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