmentExportData;
 102 import jalview.datamodel.AlignmentI;
 103 import jalview.datamodel.AlignmentOrder;
 104 import jalview.datamodel.AlignmentView;
 105 import jalview.datamodel.ColumnSelection;
 106 import jalview.datamodel.HiddenColumns;
 107 import jalview.datamodel.HiddenSequences;
 108 import jalview.datamodel.PDBEntry;
 109 import jalview.datamodel.SeqCigar;
 110 import jalview.datamodel.Sequence;
 111 import jalview.datamodel.SequenceGroup;
 112 import jalview.datamodel.SequenceI;
 113 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 114 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 115 import jalview.io.AlignmentProperties;
 116 import jalview.io.AnnotationFile;
 117 import jalview.io.BackupFiles;
 118 import jalview.io.BioJsHTMLOutput;
 119 import jalview.io.DataSourceType;
 120 import jalview.io.FileFormat;
 121 import jalview.io.FileFormatI;
 122 import jalview.io.FileFormats;
 123 import jalview.io.FileLoader;
 124 import jalview.io.FileParse;
 125 import jalview.io.FormatAdapter;
 126 import jalview.io.HtmlSvgOutput;
 127 import jalview.io.IdentifyFile;
 128 import jalview.io.JPredFile;
 129 import jalview.io.JalviewFileChooser;
 130 import jalview.io.JalviewFileView;
 131 import jalview.io.JnetAnnotationMaker;
 132 import jalview.io.NewickFile;
 133 import jalview.io.ScoreMatrixFile;
 134 import jalview.io.TCoffeeScoreFile;
 135 import jalview.io.vcf.VCFLoader;
 136 import jalview.jbgui.GAlignFrame;
 137 import jalview.schemes.ColourSchemeI;
 138 import jalview.schemes.ColourSchemes;
 139 import jalview.schemes.ResidueColourScheme;
 140 import jalview.schemes.TCoffeeColourScheme;
 141 import jalview.util.MessageManager;
 142 import jalview.util.Platform;
 143 import jalview.viewmodel.AlignmentViewport;
 144 import jalview.viewmodel.ViewportRanges;
 145 import jalview.ws.DBRefFetcher;
 146 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 147 import jalview.ws.jws1.Discoverer;
 148 import jalview.ws.jws2.Jws2Discoverer;
 149 import jalview.ws.jws2.jabaws2.Jws2Instance;
 150 import jalview.ws.seqfetcher.DbSourceProxy;
 151
 152 /**
 153  * DOCUMENT ME!
 154  *
 155  * @author $author$
 156  * @version $Revision$
 157  */
 158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 159         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 160 {
 161
 162   public static final int DEFAULT_WIDTH = 700;
 163
 164   public static final int DEFAULT_HEIGHT = 500;
 165
 166   /*
 167    * The currently displayed panel (selected tabbed view if more than one)
 168    */
 169   public AlignmentPanel alignPanel;
 170
 171   AlignViewport viewport;
 172
 173   public AlignViewControllerI avc;
 174
 175   List<AlignmentPanel> alignPanels = new ArrayList<>();
 176
 177   /**
 178    * Last format used to load or save alignments in this window
 179    */
 180   FileFormatI currentFileFormat = null;
 181
 182   /**
 183    * Current filename for this alignment
 184    */
 185   String fileName = null;
 186
 187   /**
 188    * Creates a new AlignFrame object with specific width and height.
 189    *
 190    * @param al
 191    * @param width
 192    * @param height
 193    */
 194   public AlignFrame(AlignmentI al, int width, int height)
 195   {
 196     this(al, null, width, height);
 197   }
 198
 199   /**
 200    * Creates a new AlignFrame object with specific width, height and
 201    * sequenceSetId
 202    *
 203    * @param al
 204    * @param width
 205    * @param height
 206    * @param sequenceSetId
 207    */
 208   public AlignFrame(AlignmentI al, int width, int height,
 209           String sequenceSetId)
 210   {
 211     this(al, null, width, height, sequenceSetId);
 212   }
 213
 214   /**
 215    * Creates a new AlignFrame object with specific width, height and
 216    * sequenceSetId
 217    *
 218    * @param al
 219    * @param width
 220    * @param height
 221    * @param sequenceSetId
 222    * @param viewId
 223    */
 224   public AlignFrame(AlignmentI al, int width, int height,
 225           String sequenceSetId, String viewId)
 226   {
 227     this(al, null, width, height, sequenceSetId, viewId);
 228   }
 229
 230   /**
 231    * new alignment window with hidden columns
 232    *
 233    * @param al
 234    *          AlignmentI
 235    * @param hiddenColumns
 236    *          ColumnSelection or null
 237    * @param width
 238    *          Width of alignment frame
 239    * @param height
 240    *          height of frame.
 241    */
 242   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 243           int height)
 244   {
 245     this(al, hiddenColumns, width, height, null);
 246   }
 247
 248   /**
 249    * Create alignment frame for al with hiddenColumns, a specific width and
 250    * height, and specific sequenceId
 251    *
 252    * @param al
 253    * @param hiddenColumns
 254    * @param width
 255    * @param height
 256    * @param sequenceSetId
 257    *          (may be null)
 258    */
 259   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 260           int height, String sequenceSetId)
 261   {
 262     this(al, hiddenColumns, width, height, sequenceSetId, null);
 263   }
 264
 265   /**
 266    * Create alignment frame for al with hiddenColumns, a specific width and
 267    * height, and specific sequenceId
 268    *
 269    * @param al
 270    * @param hiddenColumns
 271    * @param width
 272    * @param height
 273    * @param sequenceSetId
 274    *          (may be null)
 275    * @param viewId
 276    *          (may be null)
 277    */
 278   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 279           int height, String sequenceSetId, String viewId)
 280   {
 281     setSize(width, height);
 282
 283     if (al.getDataset() == null)
 284     {
 285       al.setDataset(null);
 286     }
 287
 288     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 289
 290     alignPanel = new AlignmentPanel(this, viewport);
 291
 292     addAlignmentPanel(alignPanel, true);
 293     init();
 294   }
 295
 296   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 297           HiddenColumns hiddenColumns, int width, int height)
 298   {
 299     setSize(width, height);
 300
 301     if (al.getDataset() == null)
 302     {
 303       al.setDataset(null);
 304     }
 305
 306     viewport = new AlignViewport(al, hiddenColumns);
 307
 308     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 309     {
 310       viewport.hideSequence(hiddenSeqs);
 311     }
 312     alignPanel = new AlignmentPanel(this, viewport);
 313     addAlignmentPanel(alignPanel, true);
 314     init();
 315   }
 316
 317   /**
 318    * Make a new AlignFrame from existing alignmentPanels
 319    *
 320    * @param ap
 321    *          AlignmentPanel
 322    * @param av
 323    *          AlignViewport
 324    */
 325   public AlignFrame(AlignmentPanel ap)
 326   {
 327     viewport = ap.av;
 328     alignPanel = ap;
 329     addAlignmentPanel(ap, false);
 330     init();
 331   }
 332
 333   /**
 334    * initalise the alignframe from the underlying viewport data and the
 335    * configurations
 336    */
 337   void init()
 338   {
 339     if (!Jalview.isHeadlessMode())
 340     {
 341       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 342     }
 343
 344     avc = new jalview.controller.AlignViewController(this, viewport,
 345             alignPanel);
 346     if (viewport.getAlignmentConservationAnnotation() == null)
 347     {
 348       // BLOSUM62Colour.setEnabled(false);
 349       conservationMenuItem.setEnabled(false);
 350       modifyConservation.setEnabled(false);
 351       // PIDColour.setEnabled(false);
 352       // abovePIDThreshold.setEnabled(false);
 353       // modifyPID.setEnabled(false);
 354     }
 355
 356     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 357             "No sort");
 358
 359     if (sortby.equals("Id"))
 360     {
 361       sortIDMenuItem_actionPerformed(null);
 362     }
 363     else if (sortby.equals("Pairwise Identity"))
 364     {
 365       sortPairwiseMenuItem_actionPerformed(null);
 366     }
 367
 368     this.alignPanel.av
 369             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 370
 371     setMenusFromViewport(viewport);
 372     buildSortByAnnotationScoresMenu();
 373     calculateTree.addActionListener(new ActionListener()
 374     {
 375
 376       @Override
 377       public void actionPerformed(ActionEvent e)
 378       {
 379         openTreePcaDialog();
 380       }
 381     });
 382     buildColourMenu();
 383
 384     if (Desktop.desktop != null)
 385     {
 386       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 387       addServiceListeners();
 388       setGUINucleotide();
 389     }
 390
 391     if (viewport.getWrapAlignment())
 392     {
 393       wrapMenuItem_actionPerformed(null);
 394     }
 395
 396     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 397     {
 398       this.overviewMenuItem_actionPerformed(null);
 399     }
 400
 401     addKeyListener();
 402
 403     final List<AlignmentPanel> selviews = new ArrayList<>();
 404     final List<AlignmentPanel> origview = new ArrayList<>();
 405     final String menuLabel = MessageManager
 406             .getString("label.copy_format_from");
 407     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 408             new ViewSetProvider()
 409             {
 410
 411               @Override
 412               public AlignmentPanel[] getAllAlignmentPanels()
 413               {
 414                 origview.clear();
 415                 origview.add(alignPanel);
 416                 // make an array of all alignment panels except for this one
 417                 List<AlignmentPanel> aps = new ArrayList<>(
 418                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 419                 aps.remove(AlignFrame.this.alignPanel);
 420                 return aps.toArray(new AlignmentPanel[aps.size()]);
 421               }
 422             }, selviews, new ItemListener()
 423             {
 424
 425               @Override
 426               public void itemStateChanged(ItemEvent e)
 427               {
 428                 if (origview.size() > 0)
 429                 {
 430                   final AlignmentPanel ap = origview.get(0);
 431
 432                   /*
 433                    * Copy the ViewStyle of the selected panel to 'this one'.
 434                    * Don't change value of 'scaleProteinAsCdna' unless copying
 435                    * from a SplitFrame.
 436                    */
 437                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 438                           .getViewStyle();
 439                   boolean fromSplitFrame = selviews.get(0)
 440                           .getAlignViewport().getCodingComplement() != null;
 441                   if (!fromSplitFrame)
 442                   {
 443                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 444                             .getViewStyle().isScaleProteinAsCdna());
 445                   }
 446                   ap.getAlignViewport().setViewStyle(vs);
 447
 448                   /*
 449                    * Also rescale ViewStyle of SplitFrame complement if there is
 450                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 451                    * the whole ViewStyle (allow cDNA protein to have different
 452                    * fonts)
 453                    */
 454                   AlignViewportI complement = ap.getAlignViewport()
 455                           .getCodingComplement();
 456                   if (complement != null && vs.isScaleProteinAsCdna())
 457                   {
 458                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 459                     ((SplitFrame) af.getSplitViewContainer())
 460                             .adjustLayout();
 461                     af.setMenusForViewport();
 462                   }
 463
 464                   ap.updateLayout();
 465                   ap.setSelected(true);
 466                   ap.alignFrame.setMenusForViewport();
 467
 468                 }
 469               }
 470             });
 471     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 472             .indexOf("devel") > -1
 473             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 474                     .indexOf("test") > -1)
 475     {
 476       formatMenu.add(vsel);
 477     }
 478     addFocusListener(new FocusAdapter()
 479     {
 480       @Override
 481       public void focusGained(FocusEvent e)
 482       {
 483         Jalview.setCurrentAlignFrame(AlignFrame.this);
 484       }
 485     });
 486
 487   }
 488
 489   /**
 490    * Change the filename and format for the alignment, and enable the 'reload'
 491    * button functionality.
 492    *
 493    * @param file
 494    *          valid filename
 495    * @param format
 496    *          format of file
 497    */
 498   public void setFileName(String file, FileFormatI format)
 499   {
 500     fileName = file;
 501     setFileFormat(format);
 502     reload.setEnabled(true);
 503   }
 504
 505   /**
 506    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 507    * events
 508    */
 509   void addKeyListener()
 510   {
 511     addKeyListener(new KeyAdapter()
 512     {
 513       @Override
 514       public void keyPressed(KeyEvent evt)
 515       {
 516         if (viewport.cursorMode
 517                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 518                         && evt.getKeyCode() <= KeyEvent.VK_9)
 519                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 520                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 521                 && Character.isDigit(evt.getKeyChar()))
 522         {
 523           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 524         }
 525
 526         switch (evt.getKeyCode())
 527         {
 528
 529         case 27: // escape key
 530           deselectAllSequenceMenuItem_actionPerformed(null);
 531
 532           break;
 533
 534         case KeyEvent.VK_DOWN:
 535           if (evt.isAltDown() || !viewport.cursorMode)
 536           {
 537             moveSelectedSequences(false);
 538           }
 539           if (viewport.cursorMode)
 540           {
 541             alignPanel.getSeqPanel().moveCursor(0, 1,
 542                     evt.isShiftDown() && !evt.isAltDown());
 543           }
 544           break;
 545
 546         case KeyEvent.VK_UP:
 547           if (evt.isAltDown() || !viewport.cursorMode)
 548           {
 549             moveSelectedSequences(true);
 550           }
 551           if (viewport.cursorMode)
 552           {
 553             alignPanel.getSeqPanel().moveCursor(0, -1,
 554                     evt.isShiftDown() && !evt.isAltDown());
 555           }
 556           break;
 557
 558         case KeyEvent.VK_LEFT:
 559           if (evt.isAltDown() || !viewport.cursorMode)
 560           {
 561             slideSequences(false,
 562                     alignPanel.getSeqPanel().getKeyboardNo1());
 563           }
 564           else
 565           {
 566             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 567           }
 568
 569           break;
 570
 571         case KeyEvent.VK_RIGHT:
 572           if (evt.isAltDown() || !viewport.cursorMode)
 573           {
 574             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 575           }
 576           else
 577           {
 578             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 579           }
 580           break;
 581
 582         case KeyEvent.VK_SPACE:
 583           if (viewport.cursorMode)
 584           {
 585             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 586                     || evt.isShiftDown() || evt.isAltDown());
 587           }
 588           break;
 589
 590         // case KeyEvent.VK_A:
 591         // if (viewport.cursorMode)
 592         // {
 593         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 594         // //System.out.println("A");
 595         // }
 596         // break;
 597         /*
 598          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 599          * System.out.println("closing bracket"); } break;
 600          */
 601         case KeyEvent.VK_DELETE:
 602         case KeyEvent.VK_BACK_SPACE:
 603           if (!viewport.cursorMode)
 604           {
 605             cut_actionPerformed(null);
 606           }
 607           else
 608           {
 609             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 610                     || evt.isShiftDown() || evt.isAltDown());
 611           }
 612
 613           break;
 614
 615         case KeyEvent.VK_S:
 616           if (viewport.cursorMode)
 617           {
 618             alignPanel.getSeqPanel().setCursorRow();
 619           }
 620           break;
 621         case KeyEvent.VK_C:
 622           if (viewport.cursorMode && !evt.isControlDown())
 623           {
 624             alignPanel.getSeqPanel().setCursorColumn();
 625           }
 626           break;
 627         case KeyEvent.VK_P:
 628           if (viewport.cursorMode)
 629           {
 630             alignPanel.getSeqPanel().setCursorPosition();
 631           }
 632           break;
 633
 634         case KeyEvent.VK_ENTER:
 635         case KeyEvent.VK_COMMA:
 636           if (viewport.cursorMode)
 637           {
 638             alignPanel.getSeqPanel().setCursorRowAndColumn();
 639           }
 640           break;
 641
 642         case KeyEvent.VK_Q:
 643           if (viewport.cursorMode)
 644           {
 645             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 646           }
 647           break;
 648         case KeyEvent.VK_M:
 649           if (viewport.cursorMode)
 650           {
 651             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 652           }
 653           break;
 654
 655         case KeyEvent.VK_F2:
 656           viewport.cursorMode = !viewport.cursorMode;
 657           statusBar.setText(MessageManager
 658                   .formatMessage("label.keyboard_editing_mode", new String[]
 659                   { (viewport.cursorMode ? "on" : "off") }));
 660           if (viewport.cursorMode)
 661           {
 662             ViewportRanges ranges = viewport.getRanges();
 663             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 664                     .getStartRes();
 665             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 666                     .getStartSeq();
 667           }
 668           alignPanel.getSeqPanel().seqCanvas.repaint();
 669           break;
 670
 671         case KeyEvent.VK_F1:
 672           try
 673           {
 674             Help.showHelpWindow();
 675           } catch (Exception ex)
 676           {
 677             ex.printStackTrace();
 678           }
 679           break;
 680         case KeyEvent.VK_H:
 681         {
 682           boolean toggleSeqs = !evt.isControlDown();
 683           boolean toggleCols = !evt.isShiftDown();
 684           toggleHiddenRegions(toggleSeqs, toggleCols);
 685           break;
 686         }
 687         case KeyEvent.VK_B:
 688         {
 689           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 690           boolean modifyExisting = true; // always modify, don't clear
 691                                          // evt.isShiftDown();
 692           boolean invertHighlighted = evt.isAltDown();
 693           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 694                   toggleSel);
 695           break;
 696         }
 697         case KeyEvent.VK_PAGE_UP:
 698           viewport.getRanges().pageUp();
 699           break;
 700         case KeyEvent.VK_PAGE_DOWN:
 701           viewport.getRanges().pageDown();
 702           break;
 703         }
 704       }
 705
 706       @Override
 707       public void keyReleased(KeyEvent evt)
 708       {
 709         switch (evt.getKeyCode())
 710         {
 711         case KeyEvent.VK_LEFT:
 712           if (evt.isAltDown() || !viewport.cursorMode)
 713           {
 714             viewport.firePropertyChange("alignment", null,
 715                     viewport.getAlignment().getSequences());
 716           }
 717           break;
 718
 719         case KeyEvent.VK_RIGHT:
 720           if (evt.isAltDown() || !viewport.cursorMode)
 721           {
 722             viewport.firePropertyChange("alignment", null,
 723                     viewport.getAlignment().getSequences());
 724           }
 725           break;
 726         }
 727       }
 728     });
 729   }
 730
 731   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 732   {
 733     ap.alignFrame = this;
 734     avc = new jalview.controller.AlignViewController(this, viewport,
 735             alignPanel);
 736
 737     alignPanels.add(ap);
 738
 739     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 740
 741     int aSize = alignPanels.size();
 742
 743     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 744
 745     if (aSize == 1 && ap.av.getViewName() == null)
 746     {
 747       this.getContentPane().add(ap, BorderLayout.CENTER);
 748     }
 749     else
 750     {
 751       if (aSize == 2)
 752       {
 753         setInitialTabVisible();
 754       }
 755
 756       expandViews.setEnabled(true);
 757       gatherViews.setEnabled(true);
 758       tabbedPane.addTab(ap.av.getViewName(), ap);
 759
 760       ap.setVisible(false);
 761     }
 762
 763     if (newPanel)
 764     {
 765       if (ap.av.isPadGaps())
 766       {
 767         ap.av.getAlignment().padGaps();
 768       }
 769       ap.av.updateConservation(ap);
 770       ap.av.updateConsensus(ap);
 771       ap.av.updateStrucConsensus(ap);
 772     }
 773   }
 774
 775   public void setInitialTabVisible()
 776   {
 777     expandViews.setEnabled(true);
 778     gatherViews.setEnabled(true);
 779     tabbedPane.setVisible(true);
 780     AlignmentPanel first = alignPanels.get(0);
 781     tabbedPane.addTab(first.av.getViewName(), first);
 782     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 783   }
 784
 785   public AlignViewport getViewport()
 786   {
 787     return viewport;
 788   }
 789
 790   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 791   private void addServiceListeners()
 792   {
 793     final java.beans.PropertyChangeListener thisListener;
 794     Desktop.instance.addJalviewPropertyChangeListener("services",
 795             thisListener = new java.beans.PropertyChangeListener()
 796             {
 797               @Override
 798               public void propertyChange(PropertyChangeEvent evt)
 799               {
 800                 // // System.out.println("Discoverer property change.");
 801                 // if (evt.getPropertyName().equals("services"))
 802                 {
 803                   SwingUtilities.invokeLater(new Runnable()
 804                   {
 805
 806                     @Override
 807                     public void run()
 808                     {
 809                       System.err.println(
 810                               "Rebuild WS Menu for service change");
 811                       BuildWebServiceMenu();
 812                     }
 813
 814                   });
 815                 }
 816               }
 817             });
 818     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 819     {
 820       @Override
 821       public void internalFrameClosed(
 822               javax.swing.event.InternalFrameEvent evt)
 823       {
 824         // System.out.println("deregistering discoverer listener");
 825         Desktop.instance.removeJalviewPropertyChangeListener("services",
 826                 thisListener);
 827         closeMenuItem_actionPerformed(true);
 828       };
 829     });
 830     // Finally, build the menu once to get current service state
 831     new Thread(new Runnable()
 832     {
 833       @Override
 834       public void run()
 835       {
 836         BuildWebServiceMenu();
 837       }
 838     }).start();
 839   }
 840
 841   /**
 842    * Configure menu items that vary according to whether the alignment is
 843    * nucleotide or protein
 844    */
 845   public void setGUINucleotide()
 846   {
 847     AlignmentI al = getViewport().getAlignment();
 848     boolean nucleotide = al.isNucleotide();
 849
 850     loadVcf.setVisible(nucleotide);
 851     showTranslation.setVisible(nucleotide);
 852     showReverse.setVisible(nucleotide);
 853     showReverseComplement.setVisible(nucleotide);
 854     conservationMenuItem.setEnabled(!nucleotide);
 855     modifyConservation
 856             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 857     showGroupConservation.setEnabled(!nucleotide);
 858
 859     showComplementMenuItem
 860             .setText(nucleotide ? MessageManager.getString("label.protein")
 861                     : MessageManager.getString("label.nucleotide"));
 862   }
 863
 864   /**
 865    * set up menus for the current viewport. This may be called after any
 866    * operation that affects the data in the current view (selection changed,
 867    * etc) to update the menus to reflect the new state.
