src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenColumns;
  57 import jalview.datamodel.HiddenMarkovModel;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  66 import jalview.hmmer.HMMAlignThread;
  67 import jalview.hmmer.HMMBuildThread;
  68 import jalview.hmmer.HMMERParamStore;
  69 import jalview.hmmer.HMMERPreset;
  70 import jalview.hmmer.HMMSearchThread;
  71 import jalview.hmmer.HmmerCommand;
  72 import jalview.io.AlignmentProperties;
  73 import jalview.io.AnnotationFile;
  74 import jalview.io.BioJsHTMLOutput;
  75 import jalview.io.DataSourceType;
  76 import jalview.io.FileFormat;
  77 import jalview.io.FileFormatI;
  78 import jalview.io.FileFormats;
  79 import jalview.io.FileLoader;
  80 import jalview.io.FileParse;
  81 import jalview.io.FormatAdapter;
  82 import jalview.io.HtmlSvgOutput;
  83 import jalview.io.IdentifyFile;
  84 import jalview.io.JPredFile;
  85 import jalview.io.JalviewFileChooser;
  86 import jalview.io.JalviewFileView;
  87 import jalview.io.JnetAnnotationMaker;
  88 import jalview.io.NewickFile;
  89 import jalview.io.ScoreMatrixFile;
  90 import jalview.io.TCoffeeScoreFile;
  91 import jalview.jbgui.GAlignFrame;
  92 import jalview.schemes.ColourSchemeI;
  93 import jalview.schemes.ColourSchemes;
  94 import jalview.schemes.ResidueColourScheme;
  95 import jalview.schemes.TCoffeeColourScheme;
  96 import jalview.util.MessageManager;
  97 import jalview.util.StringUtils;
  98 import jalview.viewmodel.AlignmentViewport;
  99 import jalview.viewmodel.ViewportRanges;
 100 import jalview.ws.DBRefFetcher;
 101 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 102 import jalview.ws.jws1.Discoverer;
 103 import jalview.ws.jws2.Jws2Discoverer;
 104 import jalview.ws.jws2.jabaws2.Jws2Instance;
 105 import jalview.ws.params.ArgumentI;
 106 import jalview.ws.params.ParamDatastoreI;
 107 import jalview.ws.params.WsParamSetI;
 108 import jalview.ws.seqfetcher.DbSourceProxy;
 109
 110 import java.awt.BorderLayout;
 111 import java.awt.Component;
 112 import java.awt.Rectangle;
 113 import java.awt.Toolkit;
 114 import java.awt.datatransfer.Clipboard;
 115 import java.awt.datatransfer.DataFlavor;
 116 import java.awt.datatransfer.StringSelection;
 117 import java.awt.datatransfer.Transferable;
 118 import java.awt.dnd.DnDConstants;
 119 import java.awt.dnd.DropTargetDragEvent;
 120 import java.awt.dnd.DropTargetDropEvent;
 121 import java.awt.dnd.DropTargetEvent;
 122 import java.awt.dnd.DropTargetListener;
 123 import java.awt.event.ActionEvent;
 124 import java.awt.event.ActionListener;
 125 import java.awt.event.FocusAdapter;
 126 import java.awt.event.FocusEvent;
 127 import java.awt.event.ItemEvent;
 128 import java.awt.event.ItemListener;
 129 import java.awt.event.KeyAdapter;
 130 import java.awt.event.KeyEvent;
 131 import java.awt.event.MouseEvent;
 132 import java.awt.print.PageFormat;
 133 import java.awt.print.PrinterJob;
 134 import java.beans.PropertyChangeEvent;
 135 import java.io.File;
 136 import java.io.FileWriter;
 137 import java.io.IOException;
 138 import java.io.PrintWriter;
 139 import java.net.URL;
 140 import java.util.ArrayList;
 141 import java.util.Arrays;
 142 import java.util.Deque;
 143 import java.util.Enumeration;
 144 import java.util.HashMap;
 145 import java.util.Hashtable;
 146 import java.util.List;
 147 import java.util.Map;
 148 import java.util.Scanner;
 149 import java.util.Vector;
 150
 151 import javax.swing.JCheckBoxMenuItem;
 152 import javax.swing.JEditorPane;
 153 import javax.swing.JFileChooser;
 154 import javax.swing.JFrame;
 155 import javax.swing.JInternalFrame;
 156 import javax.swing.JLayeredPane;
 157 import javax.swing.JMenu;
 158 import javax.swing.JMenuItem;
 159 import javax.swing.JOptionPane;
 160 import javax.swing.JScrollPane;
 161 import javax.swing.SwingUtilities;
 162
 163 /**
 164  * DOCUMENT ME!
 165  *
 166  * @author $author$
 167  * @version $Revision$
 168  */
 169 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 170         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 171 {
 172
 173   Map<String, Float> distribution = new HashMap<>(); // temporary
 174
 175   public static final int DEFAULT_WIDTH = 700;
 176
 177   public static final int DEFAULT_HEIGHT = 500;
 178
 179   /*
 180    * The currently displayed panel (selected tabbed view if more than one)
 181    */
 182   public AlignmentPanel alignPanel;
 183
 184   AlignViewport viewport;
 185
 186   ViewportRanges vpRanges;
 187
 188   public AlignViewControllerI avc;
 189   /*
 190    * The selected HMM for this align frame
 191    */
 192   SequenceI selectedHMMSequence;
 193
 194   List<AlignmentPanel> alignPanels = new ArrayList<>();
 195
 196   /**
 197    * Last format used to load or save alignments in this window
 198    */
 199   FileFormatI currentFileFormat = null;
 200
 201   /**
 202    * Current filename for this alignment
 203    */
 204   String fileName = null;
 205
 206
 207   /**
 208    * Creates a new AlignFrame object with specific width and height.
 209    *
 210    * @param al
 211    * @param width
 212    * @param height
 213    */
 214   public AlignFrame(AlignmentI al, int width, int height)
 215   {
 216     this(al, null, width, height);
 217   }
 218
 219   /**
 220    * Creates a new AlignFrame object with specific width, height and
 221    * sequenceSetId
 222    *
 223    * @param al
 224    * @param width
 225    * @param height
 226    * @param sequenceSetId
 227    */
 228   public AlignFrame(AlignmentI al, int width, int height,
 229           String sequenceSetId)
 230   {
 231     this(al, null, width, height, sequenceSetId);
 232   }
 233
 234   /**
 235    * Creates a new AlignFrame object with specific width, height and
 236    * sequenceSetId
 237    *
 238    * @param al
 239    * @param width
 240    * @param height
 241    * @param sequenceSetId
 242    * @param viewId
 243    */
 244   public AlignFrame(AlignmentI al, int width, int height,
 245           String sequenceSetId, String viewId)
 246   {
 247     this(al, null, width, height, sequenceSetId, viewId);
 248   }
 249
 250   /**
 251    * new alignment window with hidden columns
 252    *
 253    * @param al
 254    *          AlignmentI
 255    * @param hiddenColumns
 256    *          ColumnSelection or null
 257    * @param width
 258    *          Width of alignment frame
 259    * @param height
 260    *          height of frame.
 261    */
 262   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 263           int height)
 264   {
 265     this(al, hiddenColumns, width, height, null);
 266   }
 267
 268   /**
 269    * Create alignment frame for al with hiddenColumns, a specific width and
 270    * height, and specific sequenceId
 271    *
 272    * @param al
 273    * @param hiddenColumns
 274    * @param width
 275    * @param height
 276    * @param sequenceSetId
 277    *          (may be null)
 278    */
 279   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 280           int height, String sequenceSetId)
 281   {
 282     this(al, hiddenColumns, width, height, sequenceSetId, null);
 283   }
 284
 285   /**
 286    * Create alignment frame for al with hiddenColumns, a specific width and
 287    * height, and specific sequenceId
 288    *
 289    * @param al
 290    * @param hiddenColumns
 291    * @param width
 292    * @param height
 293    * @param sequenceSetId
 294    *          (may be null)
 295    * @param viewId
 296    *          (may be null)
 297    */
 298   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 299           int height, String sequenceSetId, String viewId)
 300   {
 301     setSize(width, height);
 302
 303     if (al.getDataset() == null)
 304     {
 305       al.setDataset(null);
 306     }
 307
 308     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 309
 310     alignPanel = new AlignmentPanel(this, viewport);
 311
 312     addAlignmentPanel(alignPanel, true);
 313     init();
 314   }
 315
 316   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 317           HiddenColumns hiddenColumns, int width, int height)
 318   {
 319     setSize(width, height);
 320
 321     if (al.getDataset() == null)
 322     {
 323       al.setDataset(null);
 324     }
 325
 326     viewport = new AlignViewport(al, hiddenColumns);
 327
 328     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 329     {
 330       viewport.hideSequence(hiddenSeqs);
 331     }
 332     alignPanel = new AlignmentPanel(this, viewport);
 333     addAlignmentPanel(alignPanel, true);
 334     init();
 335   }
 336
 337   /**
 338    * Make a new AlignFrame from existing alignmentPanels
 339    *
 340    * @param ap
 341    *          AlignmentPanel
 342    * @param av
 343    *          AlignViewport
 344    */
 345   public AlignFrame(AlignmentPanel ap)
 346   {
 347     viewport = ap.av;
 348     alignPanel = ap;
 349     addAlignmentPanel(ap, false);
 350     init();
 351   }
 352
 353   /**
 354    * initalise the alignframe from the underlying viewport data and the
 355    * configurations
 356    */
 357   void init()
 358   {
 359     if (!Jalview.isHeadlessMode())
 360     {
 361       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 362     }
 363
 364     vpRanges = viewport.getRanges();
 365     avc = new jalview.controller.AlignViewController(this, viewport,
 366             alignPanel);
 367     if (viewport.getAlignmentConservationAnnotation() == null)
 368     {
 369       // BLOSUM62Colour.setEnabled(false);
 370       conservationMenuItem.setEnabled(false);
 371       modifyConservation.setEnabled(false);
 372       // PIDColour.setEnabled(false);
 373       // abovePIDThreshold.setEnabled(false);
 374       // modifyPID.setEnabled(false);
 375     }
 376
 377     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 378             "No sort");
 379
 380     if (sortby.equals("Id"))
 381     {
 382       sortIDMenuItem_actionPerformed(null);
 383     }
 384     else if (sortby.equals("Pairwise Identity"))
 385     {
 386       sortPairwiseMenuItem_actionPerformed(null);
 387     }
 388
 389     this.alignPanel.av
 390             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 391
 392     setMenusFromViewport(viewport);
 393     buildSortByAnnotationScoresMenu();
 394     calculateTree.addActionListener(new ActionListener()
 395     {
 396
 397       @Override
 398       public void actionPerformed(ActionEvent e)
 399       {
 400         openTreePcaDialog();
 401       }
 402     });
 403     buildColourMenu();
 404
 405     if (Desktop.desktop != null)
 406     {
 407       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 408       addServiceListeners();
 409       setGUINucleotide();
 410     }
 411
 412     if (viewport.getWrapAlignment())
 413     {
 414       wrapMenuItem_actionPerformed(null);
 415     }
 416
 417     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 418     {
 419       this.overviewMenuItem_actionPerformed(null);
 420     }
 421
 422     addKeyListener();
 423
 424     final List<AlignmentPanel> selviews = new ArrayList<>();
 425     final List<AlignmentPanel> origview = new ArrayList<>();
 426     final String menuLabel = MessageManager
 427             .getString("label.copy_format_from");
 428     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 429             new ViewSetProvider()
 430             {
 431
 432               @Override
 433               public AlignmentPanel[] getAllAlignmentPanels()
 434               {
 435                 origview.clear();
 436                 origview.add(alignPanel);
 437                 // make an array of all alignment panels except for this one
 438                 List<AlignmentPanel> aps = new ArrayList<>(
 439                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 440                 aps.remove(AlignFrame.this.alignPanel);
 441                 return aps.toArray(new AlignmentPanel[aps.size()]);
 442               }
 443             }, selviews, new ItemListener()
 444             {
 445
 446               @Override
 447               public void itemStateChanged(ItemEvent e)
 448               {
 449                 if (origview.size() > 0)
 450                 {
 451                   final AlignmentPanel ap = origview.get(0);
 452
 453                   /*
 454                    * Copy the ViewStyle of the selected panel to 'this one'.
