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