 868    */
 869   @Override
 870   public void setMenusForViewport()
 871   {
 872     setMenusFromViewport(viewport);
 873   }
 874
 875   /**
 876    * Need to call this method when tabs are selected for multiple views, or when
 877    * loading from Jalview2XML.java
 878    *
 879    * @param av
 880    *          AlignViewport
 881    */
 882   public void setMenusFromViewport(AlignViewport av)
 883   {
 884     padGapsMenuitem.setSelected(av.isPadGaps());
 885     colourTextMenuItem.setSelected(av.isShowColourText());
 886     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 887     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 888     conservationMenuItem.setSelected(av.getConservationSelected());
 889     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 890     seqLimits.setSelected(av.getShowJVSuffix());
 891     idRightAlign.setSelected(av.isRightAlignIds());
 892     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 893     renderGapsMenuItem.setSelected(av.isRenderGaps());
 894     wrapMenuItem.setSelected(av.getWrapAlignment());
 895     scaleAbove.setVisible(av.getWrapAlignment());
 896     scaleLeft.setVisible(av.getWrapAlignment());
 897     scaleRight.setVisible(av.getWrapAlignment());
 898     annotationPanelMenuItem.setState(av.isShowAnnotation());
 899     /*
 900      * Show/hide annotations only enabled if annotation panel is shown
 901      */
 902     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 903     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 904     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 905     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 906     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 907     viewTextMenuItem.setSelected(av.getShowText());
 908     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 909     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 910     showGroupConservation.setSelected(av.isShowGroupConservation());
 911     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 912     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 913     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 914
 915     ColourMenuHelper.setColourSelected(colourMenu,
 916             av.getGlobalColourScheme());
 917
 918     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 919     hiddenMarkers.setState(av.getShowHiddenMarkers());
 920     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 921     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 922     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 923     autoCalculate.setSelected(av.autoCalculateConsensus);
 924     sortByTree.setSelected(av.sortByTree);
 925     listenToViewSelections.setSelected(av.followSelection);
 926
 927     showProducts.setEnabled(canShowProducts());
 928     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 929
 930     updateEditMenuBar();
 931   }
 932
 933   /**
 934    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 935    *
 936    * @param b
 937    */
 938   public void setGroovyEnabled(boolean b)
 939   {
 940     runGroovy.setEnabled(b);
 941   }
 942
 943   private IProgressIndicator progressBar;
 944
 945   /*
 946    * (non-Javadoc)
 947    *
 948    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 949    */
 950   @Override
 951   public void setProgressBar(String message, long id)
 952   {
 953     progressBar.setProgressBar(message, id);
 954   }
 955
 956   @Override
 957   public void registerHandler(final long id,
 958           final IProgressIndicatorHandler handler)
 959   {
 960     progressBar.registerHandler(id, handler);
 961   }
 962
 963   /**
 964    *
 965    * @return true if any progress bars are still active
 966    */
 967   @Override
 968   public boolean operationInProgress()
 969   {
 970     return progressBar.operationInProgress();
 971   }
 972
 973   /**
 974    * Sets the text of the status bar. Note that setting a null or empty value
 975    * will cause the status bar to be hidden, with possibly undesirable flicker
 976    * of the screen layout.
 977    */
 978   @Override
 979   public void setStatus(String text)
 980   {
 981     statusBar.setText(text == null || text.isEmpty() ? " " : text);
 982   }
 983
 984   /*
 985    * Added so Castor Mapping file can obtain Jalview Version
 986    */
 987   public String getVersion()
 988   {
 989     return jalview.bin.Cache.getProperty("VERSION");
 990   }
 991
 992   public FeatureRenderer getFeatureRenderer()
 993   {
 994     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 995   }
 996
 997   @Override
 998   public void fetchSequence_actionPerformed(ActionEvent e)
 999   {
1000     new jalview.gui.SequenceFetcher(this);
1001   }
1002
1003   @Override
1004   public void addFromFile_actionPerformed(ActionEvent e)
1005   {
1006     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1007   }
1008
1009   @Override
1010   public void reload_actionPerformed(ActionEvent e)
1011   {
1012     if (fileName != null)
1013     {
1014       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1015       // originating file's format
1016       // TODO: work out how to recover feature settings for correct view(s) when
1017       // file is reloaded.
1018       if (FileFormat.Jalview.equals(currentFileFormat))
1019       {
1020         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1021         for (int i = 0; i < frames.length; i++)
1022         {
1023           if (frames[i] instanceof AlignFrame && frames[i] != this
1024                   && ((AlignFrame) frames[i]).fileName != null
1025                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1026           {
1027             try
1028             {
1029               frames[i].setSelected(true);
1030               Desktop.instance.closeAssociatedWindows();
1031             } catch (java.beans.PropertyVetoException ex)
1032             {
1033             }
1034           }
1035
1036         }
1037         Desktop.instance.closeAssociatedWindows();
1038
1039         FileLoader loader = new FileLoader();
1040         DataSourceType protocol = fileName.startsWith("http:")
1041                 ? DataSourceType.URL
1042                 : DataSourceType.FILE;
1043         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1044       }
1045       else
1046       {
1047         Rectangle bounds = this.getBounds();
1048
1049         FileLoader loader = new FileLoader();
1050         DataSourceType protocol = fileName.startsWith("http:")
1051                 ? DataSourceType.URL
1052                 : DataSourceType.FILE;
1053         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1054                 protocol, currentFileFormat);
1055
1056         newframe.setBounds(bounds);
1057         if (featureSettings != null && featureSettings.isShowing())
1058         {
1059           final Rectangle fspos = featureSettings.frame.getBounds();
1060           // TODO: need a 'show feature settings' function that takes bounds -
1061           // need to refactor Desktop.addFrame
1062           newframe.featureSettings_actionPerformed(null);
1063           final FeatureSettings nfs = newframe.featureSettings;
1064           SwingUtilities.invokeLater(new Runnable()
1065           {
1066             @Override
1067             public void run()
1068             {
1069               nfs.frame.setBounds(fspos);
1070             }
1071           });
1072           this.featureSettings.close();
1073           this.featureSettings = null;
1074         }
1075         this.closeMenuItem_actionPerformed(true);
1076       }
1077     }
1078   }
1079
1080   @Override
1081   public void addFromText_actionPerformed(ActionEvent e)
1082   {
1083     Desktop.instance
1084             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1085   }
1086
1087   @Override
1088   public void addFromURL_actionPerformed(ActionEvent e)
1089   {
1090     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1091   }
1092
1093   @Override
1094   public void save_actionPerformed(ActionEvent e)
1095   {
1096     if (fileName == null || (currentFileFormat == null)
1097             || fileName.startsWith("http"))
1098     {
1099       saveAs_actionPerformed(null);
1100     }
1101     else
1102     {
1103       saveAlignment(fileName, currentFileFormat);
1104     }
1105   }
1106
1107   /**
1108    * DOCUMENT ME!
1109    *
1110    * @param e
1111    *          DOCUMENT ME!
1112    */
1113   @Override
1114   public void saveAs_actionPerformed(ActionEvent e)
1115   {
1116     String format = currentFileFormat == null ? null
1117             : currentFileFormat.getName();
1118     JalviewFileChooser chooser = JalviewFileChooser
1119             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1120
1121     chooser.setFileView(new JalviewFileView());
1122     chooser.setDialogTitle(
1123             MessageManager.getString("label.save_alignment_to_file"));
1124     chooser.setToolTipText(MessageManager.getString("action.save"));
1125
1126     int value = chooser.showSaveDialog(this);
1127
1128     if (value == JalviewFileChooser.APPROVE_OPTION)
1129     {
1130       currentFileFormat = chooser.getSelectedFormat();
1131       while (currentFileFormat == null)
1132       {
1133         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1134                 MessageManager.getString(
1135                         "label.select_file_format_before_saving"),
1136                 MessageManager.getString("label.file_format_not_specified"),
1137                 JvOptionPane.WARNING_MESSAGE);
1138         currentFileFormat = chooser.getSelectedFormat();
1139         value = chooser.showSaveDialog(this);
1140         if (value != JalviewFileChooser.APPROVE_OPTION)
1141         {
1142           return;
1143         }
1144       }
1145
1146       fileName = chooser.getSelectedFile().getPath();
1147
1148       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1149
1150       Cache.setProperty("LAST_DIRECTORY", fileName);
1151       saveAlignment(fileName, currentFileFormat);
1152     }
1153   }
1154
1155   public boolean saveAlignment(String file, FileFormatI format)
1156   {
1157     boolean success = true;
1158
1159     if (FileFormat.Jalview.equals(format))
1160     {
1161       String shortName = title;
1162
1163       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1164       {
1165         shortName = shortName.substring(
1166                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1167       }
1168
1169       success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1170               shortName);
1171
1172       statusBar.setText(MessageManager.formatMessage(
1173               "label.successfully_saved_to_file_in_format", new Object[]
1174               { file, format }));
1175
1176     }
1177     else
1178     {
1179       AlignmentExportData exportData = getAlignmentForExport(format,
1180               viewport, null);
1181       if (exportData.getSettings().isCancelled())
1182       {
1183         return false;
1184       }
1185       FormatAdapter f = new FormatAdapter(alignPanel,
1186               exportData.getSettings());
1187       String output = f.formatSequences(format, exportData.getAlignment(), // class
1188                                                                            // cast
1189                                                                            // exceptions
1190                                                                            // will
1191               // occur in the distant future
1192               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1193               f.getCacheSuffixDefault(format),
1194               viewport.getAlignment().getHiddenColumns());
1195
1196       if (output == null)
1197       {
1198         success = false;
1199       }
1200       else
1201       {
1202         // create backupfiles object and get new temp filename destination
1203         Cache.log.trace("ALIGNFRAME making backupfiles object for " + file);
1204         BackupFiles backupfiles = new BackupFiles(file);
1205
1206         try
1207         {
1208           String tempFilePath = backupfiles.getTempFilePath();
1209           Cache.log.trace(
1210                   "ALIGNFRAME setting PrintWriter to " + tempFilePath);
1211           PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1212
1213           Cache.log.trace(
1214                   "ALIGNFRAME about to write to temp file " + tempFilePath);
1215
1216           out.print(output);
1217           Cache.log.trace("ALIGNFRAME about to close file");
1218           out.close();
1219           Cache.log.trace("ALIGNFRAME closed file");
1220           this.setTitle(file);
1221           statusBar.setText(MessageManager.formatMessage(
1222                   "label.successfully_saved_to_file_in_format", new Object[]
1223                   { file, format.getName() }));
1224         } catch (IOException e)
1225         {
1226           success = false;
1227           Cache.log.error(
1228                   "ALIGNFRAME Something happened writing the temp file");
1229           Cache.log.error(e.getMessage());
1230           Cache.log.debug(Cache.getStackTraceString(e));
1231
1232         } catch (Exception ex)
1233         {
1234           success = false;
1235           Cache.log.error(
1236                   "ALIGNFRAME Something unexpected happened writing the temp file");
1237           Cache.log.error(ex.getMessage());
1238           Cache.log.debug(Cache.getStackTraceString(ex));
1239         }
1240
1241         backupfiles.setWriteSuccess(success);
1242         Cache.log.debug("ALIGNFRAME writing temp file was "
1243                 + (success ? "" : "NOT ") + "successful");
1244         // do the backup file roll and rename the temp file to actual file
1245         Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1246         success = backupfiles.rollBackupsAndRenameTempFile();
1247         Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1248                 + (success ? "" : "un") + "successfully");
1249
1250       }
1251     }
1252
1253     if (!success)
1254     {
1255       if (!Platform.isHeadless())
1256       {
1257         JvOptionPane.showInternalMessageDialog(this, MessageManager
1258                 .formatMessage("label.couldnt_save_file", new Object[]
1259                 { file }),
1260                 MessageManager.getString("label.error_saving_file"),
1261                 JvOptionPane.WARNING_MESSAGE);
1262       }
1263     }
1264
1265     return success;
1266   }
1267
1268   private void warningMessage(String warning, String title)
1269   {
1270     if (new jalview.util.Platform().isHeadless())
1271     {
1272       System.err.println("Warning: " + title + "\nWarning: " + warning);
1273
1274     }
1275     else
1276     {
1277       JvOptionPane.showInternalMessageDialog(this, warning, title,
1278               JvOptionPane.WARNING_MESSAGE);
1279     }
1280     return;
1281   }
1282
1283   /**
1284    * DOCUMENT ME!
1285    *
1286    * @param e
1287    *          DOCUMENT ME!
1288    */
1289   @Override
1290   protected void outputText_actionPerformed(ActionEvent e)
1291   {
1292     FileFormatI fileFormat = FileFormats.getInstance()
1293             .forName(e.getActionCommand());
1294     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1295             viewport, null);
1296     if (exportData.getSettings().isCancelled())
1297     {
1298       return;
1299     }
1300     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1301     cap.setForInput(null);
1302     try
1303     {
1304       FileFormatI format = fileFormat;
1305       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1306               .formatSequences(format, exportData.getAlignment(),
1307                       exportData.getOmitHidden(),
1308                       exportData.getStartEndPostions(),
1309                       viewport.getAlignment().getHiddenColumns()));
1310       Desktop.addInternalFrame(cap, MessageManager
1311               .formatMessage("label.alignment_output_command", new Object[]
1312               { e.getActionCommand() }), 600, 500);
1313     } catch (OutOfMemoryError oom)
1314     {
1315       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1316               oom);
1317       cap.dispose();
1318     }
1319
1320   }
1321
1322   public static AlignmentExportData getAlignmentForExport(
1323           FileFormatI format, AlignViewportI viewport,
1324           AlignExportSettingI exportSettings)
1325   {
1326     AlignmentI alignmentToExport = null;
1327     AlignExportSettingI settings = exportSettings;
1328     String[] omitHidden = null;
1329
1330     HiddenSequences hiddenSeqs = viewport.getAlignment()
1331             .getHiddenSequences();
1332
1333     alignmentToExport = viewport.getAlignment();
1334
1335     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1336     if (settings == null)
1337     {
1338       settings = new AlignExportSettings(hasHiddenSeqs,
1339               viewport.hasHiddenColumns(), format);
1340     }
1341     // settings.isExportAnnotations();
1342
1343     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1344     {
1345       omitHidden = viewport.getViewAsString(false,
1346               settings.isExportHiddenSequences());
1347     }
1348
1349     int[] alignmentStartEnd = new int[2];
1350     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1351     {
1352       alignmentToExport = hiddenSeqs.getFullAlignment();
1353     }
1354     else
1355     {
1356       alignmentToExport = viewport.getAlignment();
1357     }
1358     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1359             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1360     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1361             omitHidden, alignmentStartEnd, settings);
1362     return ed;
1363   }
1364
1365   /**
1366    * DOCUMENT ME!
1367    *
1368    * @param e
1369    *          DOCUMENT ME!
1370    */
1371   @Override
1372   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1373   {
1374     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1375     htmlSVG.exportHTML(null);
1376   }
1377
1378   @Override
1379   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1380   {
1381     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1382     bjs.exportHTML(null);
1383   }
1384
1385   public void createImageMap(File file, String image)
1386   {
1387     alignPanel.makePNGImageMap(file, image);
1388   }
1389
1390   /**
1391    * DOCUMENT ME!
1392    *
1393    * @param e
1394    *          DOCUMENT ME!
1395    */
1396   @Override
1397   public void createPNG(File f)
1398   {
1399     alignPanel.makePNG(f);
1400   }
1401
1402   /**
1403    * DOCUMENT ME!
1404    *
1405    * @param e
1406    *          DOCUMENT ME!
1407    */
1408   @Override
1409   public void createEPS(File f)
1410   {
1411     alignPanel.makeEPS(f);
1412   }
1413
1414   @Override
1415   public void createSVG(File f)
1416   {
1417     alignPanel.makeSVG(f);
1418   }
1419
1420   @Override
1421   public void pageSetup_actionPerformed(ActionEvent e)
1422   {
1423     PrinterJob printJob = PrinterJob.getPrinterJob();
1424     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1425   }
1426
1427   /**
1428    * DOCUMENT ME!
1429    *
1430    * @param e
1431    *          DOCUMENT ME!
1432    */
1433   @Override
1434   public void printMenuItem_actionPerformed(ActionEvent e)
1435   {
1436     // Putting in a thread avoids Swing painting problems
1437     PrintThread thread = new PrintThread(alignPanel);
1438     thread.start();
1439   }
1440
1441   @Override
1442   public void exportFeatures_actionPerformed(ActionEvent e)
1443   {
1444     new AnnotationExporter(alignPanel).exportFeatures();
1445   }
1446
1447   @Override
1448   public void exportAnnotations_actionPerformed(ActionEvent e)
1449   {
1450     new AnnotationExporter(alignPanel).exportAnnotations();
1451   }
1452
1453   @Override
1454   public void associatedData_actionPerformed(ActionEvent e)
1455   {
1456     // Pick the tree file
1457     JalviewFileChooser chooser = new JalviewFileChooser(
1458             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1459     chooser.setFileView(new JalviewFileView());
1460     chooser.setDialogTitle(
1461             MessageManager.getString("label.load_jalview_annotations"));
1462     chooser.setToolTipText(
1463             MessageManager.getString("label.load_jalview_annotations"));
1464
1465     int value = chooser.showOpenDialog(null);
1466
1467     if (value == JalviewFileChooser.APPROVE_OPTION)
1468     {
1469       String choice = chooser.getSelectedFile().getPath();
1470       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1471       loadJalviewDataFile(choice, null, null, null);
1472     }
1473
1474   }
1475
1476   /**
1477    * Close the current view or all views in the alignment frame. If the frame
1478    * only contains one view then the alignment will be removed from memory.