 455                    * Don't change value of 'scaleProteinAsCdna' unless copying
 456                    * from a SplitFrame.
 457                    */
 458                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 459                           .getViewStyle();
 460                   boolean fromSplitFrame = selviews.get(0)
 461                           .getAlignViewport().getCodingComplement() != null;
 462                   if (!fromSplitFrame)
 463                   {
 464                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 465                             .getViewStyle().isScaleProteinAsCdna());
 466                   }
 467                   ap.getAlignViewport().setViewStyle(vs);
 468
 469                   /*
 470                    * Also rescale ViewStyle of SplitFrame complement if there is
 471                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 472                    * the whole ViewStyle (allow cDNA protein to have different
 473                    * fonts)
 474                    */
 475                   AlignViewportI complement = ap.getAlignViewport()
 476                           .getCodingComplement();
 477                   if (complement != null && vs.isScaleProteinAsCdna())
 478                   {
 479                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 480                     ((SplitFrame) af.getSplitViewContainer())
 481                             .adjustLayout();
 482                     af.setMenusForViewport();
 483                   }
 484
 485                   ap.updateLayout();
 486                   ap.setSelected(true);
 487                   ap.alignFrame.setMenusForViewport();
 488
 489                 }
 490               }
 491             });
 492     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 493             .indexOf("devel") > -1
 494             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 495                     .indexOf("test") > -1)
 496     {
 497       formatMenu.add(vsel);
 498     }
 499     addFocusListener(new FocusAdapter()
 500     {
 501       @Override
 502       public void focusGained(FocusEvent e)
 503       {
 504         Jalview.setCurrentAlignFrame(AlignFrame.this);
 505       }
 506     });
 507
 508   }
 509
 510   /**
 511    * Change the filename and format for the alignment, and enable the 'reload'
 512    * button functionality.
 513    *
 514    * @param file
 515    *          valid filename
 516    * @param format
 517    *          format of file
 518    */
 519   public void setFileName(String file, FileFormatI format)
 520   {
 521     fileName = file;
 522     setFileFormat(format);
 523     reload.setEnabled(true);
 524   }
 525
 526   /**
 527    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 528    * events
 529    */
 530   void addKeyListener()
 531   {
 532     addKeyListener(new KeyAdapter()
 533     {
 534       @Override
 535       public void keyPressed(KeyEvent evt)
 536       {
 537         if (viewport.cursorMode
 538                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 539                         && evt.getKeyCode() <= KeyEvent.VK_9)
 540                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 541                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 542                 && Character.isDigit(evt.getKeyChar()))
 543         {
 544           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 545         }
 546
 547         switch (evt.getKeyCode())
 548         {
 549
 550         case 27: // escape key
 551           deselectAllSequenceMenuItem_actionPerformed(null);
 552
 553           break;
 554
 555         case KeyEvent.VK_DOWN:
 556           if (evt.isAltDown() || !viewport.cursorMode)
 557           {
 558             moveSelectedSequences(false);
 559           }
 560           if (viewport.cursorMode)
 561           {
 562             alignPanel.getSeqPanel().moveCursor(0, 1);
 563           }
 564           break;
 565
 566         case KeyEvent.VK_UP:
 567           if (evt.isAltDown() || !viewport.cursorMode)
 568           {
 569             moveSelectedSequences(true);
 570           }
 571           if (viewport.cursorMode)
 572           {
 573             alignPanel.getSeqPanel().moveCursor(0, -1);
 574           }
 575
 576           break;
 577
 578         case KeyEvent.VK_LEFT:
 579           if (evt.isAltDown() || !viewport.cursorMode)
 580           {
 581             slideSequences(false,
 582                     alignPanel.getSeqPanel().getKeyboardNo1());
 583           }
 584           else
 585           {
 586             alignPanel.getSeqPanel().moveCursor(-1, 0);
 587           }
 588
 589           break;
 590
 591         case KeyEvent.VK_RIGHT:
 592           if (evt.isAltDown() || !viewport.cursorMode)
 593           {
 594             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 595           }
 596           else
 597           {
 598             alignPanel.getSeqPanel().moveCursor(1, 0);
 599           }
 600           break;
 601
 602         case KeyEvent.VK_SPACE:
 603           if (viewport.cursorMode)
 604           {
 605             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 606                     || evt.isShiftDown() || evt.isAltDown());
 607           }
 608           break;
 609
 610         // case KeyEvent.VK_A:
 611         // if (viewport.cursorMode)
 612         // {
 613         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 614         // //System.out.println("A");
 615         // }
 616         // break;
 617         /*
 618          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 619          * System.out.println("closing bracket"); } break;
 620          */
 621         case KeyEvent.VK_DELETE:
 622         case KeyEvent.VK_BACK_SPACE:
 623           if (!viewport.cursorMode)
 624           {
 625             cut_actionPerformed(null);
 626           }
 627           else
 628           {
 629             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 630                     || evt.isShiftDown() || evt.isAltDown());
 631           }
 632
 633           break;
 634
 635         case KeyEvent.VK_S:
 636           if (viewport.cursorMode)
 637           {
 638             alignPanel.getSeqPanel().setCursorRow();
 639           }
 640           break;
 641         case KeyEvent.VK_C:
 642           if (viewport.cursorMode && !evt.isControlDown())
 643           {
 644             alignPanel.getSeqPanel().setCursorColumn();
 645           }
 646           break;
 647         case KeyEvent.VK_P:
 648           if (viewport.cursorMode)
 649           {
 650             alignPanel.getSeqPanel().setCursorPosition();
 651           }
 652           break;
 653
 654         case KeyEvent.VK_ENTER:
 655         case KeyEvent.VK_COMMA:
 656           if (viewport.cursorMode)
 657           {
 658             alignPanel.getSeqPanel().setCursorRowAndColumn();
 659           }
 660           break;
 661
 662         case KeyEvent.VK_Q:
 663           if (viewport.cursorMode)
 664           {
 665             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 666           }
 667           break;
 668         case KeyEvent.VK_M:
 669           if (viewport.cursorMode)
 670           {
 671             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 672           }
 673           break;
 674
 675         case KeyEvent.VK_F2:
 676           viewport.cursorMode = !viewport.cursorMode;
 677           statusBar.setText(MessageManager
 678                   .formatMessage("label.keyboard_editing_mode", new String[]
 679                   { (viewport.cursorMode ? "on" : "off") }));
 680           if (viewport.cursorMode)
 681           {
 682             alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
 683                     .getStartRes();
 684             alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
 685                     .getStartSeq();
 686           }
 687           alignPanel.getSeqPanel().seqCanvas.repaint();
 688           break;
 689
 690         case KeyEvent.VK_F1:
 691           try
 692           {
 693             Help.showHelpWindow();
 694           } catch (Exception ex)
 695           {
 696             ex.printStackTrace();
 697           }
 698           break;
 699         case KeyEvent.VK_H:
 700         {
 701           boolean toggleSeqs = !evt.isControlDown();
 702           boolean toggleCols = !evt.isShiftDown();
 703           toggleHiddenRegions(toggleSeqs, toggleCols);
 704           break;
 705         }
 706         case KeyEvent.VK_B:
 707         {
 708           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 709           boolean modifyExisting = true; // always modify, don't clear
 710                                          // evt.isShiftDown();
 711           boolean invertHighlighted = evt.isAltDown();
 712           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 713                   toggleSel);
 714           break;
 715         }
 716         case KeyEvent.VK_PAGE_UP:
 717           vpRanges.pageUp();
 718           break;
 719         case KeyEvent.VK_PAGE_DOWN:
 720           vpRanges.pageDown();
 721           break;
 722         }
 723       }
 724
 725       @Override
 726       public void keyReleased(KeyEvent evt)
 727       {
 728         switch (evt.getKeyCode())
 729         {
 730         case KeyEvent.VK_LEFT:
 731           if (evt.isAltDown() || !viewport.cursorMode)
 732           {
 733             viewport.firePropertyChange("alignment", null,
 734                     viewport.getAlignment().getSequences());
 735           }
 736           break;
 737
 738         case KeyEvent.VK_RIGHT:
 739           if (evt.isAltDown() || !viewport.cursorMode)
 740           {
 741             viewport.firePropertyChange("alignment", null,
 742                     viewport.getAlignment().getSequences());
 743           }
 744           break;
 745         }
 746       }
 747     });
 748   }
 749
 750   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 751   {
 752     ap.alignFrame = this;
 753     avc = new jalview.controller.AlignViewController(this, viewport,
 754             alignPanel);
 755
 756     alignPanels.add(ap);
 757
 758     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 759
 760     int aSize = alignPanels.size();
 761
 762     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 763
 764     if (aSize == 1 && ap.av.viewName == null)
 765     {
 766       this.getContentPane().add(ap, BorderLayout.CENTER);
 767     }
 768     else
 769     {
 770       if (aSize == 2)
 771       {
 772         setInitialTabVisible();
 773       }
 774
 775       expandViews.setEnabled(true);
 776       gatherViews.setEnabled(true);
 777       tabbedPane.addTab(ap.av.viewName, ap);
 778
 779       ap.setVisible(false);
 780     }
 781
 782     if (newPanel)
 783     {
 784       if (ap.av.isPadGaps())
 785       {
 786         ap.av.getAlignment().padGaps();
 787       }
 788       ap.av.updateConservation(ap);
 789       ap.av.updateConsensus(ap);
 790       ap.av.updateStrucConsensus(ap);
 791       ap.av.updateInformation(ap);
 792     }
 793   }
 794
 795   public void setInitialTabVisible()
 796   {
 797     expandViews.setEnabled(true);
 798     gatherViews.setEnabled(true);
 799     tabbedPane.setVisible(true);
 800     AlignmentPanel first = alignPanels.get(0);
 801     tabbedPane.addTab(first.av.viewName, first);
 802     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 803   }
 804
 805   public AlignViewport getViewport()
 806   {
 807     return viewport;
 808   }
 809
 810   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 811   private void addServiceListeners()
 812   {
 813     final java.beans.PropertyChangeListener thisListener;
 814     Desktop.instance.addJalviewPropertyChangeListener("services",
 815             thisListener = new java.beans.PropertyChangeListener()
 816             {
 817               @Override
 818               public void propertyChange(PropertyChangeEvent evt)
 819               {
 820                 // // System.out.println("Discoverer property change.");
 821                 // if (evt.getPropertyName().equals("services"))
 822                 {
 823                   SwingUtilities.invokeLater(new Runnable()
 824                   {
 825
 826                     @Override
 827                     public void run()
 828                     {
 829                       System.err.println(
 830                               "Rebuild WS Menu for service change");
 831                       BuildWebServiceMenu();
 832                     }
 833
 834                   });
 835                 }
 836               }
 837             });
 838     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 839     {
 840       @Override
 841       public void internalFrameClosed(
 842               javax.swing.event.InternalFrameEvent evt)
 843       {
 844         // System.out.println("deregistering discoverer listener");
 845         Desktop.instance.removeJalviewPropertyChangeListener("services",
 846                 thisListener);
 847         closeMenuItem_actionPerformed(true);
 848       };
 849     });
 850     // Finally, build the menu once to get current service state
 851     new Thread(new Runnable()
 852     {
 853       @Override
 854       public void run()
 855       {
 856         BuildWebServiceMenu();
 857       }
 858     }).start();
 859   }
 860
 861   /**
 862    * Configure menu items that vary according to whether the alignment is
 863    * nucleotide or protein
 864    */
 865   public void setGUINucleotide()
 866   {
 867     AlignmentI al = getViewport().getAlignment();
 868     boolean nucleotide = al.isNucleotide();
 869
 870     showTranslation.setVisible(nucleotide);
 871     showReverse.setVisible(nucleotide);
 872     showReverseComplement.setVisible(nucleotide);
 873     conservationMenuItem.setEnabled(!nucleotide);
 874     modifyConservation
 875             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 876     showGroupConservation.setEnabled(!nucleotide);
 877
 878     showComplementMenuItem
 879             .setText(nucleotide ? MessageManager.getString("label.protein")
 880                     : MessageManager.getString("label.nucleotide"));
 881   }
 882
 883   /**
 884    * set up menus for the current viewport. This may be called after any
 885    * operation that affects the data in the current view (selection changed,
 886    * etc) to update the menus to reflect the new state.