1479    *
1480    * @param closeAllTabs
1481    */
1482   @Override
1483   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1484   {
1485     if (alignPanels != null && alignPanels.size() < 2)
1486     {
1487       closeAllTabs = true;
1488     }
1489
1490     try
1491     {
1492       if (alignPanels != null)
1493       {
1494         if (closeAllTabs)
1495         {
1496           if (this.isClosed())
1497           {
1498             // really close all the windows - otherwise wait till
1499             // setClosed(true) is called
1500             for (int i = 0; i < alignPanels.size(); i++)
1501             {
1502               AlignmentPanel ap = alignPanels.get(i);
1503               ap.closePanel();
1504             }
1505           }
1506         }
1507         else
1508         {
1509           closeView(alignPanel);
1510         }
1511       }
1512       if (closeAllTabs)
1513       {
1514         if (featureSettings != null && featureSettings.isOpen())
1515         {
1516           featureSettings.close();
1517           featureSettings = null;
1518         }
1519         /*
1520          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1521          * be called recursively, with the frame now in 'closed' state
1522          */
1523         this.setClosed(true);
1524       }
1525     } catch (Exception ex)
1526     {
1527       ex.printStackTrace();
1528     }
1529   }
1530
1531   /**
1532    * Close the specified panel and close up tabs appropriately.
1533    *
1534    * @param panelToClose
1535    */
1536   public void closeView(AlignmentPanel panelToClose)
1537   {
1538     int index = tabbedPane.getSelectedIndex();
1539     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1540     alignPanels.remove(panelToClose);
1541     panelToClose.closePanel();
1542     panelToClose = null;
1543
1544     tabbedPane.removeTabAt(closedindex);
1545     tabbedPane.validate();
1546
1547     if (index > closedindex || index == tabbedPane.getTabCount())
1548     {
1549       // modify currently selected tab index if necessary.
1550       index--;
1551     }
1552
1553     this.tabSelectionChanged(index);
1554   }
1555
1556   /**
1557    * DOCUMENT ME!
1558    */
1559   void updateEditMenuBar()
1560   {
1561
1562     if (viewport.getHistoryList().size() > 0)
1563     {
1564       undoMenuItem.setEnabled(true);
1565       CommandI command = viewport.getHistoryList().peek();
1566       undoMenuItem.setText(MessageManager
1567               .formatMessage("label.undo_command", new Object[]
1568               { command.getDescription() }));
1569     }
1570     else
1571     {
1572       undoMenuItem.setEnabled(false);
1573       undoMenuItem.setText(MessageManager.getString("action.undo"));
1574     }
1575
1576     if (viewport.getRedoList().size() > 0)
1577     {
1578       redoMenuItem.setEnabled(true);
1579
1580       CommandI command = viewport.getRedoList().peek();
1581       redoMenuItem.setText(MessageManager
1582               .formatMessage("label.redo_command", new Object[]
1583               { command.getDescription() }));
1584     }
1585     else
1586     {
1587       redoMenuItem.setEnabled(false);
1588       redoMenuItem.setText(MessageManager.getString("action.redo"));
1589     }
1590   }
1591
1592   @Override
1593   public void addHistoryItem(CommandI command)
1594   {
1595     if (command.getSize() > 0)
1596     {
1597       viewport.addToHistoryList(command);
1598       viewport.clearRedoList();
1599       updateEditMenuBar();
1600       viewport.updateHiddenColumns();
1601       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1602       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1603       // viewport.getColumnSelection()
1604       // .getHiddenColumns().size() > 0);
1605     }
1606   }
1607
1608   /**
1609    *
1610    * @return alignment objects for all views
1611    */
1612   AlignmentI[] getViewAlignments()
1613   {
1614     if (alignPanels != null)
1615     {
1616       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1617       int i = 0;
1618       for (AlignmentPanel ap : alignPanels)
1619       {
1620         als[i++] = ap.av.getAlignment();
1621       }
1622       return als;
1623     }
1624     if (viewport != null)
1625     {
1626       return new AlignmentI[] { viewport.getAlignment() };
1627     }
1628     return null;
1629   }
1630
1631   /**
1632    * DOCUMENT ME!
1633    *
1634    * @param e
1635    *          DOCUMENT ME!
1636    */
1637   @Override
1638   protected void undoMenuItem_actionPerformed(ActionEvent e)
1639   {
1640     if (viewport.getHistoryList().isEmpty())
1641     {
1642       return;
1643     }
1644     CommandI command = viewport.getHistoryList().pop();
1645     viewport.addToRedoList(command);
1646     command.undoCommand(getViewAlignments());
1647
1648     AlignmentViewport originalSource = getOriginatingSource(command);
1649     updateEditMenuBar();
1650
1651     if (originalSource != null)
1652     {
1653       if (originalSource != viewport)
1654       {
1655         Cache.log.warn(
1656                 "Implementation worry: mismatch of viewport origin for undo");
1657       }
1658       originalSource.updateHiddenColumns();
1659       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1660       // null
1661       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1662       // viewport.getColumnSelection()
1663       // .getHiddenColumns().size() > 0);
1664       originalSource.firePropertyChange("alignment", null,
1665               originalSource.getAlignment().getSequences());
1666     }
1667   }
1668
1669   /**
1670    * DOCUMENT ME!
1671    *
1672    * @param e
1673    *          DOCUMENT ME!
1674    */
1675   @Override
1676   protected void redoMenuItem_actionPerformed(ActionEvent e)
1677   {
1678     if (viewport.getRedoList().size() < 1)
1679     {
1680       return;
1681     }
1682
1683     CommandI command = viewport.getRedoList().pop();
1684     viewport.addToHistoryList(command);
1685     command.doCommand(getViewAlignments());
1686
1687     AlignmentViewport originalSource = getOriginatingSource(command);
1688     updateEditMenuBar();
1689
1690     if (originalSource != null)
1691     {
1692
1693       if (originalSource != viewport)
1694       {
1695         Cache.log.warn(
1696                 "Implementation worry: mismatch of viewport origin for redo");
1697       }
1698       originalSource.updateHiddenColumns();
1699       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1700       // null
1701       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1702       // viewport.getColumnSelection()
1703       // .getHiddenColumns().size() > 0);
1704       originalSource.firePropertyChange("alignment", null,
1705               originalSource.getAlignment().getSequences());
1706     }
1707   }
1708
1709   AlignmentViewport getOriginatingSource(CommandI command)
1710   {
1711     AlignmentViewport originalSource = null;
1712     // For sequence removal and addition, we need to fire
1713     // the property change event FROM the viewport where the
1714     // original alignment was altered
1715     AlignmentI al = null;
1716     if (command instanceof EditCommand)
1717     {
1718       EditCommand editCommand = (EditCommand) command;
1719       al = editCommand.getAlignment();
1720       List<Component> comps = PaintRefresher.components
1721               .get(viewport.getSequenceSetId());
1722
1723       for (Component comp : comps)
1724       {
1725         if (comp instanceof AlignmentPanel)
1726         {
1727           if (al == ((AlignmentPanel) comp).av.getAlignment())
1728           {
1729             originalSource = ((AlignmentPanel) comp).av;
1730             break;
1731           }
1732         }
1733       }
1734     }
1735
1736     if (originalSource == null)
1737     {
1738       // The original view is closed, we must validate
1739       // the current view against the closed view first
1740       if (al != null)
1741       {
1742         PaintRefresher.validateSequences(al, viewport.getAlignment());
1743       }
1744
1745       originalSource = viewport;
1746     }
1747
1748     return originalSource;
1749   }
1750
1751   /**
1752    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode
1753    *
1754    * @param up
1755    *          or down (if !up)
1756    */
1757   public void moveSelectedSequences(boolean up)
1758   {
1759     SequenceGroup sg = viewport.getSelectionGroup();
1760
1761     if (sg == null)
1762     {
1763       if (viewport.cursorMode)
1764       {
1765         sg = new SequenceGroup();
1766         sg.addSequence(viewport.getAlignment()
1767                 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
1768       } else {
1769         return;
1770       }
1771     }
1772
1773     if (sg.getSize() < 1)
1774     {
1775         return;
1776     }
1777
1778     // TODO: JAL-3733 - add an event to the undo buffer for this !
1779
1780     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1781             viewport.getHiddenRepSequences(), up);
1782     alignPanel.paintAlignment(true, false);
1783   }
1784
1785   synchronized void slideSequences(boolean right, int size)
1786   {
1787     List<SequenceI> sg = new ArrayList<>();
1788     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
1789             .getSize() != viewport.getAlignment().getHeight())
1790     {
1791       sg = viewport.getSelectionGroup()
1792               .getSequences(viewport.getHiddenRepSequences());
1793     }
1794
1795     if (sg.size() == 0 && viewport.cursorMode)
1796     {
1797       sg.add(viewport.getAlignment()
1798               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1799     }
1800
1801     if (sg.size() < 1)
1802     {
1803       return;
1804     }
1805
1806     List<SequenceI> invertGroup = new ArrayList<>();
1807
1808     for (SequenceI seq : viewport.getAlignment().getSequences())
1809     {
1810       if (!sg.contains(seq))
1811       {
1812         invertGroup.add(seq);
1813       }
1814     }
1815
1816     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1817
1818     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1819     for (int i = 0; i < invertGroup.size(); i++)
1820     {
1821       seqs2[i] = invertGroup.get(i);
1822     }
1823
1824     SlideSequencesCommand ssc;
1825     if (right)
1826     {
1827       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1828               viewport.getGapCharacter());
1829     }
1830     else
1831     {
1832       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1833               viewport.getGapCharacter());
1834     }
1835
1836     int groupAdjustment = 0;
1837     if (ssc.getGapsInsertedBegin() && right)
1838     {
1839       if (viewport.cursorMode)
1840       {
1841         alignPanel.getSeqPanel().moveCursor(size, 0);
1842       }
1843       else
1844       {
1845         groupAdjustment = size;
1846       }
1847     }
1848     else if (!ssc.getGapsInsertedBegin() && !right)
1849     {
1850       if (viewport.cursorMode)
1851       {
1852         alignPanel.getSeqPanel().moveCursor(-size, 0);
1853       }
1854       else
1855       {
1856         groupAdjustment = -size;
1857       }
1858     }
1859
1860     if (groupAdjustment != 0)
1861     {
1862       viewport.getSelectionGroup().setStartRes(
1863               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1864       viewport.getSelectionGroup().setEndRes(
1865               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1866     }
1867
1868     /*
1869      * just extend the last slide command if compatible; but not if in
1870      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1871      */
1872     boolean appendHistoryItem = false;
1873     Deque<CommandI> historyList = viewport.getHistoryList();
1874     boolean inSplitFrame = getSplitViewContainer() != null;
1875     if (!inSplitFrame && historyList != null && historyList.size() > 0
1876             && historyList.peek() instanceof SlideSequencesCommand)
1877     {
1878       appendHistoryItem = ssc.appendSlideCommand(
1879               (SlideSequencesCommand) historyList.peek());
1880     }
1881
1882     if (!appendHistoryItem)
1883     {
1884       addHistoryItem(ssc);
1885     }
1886
1887     repaint();
1888   }
1889
1890   /**
1891    * DOCUMENT ME!
1892    *
1893    * @param e
1894    *          DOCUMENT ME!
1895    */
1896   @Override
1897   protected void copy_actionPerformed(ActionEvent e)
1898   {
1899     if (viewport.getSelectionGroup() == null)
1900     {
1901       return;
1902     }
1903     // TODO: preserve the ordering of displayed alignment annotation in any
1904     // internal paste (particularly sequence associated annotation)
1905     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1906     String[] omitHidden = null;
1907
1908     if (viewport.hasHiddenColumns())
1909     {
1910       omitHidden = viewport.getViewAsString(true);
1911     }
1912
1913     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1914             seqs, omitHidden, null);
1915
1916     StringSelection ss = new StringSelection(output);
1917
1918     try
1919     {
1920       jalview.gui.Desktop.internalCopy = true;
1921       // Its really worth setting the clipboard contents
1922       // to empty before setting the large StringSelection!!
1923       Toolkit.getDefaultToolkit().getSystemClipboard()
1924               .setContents(new StringSelection(""), null);
1925
1926       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1927               Desktop.instance);
1928     } catch (OutOfMemoryError er)
1929     {
1930       new OOMWarning("copying region", er);
1931       return;
1932     }
1933
1934     HiddenColumns hiddenColumns = null;
1935     if (viewport.hasHiddenColumns())
1936     {
1937       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1938       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1939
1940       // create new HiddenColumns object with copy of hidden regions
1941       // between startRes and endRes, offset by startRes
1942       hiddenColumns = new HiddenColumns(
1943               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1944               hiddenCutoff, hiddenOffset);
1945     }
1946
1947     Desktop.jalviewClipboard = new Object[] { seqs,
1948         viewport.getAlignment().getDataset(), hiddenColumns };
1949     statusBar.setText(MessageManager.formatMessage(
1950             "label.copied_sequences_to_clipboard", new Object[]
1951             { Integer.valueOf(seqs.length).toString() }));
1952   }
1953
1954   /**
1955    * DOCUMENT ME!
1956    *
1957    * @param e
1958    *          DOCUMENT ME!
1959    */
1960   @Override
1961   protected void pasteNew_actionPerformed(ActionEvent e)
1962   {
1963     paste(true);
1964   }
1965
1966   /**
1967    * DOCUMENT ME!
1968    *
1969    * @param e
1970    *          DOCUMENT ME!
1971    */
1972   @Override
1973   protected void pasteThis_actionPerformed(ActionEvent e)
1974   {
1975     paste(false);
1976   }
1977
1978   /**
1979    * Paste contents of Jalview clipboard
1980    *
1981    * @param newAlignment
1982    *          true to paste to a new alignment, otherwise add to this.
1983    */
1984   void paste(boolean newAlignment)
1985   {
1986     boolean externalPaste = true;
1987     try
1988     {
1989       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1990       Transferable contents = c.getContents(this);
1991
1992       if (contents == null)
1993       {
1994         return;
1995       }
1996
1997       String str;
1998       FileFormatI format;
1999       try
2000       {
2001         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2002         if (str.length() < 1)
2003         {
2004           return;
2005         }
2006
2007         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2008
2009       } catch (OutOfMemoryError er)
2010       {
2011         new OOMWarning("Out of memory pasting sequences!!", er);
2012         return;
2013       }
2014
2015       SequenceI[] sequences;
2016       boolean annotationAdded = false;
2017       AlignmentI alignment = null;
2018
2019       if (Desktop.jalviewClipboard != null)
2020       {
2021         // The clipboard was filled from within Jalview, we must use the
2022         // sequences
2023         // And dataset from the copied alignment
2024         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2025         // be doubly sure that we create *new* sequence objects.
2026         sequences = new SequenceI[newseq.length];
2027         for (int i = 0; i < newseq.length; i++)
2028         {
2029           sequences[i] = new Sequence(newseq[i]);
2030         }
2031         alignment = new Alignment(sequences);
2032         externalPaste = false;
2033       }
2034       else
2035       {
2036         // parse the clipboard as an alignment.
2037         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2038                 format);
2039         sequences = alignment.getSequencesArray();
2040       }
2041
2042       int alwidth = 0;
2043       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2044       int fgroup = -1;
2045
2046       if (newAlignment)
2047       {
2048
2049         if (Desktop.jalviewClipboard != null)
2050         {
2051           // dataset is inherited
2052           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2053         }
2054         else
2055         {
2056           // new dataset is constructed
2057           alignment.setDataset(null);
2058         }
2059         alwidth = alignment.getWidth() + 1;
2060       }
2061       else
2062       {
2063         AlignmentI pastedal = alignment; // preserve pasted alignment object
2064         // Add pasted sequences and dataset into existing alignment.
2065         alignment = viewport.getAlignment();
2066         alwidth = alignment.getWidth() + 1;
2067         // decide if we need to import sequences from an existing dataset
2068         boolean importDs = Desktop.jalviewClipboard != null
2069                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2070         // importDs==true instructs us to copy over new dataset sequences from
2071         // an existing alignment
2072         Vector newDs = (importDs) ? new Vector() : null; // used to create
2073         // minimum dataset set
2074
2075         for (int i = 0; i < sequences.length; i++)
2076         {
2077           if (importDs)
2078           {
2079             newDs.addElement(null);
2080           }
2081           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2082           // paste
2083           if (importDs && ds != null)
2084           {
2085             if (!newDs.contains(ds))
2086             {
2087               newDs.setElementAt(ds, i);
2088               ds = new Sequence(ds);
2089               // update with new dataset sequence
2090               sequences[i].setDatasetSequence(ds);
2091             }
2092             else
2093             {
2094               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2095             }
2096           }
2097           else
2098           {
2099             // copy and derive new dataset sequence
2100             sequences[i] = sequences[i].deriveSequence();
2101             alignment.getDataset()
2102                     .addSequence(sequences[i].getDatasetSequence());
2103             // TODO: avoid creation of duplicate dataset sequences with a
2104             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2105           }
2106           alignment.addSequence(sequences[i]); // merges dataset
2107         }
2108         if (newDs != null)
2109         {
2110           newDs.clear(); // tidy up
2111         }
2112         if (alignment.getAlignmentAnnotation() != null)
2113         {
2114           for (AlignmentAnnotation alan : alignment
2115                   .getAlignmentAnnotation())
2116           {
2117             if (alan.graphGroup > fgroup)
2118             {
2119               fgroup = alan.graphGroup;
2120             }
2121           }
2122         }
2123         if (pastedal.getAlignmentAnnotation() != null)
2124         {
2125           // Add any annotation attached to alignment.
2126           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2127           for (int i = 0; i < alann.length; i++)
2128           {
2129             annotationAdded = true;
2130             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2131             {
2132               AlignmentAnnotation newann = new AlignmentAnnotation(
2133                       alann[i]);
2134               if (newann.graphGroup > -1)
2135               {
2136                 if (newGraphGroups.size() <= newann.graphGroup
2137                         || newGraphGroups.get(newann.graphGroup) == null)
2138                 {
2139                   for (int q = newGraphGroups
2140                           .size(); q <= newann.graphGroup; q++)
2141                   {
2142                     newGraphGroups.add(q, null);
2143                   }
2144                   newGraphGroups.set(newann.graphGroup,
2145                           Integer.valueOf(++fgroup));
2146                 }
2147                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2148                         .intValue();
2149               }
2150
2151               newann.padAnnotation(alwidth);
2152               alignment.addAnnotation(newann);
2153             }
2154           }
2155         }
2156       }
2157       if (!newAlignment)
2158       {
2159         // /////
2160         // ADD HISTORY ITEM
2161         //
2162         addHistoryItem(new EditCommand(
2163                 MessageManager.getString("label.add_sequences"),
2164                 Action.PASTE, sequences, 0, alignment.getWidth(),
2165                 alignment));
2166       }
2167       // Add any annotations attached to sequences
2168       for (int i = 0; i < sequences.length; i++)
2169       {
2170         if (sequences[i].getAnnotation() != null)
2171         {
2172           AlignmentAnnotation newann;
2173           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2174           {
2175             annotationAdded = true;
2176             newann = sequences[i].getAnnotation()[a];
2177             newann.adjustForAlignment();
2178             newann.padAnnotation(alwidth);
2179             if (newann.graphGroup > -1)
2180             {
2181               if (newann.graphGroup > -1)
2182               {
2183                 if (newGraphGroups.size() <= newann.graphGroup
2184                         || newGraphGroups.get(newann.graphGroup) == null)
2185                 {
2186                   for (int q = newGraphGroups
2187                           .size(); q <= newann.graphGroup; q++)
2188                   {
2189                     newGraphGroups.add(q, null);
2190                   }
2191                   newGraphGroups.set(newann.graphGroup,
2192                           Integer.valueOf(++fgroup));
2193                 }
2194                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2195                         .intValue();
2196               }
2197             }
2198             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2199             // was
2200             // duplicated
2201             // earlier
2202             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2203                     a);
2204           }
2205         }
2206       }
2207       if (!newAlignment)
2208       {
2209
2210         // propagate alignment changed.
2211         viewport.getRanges().setEndSeq(alignment.getHeight());
2212         if (annotationAdded)
2213         {
2214           // Duplicate sequence annotation in all views.
2215           AlignmentI[] alview = this.getViewAlignments();
2216           for (int i = 0; i < sequences.length; i++)
2217           {
2218             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2219             if (sann == null)
2220             {
2221               continue;
2222             }
2223             for (int avnum = 0; avnum < alview.length; avnum++)
2224             {
2225               if (alview[avnum] != alignment)
2226               {
2227                 // duplicate in a view other than the one with input focus
2228                 int avwidth = alview[avnum].getWidth() + 1;
2229                 // this relies on sann being preserved after we
2230                 // modify the sequence's annotation array for each duplication
2231                 for (int a = 0; a < sann.length; a++)
2232                 {
2233                   AlignmentAnnotation newann = new AlignmentAnnotation(
2234                           sann[a]);
2235                   sequences[i].addAlignmentAnnotation(newann);
2236                   newann.padAnnotation(avwidth);
2237                   alview[avnum].addAnnotation(newann); // annotation was
2238                   // duplicated earlier
2239                   // TODO JAL-1145 graphGroups are not updated for sequence
2240                   // annotation added to several views. This may cause
2241                   // strangeness
2242                   alview[avnum].setAnnotationIndex(newann, a);
2243                 }
2244               }
2245             }
2246           }
2247           buildSortByAnnotationScoresMenu();
2248         }
2249         viewport.firePropertyChange("alignment", null,
2250                 alignment.getSequences());
2251         if (alignPanels != null)
2252         {
2253           for (AlignmentPanel ap : alignPanels)
2254           {
2255             ap.validateAnnotationDimensions(false);
2256           }
2257         }
2258         else
2259         {
2260           alignPanel.validateAnnotationDimensions(false);
2261         }
2262
2263       }
2264       else
2265       {
2266         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2267                 DEFAULT_HEIGHT);
2268         String newtitle = new String("Copied sequences");
2269
2270         if (Desktop.jalviewClipboard != null
2271                 && Desktop.jalviewClipboard[2] != null)
2272         {
2273           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2274           af.viewport.setHiddenColumns(hc);
2275         }
2276
2277         // >>>This is a fix for the moment, until a better solution is
2278         // found!!<<<
2279         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2280                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2281                         .getFeatureRenderer());
2282
2283         // TODO: maintain provenance of an alignment, rather than just make the
2284         // title a concatenation of operations.
2285         if (!externalPaste)
2286         {
2287           if (title.startsWith("Copied sequences"))
2288           {
2289             newtitle = title;
2290           }
2291           else
2292           {
2293             newtitle = newtitle.concat("- from " + title);
2294           }
2295         }
2296         else
2297         {
2298           newtitle = new String("Pasted sequences");
2299         }
2300
2301         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2302                 DEFAULT_HEIGHT);
2303
2304       }
2305
2306     } catch (Exception ex)
2307     {
2308       ex.printStackTrace();
2309       System.out.println("Exception whilst pasting: " + ex);
2310       // could be anything being pasted in here
2311     }
2312
2313   }
2314
2315   @Override
2316   protected void expand_newalign(ActionEvent e)
2317   {
2318     try
2319     {
2320       AlignmentI alignment = AlignmentUtils
2321               .expandContext(getViewport().getAlignment(), -1);
2322       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2323               DEFAULT_HEIGHT);
2324       String newtitle = new String("Flanking alignment");
2325
2326       if (Desktop.jalviewClipboard != null
2327               && Desktop.jalviewClipboard[2] != null)
2328       {
2329         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2330         af.viewport.setHiddenColumns(hc);
2331       }
2332
2333       // >>>This is a fix for the moment, until a better solution is
2334       // found!!<<<
2335       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2336               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2337                       .getFeatureRenderer());
2338
2339       // TODO: maintain provenance of an alignment, rather than just make the
2340       // title a concatenation of operations.
2341       {
2342         if (title.startsWith("Copied sequences"))
2343         {
2344           newtitle = title;
2345         }
2346         else
2347         {
2348           newtitle = newtitle.concat("- from " + title);
2349         }
2350       }
2351
2352       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2353
2354     } catch (Exception ex)
2355     {
2356       ex.printStackTrace();
2357       System.out.println("Exception whilst pasting: " + ex);
2358       // could be anything being pasted in here
2359     } catch (OutOfMemoryError oom)
2360     {
2361       new OOMWarning("Viewing flanking region of alignment", oom);
2362     }
2363   }
2364
2365   /**
2366    * DOCUMENT ME!
2367    *
2368    * @param e
2369    *          DOCUMENT ME!
2370    */
2371   @Override
2372   protected void cut_actionPerformed(ActionEvent e)
2373   {
2374     copy_actionPerformed(null);
2375     delete_actionPerformed(null);
2376   }
2377
2378   /**
2379    * DOCUMENT ME!
2380    *
2381    * @param e
2382    *          DOCUMENT ME!
2383    */
2384   @Override
2385   protected void delete_actionPerformed(ActionEvent evt)
2386   {
2387
2388     SequenceGroup sg = viewport.getSelectionGroup();
2389     if (sg == null)
2390     {
2391       return;
2392     }
2393
2394     /*
2395      * If the cut affects all sequences, warn, remove highlighted columns
2396      */
2397     if (sg.getSize() == viewport.getAlignment().getHeight())
2398     {
2399       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2400               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2401       if (isEntireAlignWidth)
2402       {
2403         int confirm = JvOptionPane.showConfirmDialog(this,
2404                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2405                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2406                 JvOptionPane.OK_CANCEL_OPTION);
2407
2408         if (confirm == JvOptionPane.CANCEL_OPTION
2409                 || confirm == JvOptionPane.CLOSED_OPTION)
2410         {
2411           return;
2412         }
2413       }
2414       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2415               sg.getEndRes() + 1);
2416     }
2417     SequenceI[] cut = sg.getSequences()
2418             .toArray(new SequenceI[sg.getSize()]);
2419
2420     addHistoryItem(new EditCommand(
2421             MessageManager.getString("label.cut_sequences"), Action.CUT,
2422             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2423             viewport.getAlignment()));
2424
2425     viewport.setSelectionGroup(null);
2426     viewport.sendSelection();
2427     viewport.getAlignment().deleteGroup(sg);
2428
2429     viewport.firePropertyChange("alignment", null,
2430             viewport.getAlignment().getSequences());
2431     if (viewport.getAlignment().getHeight() < 1)
2432     {
2433       try
2434       {
2435         this.setClosed(true);
2436       } catch (Exception ex)
2437       {
2438       }
2439     }
2440   }
2441
2442   /**
2443    * DOCUMENT ME!
2444    *
2445    * @param e
2446    *          DOCUMENT ME!
2447    */
2448   @Override
2449   protected void deleteGroups_actionPerformed(ActionEvent e)
2450   {
2451     if (avc.deleteGroups())
2452     {
2453       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2454       alignPanel.updateAnnotation();
2455       alignPanel.paintAlignment(true, true);
2456     }
2457   }
2458
2459   /**
2460    * DOCUMENT ME!
2461    *
2462    * @param e
2463    *          DOCUMENT ME!
2464    */
2465   @Override
2466   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2467   {
2468     SequenceGroup sg = new SequenceGroup(
2469             viewport.getAlignment().getSequences());
2470
2471     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2472     viewport.setSelectionGroup(sg);
2473     viewport.isSelectionGroupChanged(true);
2474     viewport.sendSelection();
2475     // JAL-2034 - should delegate to
2476     // alignPanel to decide if overview needs
2477     // updating.
2478     alignPanel.paintAlignment(false, false);
2479     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2480   }
2481
2482   /**
2483    * DOCUMENT ME!
2484    *
2485    * @param e
2486    *          DOCUMENT ME!
2487    */
2488   @Override
2489   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2490   {
2491     if (viewport.cursorMode)
2492     {
2493       alignPanel.getSeqPanel().keyboardNo1 = null;
2494       alignPanel.getSeqPanel().keyboardNo2 = null;
2495     }
2496     viewport.setSelectionGroup(null);
2497     viewport.getColumnSelection().clear();
2498     viewport.setSearchResults(null);
2499     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2500     // JAL-2034 - should delegate to
2501     // alignPanel to decide if overview needs
2502     // updating.
2503     alignPanel.paintAlignment(false, false);
2504     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2505     viewport.sendSelection();
2506   }
2507
2508   /**
2509    * DOCUMENT ME!
2510    *
2511    * @param e
2512    *          DOCUMENT ME!
2513    */
2514   @Override
2515   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2516   {
2517     SequenceGroup sg = viewport.getSelectionGroup();
2518
2519     if (sg == null)
2520     {
2521       selectAllSequenceMenuItem_actionPerformed(null);
2522
2523       return;
2524     }
2525
2526     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2527     {
2528       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2529     }
2530     // JAL-2034 - should delegate to
2531     // alignPanel to decide if overview needs
2532     // updating.
2533
2534     alignPanel.paintAlignment(true, false);
2535     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2536     viewport.sendSelection();
2537   }
2538
2539   @Override
2540   public void invertColSel_actionPerformed(ActionEvent e)
2541   {
2542     viewport.invertColumnSelection();
2543     alignPanel.paintAlignment(true, false);
2544     viewport.sendSelection();
2545   }
2546
2547   /**
2548    * DOCUMENT ME!
2549    *
2550    * @param e
2551    *          DOCUMENT ME!
2552    */
2553   @Override
2554   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2555   {
2556     trimAlignment(true);
2557   }
2558
2559   /**
2560    * DOCUMENT ME!
2561    *
2562    * @param e
2563    *          DOCUMENT ME!
2564    */
2565   @Override
2566   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2567   {
2568     trimAlignment(false);
2569   }
2570
2571   void trimAlignment(boolean trimLeft)
2572   {
2573     ColumnSelection colSel = viewport.getColumnSelection();
2574     int column;
2575
2576     if (!colSel.isEmpty())
2577     {
2578       if (trimLeft)
2579       {
2580         column = colSel.getMin();
2581       }
2582       else
2583       {
2584         column = colSel.getMax();
2585       }
2586
2587       SequenceI[] seqs;
2588       if (viewport.getSelectionGroup() != null)
2589       {
2590         seqs = viewport.getSelectionGroup()
2591                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2592       }
2593       else
2594       {
2595         seqs = viewport.getAlignment().getSequencesArray();
2596       }
2597
2598       TrimRegionCommand trimRegion;
2599       if (trimLeft)
2600       {
2601         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2602                 column, viewport.getAlignment());
2603         viewport.getRanges().setStartRes(0);
2604       }
2605       else
2606       {
2607         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2608                 column, viewport.getAlignment());
2609       }
2610
2611       statusBar.setText(MessageManager
2612               .formatMessage("label.removed_columns", new String[]
2613               { Integer.valueOf(trimRegion.getSize()).toString() }));
2614
2615       addHistoryItem(trimRegion);
2616
2617       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2618       {
2619         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2620                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2621         {
2622           viewport.getAlignment().deleteGroup(sg);
2623         }
2624       }
2625
2626       viewport.firePropertyChange("alignment", null,
2627               viewport.getAlignment().getSequences());
2628     }
2629   }
2630
2631   /**
2632    * DOCUMENT ME!
2633    *
2634    * @param e
2635    *          DOCUMENT ME!
2636    */
2637   @Override
2638   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2639   {
2640     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2641
2642     SequenceI[] seqs;
2643     if (viewport.getSelectionGroup() != null)
2644     {
2645       seqs = viewport.getSelectionGroup()
2646               .getSequencesAsArray(viewport.getHiddenRepSequences());
2647       start = viewport.getSelectionGroup().getStartRes();
2648       end = viewport.getSelectionGroup().getEndRes();
2649     }
2650     else
2651     {
2652       seqs = viewport.getAlignment().getSequencesArray();
2653     }
2654
2655     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2656             "Remove Gapped Columns", seqs, start, end,
2657             viewport.getAlignment());
2658
2659     addHistoryItem(removeGapCols);
2660
2661     statusBar.setText(MessageManager
2662             .formatMessage("label.removed_empty_columns", new Object[]
2663             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2664
2665     // This is to maintain viewport position on first residue
2666     // of first sequence
2667     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2668     ViewportRanges ranges = viewport.getRanges();
2669     int startRes = seq.findPosition(ranges.getStartRes());
2670     // ShiftList shifts;
2671     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2672     // edit.alColumnChanges=shifts.getInverse();
2673     // if (viewport.hasHiddenColumns)
2674     // viewport.getColumnSelection().compensateForEdits(shifts);
2675     ranges.setStartRes(seq.findIndex(startRes) - 1);
2676     viewport.firePropertyChange("alignment", null,
2677             viewport.getAlignment().getSequences());
2678
2679   }
2680
2681   /**
2682    * DOCUMENT ME!
2683    *
2684    * @param e
2685    *          DOCUMENT ME!
2686    */
2687   @Override
2688   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2689   {
2690     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2691
2692     SequenceI[] seqs;
2693     if (viewport.getSelectionGroup() != null)
2694     {
2695       seqs = viewport.getSelectionGroup()
2696               .getSequencesAsArray(viewport.getHiddenRepSequences());
2697       start = viewport.getSelectionGroup().getStartRes();
2698       end = viewport.getSelectionGroup().getEndRes();
2699     }
2700     else
2701     {
2702       seqs = viewport.getAlignment().getSequencesArray();
2703     }
2704
2705     // This is to maintain viewport position on first residue
2706     // of first sequence
2707     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2708     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2709
2710     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2711             viewport.getAlignment()));
2712
2713     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2714
2715     viewport.firePropertyChange("alignment", null,
2716             viewport.getAlignment().getSequences());
2717
2718   }
2719
2720   /**
2721    * DOCUMENT ME!
2722    *
2723    * @param e
2724    *          DOCUMENT ME!
2725    */
2726   @Override
2727   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2728   {
2729     viewport.setPadGaps(padGapsMenuitem.isSelected());
2730     viewport.firePropertyChange("alignment", null,
2731             viewport.getAlignment().getSequences());
2732   }
2733
2734   /**
2735    * Opens a Finder dialog
2736    *
2737    * @param e
2738    */
2739   @Override
2740   public void findMenuItem_actionPerformed(ActionEvent e)
2741   {
2742     new Finder(alignPanel);
2743   }
2744
2745   /**
2746    * Create a new view of the current alignment.
2747    */
2748   @Override
2749   public void newView_actionPerformed(ActionEvent e)
2750   {
2751     newView(null, true);
2752   }
2753
2754   /**
2755    * Creates and shows a new view of the current alignment.
2756    *
2757    * @param viewTitle
2758    *          title of newly created view; if null, one will be generated
2759    * @param copyAnnotation
2760    *          if true then duplicate all annnotation, groups and settings
2761    * @return new alignment panel, already displayed.
2762    */
2763   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2764   {
2765     /*
2766      * Create a new AlignmentPanel (with its own, new Viewport)
2767      */
2768     AlignmentPanel newap = new jalview.project.Jalview2XML()
2769             .copyAlignPanel(alignPanel);
2770     if (!copyAnnotation)
2771     {
2772       /*
2773        * remove all groups and annotation except for the automatic stuff
2774        */
2775       newap.av.getAlignment().deleteAllGroups();
2776       newap.av.getAlignment().deleteAllAnnotations(false);
2777     }
2778
2779     newap.av.setGatherViewsHere(false);
2780
2781     if (viewport.getViewName() == null)
2782     {
2783       viewport.setViewName(
2784               MessageManager.getString("label.view_name_original"));
2785     }
2786
2787     /*
2788      * Views share the same edits undo and redo stacks
2789      */
2790     newap.av.setHistoryList(viewport.getHistoryList());
2791     newap.av.setRedoList(viewport.getRedoList());
2792
2793     /*
2794      * copy any visualisation settings that are not saved in the project
2795      */
2796     newap.av.setColourAppliesToAllGroups(
2797             viewport.getColourAppliesToAllGroups());
2798
2799     /*
2800      * Views share the same mappings; need to deregister any new mappings
2801      * created by copyAlignPanel, and register the new reference to the shared
2802      * mappings
2803      */
2804     newap.av.replaceMappings(viewport.getAlignment());
2805
2806     /*
2807      * start up cDNA consensus (if applicable) now mappings are in place
2808      */
2809     if (newap.av.initComplementConsensus())
2810     {
2811       newap.refresh(true); // adjust layout of annotations
2812     }
2813
2814     newap.av.setViewName(getNewViewName(viewTitle));
2815
2816     addAlignmentPanel(newap, true);
2817     newap.alignmentChanged();
2818
2819     if (alignPanels.size() == 2)
2820     {
2821       viewport.setGatherViewsHere(true);
2822     }
2823     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2824     return newap;
2825   }
2826
2827   /**
2828    * Make a new name for the view, ensuring it is unique within the current
2829    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2830    * these now use viewId. Unique view names are still desirable for usability.)
2831    *
2832    * @param viewTitle
2833    * @return
2834    */
2835   protected String getNewViewName(String viewTitle)
2836   {
2837     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2838     boolean addFirstIndex = false;
2839     if (viewTitle == null || viewTitle.trim().length() == 0)
2840     {
2841       viewTitle = MessageManager.getString("action.view");
2842       addFirstIndex = true;
2843     }
2844     else
2845     {
2846       index = 1;// we count from 1 if given a specific name
2847     }
2848     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2849
2850     List<Component> comps = PaintRefresher.components
2851             .get(viewport.getSequenceSetId());
2852
2853     List<String> existingNames = getExistingViewNames(comps);
2854
2855     while (existingNames.contains(newViewName))
2856     {
2857       newViewName = viewTitle + " " + (++index);
2858     }
2859     return newViewName;
2860   }
2861
2862   /**
2863    * Returns a list of distinct view names found in the given list of
2864    * components. View names are held on the viewport of an AlignmentPanel.
2865    *
2866    * @param comps
2867    * @return
2868    */
2869   protected List<String> getExistingViewNames(List<Component> comps)
2870   {
2871     List<String> existingNames = new ArrayList<>();
2872     for (Component comp : comps)
2873     {
2874       if (comp instanceof AlignmentPanel)
2875       {
2876         AlignmentPanel ap = (AlignmentPanel) comp;
2877         if (!existingNames.contains(ap.av.getViewName()))
2878         {
2879           existingNames.add(ap.av.getViewName());
2880         }
2881       }
2882     }
2883     return existingNames;
2884   }
2885
2886   /**
2887    * Explode tabbed views into separate windows.
2888    */
2889   @Override
2890   public void expandViews_actionPerformed(ActionEvent e)
2891   {
2892     Desktop.explodeViews(this);
2893   }
2894
2895   /**
2896    * Gather views in separate windows back into a tabbed presentation.
2897    */
2898   @Override
2899   public void gatherViews_actionPerformed(ActionEvent e)
2900   {
2901     Desktop.instance.gatherViews(this);
2902   }
2903
2904   /**
2905    * DOCUMENT ME!
2906    *
2907    * @param e
2908    *          DOCUMENT ME!
2909    */
2910   @Override
2911   public void font_actionPerformed(ActionEvent e)
2912   {
2913     new FontChooser(alignPanel);
2914   }
2915
2916   /**
2917    * DOCUMENT ME!
2918    *
2919    * @param e
2920    *          DOCUMENT ME!
2921    */
2922   @Override
2923   protected void seqLimit_actionPerformed(ActionEvent e)
2924   {
2925     viewport.setShowJVSuffix(seqLimits.isSelected());
2926
2927     alignPanel.getIdPanel().getIdCanvas()
2928             .setPreferredSize(alignPanel.calculateIdWidth());
2929     alignPanel.paintAlignment(true, false);
2930   }
2931
2932   @Override
2933   public void idRightAlign_actionPerformed(ActionEvent e)
2934   {
2935     viewport.setRightAlignIds(idRightAlign.isSelected());
2936     alignPanel.paintAlignment(false, false);
2937   }
2938
2939   @Override
2940   public void centreColumnLabels_actionPerformed(ActionEvent e)
2941   {
2942     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2943     alignPanel.paintAlignment(false, false);
2944   }
2945
2946   /*
2947    * (non-Javadoc)
2948    *
2949    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2950    */
2951   @Override
2952   protected void followHighlight_actionPerformed()
2953   {
2954     /*
2955      * Set the 'follow' flag on the Viewport (and scroll to position if now
2956      * true).