 887    */
 888   @Override
 889   public void setMenusForViewport()
 890   {
 891     setMenusFromViewport(viewport);
 892   }
 893
 894   /**
 895    * Need to call this method when tabs are selected for multiple views, or when
 896    * loading from Jalview2XML.java
 897    *
 898    * @param av
 899    *          AlignViewport
 900    */
 901   void setMenusFromViewport(AlignViewport av)
 902   {
 903     padGapsMenuitem.setSelected(av.isPadGaps());
 904     colourTextMenuItem.setSelected(av.isShowColourText());
 905     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 906     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 907     conservationMenuItem.setSelected(av.getConservationSelected());
 908     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 909     seqLimits.setSelected(av.getShowJVSuffix());
 910     idRightAlign.setSelected(av.isRightAlignIds());
 911     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 912     renderGapsMenuItem.setSelected(av.isRenderGaps());
 913     wrapMenuItem.setSelected(av.getWrapAlignment());
 914     scaleAbove.setVisible(av.getWrapAlignment());
 915     scaleLeft.setVisible(av.getWrapAlignment());
 916     scaleRight.setVisible(av.getWrapAlignment());
 917     annotationPanelMenuItem.setState(av.isShowAnnotation());
 918     /*
 919      * Show/hide annotations only enabled if annotation panel is shown
 920      */
 921     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 922     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 923     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 924     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 925     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 926     viewTextMenuItem.setSelected(av.getShowText());
 927     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 928     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 929     showGroupConservation.setSelected(av.isShowGroupConservation());
 930     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 931     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 932     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 933     showInformationHistogram.setSelected(av.isShowInformationHistogram());
 934     showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
 935     normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 936
 937     ColourMenuHelper.setColourSelected(colourMenu,
 938             av.getGlobalColourScheme());
 939
 940     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 941     hiddenMarkers.setState(av.getShowHiddenMarkers());
 942     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 943     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 944     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 945     autoCalculate.setSelected(av.autoCalculateConsensus);
 946     sortByTree.setSelected(av.sortByTree);
 947     listenToViewSelections.setSelected(av.followSelection);
 948
 949     showProducts.setEnabled(canShowProducts());
 950     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 951
 952     updateEditMenuBar();
 953   }
 954
 955   /**
 956    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 957    *
 958    * @param b
 959    */
 960   public void setGroovyEnabled(boolean b)
 961   {
 962     runGroovy.setEnabled(b);
 963   }
 964
 965   private IProgressIndicator progressBar;
 966
 967   /*
 968    * (non-Javadoc)
 969    *
 970    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 971    */
 972   @Override
 973   public void setProgressBar(String message, long id)
 974   {
 975     progressBar.setProgressBar(message, id);
 976   }
 977
 978   @Override
 979   public void registerHandler(final long id,
 980           final IProgressIndicatorHandler handler)
 981   {
 982     progressBar.registerHandler(id, handler);
 983   }
 984
 985   /**
 986    *
 987    * @return true if any progress bars are still active
 988    */
 989   @Override
 990   public boolean operationInProgress()
 991   {
 992     return progressBar.operationInProgress();
 993   }
 994
 995   @Override
 996   public void setStatus(String text)
 997   {
 998     statusBar.setText(text);
 999   }
1000
1001   /*
1002    * Added so Castor Mapping file can obtain Jalview Version
1003    */
1004   public String getVersion()
1005   {
1006     return jalview.bin.Cache.getProperty("VERSION");
1007   }
1008
1009   public FeatureRenderer getFeatureRenderer()
1010   {
1011     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1012   }
1013
1014   @Override
1015   public void fetchSequence_actionPerformed(ActionEvent e)
1016   {
1017     new jalview.gui.SequenceFetcher(this);
1018   }
1019
1020   @Override
1021   public void addFromFile_actionPerformed(ActionEvent e)
1022   {
1023     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1024   }
1025
1026   @Override
1027   public void hmmBuildSettings_actionPerformed()
1028   {
1029     if (!(alignmentIsSufficient(1)))
1030     {
1031       return;
1032     }
1033     WsParamSetI set = new HMMERPreset();
1034     List<ArgumentI> args = new ArrayList<>();
1035     ParamDatastoreI store = new HMMERParamStore("hmmbuild");
1036     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1037             args);
1038     if (params.showRunDialog())
1039     {
1040       new Thread(new HMMBuildThread(this, params.getJobParams())).start();
1041     }
1042     alignPanel.repaint();
1043
1044   }
1045
1046   @Override
1047   public void hmmAlignSettings_actionPerformed()
1048   {
1049     if (!(checkForHMM() && alignmentIsSufficient(2)))
1050     {
1051       return;
1052     }
1053     WsParamSetI set = new HMMERPreset();
1054     List<ArgumentI> args = new ArrayList<>();
1055     ParamDatastoreI store = new HMMERParamStore("hmmalign");
1056     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1057             args);
1058     if (params.showRunDialog())
1059     {
1060       new Thread(new HMMAlignThread(this, true, params.getJobParams()))
1061             .start();
1062     }
1063     alignPanel.repaint();
1064   }
1065
1066   @Override
1067   public void hmmSearchSettings_actionPerformed()
1068   {
1069     if (!checkForHMM())
1070     {
1071       return;
1072     }
1073     WsParamSetI set = new HMMERPreset();
1074     List<ArgumentI> args = new ArrayList<>();
1075     ParamDatastoreI store = new HMMERParamStore("hmmsearch");
1076     WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1077             args);
1078     if (params.showRunDialog())
1079     {
1080       new Thread(new HMMSearchThread(this, true, params.getJobParams()))
1081             .start();
1082     }
1083     alignPanel.repaint();
1084   }
1085
1086   @Override
1087   public void hmmBuildRun_actionPerformed()
1088   {
1089     if (!alignmentIsSufficient(1))
1090     {
1091       return;
1092     }
1093     new Thread(new HMMBuildThread(this, null))
1094             .start();
1095   }
1096
1097   @Override
1098   public void hmmAlignRun_actionPerformed()
1099   {
1100     if (!(checkForHMM() && alignmentIsSufficient(2)))
1101     {
1102       return;
1103     }
1104     new Thread(new HMMAlignThread(this, true, null))
1105             .start();
1106   }
1107
1108   @Override
1109   public void hmmSearchRun_actionPerformed()
1110   {
1111     if (!checkForHMM())
1112     {
1113       return;
1114     }
1115     new Thread(new HMMSearchThread(this, true, null))
1116             .start();
1117   }
1118
1119   /**
1120    * Checks if the frame has a selected hidden Markov model
1121    *
1122    * @return
1123    */
1124   private boolean checkForHMM()
1125   {
1126     if (getSelectedHMM() == null)
1127     {
1128       JOptionPane.showMessageDialog(this,
1129               MessageManager.getString("warn.no_selected_hmm"));
1130       return false;
1131     }
1132     return true;
1133   }
1134
1135   /**
1136    * Checks if the alignment contains the required number of sequences.
1137    *
1138    * @param required
1139    * @return
1140    */
1141   public boolean alignmentIsSufficient(int required)
1142   {
1143     if (getViewport().getAlignment().getSequences().size() < required)
1144     {
1145       JOptionPane.showMessageDialog(this,
1146               MessageManager.getString("warn.not_enough_sequences"));
1147       return false;
1148     }
1149     return true;
1150   }
1151
1152   @Override
1153   public void addDatabase_actionPerformed() throws IOException
1154   {
1155     if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
1156     {
1157       Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1158       Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
1159     }
1160
1161     String path = openFileChooser(false);
1162     if (new File(path).exists())
1163     {
1164       IdentifyFile identifier = new IdentifyFile();
1165       FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1166       if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1167               || format == FileFormat.Pfam)
1168       {
1169         String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
1170         String currentDbPaths = Cache
1171                 .getProperty(Preferences.HMMSEARCH_DB_PATHS);
1172         currentDbPaths += " " + path;
1173
1174         String fileName = StringUtils.getLastToken(path, File.separator);
1175         Scanner scanner = new Scanner(fileName).useDelimiter(".");
1176         String name = scanner.next();
1177         scanner.close();
1178         currentDbs += " " + path; // TODO remove path from file name
1179         scanner.close();
1180
1181         Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
1182         Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1183       }
1184       else
1185       {
1186         JOptionPane.showMessageDialog(this,
1187                 MessageManager.getString("warn.invalid_format"));
1188       }
1189     }
1190     else
1191     {
1192       JOptionPane.showMessageDialog(this,
1193               MessageManager.getString("warn.not_enough_sequences"));
1194     }
1195   }
1196
1197   /**
1198    * Opens a file chooser
1199    *
1200    * @param forFolder
1201    * @return
1202    */
1203   protected String openFileChooser(boolean forFolder)
1204   {
1205     String choice = null;
1206     JFileChooser chooser = new JFileChooser();
1207     if (forFolder)
1208     {
1209       chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1210     }
1211     chooser.setDialogTitle(
1212             MessageManager.getString("label.open_local_file"));
1213     chooser.setToolTipText(MessageManager.getString("action.open"));
1214
1215     int value = chooser.showOpenDialog(this);
1216
1217     if (value == JFileChooser.APPROVE_OPTION)
1218     {
1219       choice = chooser.getSelectedFile().getPath();
1220     }
1221     return choice;
1222   }
1223
1224   @Override
1225   public void reload_actionPerformed(ActionEvent e)
1226   {
1227     if (fileName != null)
1228     {
1229       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1230       // originating file's format
1231       // TODO: work out how to recover feature settings for correct view(s) when
1232       // file is reloaded.
1233       if (FileFormat.Jalview.equals(currentFileFormat))
1234       {
1235         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1236         for (int i = 0; i < frames.length; i++)
1237         {
1238           if (frames[i] instanceof AlignFrame && frames[i] != this
1239                   && ((AlignFrame) frames[i]).fileName != null
1240                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1241           {
1242             try
1243             {
1244               frames[i].setSelected(true);
1245               Desktop.instance.closeAssociatedWindows();
1246             } catch (java.beans.PropertyVetoException ex)
1247             {
1248             }
1249           }
1250
1251         }
1252         Desktop.instance.closeAssociatedWindows();
1253
1254         FileLoader loader = new FileLoader();
1255         DataSourceType protocol = fileName.startsWith("http:")
1256                 ? DataSourceType.URL
1257                 : DataSourceType.FILE;
1258         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1259       }
1260       else
1261       {
1262         Rectangle bounds = this.getBounds();
1263
1264         FileLoader loader = new FileLoader();
1265         DataSourceType protocol = fileName.startsWith("http:")
1266                 ? DataSourceType.URL
1267                 : DataSourceType.FILE;
1268         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1269                 protocol, currentFileFormat);
1270
1271         newframe.setBounds(bounds);
1272         if (featureSettings != null && featureSettings.isShowing())
1273         {
1274           final Rectangle fspos = featureSettings.frame.getBounds();
1275           // TODO: need a 'show feature settings' function that takes bounds -
1276           // need to refactor Desktop.addFrame
1277           newframe.featureSettings_actionPerformed(null);
1278           final FeatureSettings nfs = newframe.featureSettings;
1279           SwingUtilities.invokeLater(new Runnable()
1280           {
1281             @Override
1282             public void run()
1283             {
1284               nfs.frame.setBounds(fspos);
1285             }
1286           });
1287           this.featureSettings.close();
1288           this.featureSettings = null;
1289         }
1290         this.closeMenuItem_actionPerformed(true);
1291       }
1292     }
1293   }
1294
1295   @Override
1296   public void addFromText_actionPerformed(ActionEvent e)
1297   {
1298     Desktop.instance
1299             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1300   }
1301
1302   @Override
1303   public void addFromURL_actionPerformed(ActionEvent e)
1304   {
1305     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1306   }
1307
1308   @Override
1309   public void save_actionPerformed(ActionEvent e)
1310   {
1311     if (fileName == null || (currentFileFormat == null)
1312             || fileName.startsWith("http"))
1313     {
1314       saveAs_actionPerformed(null);
1315     }
1316     else
1317     {
1318       saveAlignment(fileName, currentFileFormat);
1319     }
1320   }
1321
1322   /**
1323    * DOCUMENT ME!
1324    *
1325    * @param e
1326    *          DOCUMENT ME!
1327    */
1328   @Override
1329   public void saveAs_actionPerformed(ActionEvent e)
1330   {
1331     String format = currentFileFormat == null ? null
1332             : currentFileFormat.getName();
1333     JalviewFileChooser chooser = JalviewFileChooser
1334             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1335
1336     chooser.setFileView(new JalviewFileView());
1337     chooser.setDialogTitle(
1338             MessageManager.getString("label.save_alignment_to_file"));
1339     chooser.setToolTipText(MessageManager.getString("action.save"));
1340
1341     int value = chooser.showSaveDialog(this);
1342
1343     if (value == JalviewFileChooser.APPROVE_OPTION)
1344     {
1345       currentFileFormat = chooser.getSelectedFormat();
1346       while (currentFileFormat == null)
1347       {
1348         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1349                 MessageManager.getString(
1350                         "label.select_file_format_before_saving"),
1351                 MessageManager.getString("label.file_format_not_specified"),
1352                 JvOptionPane.WARNING_MESSAGE);
1353         currentFileFormat = chooser.getSelectedFormat();
1354         value = chooser.showSaveDialog(this);
1355         if (value != JalviewFileChooser.APPROVE_OPTION)
1356         {
1357           return;
1358         }
1359       }
1360
1361       fileName = chooser.getSelectedFile().getPath();
1362
1363       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1364
1365       Cache.setProperty("LAST_DIRECTORY", fileName);
1366       saveAlignment(fileName, currentFileFormat);
1367     }
1368   }
1369
1370   public boolean saveAlignment(String file, FileFormatI format)
1371   {
1372     boolean success = true;
1373
1374     if (FileFormat.Jalview.equals(format))
1375     {
1376       String shortName = title;
1377
1378       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1379       {
1380         shortName = shortName.substring(
1381                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1382       }
1383
1384       success = new Jalview2XML().saveAlignment(this, file, shortName);
1385
1386       statusBar.setText(MessageManager.formatMessage(
1387               "label.successfully_saved_to_file_in_format", new Object[]
1388               { fileName, format }));
1389
1390     }
1391     else
1392     {
1393       AlignmentExportData exportData = getAlignmentForExport(format,
1394               viewport, null);
1395       if (exportData.getSettings().isCancelled())
1396       {
1397         return false;
1398       }
1399       FormatAdapter f = new FormatAdapter(alignPanel,
1400               exportData.getSettings());
1401       String output = f.formatSequences(format, exportData.getAlignment(), // class
1402                                                                            // cast
1403                                                                            // exceptions
1404                                                                            // will
1405               // occur in the distant future
1406               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1407               f.getCacheSuffixDefault(format),
1408               viewport.getAlignment().getHiddenColumns());
1409
1410       if (output == null)
1411       {
1412         success = false;
1413       }
1414       else
1415       {
1416         try
1417         {
1418           PrintWriter out = new PrintWriter(new FileWriter(file));
1419
1420           out.print(output);
1421           out.close();
1422           this.setTitle(file);
1423           statusBar.setText(MessageManager.formatMessage(
1424                   "label.successfully_saved_to_file_in_format", new Object[]
1425                   { fileName, format.getName() }));
1426         } catch (Exception ex)
1427         {
1428           success = false;
1429           ex.printStackTrace();
1430         }
1431       }
1432     }
1433
1434     if (!success)
1435     {
1436       JvOptionPane.showInternalMessageDialog(this, MessageManager
1437               .formatMessage("label.couldnt_save_file", new Object[]
1438               { fileName }),
1439               MessageManager.getString("label.error_saving_file"),
1440               JvOptionPane.WARNING_MESSAGE);
1441     }
1442
1443     return success;
1444   }
1445
1446   private void warningMessage(String warning, String title)
1447   {
1448     if (new jalview.util.Platform().isHeadless())
1449     {
1450       System.err.println("Warning: " + title + "\nWarning: " + warning);
1451
1452     }
1453     else
1454     {
1455       JvOptionPane.showInternalMessageDialog(this, warning, title,
1456               JvOptionPane.WARNING_MESSAGE);
1457     }
1458     return;
1459   }
1460
1461   /**
1462    * DOCUMENT ME!
1463    *
1464    * @param e
1465    *          DOCUMENT ME!
1466    */
1467   @Override
1468   protected void outputText_actionPerformed(ActionEvent e)
1469   {
1470     FileFormatI fileFormat = FileFormats.getInstance()
1471             .forName(e.getActionCommand());
1472     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1473             viewport, null);
1474     if (exportData.getSettings().isCancelled())
1475     {
1476       return;
1477     }
1478     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1479     cap.setForInput(null);
1480     try
1481     {
1482       FileFormatI format = fileFormat;
1483       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1484               .formatSequences(format, exportData.getAlignment(),
1485                       exportData.getOmitHidden(),
1486                       exportData.getStartEndPostions(),
1487                       viewport.getAlignment().getHiddenColumns()));
1488       Desktop.addInternalFrame(cap, MessageManager
1489               .formatMessage("label.alignment_output_command", new Object[]
1490               { e.getActionCommand() }), 600, 500);
1491     } catch (OutOfMemoryError oom)
1492     {
1493       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1494               oom);
1495       cap.dispose();
1496     }
1497
1498   }
1499
1500   public static AlignmentExportData getAlignmentForExport(
1501           FileFormatI format, AlignViewportI viewport,
1502           AlignExportSettingI exportSettings)
1503   {
1504     AlignmentI alignmentToExport = null;
1505     AlignExportSettingI settings = exportSettings;
1506     String[] omitHidden = null;
1507
1508     HiddenSequences hiddenSeqs = viewport.getAlignment()
1509             .getHiddenSequences();
1510
1511     alignmentToExport = viewport.getAlignment();
1512
1513     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1514     if (settings == null)
1515     {
1516       settings = new AlignExportSettings(hasHiddenSeqs,
1517               viewport.hasHiddenColumns(), format);
1518     }
1519     // settings.isExportAnnotations();
1520
1521     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1522     {
1523       omitHidden = viewport.getViewAsString(false,
1524               settings.isExportHiddenSequences());
1525     }
1526
1527     int[] alignmentStartEnd = new int[2];
1528     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1529     {
1530       alignmentToExport = hiddenSeqs.getFullAlignment();
1531     }
1532     else
1533     {
1534       alignmentToExport = viewport.getAlignment();
1535     }
1536     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1537             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1538     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1539             omitHidden, alignmentStartEnd, settings);
1540     return ed;
1541   }
1542
1543   /**
1544    * DOCUMENT ME!
1545    *
1546    * @param e
1547    *          DOCUMENT ME!