2957      */
2958     final boolean state = this.followHighlightMenuItem.getState();
2959     viewport.setFollowHighlight(state);
2960     if (state)
2961     {
2962       alignPanel.scrollToPosition(viewport.getSearchResults());
2963     }
2964   }
2965
2966   /**
2967    * DOCUMENT ME!
2968    *
2969    * @param e
2970    *          DOCUMENT ME!
2971    */
2972   @Override
2973   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2974   {
2975     viewport.setColourText(colourTextMenuItem.isSelected());
2976     alignPanel.paintAlignment(false, false);
2977   }
2978
2979   /**
2980    * DOCUMENT ME!
2981    *
2982    * @param e
2983    *          DOCUMENT ME!
2984    */
2985   @Override
2986   public void wrapMenuItem_actionPerformed(ActionEvent e)
2987   {
2988     scaleAbove.setVisible(wrapMenuItem.isSelected());
2989     scaleLeft.setVisible(wrapMenuItem.isSelected());
2990     scaleRight.setVisible(wrapMenuItem.isSelected());
2991     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2992     alignPanel.updateLayout();
2993   }
2994
2995   @Override
2996   public void showAllSeqs_actionPerformed(ActionEvent e)
2997   {
2998     viewport.showAllHiddenSeqs();
2999   }
3000
3001   @Override
3002   public void showAllColumns_actionPerformed(ActionEvent e)
3003   {
3004     viewport.showAllHiddenColumns();
3005     alignPanel.paintAlignment(true, true);
3006     viewport.sendSelection();
3007   }
3008
3009   @Override
3010   public void hideSelSequences_actionPerformed(ActionEvent e)
3011   {
3012     viewport.hideAllSelectedSeqs();
3013   }
3014
3015   /**
3016    * called by key handler and the hide all/show all menu items
3017    *
3018    * @param toggleSeqs
3019    * @param toggleCols
3020    */
3021   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3022   {
3023
3024     boolean hide = false;
3025     SequenceGroup sg = viewport.getSelectionGroup();
3026     if (!toggleSeqs && !toggleCols)
3027     {
3028       // Hide everything by the current selection - this is a hack - we do the
3029       // invert and then hide
3030       // first check that there will be visible columns after the invert.
3031       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3032               && sg.getStartRes() <= sg.getEndRes()))
3033       {
3034         // now invert the sequence set, if required - empty selection implies
3035         // that no hiding is required.
3036         if (sg != null)
3037         {
3038           invertSequenceMenuItem_actionPerformed(null);
3039           sg = viewport.getSelectionGroup();
3040           toggleSeqs = true;
3041
3042         }
3043         viewport.expandColSelection(sg, true);
3044         // finally invert the column selection and get the new sequence
3045         // selection.
3046         invertColSel_actionPerformed(null);
3047         toggleCols = true;
3048       }
3049     }
3050
3051     if (toggleSeqs)
3052     {
3053       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3054       {
3055         hideSelSequences_actionPerformed(null);
3056         hide = true;
3057       }
3058       else if (!(toggleCols && viewport.hasSelectedColumns()))
3059       {
3060         showAllSeqs_actionPerformed(null);
3061       }
3062     }
3063
3064     if (toggleCols)
3065     {
3066       if (viewport.hasSelectedColumns())
3067       {
3068         hideSelColumns_actionPerformed(null);
3069         if (!toggleSeqs)
3070         {
3071           viewport.setSelectionGroup(sg);
3072         }
3073       }
3074       else if (!hide)
3075       {
3076         showAllColumns_actionPerformed(null);
3077       }
3078     }
3079   }
3080
3081   /*
3082    * (non-Javadoc)
3083    *
3084    * @see
3085    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3086    * event.ActionEvent)
3087    */
3088   @Override
3089   public void hideAllButSelection_actionPerformed(ActionEvent e)
3090   {
3091     toggleHiddenRegions(false, false);
3092     viewport.sendSelection();
3093   }
3094
3095   /*
3096    * (non-Javadoc)
3097    *
3098    * @see
3099    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3100    * .ActionEvent)
3101    */
3102   @Override
3103   public void hideAllSelection_actionPerformed(ActionEvent e)
3104   {
3105     SequenceGroup sg = viewport.getSelectionGroup();
3106     viewport.expandColSelection(sg, false);
3107     viewport.hideAllSelectedSeqs();
3108     viewport.hideSelectedColumns();
3109     alignPanel.updateLayout();
3110     alignPanel.paintAlignment(true, true);
3111     viewport.sendSelection();
3112   }
3113
3114   /*
3115    * (non-Javadoc)
3116    *
3117    * @see
3118    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3119    * ActionEvent)
3120    */
3121   @Override
3122   public void showAllhidden_actionPerformed(ActionEvent e)
3123   {
3124     viewport.showAllHiddenColumns();
3125     viewport.showAllHiddenSeqs();
3126     alignPanel.paintAlignment(true, true);
3127     viewport.sendSelection();
3128   }
3129
3130   @Override
3131   public void hideSelColumns_actionPerformed(ActionEvent e)
3132   {
3133     viewport.hideSelectedColumns();
3134     alignPanel.updateLayout();
3135     alignPanel.paintAlignment(true, true);
3136     viewport.sendSelection();
3137   }
3138
3139   @Override
3140   public void hiddenMarkers_actionPerformed(ActionEvent e)
3141   {
3142     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3143     repaint();
3144   }
3145
3146   /**
3147    * DOCUMENT ME!
3148    *
3149    * @param e
3150    *          DOCUMENT ME!
3151    */
3152   @Override
3153   protected void scaleAbove_actionPerformed(ActionEvent e)
3154   {
3155     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3156     alignPanel.updateLayout();
3157     alignPanel.paintAlignment(true, false);
3158   }
3159
3160   /**
3161    * DOCUMENT ME!
3162    *
3163    * @param e
3164    *          DOCUMENT ME!
3165    */
3166   @Override
3167   protected void scaleLeft_actionPerformed(ActionEvent e)
3168   {
3169     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3170     alignPanel.updateLayout();
3171     alignPanel.paintAlignment(true, false);
3172   }
3173
3174   /**
3175    * DOCUMENT ME!
3176    *
3177    * @param e
3178    *          DOCUMENT ME!
3179    */
3180   @Override
3181   protected void scaleRight_actionPerformed(ActionEvent e)
3182   {
3183     viewport.setScaleRightWrapped(scaleRight.isSelected());
3184     alignPanel.updateLayout();
3185     alignPanel.paintAlignment(true, false);
3186   }
3187
3188   /**
3189    * DOCUMENT ME!
3190    *
3191    * @param e
3192    *          DOCUMENT ME!
3193    */
3194   @Override
3195   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3196   {
3197     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3198     alignPanel.paintAlignment(false, false);
3199   }
3200
3201   /**
3202    * DOCUMENT ME!
3203    *
3204    * @param e
3205    *          DOCUMENT ME!
3206    */
3207   @Override
3208   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3209   {
3210     viewport.setShowText(viewTextMenuItem.isSelected());
3211     alignPanel.paintAlignment(false, false);
3212   }
3213
3214   /**
3215    * DOCUMENT ME!
3216    *
3217    * @param e
3218    *          DOCUMENT ME!
3219    */
3220   @Override
3221   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3222   {
3223     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3224     alignPanel.paintAlignment(false, false);
3225   }
3226
3227   public FeatureSettings featureSettings;
3228
3229   @Override
3230   public FeatureSettingsControllerI getFeatureSettingsUI()
3231   {
3232     return featureSettings;
3233   }
3234
3235   @Override
3236   public void featureSettings_actionPerformed(ActionEvent e)
3237   {
3238     showFeatureSettingsUI();
3239   }
3240
3241   @Override
3242   public FeatureSettingsControllerI showFeatureSettingsUI()
3243   {
3244     if (featureSettings != null)
3245     {
3246       featureSettings.closeOldSettings();
3247       featureSettings = null;
3248     }
3249     if (!showSeqFeatures.isSelected())
3250     {
3251       // make sure features are actually displayed
3252       showSeqFeatures.setSelected(true);
3253       showSeqFeatures_actionPerformed(null);
3254     }
3255     featureSettings = new FeatureSettings(this);
3256     return featureSettings;
3257   }
3258
3259   /**
3260    * Set or clear 'Show Sequence Features'
3261    *
3262    * @param evt
3263    *          DOCUMENT ME!
3264    */
3265   @Override
3266   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3267   {
3268     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3269     alignPanel.paintAlignment(true, true);
3270   }
3271
3272   /**
3273    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3274    * the annotations panel as a whole.
3275    *
3276    * The options to show/hide all annotations should be enabled when the panel
3277    * is shown, and disabled when the panel is hidden.
3278    *
3279    * @param e
3280    */
3281   @Override
3282   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3283   {
3284     final boolean setVisible = annotationPanelMenuItem.isSelected();
3285     viewport.setShowAnnotation(setVisible);
3286     this.showAllSeqAnnotations.setEnabled(setVisible);
3287     this.hideAllSeqAnnotations.setEnabled(setVisible);
3288     this.showAllAlAnnotations.setEnabled(setVisible);
3289     this.hideAllAlAnnotations.setEnabled(setVisible);
3290     alignPanel.updateLayout();
3291   }
3292
3293   @Override
3294   public void alignmentProperties()
3295   {
3296     JEditorPane editPane = new JEditorPane("text/html", "");
3297     editPane.setEditable(false);
3298     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3299             .formatAsHtml();
3300     editPane.setText(
3301             MessageManager.formatMessage("label.html_content", new Object[]
3302             { contents.toString() }));
3303     JInternalFrame frame = new JInternalFrame();
3304     frame.getContentPane().add(new JScrollPane(editPane));
3305
3306     Desktop.addInternalFrame(frame, MessageManager
3307             .formatMessage("label.alignment_properties", new Object[]
3308             { getTitle() }), 500, 400);
3309   }
3310
3311   /**
3312    * DOCUMENT ME!
3313    *
3314    * @param e
3315    *          DOCUMENT ME!
3316    */
3317   @Override
3318   public void overviewMenuItem_actionPerformed(ActionEvent e)
3319   {
3320     if (alignPanel.overviewPanel != null)
3321     {
3322       return;
3323     }
3324
3325     JInternalFrame frame = new JInternalFrame();
3326     final OverviewPanel overview = new OverviewPanel(alignPanel);
3327     frame.setContentPane(overview);
3328     Desktop.addInternalFrame(frame, MessageManager
3329             .formatMessage("label.overview_params", new Object[]
3330             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3331             true, true);
3332     frame.pack();
3333     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3334     frame.addInternalFrameListener(
3335             new javax.swing.event.InternalFrameAdapter()
3336             {
3337               @Override
3338               public void internalFrameClosed(
3339                       javax.swing.event.InternalFrameEvent evt)
3340               {
3341                 overview.dispose();
3342                 alignPanel.setOverviewPanel(null);
3343               };
3344             });
3345     if (getKeyListeners().length > 0)
3346     {
3347       frame.addKeyListener(getKeyListeners()[0]);
3348     }
3349
3350     alignPanel.setOverviewPanel(overview);
3351   }
3352
3353   @Override
3354   public void textColour_actionPerformed()
3355   {
3356     new TextColourChooser().chooseColour(alignPanel, null);
3357   }
3358
3359   /*
3360    * public void covariationColour_actionPerformed() {
3361    * changeColour(new
3362    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3363    * ()[0])); }
3364    */
3365   @Override
3366   public void annotationColour_actionPerformed()
3367   {
3368     new AnnotationColourChooser(viewport, alignPanel);
3369   }
3370
3371   @Override
3372   public void annotationColumn_actionPerformed(ActionEvent e)
3373   {
3374     new AnnotationColumnChooser(viewport, alignPanel);
3375   }
3376
3377   /**
3378    * Action on the user checking or unchecking the option to apply the selected
3379    * colour scheme to all groups. If unchecked, groups may have their own
3380    * independent colour schemes.
3381    *
3382    * @param selected
3383    */
3384   @Override
3385   public void applyToAllGroups_actionPerformed(boolean selected)
3386   {
3387     viewport.setColourAppliesToAllGroups(selected);
3388   }
3389
3390   /**
3391    * Action on user selecting a colour from the colour menu
3392    *
3393    * @param name
3394    *          the name (not the menu item label!) of the colour scheme
3395    */
3396   @Override
3397   public void changeColour_actionPerformed(String name)
3398   {
3399     /*
3400      * 'User Defined' opens a panel to configure or load a
3401      * user-defined colour scheme
3402      */
3403     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3404     {
3405       new UserDefinedColours(alignPanel);
3406       return;
3407     }
3408
3409     /*
3410      * otherwise set the chosen colour scheme (or null for 'None')
3411      */
3412     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3413             viewport, viewport.getAlignment(),
3414             viewport.getHiddenRepSequences());
3415     changeColour(cs);
3416   }
3417
3418   /**
3419    * Actions on setting or changing the alignment colour scheme
3420    *
3421    * @param cs
3422    */
3423   @Override
3424   public void changeColour(ColourSchemeI cs)
3425   {
3426     // TODO: pull up to controller method
3427     ColourMenuHelper.setColourSelected(colourMenu, cs);
3428
3429     viewport.setGlobalColourScheme(cs);
3430
3431     alignPanel.paintAlignment(true, true);
3432   }
3433
3434   /**
3435    * Show the PID threshold slider panel
3436    */
3437   @Override
3438   protected void modifyPID_actionPerformed()
3439   {
3440     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3441             alignPanel.getViewName());
3442     SliderPanel.showPIDSlider();
3443   }
3444
3445   /**
3446    * Show the Conservation slider panel
3447    */
3448   @Override
3449   protected void modifyConservation_actionPerformed()
3450   {
3451     SliderPanel.setConservationSlider(alignPanel,
3452             viewport.getResidueShading(), alignPanel.getViewName());
3453     SliderPanel.showConservationSlider();
3454   }
3455
3456   /**
3457    * Action on selecting or deselecting (Colour) By Conservation
3458    */
3459   @Override
3460   public void conservationMenuItem_actionPerformed(boolean selected)
3461   {
3462     modifyConservation.setEnabled(selected);
3463     viewport.setConservationSelected(selected);
3464     viewport.getResidueShading().setConservationApplied(selected);
3465
3466     changeColour(viewport.getGlobalColourScheme());
3467     if (selected)
3468     {
3469       modifyConservation_actionPerformed();
3470     }
3471     else
3472     {
3473       SliderPanel.hideConservationSlider();
3474     }
3475   }
3476
3477   /**
3478    * Action on selecting or deselecting (Colour) Above PID Threshold
3479    */
3480   @Override
3481   public void abovePIDThreshold_actionPerformed(boolean selected)
3482   {
3483     modifyPID.setEnabled(selected);
3484     viewport.setAbovePIDThreshold(selected);
3485     if (!selected)
3486     {
3487       viewport.getResidueShading().setThreshold(0,
3488               viewport.isIgnoreGapsConsensus());
3489     }
3490
3491     changeColour(viewport.getGlobalColourScheme());
3492     if (selected)
3493     {
3494       modifyPID_actionPerformed();
3495     }
3496     else
3497     {
3498       SliderPanel.hidePIDSlider();
3499     }
3500   }
3501
3502   /**
3503    * DOCUMENT ME!
3504    *
3505    * @param e
3506    *          DOCUMENT ME!
3507    */
3508   @Override
3509   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3510   {
3511     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3512     AlignmentSorter.sortByPID(viewport.getAlignment(),
3513             viewport.getAlignment().getSequenceAt(0));
3514     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3515             viewport.getAlignment()));
3516     alignPanel.paintAlignment(true, false);
3517   }
3518
3519   /**
3520    * DOCUMENT ME!
3521    *
3522    * @param e
3523    *          DOCUMENT ME!
3524    */
3525   @Override
3526   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3527   {
3528     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3529     AlignmentSorter.sortByID(viewport.getAlignment());
3530     addHistoryItem(
3531             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3532     alignPanel.paintAlignment(true, false);
3533   }
3534
3535   /**
3536    * DOCUMENT ME!
3537    *
3538    * @param e
3539    *          DOCUMENT ME!
3540    */
3541   @Override
3542   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3543   {
3544     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3545     AlignmentSorter.sortByLength(viewport.getAlignment());
3546     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3547             viewport.getAlignment()));
3548     alignPanel.paintAlignment(true, false);
3549   }
3550
3551   /**
3552    * DOCUMENT ME!
3553    *
3554    * @param e
3555    *          DOCUMENT ME!
3556    */
3557   @Override
3558   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3559   {
3560     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3561     AlignmentSorter.sortByGroup(viewport.getAlignment());
3562     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3563             viewport.getAlignment()));
3564
3565     alignPanel.paintAlignment(true, false);
3566   }
3567
3568   /**
3569    * DOCUMENT ME!
3570    *
3571    * @param e
3572    *          DOCUMENT ME!
3573    */
3574   @Override
3575   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3576   {
3577     new RedundancyPanel(alignPanel, this);
3578   }
3579
3580   /**
3581    * DOCUMENT ME!
3582    *
3583    * @param e
3584    *          DOCUMENT ME!
3585    */
3586   @Override
3587   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3588   {
3589     if ((viewport.getSelectionGroup() == null)
3590             || (viewport.getSelectionGroup().getSize() < 2))
3591     {
3592       JvOptionPane.showInternalMessageDialog(this,
3593               MessageManager.getString(
3594                       "label.you_must_select_least_two_sequences"),
3595               MessageManager.getString("label.invalid_selection"),
3596               JvOptionPane.WARNING_MESSAGE);
3597     }
3598     else
3599     {
3600       JInternalFrame frame = new JInternalFrame();
3601       frame.setContentPane(new PairwiseAlignPanel(viewport));
3602       Desktop.addInternalFrame(frame,
3603               MessageManager.getString("action.pairwise_alignment"), 600,
3604               500);
3605     }
3606   }
3607
3608   @Override
3609   public void autoCalculate_actionPerformed(ActionEvent e)
3610   {
3611     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3612     if (viewport.autoCalculateConsensus)
3613     {
3614       viewport.firePropertyChange("alignment", null,
3615               viewport.getAlignment().getSequences());
3616     }
3617   }
3618
3619   @Override
3620   public void sortByTreeOption_actionPerformed(ActionEvent e)
3621   {
3622     viewport.sortByTree = sortByTree.isSelected();
3623   }
3624
3625   @Override
3626   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3627   {
3628     viewport.followSelection = listenToViewSelections.isSelected();
3629   }
3630
3631   /**
3632    * Constructs a tree panel and adds it to the desktop
3633    *
3634    * @param type
3635    *          tree type (NJ or AV)
3636    * @param modelName
3637    *          name of score model used to compute the tree
3638    * @param options
3639    *          parameters for the distance or similarity calculation
3640    */
3641   void newTreePanel(String type, String modelName,
3642           SimilarityParamsI options)
3643   {
3644     String frameTitle = "";
3645     TreePanel tp;
3646
3647     boolean onSelection = false;
3648     if (viewport.getSelectionGroup() != null
3649             && viewport.getSelectionGroup().getSize() > 0)
3650     {
3651       SequenceGroup sg = viewport.getSelectionGroup();
3652
3653       /* Decide if the selection is a column region */
3654       for (SequenceI _s : sg.getSequences())
3655       {
3656         if (_s.getLength() < sg.getEndRes())
3657         {
3658           JvOptionPane.showMessageDialog(Desktop.desktop,
3659                   MessageManager.getString(
3660                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3661                   MessageManager.getString(
3662                           "label.sequences_selection_not_aligned"),
3663                   JvOptionPane.WARNING_MESSAGE);
3664
3665           return;
3666         }
3667       }
3668       onSelection = true;
3669     }
3670     else
3671     {
3672       if (viewport.getAlignment().getHeight() < 2)
3673       {
3674         return;
3675       }
3676     }
3677
3678     tp = new TreePanel(alignPanel, type, modelName, options);
3679     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3680
3681     frameTitle += " from ";
3682
3683     if (viewport.getViewName() != null)
3684     {
3685       frameTitle += viewport.getViewName() + " of ";
3686     }
3687
3688     frameTitle += this.title;
3689
3690     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3691   }
3692
3693   /**
3694    * DOCUMENT ME!