1548    */
1549   @Override
1550   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1551   {
1552     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1553     htmlSVG.exportHTML(null);
1554   }
1555
1556   @Override
1557   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1558   {
1559     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1560     bjs.exportHTML(null);
1561   }
1562
1563   public void createImageMap(File file, String image)
1564   {
1565     alignPanel.makePNGImageMap(file, image);
1566   }
1567
1568   /**
1569    * DOCUMENT ME!
1570    *
1571    * @param e
1572    *          DOCUMENT ME!
1573    */
1574   @Override
1575   public void createPNG(File f)
1576   {
1577     alignPanel.makePNG(f);
1578   }
1579
1580   /**
1581    * DOCUMENT ME!
1582    *
1583    * @param e
1584    *          DOCUMENT ME!
1585    */
1586   @Override
1587   public void createEPS(File f)
1588   {
1589     alignPanel.makeEPS(f);
1590   }
1591
1592   @Override
1593   public void createSVG(File f)
1594   {
1595     alignPanel.makeSVG(f);
1596   }
1597
1598   @Override
1599   public void pageSetup_actionPerformed(ActionEvent e)
1600   {
1601     PrinterJob printJob = PrinterJob.getPrinterJob();
1602     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1603   }
1604
1605   /**
1606    * DOCUMENT ME!
1607    *
1608    * @param e
1609    *          DOCUMENT ME!
1610    */
1611   @Override
1612   public void printMenuItem_actionPerformed(ActionEvent e)
1613   {
1614     // Putting in a thread avoids Swing painting problems
1615     PrintThread thread = new PrintThread(alignPanel);
1616     thread.start();
1617   }
1618
1619   @Override
1620   public void exportFeatures_actionPerformed(ActionEvent e)
1621   {
1622     new AnnotationExporter().exportFeatures(alignPanel);
1623   }
1624
1625   @Override
1626   public void exportAnnotations_actionPerformed(ActionEvent e)
1627   {
1628     new AnnotationExporter().exportAnnotations(alignPanel);
1629   }
1630
1631   @Override
1632   public void associatedData_actionPerformed(ActionEvent e)
1633           throws IOException, InterruptedException
1634   {
1635     // Pick the tree file
1636     JalviewFileChooser chooser = new JalviewFileChooser(
1637             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1638     chooser.setFileView(new JalviewFileView());
1639     chooser.setDialogTitle(
1640             MessageManager.getString("label.load_jalview_annotations"));
1641     chooser.setToolTipText(
1642             MessageManager.getString("label.load_jalview_annotations"));
1643
1644     int value = chooser.showOpenDialog(null);
1645
1646     if (value == JalviewFileChooser.APPROVE_OPTION)
1647     {
1648       String choice = chooser.getSelectedFile().getPath();
1649       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1650       loadJalviewDataFile(choice, null, null, null);
1651     }
1652
1653   }
1654
1655   /**
1656    * Close the current view or all views in the alignment frame. If the frame
1657    * only contains one view then the alignment will be removed from memory.
1658    *
1659    * @param closeAllTabs
1660    */
1661   @Override
1662   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1663   {
1664     if (alignPanels != null && alignPanels.size() < 2)
1665     {
1666       closeAllTabs = true;
1667     }
1668
1669     try
1670     {
1671       if (alignPanels != null)
1672       {
1673         if (closeAllTabs)
1674         {
1675           if (this.isClosed())
1676           {
1677             // really close all the windows - otherwise wait till
1678             // setClosed(true) is called
1679             for (int i = 0; i < alignPanels.size(); i++)
1680             {
1681               AlignmentPanel ap = alignPanels.get(i);
1682               ap.closePanel();
1683             }
1684           }
1685         }
1686         else
1687         {
1688           closeView(alignPanel);
1689         }
1690       }
1691
1692       if (closeAllTabs)
1693       {
1694         /*
1695          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1696          * be called recursively, with the frame now in 'closed' state
1697          */
1698         this.setClosed(true);
1699       }
1700     } catch (Exception ex)
1701     {
1702       ex.printStackTrace();
1703     }
1704   }
1705
1706   /**
1707    * Close the specified panel and close up tabs appropriately.
1708    *
1709    * @param panelToClose
1710    */
1711   public void closeView(AlignmentPanel panelToClose)
1712   {
1713     int index = tabbedPane.getSelectedIndex();
1714     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1715     alignPanels.remove(panelToClose);
1716     panelToClose.closePanel();
1717     panelToClose = null;
1718
1719     tabbedPane.removeTabAt(closedindex);
1720     tabbedPane.validate();
1721
1722     if (index > closedindex || index == tabbedPane.getTabCount())
1723     {
1724       // modify currently selected tab index if necessary.
1725       index--;
1726     }
1727
1728     this.tabSelectionChanged(index);
1729   }
1730
1731   /**
1732    * DOCUMENT ME!
1733    */
1734   void updateEditMenuBar()
1735   {
1736
1737     if (viewport.getHistoryList().size() > 0)
1738     {
1739       undoMenuItem.setEnabled(true);
1740       CommandI command = viewport.getHistoryList().peek();
1741       undoMenuItem.setText(MessageManager
1742               .formatMessage("label.undo_command", new Object[]
1743               { command.getDescription() }));
1744     }
1745     else
1746     {
1747       undoMenuItem.setEnabled(false);
1748       undoMenuItem.setText(MessageManager.getString("action.undo"));
1749     }
1750
1751     if (viewport.getRedoList().size() > 0)
1752     {
1753       redoMenuItem.setEnabled(true);
1754
1755       CommandI command = viewport.getRedoList().peek();
1756       redoMenuItem.setText(MessageManager
1757               .formatMessage("label.redo_command", new Object[]
1758               { command.getDescription() }));
1759     }
1760     else
1761     {
1762       redoMenuItem.setEnabled(false);
1763       redoMenuItem.setText(MessageManager.getString("action.redo"));
1764     }
1765   }
1766
1767   @Override
1768   public void addHistoryItem(CommandI command)
1769   {
1770     if (command.getSize() > 0)
1771     {
1772       viewport.addToHistoryList(command);
1773       viewport.clearRedoList();
1774       updateEditMenuBar();
1775       viewport.updateHiddenColumns();
1776       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1777       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1778       // viewport.getColumnSelection()
1779       // .getHiddenColumns().size() > 0);
1780     }
1781   }
1782
1783   /**
1784    *
1785    * @return alignment objects for all views
1786    */
1787   AlignmentI[] getViewAlignments()
1788   {
1789     if (alignPanels != null)
1790     {
1791       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1792       int i = 0;
1793       for (AlignmentPanel ap : alignPanels)
1794       {
1795         als[i++] = ap.av.getAlignment();
1796       }
1797       return als;
1798     }
1799     if (viewport != null)
1800     {
1801       return new AlignmentI[] { viewport.getAlignment() };
1802     }
1803     return null;
1804   }
1805
1806   /**
1807    * DOCUMENT ME!
1808    *
1809    * @param e
1810    *          DOCUMENT ME!
1811    */
1812   @Override
1813   protected void undoMenuItem_actionPerformed(ActionEvent e)
1814   {
1815     if (viewport.getHistoryList().isEmpty())
1816     {
1817       return;
1818     }
1819     CommandI command = viewport.getHistoryList().pop();
1820     viewport.addToRedoList(command);
1821     command.undoCommand(getViewAlignments());
1822
1823     AlignmentViewport originalSource = getOriginatingSource(command);
1824     updateEditMenuBar();
1825
1826     if (originalSource != null)
1827     {
1828       if (originalSource != viewport)
1829       {
1830         Cache.log.warn(
1831                 "Implementation worry: mismatch of viewport origin for undo");
1832       }
1833       originalSource.updateHiddenColumns();
1834       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1835       // null
1836       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1837       // viewport.getColumnSelection()
1838       // .getHiddenColumns().size() > 0);
1839       originalSource.firePropertyChange("alignment", null,
1840               originalSource.getAlignment().getSequences());
1841     }
1842   }
1843
1844   /**
1845    * DOCUMENT ME!
1846    *
1847    * @param e
1848    *          DOCUMENT ME!
1849    */
1850   @Override
1851   protected void redoMenuItem_actionPerformed(ActionEvent e)
1852   {
1853     if (viewport.getRedoList().size() < 1)
1854     {
1855       return;
1856     }
1857
1858     CommandI command = viewport.getRedoList().pop();
1859     viewport.addToHistoryList(command);
1860     command.doCommand(getViewAlignments());
1861
1862     AlignmentViewport originalSource = getOriginatingSource(command);
1863     updateEditMenuBar();
1864
1865     if (originalSource != null)
1866     {
1867
1868       if (originalSource != viewport)
1869       {
1870         Cache.log.warn(
1871                 "Implementation worry: mismatch of viewport origin for redo");
1872       }
1873       originalSource.updateHiddenColumns();
1874       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1875       // null
1876       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1877       // viewport.getColumnSelection()
1878       // .getHiddenColumns().size() > 0);
1879       originalSource.firePropertyChange("alignment", null,
1880               originalSource.getAlignment().getSequences());
1881     }
1882   }
1883
1884   AlignmentViewport getOriginatingSource(CommandI command)
1885   {
1886     AlignmentViewport originalSource = null;
1887     // For sequence removal and addition, we need to fire
1888     // the property change event FROM the viewport where the
1889     // original alignment was altered
1890     AlignmentI al = null;
1891     if (command instanceof EditCommand)
1892     {
1893       EditCommand editCommand = (EditCommand) command;
1894       al = editCommand.getAlignment();
1895       List<Component> comps = PaintRefresher.components
1896               .get(viewport.getSequenceSetId());
1897
1898       for (Component comp : comps)
1899       {
1900         if (comp instanceof AlignmentPanel)
1901         {
1902           if (al == ((AlignmentPanel) comp).av.getAlignment())
1903           {
1904             originalSource = ((AlignmentPanel) comp).av;
1905             break;
1906           }
1907         }
1908       }
1909     }
1910
1911     if (originalSource == null)
1912     {
1913       // The original view is closed, we must validate
1914       // the current view against the closed view first
1915       if (al != null)
1916       {
1917         PaintRefresher.validateSequences(al, viewport.getAlignment());
1918       }
1919
1920       originalSource = viewport;
1921     }
1922
1923     return originalSource;
1924   }
1925
1926   /**
1927    * DOCUMENT ME!
1928    *
1929    * @param up
1930    *          DOCUMENT ME!