3695    *
3696    * @param title
3697    *          DOCUMENT ME!
3698    * @param order
3699    *          DOCUMENT ME!
3700    */
3701   public void addSortByOrderMenuItem(String title,
3702           final AlignmentOrder order)
3703   {
3704     final JMenuItem item = new JMenuItem(MessageManager
3705             .formatMessage("action.by_title_param", new Object[]
3706             { title }));
3707     sort.add(item);
3708     item.addActionListener(new java.awt.event.ActionListener()
3709     {
3710       @Override
3711       public void actionPerformed(ActionEvent e)
3712       {
3713         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3714
3715         // TODO: JBPNote - have to map order entries to curent SequenceI
3716         // pointers
3717         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3718
3719         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3720                 viewport.getAlignment()));
3721
3722         alignPanel.paintAlignment(true, false);
3723       }
3724     });
3725   }
3726
3727   /**
3728    * Add a new sort by annotation score menu item
3729    *
3730    * @param sort
3731    *          the menu to add the option to
3732    * @param scoreLabel
3733    *          the label used to retrieve scores for each sequence on the
3734    *          alignment
3735    */
3736   public void addSortByAnnotScoreMenuItem(JMenu sort,
3737           final String scoreLabel)
3738   {
3739     final JMenuItem item = new JMenuItem(scoreLabel);
3740     sort.add(item);
3741     item.addActionListener(new java.awt.event.ActionListener()
3742     {
3743       @Override
3744       public void actionPerformed(ActionEvent e)
3745       {
3746         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3747         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3748                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3749         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3750                 viewport.getAlignment()));
3751         alignPanel.paintAlignment(true, false);
3752       }
3753     });
3754   }
3755
3756   /**
3757    * last hash for alignment's annotation array - used to minimise cost of
3758    * rebuild.
3759    */
3760   protected int _annotationScoreVectorHash;
3761
3762   /**
3763    * search the alignment and rebuild the sort by annotation score submenu the
3764    * last alignment annotation vector hash is stored to minimize cost of
3765    * rebuilding in subsequence calls.
3766    *
3767    */
3768   @Override
3769   public void buildSortByAnnotationScoresMenu()
3770   {
3771     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3772     {
3773       return;
3774     }
3775
3776     if (viewport.getAlignment().getAlignmentAnnotation()
3777             .hashCode() != _annotationScoreVectorHash)
3778     {
3779       sortByAnnotScore.removeAll();
3780       // almost certainly a quicker way to do this - but we keep it simple
3781       Hashtable scoreSorts = new Hashtable();
3782       AlignmentAnnotation aann[];
3783       for (SequenceI sqa : viewport.getAlignment().getSequences())
3784       {
3785         aann = sqa.getAnnotation();
3786         for (int i = 0; aann != null && i < aann.length; i++)
3787         {
3788           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3789           {
3790             scoreSorts.put(aann[i].label, aann[i].label);
3791           }
3792         }
3793       }
3794       Enumeration labels = scoreSorts.keys();
3795       while (labels.hasMoreElements())
3796       {
3797         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3798                 (String) labels.nextElement());
3799       }
3800       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3801       scoreSorts.clear();
3802
3803       _annotationScoreVectorHash = viewport.getAlignment()
3804               .getAlignmentAnnotation().hashCode();
3805     }
3806   }
3807
3808   /**
3809    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3810    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3811    * call. Listeners are added to remove the menu item when the treePanel is
3812    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3813    * modified.
3814    */
3815   @Override
3816   public void buildTreeSortMenu()
3817   {
3818     sortByTreeMenu.removeAll();
3819
3820     List<Component> comps = PaintRefresher.components
3821             .get(viewport.getSequenceSetId());
3822     List<TreePanel> treePanels = new ArrayList<>();
3823     for (Component comp : comps)
3824     {
3825       if (comp instanceof TreePanel)
3826       {
3827         treePanels.add((TreePanel) comp);
3828       }
3829     }
3830
3831     if (treePanels.size() < 1)
3832     {
3833       sortByTreeMenu.setVisible(false);
3834       return;
3835     }
3836
3837     sortByTreeMenu.setVisible(true);
3838
3839     for (final TreePanel tp : treePanels)
3840     {
3841       final JMenuItem item = new JMenuItem(tp.getTitle());
3842       item.addActionListener(new java.awt.event.ActionListener()
3843       {
3844         @Override
3845         public void actionPerformed(ActionEvent e)
3846         {
3847           tp.sortByTree_actionPerformed();
3848           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3849
3850         }
3851       });
3852
3853       sortByTreeMenu.add(item);
3854     }
3855   }
3856
3857   public boolean sortBy(AlignmentOrder alorder, String undoname)
3858   {
3859     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3860     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3861     if (undoname != null)
3862     {
3863       addHistoryItem(new OrderCommand(undoname, oldOrder,
3864               viewport.getAlignment()));
3865     }
3866     alignPanel.paintAlignment(true, false);
3867     return true;
3868   }
3869
3870   /**
3871    * Work out whether the whole set of sequences or just the selected set will
3872    * be submitted for multiple alignment.
3873    *
3874    */
3875   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3876   {
3877     // Now, check we have enough sequences
3878     AlignmentView msa = null;
3879
3880     if ((viewport.getSelectionGroup() != null)
3881             && (viewport.getSelectionGroup().getSize() > 1))
3882     {
3883       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3884       // some common interface!
3885       /*
3886        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3887        * SequenceI[sz = seqs.getSize(false)];
3888        *
3889        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3890        * seqs.getSequenceAt(i); }
3891        */
3892       msa = viewport.getAlignmentView(true);
3893     }
3894     else if (viewport.getSelectionGroup() != null
3895             && viewport.getSelectionGroup().getSize() == 1)
3896     {
3897       int option = JvOptionPane.showConfirmDialog(this,
3898               MessageManager.getString("warn.oneseq_msainput_selection"),
3899               MessageManager.getString("label.invalid_selection"),
3900               JvOptionPane.OK_CANCEL_OPTION);
3901       if (option == JvOptionPane.OK_OPTION)
3902       {
3903         msa = viewport.getAlignmentView(false);
3904       }
3905     }
3906     else
3907     {
3908       msa = viewport.getAlignmentView(false);
3909     }
3910     return msa;
3911   }
3912
3913   /**
3914    * Decides what is submitted to a secondary structure prediction service: the
3915    * first sequence in the alignment, or in the current selection, or, if the
3916    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3917    * region or the whole alignment. (where the first sequence in the set is the
3918    * one that the prediction will be for).
3919    */
3920   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3921   {
3922     AlignmentView seqs = null;
3923
3924     if ((viewport.getSelectionGroup() != null)
3925             && (viewport.getSelectionGroup().getSize() > 0))
3926     {
3927       seqs = viewport.getAlignmentView(true);
3928     }
3929     else
3930     {
3931       seqs = viewport.getAlignmentView(false);
3932     }
3933     // limit sequences - JBPNote in future - could spawn multiple prediction
3934     // jobs
3935     // TODO: viewport.getAlignment().isAligned is a global state - the local
3936     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3937     if (!viewport.getAlignment().isAligned(false))
3938     {
3939       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3940       // TODO: if seqs.getSequences().length>1 then should really have warned
3941       // user!
3942
3943     }
3944     return seqs;
3945   }
3946
3947   /**
3948    * DOCUMENT ME!
3949    *
3950    * @param e
3951    *          DOCUMENT ME!
3952    */
3953   @Override
3954   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3955   {
3956     // Pick the tree file
3957     JalviewFileChooser chooser = new JalviewFileChooser(
3958             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3959     chooser.setFileView(new JalviewFileView());
3960     chooser.setDialogTitle(
3961             MessageManager.getString("label.select_newick_like_tree_file"));
3962     chooser.setToolTipText(
3963             MessageManager.getString("label.load_tree_file"));
3964
3965     int value = chooser.showOpenDialog(null);
3966
3967     if (value == JalviewFileChooser.APPROVE_OPTION)
3968     {
3969       String filePath = chooser.getSelectedFile().getPath();
3970       Cache.setProperty("LAST_DIRECTORY", filePath);
3971       NewickFile fin = null;
3972       try
3973       {
3974         fin = new NewickFile(filePath, DataSourceType.FILE);
3975         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3976       } catch (Exception ex)
3977       {
3978         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3979                 MessageManager.getString("label.problem_reading_tree_file"),
3980                 JvOptionPane.WARNING_MESSAGE);
3981         ex.printStackTrace();
3982       }
3983       if (fin != null && fin.hasWarningMessage())
3984       {
3985         JvOptionPane.showMessageDialog(Desktop.desktop,
3986                 fin.getWarningMessage(),
3987                 MessageManager
3988                         .getString("label.possible_problem_with_tree_file"),
3989                 JvOptionPane.WARNING_MESSAGE);
3990       }
3991     }
3992   }
3993
3994   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3995   {
3996     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3997   }
3998
3999   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4000           int h, int x, int y)
4001   {
4002     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4003   }
4004
4005   /**
4006    * Add a treeviewer for the tree extracted from a Newick file object to the
4007    * current alignment view
4008    *
4009    * @param nf
4010    *          the tree
4011    * @param title
4012    *          tree viewer title
4013    * @param input
4014    *          Associated alignment input data (or null)
4015    * @param w
4016    *          width
4017    * @param h
4018    *          height
4019    * @param x
4020    *          position
4021    * @param y
4022    *          position
4023    * @return TreePanel handle
4024    */
4025   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4026           AlignmentView input, int w, int h, int x, int y)
4027   {
4028     TreePanel tp = null;
4029
4030     try
4031     {
4032       nf.parse();
4033
4034       if (nf.getTree() != null)
4035       {
4036         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4037
4038         tp.setSize(w, h);
4039
4040         if (x > 0 && y > 0)
4041         {
4042           tp.setLocation(x, y);
4043         }
4044
4045         Desktop.addInternalFrame(tp, treeTitle, w, h);
4046       }
4047     } catch (Exception ex)
4048     {
4049       ex.printStackTrace();
4050     }
4051
4052     return tp;
4053   }
4054
4055   private boolean buildingMenu = false;
4056
4057   /**
4058    * Generates menu items and listener event actions for web service clients
4059    *
4060    */
4061   public void BuildWebServiceMenu()
4062   {
4063     while (buildingMenu)
4064     {
4065       try
4066       {
4067         System.err.println("Waiting for building menu to finish.");
4068         Thread.sleep(10);
4069       } catch (Exception e)
4070       {
4071       }
4072     }
4073     final AlignFrame me = this;
4074     buildingMenu = true;
4075     new Thread(new Runnable()
4076     {
4077       @Override
4078       public void run()
4079       {
4080         final List<JMenuItem> legacyItems = new ArrayList<>();
4081         try
4082         {
4083           // System.err.println("Building ws menu again "
4084           // + Thread.currentThread());
4085           // TODO: add support for context dependent disabling of services based
4086           // on
4087           // alignment and current selection
4088           // TODO: add additional serviceHandle parameter to specify abstract
4089           // handler
4090           // class independently of AbstractName
4091           // TODO: add in rediscovery GUI function to restart discoverer
4092           // TODO: group services by location as well as function and/or
4093           // introduce
4094           // object broker mechanism.
4095           final Vector<JMenu> wsmenu = new Vector<>();
4096           final IProgressIndicator af = me;
4097
4098           /*
4099            * do not i18n these strings - they are hard-coded in class
4100            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4101            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4102            */
4103           final JMenu msawsmenu = new JMenu("Alignment");
4104           final JMenu secstrmenu = new JMenu(
4105                   "Secondary Structure Prediction");
4106           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4107           final JMenu analymenu = new JMenu("Analysis");
4108           final JMenu dismenu = new JMenu("Protein Disorder");
4109           // JAL-940 - only show secondary structure prediction services from
4110           // the legacy server
4111           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4112               // &&
4113           Discoverer.services != null && (Discoverer.services.size() > 0))
4114           {
4115             // TODO: refactor to allow list of AbstractName/Handler bindings to
4116             // be
4117             // stored or retrieved from elsewhere
4118             // No MSAWS used any more:
4119             // Vector msaws = null; // (Vector)
4120             // Discoverer.services.get("MsaWS");
4121             Vector secstrpr = (Vector) Discoverer.services
4122                     .get("SecStrPred");
4123             if (secstrpr != null)
4124             {
4125               // Add any secondary structure prediction services
4126               for (int i = 0, j = secstrpr.size(); i < j; i++)
4127               {
4128                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4129                         .get(i);
4130                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4131                         .getServiceClient(sh);
4132                 int p = secstrmenu.getItemCount();
4133                 impl.attachWSMenuEntry(secstrmenu, me);
4134                 int q = secstrmenu.getItemCount();
4135                 for (int litm = p; litm < q; litm++)
4136                 {
4137                   legacyItems.add(secstrmenu.getItem(litm));
4138                 }
4139               }
4140             }
4141           }
4142
4143           // Add all submenus in the order they should appear on the web
4144           // services menu
4145           wsmenu.add(msawsmenu);
4146           wsmenu.add(secstrmenu);
4147           wsmenu.add(dismenu);
4148           wsmenu.add(analymenu);
4149           // No search services yet
4150           // wsmenu.add(seqsrchmenu);
4151
4152           javax.swing.SwingUtilities.invokeLater(new Runnable()
4153           {
4154             @Override
4155             public void run()
4156             {
4157               try
4158               {
4159                 webService.removeAll();
4160                 // first, add discovered services onto the webservices menu
4161                 if (wsmenu.size() > 0)
4162                 {
4163                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4164                   {
4165                     webService.add(wsmenu.get(i));
4166                   }
4167                 }
4168                 else
4169                 {
4170                   webService.add(me.webServiceNoServices);
4171                 }
4172                 // TODO: move into separate menu builder class.
4173                 boolean new_sspred = false;
4174                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4175                 {
4176                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4177                   if (jws2servs != null)
4178                   {
4179                     if (jws2servs.hasServices())
4180                     {
4181                       jws2servs.attachWSMenuEntry(webService, me);
4182                       for (Jws2Instance sv : jws2servs.getServices())
4183                       {
4184                         if (sv.description.toLowerCase().contains("jpred"))
4185                         {
4186                           for (JMenuItem jmi : legacyItems)
4187                           {
4188                             jmi.setVisible(false);
4189                           }
4190                         }
4191                       }
4192
4193                     }
4194                     if (jws2servs.isRunning())
4195                     {
4196                       JMenuItem tm = new JMenuItem(
4197                               "Still discovering JABA Services");
4198                       tm.setEnabled(false);
4199                       webService.add(tm);
4200                     }
4201                   }
4202                 }
4203                 build_urlServiceMenu(me.webService);
4204                 build_fetchdbmenu(webService);
4205                 for (JMenu item : wsmenu)
4206                 {
4207                   if (item.getItemCount() == 0)
4208                   {
4209                     item.setEnabled(false);
4210                   }
4211                   else
4212                   {
4213                     item.setEnabled(true);
4214                   }
4215                 }
4216               } catch (Exception e)
4217               {
4218                 Cache.log.debug(
4219                         "Exception during web service menu building process.",
4220                         e);
4221               }
4222             }
4223           });
4224         } catch (Exception e)
4225         {
4226         }
4227         buildingMenu = false;
4228       }
4229     }).start();
4230
4231   }
4232
4233   /**
4234    * construct any groupURL type service menu entries.
4235    *
4236    * @param webService
4237    */
4238   private void build_urlServiceMenu(JMenu webService)
4239   {
4240     // TODO: remove this code when 2.7 is released
4241     // DEBUG - alignmentView
4242     /*
4243      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4244      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4245      *
4246      * @Override public void actionPerformed(ActionEvent e) {
4247      * jalview.datamodel.AlignmentView
4248      * .testSelectionViews(af.viewport.getAlignment(),
4249      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4250      *
4251      * }); webService.add(testAlView);
4252      */
4253     // TODO: refactor to RestClient discoverer and merge menu entries for
4254     // rest-style services with other types of analysis/calculation service
4255     // SHmmr test client - still being implemented.
4256     // DEBUG - alignmentView
4257
4258     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4259             .getRestClients())
4260     {
4261       client.attachWSMenuEntry(
4262               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4263               this);
4264     }
4265   }
4266
4267   /**
4268    * Searches the alignment sequences for xRefs and builds the Show
4269    * Cross-References menu (formerly called Show Products), with database
4270    * sources for which cross-references are found (protein sources for a
4271    * nucleotide alignment and vice versa)
4272    *
4273    * @return true if Show Cross-references menu should be enabled
4274    */
4275   public boolean canShowProducts()
4276   {
4277     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4278     AlignmentI dataset = viewport.getAlignment().getDataset();
4279
4280     showProducts.removeAll();
4281     final boolean dna = viewport.getAlignment().isNucleotide();
4282
4283     if (seqs == null || seqs.length == 0)
4284     {
4285       // nothing to see here.
4286       return false;
4287     }
4288
4289     boolean showp = false;
4290     try
4291     {
4292       List<String> ptypes = new CrossRef(seqs, dataset)
4293               .findXrefSourcesForSequences(dna);
4294
4295       for (final String source : ptypes)
4296       {
4297         showp = true;
4298         final AlignFrame af = this;
4299         JMenuItem xtype = new JMenuItem(source);
4300         xtype.addActionListener(new ActionListener()
4301         {
4302           @Override
4303           public void actionPerformed(ActionEvent e)
4304           {
4305             showProductsFor(af.viewport.getSequenceSelection(), dna,
4306                     source);
4307           }
4308         });
4309         showProducts.add(xtype);
4310       }
4311       showProducts.setVisible(showp);
4312       showProducts.setEnabled(showp);
4313     } catch (Exception e)
4314     {
4315       Cache.log.warn(
4316               "canShowProducts threw an exception - please report to help@jalview.org",
4317               e);
4318       return false;
4319     }
4320     return showp;
4321   }
4322
4323   /**
4324    * Finds and displays cross-references for the selected sequences (protein
4325    * products for nucleotide sequences, dna coding sequences for peptides).
4326    *
4327    * @param sel
4328    *          the sequences to show cross-references for
4329    * @param dna
4330    *          true if from a nucleotide alignment (so showing proteins)
4331    * @param source
4332    *          the database to show cross-references for
4333    */
4334   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4335           final String source)
4336   {
4337     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4338             .start();
4339   }
4340
4341   /**
4342    * Construct and display a new frame containing the translation of this
4343    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4344    */
4345   @Override
4346   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4347   {
4348     AlignmentI al = null;
4349     try
4350     {
4351       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4352
4353       al = dna.translateCdna(codeTable);
4354     } catch (Exception ex)
4355     {
4356       jalview.bin.Cache.log.error(
4357               "Exception during translation. Please report this !", ex);
4358       final String msg = MessageManager.getString(
4359               "label.error_when_translating_sequences_submit_bug_report");
4360       final String errorTitle = MessageManager
4361               .getString("label.implementation_error")
4362               + MessageManager.getString("label.translation_failed");
4363       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4364               JvOptionPane.ERROR_MESSAGE);
4365       return;
4366     }
4367     if (al == null || al.getHeight() == 0)
4368     {
4369       final String msg = MessageManager.getString(
4370               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4371       final String errorTitle = MessageManager
4372               .getString("label.translation_failed");
4373       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4374               JvOptionPane.WARNING_MESSAGE);
4375     }
4376     else
4377     {
4378       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4379       af.setFileFormat(this.currentFileFormat);
4380       final String newTitle = MessageManager
4381               .formatMessage("label.translation_of_params", new Object[]
4382               { this.getTitle(), codeTable.getId() });
4383       af.setTitle(newTitle);
4384       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4385       {
4386         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4387         viewport.openSplitFrame(af, new Alignment(seqs));
4388       }
4389       else
4390       {
4391         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4392                 DEFAULT_HEIGHT);
4393       }
4394     }
4395   }
4396
4397   /**
4398    * Set the file format
4399    *
4400    * @param format
4401    */
4402   public void setFileFormat(FileFormatI format)
4403   {
4404     this.currentFileFormat = format;
4405   }
4406
4407   /**
4408    * Try to load a features file onto the alignment.