1931    */
1932   public void moveSelectedSequences(boolean up)
1933   {
1934     SequenceGroup sg = viewport.getSelectionGroup();
1935
1936     if (sg == null)
1937     {
1938       return;
1939     }
1940     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1941             viewport.getHiddenRepSequences(), up);
1942     alignPanel.paintAlignment(true);
1943   }
1944
1945   synchronized void slideSequences(boolean right, int size)
1946   {
1947     List<SequenceI> sg = new ArrayList<>();
1948     if (viewport.cursorMode)
1949     {
1950       sg.add(viewport.getAlignment()
1951               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1952     }
1953     else if (viewport.getSelectionGroup() != null
1954             && viewport.getSelectionGroup().getSize() != viewport
1955                     .getAlignment().getHeight())
1956     {
1957       sg = viewport.getSelectionGroup()
1958               .getSequences(viewport.getHiddenRepSequences());
1959     }
1960
1961     if (sg.size() < 1)
1962     {
1963       return;
1964     }
1965
1966     List<SequenceI> invertGroup = new ArrayList<>();
1967
1968     for (SequenceI seq : viewport.getAlignment().getSequences())
1969     {
1970       if (!sg.contains(seq))
1971       {
1972         invertGroup.add(seq);
1973       }
1974     }
1975
1976     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1977
1978     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1979     for (int i = 0; i < invertGroup.size(); i++)
1980     {
1981       seqs2[i] = invertGroup.get(i);
1982     }
1983
1984     SlideSequencesCommand ssc;
1985     if (right)
1986     {
1987       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1988               viewport.getGapCharacter());
1989     }
1990     else
1991     {
1992       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1993               viewport.getGapCharacter());
1994     }
1995
1996     int groupAdjustment = 0;
1997     if (ssc.getGapsInsertedBegin() && right)
1998     {
1999       if (viewport.cursorMode)
2000       {
2001         alignPanel.getSeqPanel().moveCursor(size, 0);
2002       }
2003       else
2004       {
2005         groupAdjustment = size;
2006       }
2007     }
2008     else if (!ssc.getGapsInsertedBegin() && !right)
2009     {
2010       if (viewport.cursorMode)
2011       {
2012         alignPanel.getSeqPanel().moveCursor(-size, 0);
2013       }
2014       else
2015       {
2016         groupAdjustment = -size;
2017       }
2018     }
2019
2020     if (groupAdjustment != 0)
2021     {
2022       viewport.getSelectionGroup().setStartRes(
2023               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2024       viewport.getSelectionGroup().setEndRes(
2025               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2026     }
2027
2028     /*
2029      * just extend the last slide command if compatible; but not if in
2030      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2031      */
2032     boolean appendHistoryItem = false;
2033     Deque<CommandI> historyList = viewport.getHistoryList();
2034     boolean inSplitFrame = getSplitViewContainer() != null;
2035     if (!inSplitFrame && historyList != null && historyList.size() > 0
2036             && historyList.peek() instanceof SlideSequencesCommand)
2037     {
2038       appendHistoryItem = ssc.appendSlideCommand(
2039               (SlideSequencesCommand) historyList.peek());
2040     }
2041
2042     if (!appendHistoryItem)
2043     {
2044       addHistoryItem(ssc);
2045     }
2046
2047     repaint();
2048   }
2049
2050   /**
2051    * DOCUMENT ME!
2052    *
2053    * @param e
2054    *          DOCUMENT ME!
2055    */
2056   @Override
2057   protected void copy_actionPerformed(ActionEvent e)
2058   {
2059     System.gc();
2060     if (viewport.getSelectionGroup() == null)
2061     {
2062       return;
2063     }
2064     // TODO: preserve the ordering of displayed alignment annotation in any
2065     // internal paste (particularly sequence associated annotation)
2066     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2067     String[] omitHidden = null;
2068
2069     if (viewport.hasHiddenColumns())
2070     {
2071       omitHidden = viewport.getViewAsString(true);
2072     }
2073
2074     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2075             seqs, omitHidden, null);
2076
2077     StringSelection ss = new StringSelection(output);
2078
2079     try
2080     {
2081       jalview.gui.Desktop.internalCopy = true;
2082       // Its really worth setting the clipboard contents
2083       // to empty before setting the large StringSelection!!
2084       Toolkit.getDefaultToolkit().getSystemClipboard()
2085               .setContents(new StringSelection(""), null);
2086
2087       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2088               Desktop.instance);
2089     } catch (OutOfMemoryError er)
2090     {
2091       new OOMWarning("copying region", er);
2092       return;
2093     }
2094
2095     ArrayList<int[]> hiddenColumns = null;
2096     if (viewport.hasHiddenColumns())
2097     {
2098       hiddenColumns = new ArrayList<>();
2099
2100       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2101       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2102       ArrayList<int[]> hiddenRegions = viewport.getAlignment()
2103               .getHiddenColumns().getHiddenColumnsCopy();
2104       for (int[] region : hiddenRegions)
2105
2106       {
2107         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
2108         {
2109           hiddenColumns
2110                   .add(new int[]
2111                   { region[0] - hiddenOffset, region[1] - hiddenOffset });
2112         }
2113       }
2114     }
2115
2116     Desktop.jalviewClipboard = new Object[] { seqs,
2117         viewport.getAlignment().getDataset(), hiddenColumns };
2118     statusBar.setText(MessageManager.formatMessage(
2119             "label.copied_sequences_to_clipboard", new Object[]
2120             { Integer.valueOf(seqs.length).toString() }));
2121   }
2122
2123   /**
2124    * DOCUMENT ME!
2125    *
2126    * @param e
2127    *          DOCUMENT ME!
2128    * @throws InterruptedException
2129    * @throws IOException
2130    */
2131   @Override
2132   protected void pasteNew_actionPerformed(ActionEvent e)
2133           throws IOException, InterruptedException
2134   {
2135     paste(true);
2136   }
2137
2138   /**
2139    * DOCUMENT ME!
2140    *
2141    * @param e
2142    *          DOCUMENT ME!
2143    * @throws InterruptedException
2144    * @throws IOException
2145    */
2146   @Override
2147   protected void pasteThis_actionPerformed(ActionEvent e)
2148           throws IOException, InterruptedException
2149   {
2150     paste(false);
2151   }
2152
2153   /**
2154    * Paste contents of Jalview clipboard
2155    *
2156    * @param newAlignment
2157    *          true to paste to a new alignment, otherwise add to this.
2158    * @throws InterruptedException
2159    * @throws IOException
2160    */
2161   void paste(boolean newAlignment) throws IOException, InterruptedException
2162   {
2163     boolean externalPaste = true;
2164     try
2165     {
2166       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2167       Transferable contents = c.getContents(this);
2168
2169       if (contents == null)
2170       {
2171         return;
2172       }
2173
2174       String str;
2175       FileFormatI format;
2176       try
2177       {
2178         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2179         if (str.length() < 1)
2180         {
2181           return;
2182         }
2183
2184         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2185
2186       } catch (OutOfMemoryError er)
2187       {
2188         new OOMWarning("Out of memory pasting sequences!!", er);
2189         return;
2190       }
2191
2192       SequenceI[] sequences;
2193       boolean annotationAdded = false;
2194       AlignmentI alignment = null;
2195
2196       if (Desktop.jalviewClipboard != null)
2197       {
2198         // The clipboard was filled from within Jalview, we must use the
2199         // sequences
2200         // And dataset from the copied alignment
2201         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2202         // be doubly sure that we create *new* sequence objects.
2203         sequences = new SequenceI[newseq.length];
2204         for (int i = 0; i < newseq.length; i++)
2205         {
2206           sequences[i] = new Sequence(newseq[i]);
2207         }
2208         alignment = new Alignment(sequences);
2209         externalPaste = false;
2210       }
2211       else
2212       {
2213         // parse the clipboard as an alignment.
2214         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2215                 format);
2216         sequences = alignment.getSequencesArray();
2217       }
2218
2219       int alwidth = 0;
2220       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2221       int fgroup = -1;
2222
2223       if (newAlignment)
2224       {
2225
2226         if (Desktop.jalviewClipboard != null)
2227         {
2228           // dataset is inherited
2229           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2230         }
2231         else
2232         {
2233           // new dataset is constructed
2234           alignment.setDataset(null);
2235         }
2236         alwidth = alignment.getWidth() + 1;
2237       }
2238       else
2239       {
2240         AlignmentI pastedal = alignment; // preserve pasted alignment object
2241         // Add pasted sequences and dataset into existing alignment.
2242         alignment = viewport.getAlignment();
2243         alwidth = alignment.getWidth() + 1;
2244         // decide if we need to import sequences from an existing dataset
2245         boolean importDs = Desktop.jalviewClipboard != null
2246                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2247         // importDs==true instructs us to copy over new dataset sequences from
2248         // an existing alignment
2249         Vector newDs = (importDs) ? new Vector() : null; // used to create
2250         // minimum dataset set
2251
2252         for (int i = 0; i < sequences.length; i++)
2253         {
2254           if (importDs)
2255           {
2256             newDs.addElement(null);
2257           }
2258           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2259           // paste
2260           if (importDs && ds != null)
2261           {
2262             if (!newDs.contains(ds))
2263             {
2264               newDs.setElementAt(ds, i);
2265               ds = new Sequence(ds);
2266               // update with new dataset sequence
2267               sequences[i].setDatasetSequence(ds);
2268             }
2269             else
2270             {
2271               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2272             }
2273           }
2274           else
2275           {
2276             // copy and derive new dataset sequence
2277             sequences[i] = sequences[i].deriveSequence();
2278             alignment.getDataset()
2279                     .addSequence(sequences[i].getDatasetSequence());
2280             // TODO: avoid creation of duplicate dataset sequences with a
2281             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2282           }
2283           alignment.addSequence(sequences[i]); // merges dataset
2284         }
2285         if (newDs != null)
2286         {
2287           newDs.clear(); // tidy up
2288         }
2289         if (alignment.getAlignmentAnnotation() != null)
2290         {
2291           for (AlignmentAnnotation alan : alignment
2292                   .getAlignmentAnnotation())
2293           {
2294             if (alan.graphGroup > fgroup)
2295             {
2296               fgroup = alan.graphGroup;
2297             }
2298           }
2299         }
2300         if (pastedal.getAlignmentAnnotation() != null)
2301         {
2302           // Add any annotation attached to alignment.
2303           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2304           for (int i = 0; i < alann.length; i++)
2305           {
2306             annotationAdded = true;
2307             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2308             {
2309               AlignmentAnnotation newann = new AlignmentAnnotation(
2310                       alann[i]);
2311               if (newann.graphGroup > -1)
2312               {
2313                 if (newGraphGroups.size() <= newann.graphGroup
2314                         || newGraphGroups.get(newann.graphGroup) == null)
2315                 {
2316                   for (int q = newGraphGroups
2317                           .size(); q <= newann.graphGroup; q++)
2318                   {
2319                     newGraphGroups.add(q, null);
2320                   }
2321                   newGraphGroups.set(newann.graphGroup,
2322                           new Integer(++fgroup));
2323                 }
2324                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2325                         .intValue();
2326               }
2327
2328               newann.padAnnotation(alwidth);
2329               alignment.addAnnotation(newann);
2330             }
2331           }
2332         }
2333       }
2334       if (!newAlignment)
2335       {
2336         // /////
2337         // ADD HISTORY ITEM
2338         //
2339         addHistoryItem(new EditCommand(
2340                 MessageManager.getString("label.add_sequences"),
2341                 Action.PASTE, sequences, 0, alignment.getWidth(),
2342                 alignment));
2343       }
2344       // Add any annotations attached to sequences
2345       for (int i = 0; i < sequences.length; i++)
2346       {
2347         if (sequences[i].getAnnotation() != null)
2348         {
2349           AlignmentAnnotation newann;
2350           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2351           {
2352             annotationAdded = true;
2353             newann = sequences[i].getAnnotation()[a];
2354             newann.adjustForAlignment();
2355             newann.padAnnotation(alwidth);
2356             if (newann.graphGroup > -1)
2357             {
2358               if (newann.graphGroup > -1)
2359               {
2360                 if (newGraphGroups.size() <= newann.graphGroup
2361                         || newGraphGroups.get(newann.graphGroup) == null)
2362                 {
2363                   for (int q = newGraphGroups
2364                           .size(); q <= newann.graphGroup; q++)
2365                   {
2366                     newGraphGroups.add(q, null);
2367                   }
2368                   newGraphGroups.set(newann.graphGroup,
2369                           new Integer(++fgroup));
2370                 }
2371                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2372                         .intValue();
2373               }
2374             }
2375             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2376             // was
2377             // duplicated
2378             // earlier
2379             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2380                     a);
2381           }
2382         }
2383       }
2384       if (!newAlignment)
2385       {
2386
2387         // propagate alignment changed.
2388         vpRanges.setEndSeq(alignment.getHeight());
2389         if (annotationAdded)
2390         {
2391           // Duplicate sequence annotation in all views.
2392           AlignmentI[] alview = this.getViewAlignments();
2393           for (int i = 0; i < sequences.length; i++)
2394           {
2395             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2396             if (sann == null)
2397             {
2398               continue;
2399             }
2400             for (int avnum = 0; avnum < alview.length; avnum++)
2401             {
2402               if (alview[avnum] != alignment)
2403               {
2404                 // duplicate in a view other than the one with input focus
2405                 int avwidth = alview[avnum].getWidth() + 1;
2406                 // this relies on sann being preserved after we
2407                 // modify the sequence's annotation array for each duplication
2408                 for (int a = 0; a < sann.length; a++)
2409                 {
2410                   AlignmentAnnotation newann = new AlignmentAnnotation(
2411                           sann[a]);
2412                   sequences[i].addAlignmentAnnotation(newann);
2413                   newann.padAnnotation(avwidth);
2414                   alview[avnum].addAnnotation(newann); // annotation was
2415                   // duplicated earlier
2416                   // TODO JAL-1145 graphGroups are not updated for sequence
2417                   // annotation added to several views. This may cause
2418                   // strangeness
2419                   alview[avnum].setAnnotationIndex(newann, a);
2420                 }
2421               }
2422             }
2423           }
2424           buildSortByAnnotationScoresMenu();
2425         }
2426         viewport.firePropertyChange("alignment", null,
2427                 alignment.getSequences());
2428         if (alignPanels != null)
2429         {
2430           for (AlignmentPanel ap : alignPanels)
2431           {
2432             ap.validateAnnotationDimensions(false);
2433           }
2434         }
2435         else
2436         {
2437           alignPanel.validateAnnotationDimensions(false);
2438         }
2439
2440       }
2441       else
2442       {
2443         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2444                 DEFAULT_HEIGHT);
2445         String newtitle = new String("Copied sequences");
2446
2447         if (Desktop.jalviewClipboard != null
2448                 && Desktop.jalviewClipboard[2] != null)
2449         {
2450           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2451           for (int[] region : hc)
2452           {
2453             af.viewport.hideColumns(region[0], region[1]);
2454           }
2455         }
2456
2457         // >>>This is a fix for the moment, until a better solution is
2458         // found!!<<<
2459         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2460                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2461                         .getFeatureRenderer());
2462
2463         // TODO: maintain provenance of an alignment, rather than just make the
2464         // title a concatenation of operations.
2465         if (!externalPaste)
2466         {
2467           if (title.startsWith("Copied sequences"))
2468           {
2469             newtitle = title;
2470           }
2471           else
2472           {
2473             newtitle = newtitle.concat("- from " + title);
2474           }
2475         }
2476         else
2477         {
2478           newtitle = new String("Pasted sequences");
2479         }
2480
2481         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2482                 DEFAULT_HEIGHT);
2483
2484       }
2485
2486     } catch (Exception ex)
2487     {
2488       ex.printStackTrace();
2489       System.out.println("Exception whilst pasting: " + ex);
2490       // could be anything being pasted in here
2491     }
2492   }
2493
2494   @Override
2495   protected void expand_newalign(ActionEvent e)
2496   {
2497     try
2498     {
2499       AlignmentI alignment = AlignmentUtils
2500               .expandContext(getViewport().getAlignment(), -1);
2501       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2502               DEFAULT_HEIGHT);
2503       String newtitle = new String("Flanking alignment");
2504
2505       if (Desktop.jalviewClipboard != null
2506               && Desktop.jalviewClipboard[2] != null)
2507       {
2508         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2509         for (int region[] : hc)
2510         {
2511           af.viewport.hideColumns(region[0], region[1]);
2512         }
2513       }
2514
2515       // >>>This is a fix for the moment, until a better solution is
2516       // found!!<<<
2517       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2518               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2519                       .getFeatureRenderer());
2520
2521       // TODO: maintain provenance of an alignment, rather than just make the
2522       // title a concatenation of operations.
2523       {
2524         if (title.startsWith("Copied sequences"))
2525         {
2526           newtitle = title;
2527         }
2528         else
2529         {
2530           newtitle = newtitle.concat("- from " + title);
2531         }
2532       }
2533
2534       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2535
2536     } catch (Exception ex)
2537     {
2538       ex.printStackTrace();
2539       System.out.println("Exception whilst pasting: " + ex);
2540       // could be anything being pasted in here
2541     } catch (OutOfMemoryError oom)
2542     {
2543       new OOMWarning("Viewing flanking region of alignment", oom);
2544     }
2545   }
2546
2547   /**
2548    * DOCUMENT ME!
2549    *
2550    * @param e
2551    *          DOCUMENT ME!
2552    */
2553   @Override
2554   protected void cut_actionPerformed(ActionEvent e)
2555   {
2556     copy_actionPerformed(null);
2557     delete_actionPerformed(null);
2558   }
2559
2560   /**
2561    * DOCUMENT ME!
2562    *
2563    * @param e
2564    *          DOCUMENT ME!
2565    */
2566   @Override
2567   protected void delete_actionPerformed(ActionEvent evt)
2568   {
2569
2570     SequenceGroup sg = viewport.getSelectionGroup();
2571     if (sg == null)
2572     {
2573       return;
2574     }
2575
2576     /*
2577      * If the cut affects all sequences, warn, remove highlighted columns
2578      */
2579     if (sg.getSize() == viewport.getAlignment().getHeight())
2580     {
2581       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2582               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2583       if (isEntireAlignWidth)
2584       {
2585         int confirm = JvOptionPane.showConfirmDialog(this,
2586                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2587                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2588                 JvOptionPane.OK_CANCEL_OPTION);
2589
2590         if (confirm == JvOptionPane.CANCEL_OPTION
2591                 || confirm == JvOptionPane.CLOSED_OPTION)
2592         {
2593           return;
2594         }
2595       }
2596       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2597               sg.getEndRes() + 1);
2598     }
2599     SequenceI[] cut = sg.getSequences()
2600             .toArray(new SequenceI[sg.getSize()]);
2601
2602     addHistoryItem(new EditCommand(
2603             MessageManager.getString("label.cut_sequences"), Action.CUT,
2604             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2605             viewport.getAlignment()));
2606
2607     viewport.setSelectionGroup(null);
2608     viewport.sendSelection();
2609     viewport.getAlignment().deleteGroup(sg);
2610
2611     viewport.firePropertyChange("alignment", null,
2612             viewport.getAlignment().getSequences());
2613     if (viewport.getAlignment().getHeight() < 1)
2614     {
2615       try
2616       {
2617         this.setClosed(true);
2618       } catch (Exception ex)
2619       {
2620       }
2621     }
2622   }
2623
2624   /**
2625    * DOCUMENT ME!
2626    *
2627    * @param e
2628    *          DOCUMENT ME!
2629    */
2630   @Override
2631   protected void deleteGroups_actionPerformed(ActionEvent e)
2632   {
2633     if (avc.deleteGroups())
2634     {
2635       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2636       alignPanel.updateAnnotation();
2637       alignPanel.paintAlignment(true);
2638     }
2639   }
2640
2641   /**
2642    * DOCUMENT ME!
2643    *
2644    * @param e
2645    *          DOCUMENT ME!
2646    */
2647   @Override
2648   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2649   {
2650     SequenceGroup sg = new SequenceGroup();
2651
2652     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2653     {
2654       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2655     }
2656
2657     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2658     viewport.setSelectionGroup(sg);
2659     viewport.sendSelection();
2660     // JAL-2034 - should delegate to
2661     // alignPanel to decide if overview needs
2662     // updating.
2663     alignPanel.paintAlignment(false);
2664     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2665   }
2666
2667   /**
2668    * DOCUMENT ME!
2669    *
2670    * @param e
2671    *          DOCUMENT ME!
2672    */
2673   @Override
2674   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2675   {
2676     if (viewport.cursorMode)
2677     {
2678       alignPanel.getSeqPanel().keyboardNo1 = null;
2679       alignPanel.getSeqPanel().keyboardNo2 = null;
2680     }
2681     viewport.setSelectionGroup(null);
2682     viewport.getColumnSelection().clear();
2683     viewport.setSelectionGroup(null);
2684     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2685     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2686     // JAL-2034 - should delegate to
2687     // alignPanel to decide if overview needs
2688     // updating.
2689     alignPanel.paintAlignment(false);
2690     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2691     viewport.sendSelection();
2692   }
2693
2694   /**
2695    * DOCUMENT ME!
2696    *
2697    * @param e
2698    *          DOCUMENT ME!
2699    */
2700   @Override
2701   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2702   {
2703     SequenceGroup sg = viewport.getSelectionGroup();
2704
2705     if (sg == null)
2706     {
2707       selectAllSequenceMenuItem_actionPerformed(null);
2708
2709       return;
2710     }
2711
2712     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2713     {
2714       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2715     }
2716     // JAL-2034 - should delegate to
2717     // alignPanel to decide if overview needs
2718     // updating.
2719
2720     alignPanel.paintAlignment(true);
2721     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2722     viewport.sendSelection();
2723   }
2724
2725   @Override
2726   public void invertColSel_actionPerformed(ActionEvent e)
2727   {
2728     viewport.invertColumnSelection();
2729     alignPanel.paintAlignment(true);
2730     viewport.sendSelection();
2731   }
2732
2733   /**
2734    * DOCUMENT ME!