4409    *
4410    * @param file
4411    *          contents or path to retrieve file
4412    * @param sourceType
4413    *          access mode of file (see jalview.io.AlignFile)
4414    * @return true if features file was parsed correctly.
4415    */
4416   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4417   {
4418     return avc.parseFeaturesFile(file, sourceType,
4419             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4420
4421   }
4422
4423   @Override
4424   public void refreshFeatureUI(boolean enableIfNecessary)
4425   {
4426     // note - currently this is only still here rather than in the controller
4427     // because of the featureSettings hard reference that is yet to be
4428     // abstracted
4429     if (enableIfNecessary)
4430     {
4431       viewport.setShowSequenceFeatures(true);
4432       showSeqFeatures.setSelected(true);
4433     }
4434
4435   }
4436
4437   @Override
4438   public void dragEnter(DropTargetDragEvent evt)
4439   {
4440   }
4441
4442   @Override
4443   public void dragExit(DropTargetEvent evt)
4444   {
4445   }
4446
4447   @Override
4448   public void dragOver(DropTargetDragEvent evt)
4449   {
4450   }
4451
4452   @Override
4453   public void dropActionChanged(DropTargetDragEvent evt)
4454   {
4455   }
4456
4457   @Override
4458   public void drop(DropTargetDropEvent evt)
4459   {
4460     // JAL-1552 - acceptDrop required before getTransferable call for
4461     // Java's Transferable for native dnd
4462     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4463     Transferable t = evt.getTransferable();
4464     final AlignFrame thisaf = this;
4465     final List<String> files = new ArrayList<>();
4466     List<DataSourceType> protocols = new ArrayList<>();
4467
4468     try
4469     {
4470       Desktop.transferFromDropTarget(files, protocols, evt, t);
4471     } catch (Exception e)
4472     {
4473       e.printStackTrace();
4474     }
4475     if (files != null)
4476     {
4477       new Thread(new Runnable()
4478       {
4479         @Override
4480         public void run()
4481         {
4482           try
4483           {
4484             // check to see if any of these files have names matching sequences
4485             // in
4486             // the alignment
4487             SequenceIdMatcher idm = new SequenceIdMatcher(
4488                     viewport.getAlignment().getSequencesArray());
4489             /**
4490              * Object[] { String,SequenceI}
4491              */
4492             ArrayList<Object[]> filesmatched = new ArrayList<>();
4493             ArrayList<String> filesnotmatched = new ArrayList<>();
4494             for (int i = 0; i < files.size(); i++)
4495             {
4496               String file = files.get(i).toString();
4497               String pdbfn = "";
4498               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4499               if (protocol == DataSourceType.FILE)
4500               {
4501                 File fl = new File(file);
4502                 pdbfn = fl.getName();
4503               }
4504               else if (protocol == DataSourceType.URL)
4505               {
4506                 URL url = new URL(file);
4507                 pdbfn = url.getFile();
4508               }
4509               if (pdbfn.length() > 0)
4510               {
4511                 // attempt to find a match in the alignment
4512                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4513                 int l = 0, c = pdbfn.indexOf(".");
4514                 while (mtch == null && c != -1)
4515                 {
4516                   do
4517                   {
4518                     l = c;
4519                   } while ((c = pdbfn.indexOf(".", l)) > l);
4520                   if (l > -1)
4521                   {
4522                     pdbfn = pdbfn.substring(0, l);
4523                   }
4524                   mtch = idm.findAllIdMatches(pdbfn);
4525                 }
4526                 if (mtch != null)
4527                 {
4528                   FileFormatI type = null;
4529                   try
4530                   {
4531                     type = new IdentifyFile().identify(file, protocol);
4532                   } catch (Exception ex)
4533                   {
4534                     type = null;
4535                   }
4536                   if (type != null && type.isStructureFile())
4537                   {
4538                     filesmatched.add(new Object[] { file, protocol, mtch });
4539                     continue;
4540                   }
4541                 }
4542                 // File wasn't named like one of the sequences or wasn't a PDB
4543                 // file.
4544                 filesnotmatched.add(file);
4545               }
4546             }
4547             int assocfiles = 0;
4548             if (filesmatched.size() > 0)
4549             {
4550               boolean autoAssociate = Cache
4551                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4552               if (!autoAssociate)
4553               {
4554                 String msg = MessageManager.formatMessage(
4555                         "label.automatically_associate_structure_files_with_sequences_same_name",
4556                         new Object[]
4557                         { Integer.valueOf(filesmatched.size())
4558                                 .toString() });
4559                 String ttl = MessageManager.getString(
4560                         "label.automatically_associate_structure_files_by_name");
4561                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4562                         ttl, JvOptionPane.YES_NO_OPTION);
4563                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4564               }
4565               if (autoAssociate)
4566               {
4567                 for (Object[] fm : filesmatched)
4568                 {
4569                   // try and associate
4570                   // TODO: may want to set a standard ID naming formalism for
4571                   // associating PDB files which have no IDs.
4572                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4573                   {
4574                     PDBEntry pe = new AssociatePdbFileWithSeq()
4575                             .associatePdbWithSeq((String) fm[0],
4576                                     (DataSourceType) fm[1], toassoc, false,
4577                                     Desktop.instance);
4578                     if (pe != null)
4579                     {
4580                       System.err.println("Associated file : "
4581                               + ((String) fm[0]) + " with "
4582                               + toassoc.getDisplayId(true));
4583                       assocfiles++;
4584                     }
4585                   }
4586                   // TODO: do we need to update overview ? only if features are
4587                   // shown I guess
4588                   alignPanel.paintAlignment(true, false);
4589                 }
4590               }
4591               else
4592               {
4593                 /*
4594                  * add declined structures as sequences
4595                  */
4596                 for (Object[] o : filesmatched)
4597                 {
4598                   filesnotmatched.add((String) o[0]);
4599                 }
4600               }
4601             }
4602             if (filesnotmatched.size() > 0)
4603             {
4604               if (assocfiles > 0 && (Cache.getDefault(
4605                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4606                       || JvOptionPane.showConfirmDialog(thisaf,
4607                               "<html>" + MessageManager.formatMessage(
4608                                       "label.ignore_unmatched_dropped_files_info",
4609                                       new Object[]
4610                                       { Integer.valueOf(
4611                                               filesnotmatched.size())
4612                                               .toString() })
4613                                       + "</html>",
4614                               MessageManager.getString(
4615                                       "label.ignore_unmatched_dropped_files"),
4616                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4617               {
4618                 return;
4619               }
4620               for (String fn : filesnotmatched)
4621               {
4622                 loadJalviewDataFile(fn, null, null, null);
4623               }
4624
4625             }
4626           } catch (Exception ex)
4627           {
4628             ex.printStackTrace();
4629           }
4630         }
4631       }).start();
4632     }
4633   }
4634
4635   /**
4636    * Attempt to load a "dropped" file or URL string, by testing in turn for
4637    * <ul>
4638    * <li>an Annotation file</li>
4639    * <li>a JNet file</li>
4640    * <li>a features file</li>
4641    * <li>else try to interpret as an alignment file</li>
4642    * </ul>
4643    *
4644    * @param file
4645    *          either a filename or a URL string.
4646    */
4647   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4648           FileFormatI format, SequenceI assocSeq)
4649   {
4650     try
4651     {
4652       if (sourceType == null)
4653       {
4654         sourceType = FormatAdapter.checkProtocol(file);
4655       }
4656       // if the file isn't identified, or not positively identified as some
4657       // other filetype (PFAM is default unidentified alignment file type) then
4658       // try to parse as annotation.
4659       boolean isAnnotation = (format == null
4660               || FileFormat.Pfam.equals(format))
4661                       ? new AnnotationFile().annotateAlignmentView(viewport,
4662                               file, sourceType)
4663                       : false;
4664
4665       if (!isAnnotation)
4666       {
4667         // first see if its a T-COFFEE score file
4668         TCoffeeScoreFile tcf = null;
4669         try
4670         {
4671           tcf = new TCoffeeScoreFile(file, sourceType);
4672           if (tcf.isValid())
4673           {
4674             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4675             {
4676               buildColourMenu();
4677               changeColour(
4678                       new TCoffeeColourScheme(viewport.getAlignment()));
4679               isAnnotation = true;
4680               statusBar.setText(MessageManager.getString(
4681                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4682             }
4683             else
4684             {
4685               // some problem - if no warning its probable that the ID matching
4686               // process didn't work
4687               JvOptionPane.showMessageDialog(Desktop.desktop,
4688                       tcf.getWarningMessage() == null
4689                               ? MessageManager.getString(
4690                                       "label.check_file_matches_sequence_ids_alignment")
4691                               : tcf.getWarningMessage(),
4692                       MessageManager.getString(
4693                               "label.problem_reading_tcoffee_score_file"),
4694                       JvOptionPane.WARNING_MESSAGE);
4695             }
4696           }
4697           else
4698           {
4699             tcf = null;
4700           }
4701         } catch (Exception x)
4702         {
4703           Cache.log.debug(
4704                   "Exception when processing data source as T-COFFEE score file",
4705                   x);
4706           tcf = null;
4707         }
4708         if (tcf == null)
4709         {
4710           // try to see if its a JNet 'concise' style annotation file *before*
4711           // we
4712           // try to parse it as a features file
4713           if (format == null)
4714           {
4715             format = new IdentifyFile().identify(file, sourceType);
4716           }
4717           if (FileFormat.ScoreMatrix == format)
4718           {
4719             ScoreMatrixFile sm = new ScoreMatrixFile(
4720                     new FileParse(file, sourceType));
4721             sm.parse();
4722             // todo: i18n this message
4723             statusBar.setText(MessageManager.formatMessage(
4724                     "label.successfully_loaded_matrix",
4725                     sm.getMatrixName()));
4726           }
4727           else if (FileFormat.Jnet.equals(format))
4728           {
4729             JPredFile predictions = new JPredFile(file, sourceType);
4730             new JnetAnnotationMaker();
4731             JnetAnnotationMaker.add_annotation(predictions,
4732                     viewport.getAlignment(), 0, false);
4733             viewport.getAlignment().setupJPredAlignment();
4734             isAnnotation = true;
4735           }
4736           // else if (IdentifyFile.FeaturesFile.equals(format))
4737           else if (FileFormat.Features.equals(format))
4738           {
4739             if (parseFeaturesFile(file, sourceType))
4740             {
4741               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4742               if (splitFrame != null)
4743               {
4744                 splitFrame.repaint();
4745               }
4746               else
4747               {
4748                 alignPanel.paintAlignment(true, true);
4749               }
4750             }
4751           }
4752           else
4753           {
4754             new FileLoader().LoadFile(viewport, file, sourceType, format);
4755           }
4756         }
4757       }
4758       if (isAnnotation)
4759       {
4760
4761         alignPanel.adjustAnnotationHeight();
4762         viewport.updateSequenceIdColours();
4763         buildSortByAnnotationScoresMenu();
4764         alignPanel.paintAlignment(true, true);
4765       }
4766     } catch (Exception ex)
4767     {
4768       ex.printStackTrace();
4769     } catch (OutOfMemoryError oom)
4770     {
4771       try
4772       {
4773         System.gc();
4774       } catch (Exception x)
4775       {
4776       }
4777       new OOMWarning(
4778               "loading data "
4779                       + (sourceType != null
4780                               ? (sourceType == DataSourceType.PASTE
4781                                       ? "from clipboard."
4782                                       : "using " + sourceType + " from "
4783                                               + file)
4784                               : ".")
4785                       + (format != null
4786                               ? "(parsing as '" + format + "' file)"
4787                               : ""),
4788               oom, Desktop.desktop);
4789     }
4790   }
4791
4792   /**
4793    * Method invoked by the ChangeListener on the tabbed pane, in other words
4794    * when a different tabbed pane is selected by the user or programmatically.
4795    */
4796   @Override
4797   public void tabSelectionChanged(int index)
4798   {
4799     if (index > -1)
4800     {
4801       alignPanel = alignPanels.get(index);
4802       viewport = alignPanel.av;
4803       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4804       setMenusFromViewport(viewport);
4805       if (featureSettings != null && featureSettings.isOpen()
4806               && featureSettings.fr.getViewport() != viewport)
4807       {
4808         if (viewport.isShowSequenceFeatures())
4809         {
4810           // refresh the featureSettings to reflect UI change
4811           showFeatureSettingsUI();
4812         }
4813         else
4814         {
4815           // close feature settings for this view.
4816           featureSettings.close();
4817         }
4818       }
4819
4820     }
4821
4822     /*
4823      * 'focus' any colour slider that is open to the selected viewport
4824      */
4825     if (viewport.getConservationSelected())
4826     {
4827       SliderPanel.setConservationSlider(alignPanel,
4828               viewport.getResidueShading(), alignPanel.getViewName());
4829     }
4830     else
4831     {
4832       SliderPanel.hideConservationSlider();
4833     }
4834     if (viewport.getAbovePIDThreshold())
4835     {
4836       SliderPanel.setPIDSliderSource(alignPanel,
4837               viewport.getResidueShading(), alignPanel.getViewName());
4838     }
4839     else
4840     {
4841       SliderPanel.hidePIDSlider();
4842     }
4843
4844     /*
4845      * If there is a frame linked to this one in a SplitPane, switch it to the
4846      * same view tab index. No infinite recursion of calls should happen, since
4847      * tabSelectionChanged() should not get invoked on setting the selected
4848      * index to an unchanged value. Guard against setting an invalid index
4849      * before the new view peer tab has been created.
4850      */
4851     final AlignViewportI peer = viewport.getCodingComplement();
4852     if (peer != null)
4853     {
4854       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4855               .getAlignPanel().alignFrame;
4856       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4857       {
4858         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4859       }
4860     }
4861   }
4862
4863   /**
4864    * On right mouse click on view tab, prompt for and set new view name.
4865    */
4866   @Override
4867   public void tabbedPane_mousePressed(MouseEvent e)
4868   {
4869     if (e.isPopupTrigger())
4870     {
4871       String msg = MessageManager.getString("label.enter_view_name");
4872       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4873               JvOptionPane.QUESTION_MESSAGE);
4874
4875       if (reply != null)
4876       {
4877         viewport.setViewName(reply);
4878         // TODO warn if reply is in getExistingViewNames()?
4879         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4880       }
4881     }
4882   }
4883
4884   public AlignViewport getCurrentView()
4885   {
4886     return viewport;
4887   }
4888
4889   /**
4890    * Open the dialog for regex description parsing.
4891    */
4892   @Override
4893   protected void extractScores_actionPerformed(ActionEvent e)
4894   {
4895     ParseProperties pp = new jalview.analysis.ParseProperties(
4896             viewport.getAlignment());
4897     // TODO: verify regex and introduce GUI dialog for version 2.5
4898     // if (pp.getScoresFromDescription("col", "score column ",
4899     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4900     // true)>0)
4901     if (pp.getScoresFromDescription("description column",
4902             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4903     {
4904       buildSortByAnnotationScoresMenu();
4905     }
4906   }
4907
4908   /*
4909    * (non-Javadoc)
4910    *
4911    * @see
4912    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4913    * )
4914    */
4915   @Override
4916   protected void showDbRefs_actionPerformed(ActionEvent e)
4917   {
4918     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4919   }
4920
4921   /*
4922    * (non-Javadoc)
4923    *
4924    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4925    * ActionEvent)
4926    */
4927   @Override
4928   protected void showNpFeats_actionPerformed(ActionEvent e)
4929   {
4930     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4931   }
4932
4933   /**
4934    * find the viewport amongst the tabs in this alignment frame and close that
4935    * tab
4936    *
4937    * @param av
4938    */
4939   public boolean closeView(AlignViewportI av)
4940   {
4941     if (viewport == av)
4942     {
4943       this.closeMenuItem_actionPerformed(false);
4944       return true;
4945     }
4946     Component[] comp = tabbedPane.getComponents();
4947     for (int i = 0; comp != null && i < comp.length; i++)
4948     {
4949       if (comp[i] instanceof AlignmentPanel)
4950       {
4951         if (((AlignmentPanel) comp[i]).av == av)
4952         {
4953           // close the view.
4954           closeView((AlignmentPanel) comp[i]);
4955           return true;
4956         }
4957       }
4958     }
4959     return false;
4960   }
4961
4962   protected void build_fetchdbmenu(JMenu webService)
4963   {
4964     // Temporary hack - DBRef Fetcher always top level ws entry.
4965     // TODO We probably want to store a sequence database checklist in
4966     // preferences and have checkboxes.. rather than individual sources selected
4967     // here
4968     final JMenu rfetch = new JMenu(
4969             MessageManager.getString("action.fetch_db_references"));
4970     rfetch.setToolTipText(MessageManager.getString(
4971             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4972     webService.add(rfetch);
4973
4974     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4975             MessageManager.getString("option.trim_retrieved_seqs"));
4976     trimrs.setToolTipText(
4977             MessageManager.getString("label.trim_retrieved_sequences"));
4978     trimrs.setSelected(
4979             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4980     trimrs.addActionListener(new ActionListener()
4981     {
4982       @Override
4983       public void actionPerformed(ActionEvent e)
4984       {
4985         trimrs.setSelected(trimrs.isSelected());
4986         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4987                 Boolean.valueOf(trimrs.isSelected()).toString());
4988       };
4989     });
4990     rfetch.add(trimrs);
4991     JMenuItem fetchr = new JMenuItem(
4992             MessageManager.getString("label.standard_databases"));
4993     fetchr.setToolTipText(
4994             MessageManager.getString("label.fetch_embl_uniprot"));
4995     fetchr.addActionListener(new ActionListener()
4996     {
4997
4998       @Override
4999       public void actionPerformed(ActionEvent e)
5000       {
5001         new Thread(new Runnable()
5002         {
5003           @Override
5004           public void run()
5005           {
5006             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5007                     .getAlignment().isNucleotide();
5008             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5009                     alignPanel.av.getSequenceSelection(),
5010                     alignPanel.alignFrame, null,
5011                     alignPanel.alignFrame.featureSettings, isNucleotide);
5012             dbRefFetcher.addListener(new FetchFinishedListenerI()
5013             {
5014               @Override
5015               public void finished()
5016               {
5017
5018                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5019                         .getFeatureSettingsModels())
5020                 {
5021
5022                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5023                 }
5024                 AlignFrame.this.setMenusForViewport();
5025               }
5026             });
5027             dbRefFetcher.fetchDBRefs(false);
5028           }
5029         }).start();
5030
5031       }
5032
5033     });
5034     rfetch.add(fetchr);
5035     final AlignFrame me = this;
5036     new Thread(new Runnable()
5037     {
5038       @Override
5039       public void run()
5040       {
5041         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5042                 .getSequenceFetcherSingleton(me);
5043         javax.swing.SwingUtilities.invokeLater(new Runnable()
5044         {
5045           @Override
5046           public void run()
5047           {
5048             String[] dbclasses = sf.getOrderedSupportedSources();
5049             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5050             // jalview.util.QuickSort.sort(otherdb, otherdb);
5051             List<DbSourceProxy> otherdb;
5052             JMenu dfetch = new JMenu();
5053             JMenu ifetch = new JMenu();
5054             JMenuItem fetchr = null;
5055             int comp = 0, icomp = 0, mcomp = 15;
5056             String mname = null;
5057             int dbi = 0;
5058             for (String dbclass : dbclasses)
5059             {
5060               otherdb = sf.getSourceProxy(dbclass);
5061               // add a single entry for this class, or submenu allowing 'fetch
5062               // all' or pick one
5063               if (otherdb == null || otherdb.size() < 1)
5064               {
5065                 continue;
5066               }
5067               // List<DbSourceProxy> dbs=otherdb;
5068               // otherdb=new ArrayList<DbSourceProxy>();
5069               // for (DbSourceProxy db:dbs)
5070               // {
5071               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5072               // }
5073               if (mname == null)
5074               {
5075                 mname = "From " + dbclass;
5076               }
5077               if (otherdb.size() == 1)
5078               {
5079                 final DbSourceProxy[] dassource = otherdb
5080                         .toArray(new DbSourceProxy[0]);
5081                 DbSourceProxy src = otherdb.get(0);
5082                 fetchr = new JMenuItem(src.getDbSource());
5083                 fetchr.addActionListener(new ActionListener()
5084                 {
5085
5086                   @Override
5087                   public void actionPerformed(ActionEvent e)
5088                   {
5089                     new Thread(new Runnable()
5090                     {
5091
5092                       @Override
5093                       public void run()
5094                       {
5095                         boolean isNucleotide = alignPanel.alignFrame
5096                                 .getViewport().getAlignment()
5097                                 .isNucleotide();
5098                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5099                                 alignPanel.av.getSequenceSelection(),
5100                                 alignPanel.alignFrame, dassource,
5101                                 alignPanel.alignFrame.featureSettings,
5102                                 isNucleotide);
5103                         dbRefFetcher
5104                                 .addListener(new FetchFinishedListenerI()
5105                                 {
5106                                   @Override
5107                                   public void finished()
5108                                   {
5109                                     FeatureSettingsModelI srcSettings = dassource[0]
5110                                             .getFeatureColourScheme();
5111                                     alignPanel.av.mergeFeaturesStyle(
5112                                             srcSettings);
5113                                     AlignFrame.this.setMenusForViewport();
5114                                   }
5115                                 });
5116                         dbRefFetcher.fetchDBRefs(false);
5117                       }
5118                     }).start();
5119                   }
5120
5121                 });
5122                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5123                         MessageManager.formatMessage(
5124                                 "label.fetch_retrieve_from", new Object[]
5125                                 { src.getDbName() })));
5126                 dfetch.add(fetchr);
5127                 comp++;
5128               }
5129               else
5130               {
5131                 final DbSourceProxy[] dassource = otherdb
5132                         .toArray(new DbSourceProxy[0]);
5133                 // fetch all entry
5134                 DbSourceProxy src = otherdb.get(0);
5135                 fetchr = new JMenuItem(MessageManager
5136                         .formatMessage("label.fetch_all_param", new Object[]
5137                         { src.getDbSource() }));
5138                 fetchr.addActionListener(new ActionListener()
5139                 {
5140                   @Override
5141                   public void actionPerformed(ActionEvent e)
5142                   {
5143                     new Thread(new Runnable()
5144                     {
5145
5146                       @Override
5147                       public void run()
5148                       {
5149                         boolean isNucleotide = alignPanel.alignFrame
5150                                 .getViewport().getAlignment()
5151                                 .isNucleotide();
5152                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5153                                 alignPanel.av.getSequenceSelection(),
5154                                 alignPanel.alignFrame, dassource,
5155                                 alignPanel.alignFrame.featureSettings,
5156                                 isNucleotide);
5157                         dbRefFetcher
5158                                 .addListener(new FetchFinishedListenerI()
5159                                 {
5160                                   @Override
5161                                   public void finished()
5162                                   {
5163                                     AlignFrame.this.setMenusForViewport();
5164                                   }
5165                                 });
5166                         dbRefFetcher.fetchDBRefs(false);
5167                       }
5168                     }).start();
5169                   }
5170                 });
5171
5172                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5173                         MessageManager.formatMessage(
5174                                 "label.fetch_retrieve_from_all_sources",
5175                                 new Object[]
5176                                 { Integer.valueOf(otherdb.size())
5177                                         .toString(),
5178                                     src.getDbSource(), src.getDbName() })));
5179                 dfetch.add(fetchr);
5180                 comp++;
5181                 // and then build the rest of the individual menus
5182                 ifetch = new JMenu(MessageManager.formatMessage(
5183                         "label.source_from_db_source", new Object[]
5184                         { src.getDbSource() }));
5185                 icomp = 0;
5186                 String imname = null;
5187                 int i = 0;
5188                 for (DbSourceProxy sproxy : otherdb)
5189                 {
5190                   String dbname = sproxy.getDbName();
5191                   String sname = dbname.length() > 5
5192                           ? dbname.substring(0, 5) + "..."
5193                           : dbname;
5194                   String msname = dbname.length() > 10
5195                           ? dbname.substring(0, 10) + "..."
5196                           : dbname;
5197                   if (imname == null)
5198                   {
5199                     imname = MessageManager
5200                             .formatMessage("label.from_msname", new Object[]
5201                             { sname });
5202                   }
5203                   fetchr = new JMenuItem(msname);
5204                   final DbSourceProxy[] dassrc = { sproxy };
5205                   fetchr.addActionListener(new ActionListener()
5206                   {
5207
5208                     @Override
5209                     public void actionPerformed(ActionEvent e)
5210                     {
5211                       new Thread(new Runnable()
5212                       {
5213
5214                         @Override
5215                         public void run()
5216                         {
5217                           boolean isNucleotide = alignPanel.alignFrame
5218                                   .getViewport().getAlignment()
5219                                   .isNucleotide();
5220                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5221                                   alignPanel.av.getSequenceSelection(),
5222                                   alignPanel.alignFrame, dassrc,
5223                                   alignPanel.alignFrame.featureSettings,
5224                                   isNucleotide);
5225                           dbRefFetcher
5226                                   .addListener(new FetchFinishedListenerI()
5227                                   {
5228                                     @Override
5229                                     public void finished()
5230                                     {
5231                                       AlignFrame.this.setMenusForViewport();
5232                                     }
5233                                   });
5234                           dbRefFetcher.fetchDBRefs(false);
5235                         }
5236                       }).start();
5237                     }
5238
5239                   });
5240                   fetchr.setToolTipText(
5241                           "<html>" + MessageManager.formatMessage(
5242                                   "label.fetch_retrieve_from", new Object[]
5243                                   { dbname }));
5244                   ifetch.add(fetchr);
5245                   ++i;
5246                   if (++icomp >= mcomp || i == (otherdb.size()))
5247                   {
5248                     ifetch.setText(MessageManager.formatMessage(
5249                             "label.source_to_target", imname, sname));
5250                     dfetch.add(ifetch);
5251                     ifetch = new JMenu();
5252                     imname = null;
5253                     icomp = 0;
5254                     comp++;
5255                   }
5256                 }
5257               }
5258               ++dbi;
5259               if (comp >= mcomp || dbi >= (dbclasses.length))
5260               {
5261                 dfetch.setText(MessageManager.formatMessage(
5262                         "label.source_to_target", mname, dbclass));
5263                 rfetch.add(dfetch);
5264                 dfetch = new JMenu();
5265                 mname = null;
5266                 comp = 0;
5267               }
5268             }
5269           }
5270         });
5271       }
5272     }).start();
5273
5274   }
5275
5276   /**
5277    * Left justify the whole alignment.
5278    */
5279   @Override
5280   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5281   {
5282     AlignmentI al = viewport.getAlignment();
5283     al.justify(false);
5284     viewport.firePropertyChange("alignment", null, al);
5285   }
5286
5287   /**
5288    * Right justify the whole alignment.
5289    */
5290   @Override
5291   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5292   {
5293     AlignmentI al = viewport.getAlignment();
5294     al.justify(true);
5295     viewport.firePropertyChange("alignment", null, al);
5296   }
5297
5298   @Override
5299   public void setShowSeqFeatures(boolean b)
5300   {
5301     showSeqFeatures.setSelected(b);
5302     viewport.setShowSequenceFeatures(b);
5303   }
5304
5305   /*
5306    * (non-Javadoc)
5307    *
5308    * @see
5309    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5310    * awt.event.ActionEvent)
5311    */
5312   @Override
5313   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5314   {
5315     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5316     alignPanel.paintAlignment(false, false);
5317   }
5318
5319   /*
5320    * (non-Javadoc)
5321    *
5322    * @see
5323    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5324    * .ActionEvent)
5325    */
5326   @Override
5327   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5328   {
5329     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5330     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5331
5332   }
5333
5334   /*
5335    * (non-Javadoc)
5336    *
5337    * @see
5338    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5339    * .event.ActionEvent)
5340    */
5341   @Override
5342   protected void showGroupConservation_actionPerformed(ActionEvent e)
5343   {
5344     viewport.setShowGroupConservation(showGroupConservation.getState());
5345     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5346   }
5347
5348   /*
5349    * (non-Javadoc)
5350    *
5351    * @see
5352    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5353    * .event.ActionEvent)
5354    */
5355   @Override
5356   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5357   {
5358     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5359     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5360   }
5361
5362   /*
5363    * (non-Javadoc)
5364    *
5365    * @see
5366    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5367    * .event.ActionEvent)
5368    */
5369   @Override
5370   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5371   {
5372     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5373     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5374   }
5375
5376   @Override
5377   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5378   {
5379     showSequenceLogo.setState(true);
5380     viewport.setShowSequenceLogo(true);
5381     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5382     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5383   }
5384
5385   @Override
5386   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5387   {
5388     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5389   }
5390
5391   /*
5392    * (non-Javadoc)
5393    *
5394    * @see
5395    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5396    * .event.ActionEvent)
5397    */
5398   @Override
5399   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5400   {
5401     if (avc.makeGroupsFromSelection())
5402     {
5403       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5404       alignPanel.updateAnnotation();
5405       alignPanel.paintAlignment(true,
5406               viewport.needToUpdateStructureViews());
5407     }
5408   }
5409
5410   public void clearAlignmentSeqRep()
5411   {
5412     // TODO refactor alignmentseqrep to controller
5413     if (viewport.getAlignment().hasSeqrep())
5414     {
5415       viewport.getAlignment().setSeqrep(null);
5416       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5417       alignPanel.updateAnnotation();
5418       alignPanel.paintAlignment(true, true);
5419     }
5420   }
5421
5422   @Override
5423   protected void createGroup_actionPerformed(ActionEvent e)
5424   {
5425     if (avc.createGroup())
5426     {
5427       if (applyAutoAnnotationSettings.isSelected())
5428       {
5429         alignPanel.updateAnnotation(true, false);
5430       }
5431       alignPanel.alignmentChanged();
5432     }
5433   }
5434
5435   @Override
5436   protected void unGroup_actionPerformed(ActionEvent e)
5437   {
5438     if (avc.unGroup())
5439     {
5440       alignPanel.alignmentChanged();
5441     }
5442   }
5443
5444   /**
5445    * make the given alignmentPanel the currently selected tab
5446    *
5447    * @param alignmentPanel
5448    */
5449   public void setDisplayedView(AlignmentPanel alignmentPanel)
5450   {
5451     if (!viewport.getSequenceSetId()
5452             .equals(alignmentPanel.av.getSequenceSetId()))
5453     {
5454       throw new Error(MessageManager.getString(
5455               "error.implementation_error_cannot_show_view_alignment_frame"));
5456     }
5457     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5458             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5459     {
5460       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5461     }
5462   }
5463
5464   /**
5465    * Action on selection of menu options to Show or Hide annotations.
5466    *
5467    * @param visible
5468    * @param forSequences
5469    *          update sequence-related annotations
5470    * @param forAlignment
5471    *          update non-sequence-related annotations
5472    */
5473   @Override
5474   protected void setAnnotationsVisibility(boolean visible,
5475           boolean forSequences, boolean forAlignment)
5476   {
5477     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5478             .getAlignmentAnnotation();
5479     if (anns == null)
5480     {
5481       return;
5482     }
5483     for (AlignmentAnnotation aa : anns)
5484     {
5485       /*
5486        * don't display non-positional annotations on an alignment
5487        */
5488       if (aa.annotations == null)
5489       {
5490         continue;
5491       }
5492       boolean apply = (aa.sequenceRef == null && forAlignment)
5493               || (aa.sequenceRef != null && forSequences);
5494       if (apply)
5495       {
5496         aa.visible = visible;
5497       }
5498     }
5499     alignPanel.validateAnnotationDimensions(true);
5500     alignPanel.alignmentChanged();
5501   }
5502
5503   /**
5504    * Store selected annotation sort order for the view and repaint.
5505    */
5506   @Override
5507   protected void sortAnnotations_actionPerformed()
5508   {
5509     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5510     this.alignPanel.av
5511             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5512     alignPanel.paintAlignment(false, false);
5513   }
5514
5515   /**
5516    *
5517    * @return alignment panels in this alignment frame
5518    */
5519   public List<? extends AlignmentViewPanel> getAlignPanels()
5520   {
5521     // alignPanels is never null
5522     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5523     return alignPanels;
5524   }
5525
5526   /**
5527    * Open a new alignment window, with the cDNA associated with this (protein)
5528    * alignment, aligned as is the protein.
5529    */
5530   protected void viewAsCdna_actionPerformed()
5531   {
5532     // TODO no longer a menu action - refactor as required
5533     final AlignmentI alignment = getViewport().getAlignment();
5534     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5535     if (mappings == null)
5536     {
5537       return;
5538     }
5539     List<SequenceI> cdnaSeqs = new ArrayList<>();
5540     for (SequenceI aaSeq : alignment.getSequences())
5541     {
5542       for (AlignedCodonFrame acf : mappings)
5543       {
5544         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5545         if (dnaSeq != null)
5546         {
5547           /*
5548            * There is a cDNA mapping for this protein sequence - add to new
5549            * alignment. It will share the same dataset sequence as other mapped
5550            * cDNA (no new mappings need to be created).
5551            */
5552           final Sequence newSeq = new Sequence(dnaSeq);
5553           newSeq.setDatasetSequence(dnaSeq);
5554           cdnaSeqs.add(newSeq);
5555         }
5556       }
5557     }
5558     if (cdnaSeqs.size() == 0)
5559     {
5560       // show a warning dialog no mapped cDNA
5561       return;
5562     }
5563     AlignmentI cdna = new Alignment(
5564             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5565     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5566             AlignFrame.DEFAULT_HEIGHT);
5567     cdna.alignAs(alignment);
5568     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5569             + this.title;
5570     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5571             AlignFrame.DEFAULT_HEIGHT);
5572   }
5573
5574   /**
5575    * Set visibility of dna/protein complement view (available when shown in a
5576    * split frame).
5577    *
5578    * @param show
5579    */
5580   @Override
5581   protected void showComplement_actionPerformed(boolean show)
5582   {
5583     SplitContainerI sf = getSplitViewContainer();
5584     if (sf != null)
5585     {
5586       sf.setComplementVisible(this, show);
5587     }
5588   }
5589
5590   /**
5591    * Generate the reverse (optionally complemented) of the selected sequences,
5592    * and add them to the alignment
5593    */
5594   @Override
5595   protected void showReverse_actionPerformed(boolean complement)
5596   {
5597     AlignmentI al = null;
5598     try
5599     {
5600       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5601       al = dna.reverseCdna(complement);
5602       viewport.addAlignment(al, "");
5603       addHistoryItem(new EditCommand(
5604               MessageManager.getString("label.add_sequences"), Action.PASTE,
5605               al.getSequencesArray(), 0, al.getWidth(),
5606               viewport.getAlignment()));
5607     } catch (Exception ex)
5608     {
5609       System.err.println(ex.getMessage());
5610       return;
5611     }
5612   }
5613
5614   /**
5615    * Try to run a script in the Groovy console, having first ensured that this
5616    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5617    * be targeted at this alignment.
5618    */
5619   @Override
5620   protected void runGroovy_actionPerformed()
5621   {
5622     Jalview.setCurrentAlignFrame(this);
5623     groovy.ui.Console console = Desktop.getGroovyConsole();
5624     if (console != null)
5625     {
5626       try
5627       {
5628         console.runScript();
5629       } catch (Exception ex)
5630       {
5631         System.err.println((ex.toString()));
5632         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5633                 MessageManager.getString("label.couldnt_run_groovy_script"),
5634                 MessageManager.getString("label.groovy_support_failed"),
5635                 JvOptionPane.ERROR_MESSAGE);
5636       }
5637     }
5638     else
5639     {
5640       System.err.println("Can't run Groovy script as console not found");
5641     }
5642   }
5643
5644   /**
5645    * Hides columns containing (or not containing) a specified feature, provided
5646    * that would not leave all columns hidden
5647    *
5648    * @param featureType
5649    * @param columnsContaining
5650    * @return
5651    */
5652   public boolean hideFeatureColumns(String featureType,
5653           boolean columnsContaining)
5654   {
5655     boolean notForHiding = avc.markColumnsContainingFeatures(
5656             columnsContaining, false, false, featureType);
5657     if (notForHiding)
5658     {
5659       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5660               false, featureType))
5661       {
5662         getViewport().hideSelectedColumns();
5663         return true;
5664       }
5665     }
5666     return false;
5667   }
5668
5669   @Override
5670   protected void selectHighlightedColumns_actionPerformed(
5671           ActionEvent actionEvent)
5672   {
5673     // include key modifier check in case user selects from menu
5674     avc.markHighlightedColumns(
5675             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5676             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5677                     | ActionEvent.CTRL_MASK)) != 0);
5678   }
5679
5680   /**
5681    * Rebuilds the Colour menu, including any user-defined colours which have
5682    * been loaded either on startup or during the session
5683    */
5684   public void buildColourMenu()
5685   {
5686     colourMenu.removeAll();
5687
5688     colourMenu.add(applyToAllGroups);
5689     colourMenu.add(textColour);
5690     colourMenu.addSeparator();
5691
5692     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5693             viewport.getAlignment(), false);
5694
5695     colourMenu.add(annotationColour);
5696     bg.add(annotationColour);
5697     colourMenu.addSeparator();
5698     colourMenu.add(conservationMenuItem);
5699     colourMenu.add(modifyConservation);
5700     colourMenu.add(abovePIDThreshold);
5701     colourMenu.add(modifyPID);
5702
5703     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5704     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5705   }
5706
5707   /**
5708    * Open a dialog (if not already open) that allows the user to select and
5709    * calculate PCA or Tree analysis
5710    */
5711   protected void openTreePcaDialog()
5712   {
5713     if (alignPanel.getCalculationDialog() == null)
5714     {
5715       new CalculationChooser(AlignFrame.this);
5716     }
5717   }
5718
5719   @Override
5720   protected void loadVcf_actionPerformed()
5721   {
5722     JalviewFileChooser chooser = new JalviewFileChooser(
5723             Cache.getProperty("LAST_DIRECTORY"));
5724     chooser.setFileView(new JalviewFileView());
5725     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5726     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5727
5728     int value = chooser.showOpenDialog(null);
5729
5730     if (value == JalviewFileChooser.APPROVE_OPTION)
5731     {
5732       String choice = chooser.getSelectedFile().getPath();
5733       Cache.setProperty("LAST_DIRECTORY", choice);
5734       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5735       new VCFLoader(choice).loadVCF(seqs, this);
5736     }
5737
5738   }
5739
5740   private Rectangle lastFeatureSettingsBounds = null;
5741
5742   @Override
5743   public void setFeatureSettingsGeometry(Rectangle bounds)
5744   {
5745     lastFeatureSettingsBounds = bounds;
5746   }
5747
5748   @Override
5749   public Rectangle getFeatureSettingsGeometry()
5750   {
5751     return lastFeatureSettingsBounds;
5752   }
5753 }
5754
5755 class PrintThread extends Thread
5756 {
5757   AlignmentPanel ap;
5758
5759   public PrintThread(AlignmentPanel ap)
5760   {
5761     this.ap = ap;
5762   }
5763
5764   static PageFormat pf;
5765
5766   @Override
5767   public void run()
5768   {
5769     PrinterJob printJob = PrinterJob.getPrinterJob();
5770
5771     if (pf != null)
5772     {
5773       printJob.setPrintable(ap, pf);
5774     }
5775     else
5776     {
5777       printJob.setPrintable(ap);
5778     }
5779
5780     if (printJob.printDialog())
5781     {
5782       try
5783       {
5784         printJob.print();
5785       } catch (Exception PrintException)
5786       {
5787         PrintException.printStackTrace();
5788       }
5789     }
5790   }
5791 }