2735    *
2736    * @param e
2737    *          DOCUMENT ME!
2738    */
2739   @Override
2740   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2741   {
2742     trimAlignment(true);
2743   }
2744
2745   /**
2746    * DOCUMENT ME!
2747    *
2748    * @param e
2749    *          DOCUMENT ME!
2750    */
2751   @Override
2752   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2753   {
2754     trimAlignment(false);
2755   }
2756
2757   void trimAlignment(boolean trimLeft)
2758   {
2759     ColumnSelection colSel = viewport.getColumnSelection();
2760     int column;
2761
2762     if (!colSel.isEmpty())
2763     {
2764       if (trimLeft)
2765       {
2766         column = colSel.getMin();
2767       }
2768       else
2769       {
2770         column = colSel.getMax();
2771       }
2772
2773       SequenceI[] seqs;
2774       if (viewport.getSelectionGroup() != null)
2775       {
2776         seqs = viewport.getSelectionGroup()
2777                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2778       }
2779       else
2780       {
2781         seqs = viewport.getAlignment().getSequencesArray();
2782       }
2783
2784       TrimRegionCommand trimRegion;
2785       if (trimLeft)
2786       {
2787         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2788                 column, viewport.getAlignment());
2789         vpRanges.setStartRes(0);
2790       }
2791       else
2792       {
2793         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2794                 column, viewport.getAlignment());
2795       }
2796
2797       statusBar.setText(MessageManager
2798               .formatMessage("label.removed_columns", new String[]
2799               { Integer.valueOf(trimRegion.getSize()).toString() }));
2800
2801       addHistoryItem(trimRegion);
2802
2803       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2804       {
2805         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2806                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2807         {
2808           viewport.getAlignment().deleteGroup(sg);
2809         }
2810       }
2811
2812       viewport.firePropertyChange("alignment", null,
2813               viewport.getAlignment().getSequences());
2814     }
2815   }
2816
2817   /**
2818    * DOCUMENT ME!
2819    *
2820    * @param e
2821    *          DOCUMENT ME!
2822    */
2823   @Override
2824   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2825   {
2826     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2827
2828     SequenceI[] seqs;
2829     if (viewport.getSelectionGroup() != null)
2830     {
2831       seqs = viewport.getSelectionGroup()
2832               .getSequencesAsArray(viewport.getHiddenRepSequences());
2833       start = viewport.getSelectionGroup().getStartRes();
2834       end = viewport.getSelectionGroup().getEndRes();
2835     }
2836     else
2837     {
2838       seqs = viewport.getAlignment().getSequencesArray();
2839     }
2840
2841     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2842             "Remove Gapped Columns", seqs, start, end,
2843             viewport.getAlignment());
2844
2845     addHistoryItem(removeGapCols);
2846
2847     statusBar.setText(MessageManager
2848             .formatMessage("label.removed_empty_columns", new Object[]
2849             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2850
2851     // This is to maintain viewport position on first residue
2852     // of first sequence
2853     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2854     int startRes = seq.findPosition(vpRanges.getStartRes());
2855     // ShiftList shifts;
2856     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2857     // edit.alColumnChanges=shifts.getInverse();
2858     // if (viewport.hasHiddenColumns)
2859     // viewport.getColumnSelection().compensateForEdits(shifts);
2860     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2861     viewport.firePropertyChange("alignment", null,
2862             viewport.getAlignment().getSequences());
2863
2864   }
2865
2866   /**
2867    * DOCUMENT ME!
2868    *
2869    * @param e
2870    *          DOCUMENT ME!
2871    */
2872   @Override
2873   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2874   {
2875     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2876
2877     SequenceI[] seqs;
2878     if (viewport.getSelectionGroup() != null)
2879     {
2880       seqs = viewport.getSelectionGroup()
2881               .getSequencesAsArray(viewport.getHiddenRepSequences());
2882       start = viewport.getSelectionGroup().getStartRes();
2883       end = viewport.getSelectionGroup().getEndRes();
2884     }
2885     else
2886     {
2887       seqs = viewport.getAlignment().getSequencesArray();
2888     }
2889
2890     // This is to maintain viewport position on first residue
2891     // of first sequence
2892     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2893     int startRes = seq.findPosition(vpRanges.getStartRes());
2894
2895     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2896             viewport.getAlignment()));
2897
2898     vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2899
2900     viewport.firePropertyChange("alignment", null,
2901             viewport.getAlignment().getSequences());
2902
2903   }
2904
2905   /**
2906    * DOCUMENT ME!
2907    *
2908    * @param e
2909    *          DOCUMENT ME!
2910    */
2911   @Override
2912   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2913   {
2914     viewport.setPadGaps(padGapsMenuitem.isSelected());
2915     viewport.firePropertyChange("alignment", null,
2916             viewport.getAlignment().getSequences());
2917   }
2918
2919   /**
2920    * DOCUMENT ME!
2921    *
2922    * @param e
2923    *          DOCUMENT ME!
2924    */
2925   @Override
2926   public void findMenuItem_actionPerformed(ActionEvent e)
2927   {
2928     new Finder();
2929   }
2930
2931   /**
2932    * Create a new view of the current alignment.
2933    */
2934   @Override
2935   public void newView_actionPerformed(ActionEvent e)
2936   {
2937     newView(null, true);
2938   }
2939
2940   /**
2941    * Creates and shows a new view of the current alignment.
2942    *
2943    * @param viewTitle
2944    *          title of newly created view; if null, one will be generated
2945    * @param copyAnnotation
2946    *          if true then duplicate all annnotation, groups and settings
2947    * @return new alignment panel, already displayed.
2948    */
2949   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2950   {
2951     /*
2952      * Create a new AlignmentPanel (with its own, new Viewport)
2953      */
2954     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2955             true);
2956     if (!copyAnnotation)
2957     {
2958       /*
2959        * remove all groups and annotation except for the automatic stuff
2960        */
2961       newap.av.getAlignment().deleteAllGroups();
2962       newap.av.getAlignment().deleteAllAnnotations(false);
2963     }
2964
2965     newap.av.setGatherViewsHere(false);
2966
2967     if (viewport.viewName == null)
2968     {
2969       viewport.viewName = MessageManager
2970               .getString("label.view_name_original");
2971     }
2972
2973     /*
2974      * Views share the same edits undo and redo stacks
2975      */
2976     newap.av.setHistoryList(viewport.getHistoryList());
2977     newap.av.setRedoList(viewport.getRedoList());
2978
2979     /*
2980      * Views share the same mappings; need to deregister any new mappings
2981      * created by copyAlignPanel, and register the new reference to the shared
2982      * mappings
2983      */
2984     newap.av.replaceMappings(viewport.getAlignment());
2985
2986     /*
2987      * start up cDNA consensus (if applicable) now mappings are in place
2988      */
2989     if (newap.av.initComplementConsensus())
2990     {
2991       newap.refresh(true); // adjust layout of annotations
2992     }
2993
2994     newap.av.viewName = getNewViewName(viewTitle);
2995
2996     addAlignmentPanel(newap, true);
2997     newap.alignmentChanged();
2998
2999     if (alignPanels.size() == 2)
3000     {
3001       viewport.setGatherViewsHere(true);
3002     }
3003     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3004     return newap;
3005   }
3006
3007   /**
3008    * Make a new name for the view, ensuring it is unique within the current
3009    * sequenceSetId. (This used to be essential for Jalview Project archives, but
3010    * these now use viewId. Unique view names are still desirable for usability.)
3011    *
3012    * @param viewTitle
3013    * @return
3014    */
3015   protected String getNewViewName(String viewTitle)
3016   {
3017     int index = Desktop.getViewCount(viewport.getSequenceSetId());
3018     boolean addFirstIndex = false;
3019     if (viewTitle == null || viewTitle.trim().length() == 0)
3020     {
3021       viewTitle = MessageManager.getString("action.view");
3022       addFirstIndex = true;
3023     }
3024     else
3025     {
3026       index = 1;// we count from 1 if given a specific name
3027     }
3028     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3029
3030     List<Component> comps = PaintRefresher.components
3031             .get(viewport.getSequenceSetId());
3032
3033     List<String> existingNames = getExistingViewNames(comps);
3034
3035     while (existingNames.contains(newViewName))
3036     {
3037       newViewName = viewTitle + " " + (++index);
3038     }
3039     return newViewName;
3040   }
3041
3042   /**
3043    * Returns a list of distinct view names found in the given list of
3044    * components. View names are held on the viewport of an AlignmentPanel.
3045    *
3046    * @param comps
3047    * @return
3048    */
3049   protected List<String> getExistingViewNames(List<Component> comps)
3050   {
3051     List<String> existingNames = new ArrayList<>();
3052     for (Component comp : comps)
3053     {
3054       if (comp instanceof AlignmentPanel)
3055       {
3056         AlignmentPanel ap = (AlignmentPanel) comp;
3057         if (!existingNames.contains(ap.av.viewName))
3058         {
3059           existingNames.add(ap.av.viewName);
3060         }
3061       }
3062     }
3063     return existingNames;
3064   }
3065
3066   /**
3067    * Explode tabbed views into separate windows.
3068    */
3069   @Override
3070   public void expandViews_actionPerformed(ActionEvent e)
3071   {
3072     Desktop.explodeViews(this);
3073   }
3074
3075   /**
3076    * Gather views in separate windows back into a tabbed presentation.
3077    */
3078   @Override
3079   public void gatherViews_actionPerformed(ActionEvent e)
3080   {
3081     Desktop.instance.gatherViews(this);
3082   }
3083
3084   /**
3085    * DOCUMENT ME!
3086    *
3087    * @param e
3088    *          DOCUMENT ME!
3089    */
3090   @Override
3091   public void font_actionPerformed(ActionEvent e)
3092   {
3093     new FontChooser(alignPanel);
3094   }
3095
3096   /**
3097    * DOCUMENT ME!
3098    *
3099    * @param e
3100    *          DOCUMENT ME!
3101    */
3102   @Override
3103   protected void seqLimit_actionPerformed(ActionEvent e)
3104   {
3105     viewport.setShowJVSuffix(seqLimits.isSelected());
3106
3107     alignPanel.getIdPanel().getIdCanvas()
3108             .setPreferredSize(alignPanel.calculateIdWidth());
3109     alignPanel.paintAlignment(true);
3110   }
3111
3112   @Override
3113   public void idRightAlign_actionPerformed(ActionEvent e)
3114   {
3115     viewport.setRightAlignIds(idRightAlign.isSelected());
3116     alignPanel.paintAlignment(true);
3117   }
3118
3119   @Override
3120   public void centreColumnLabels_actionPerformed(ActionEvent e)
3121   {
3122     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3123     alignPanel.paintAlignment(true);
3124   }
3125
3126   /*
3127    * (non-Javadoc)
3128    *
3129    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3130    */
3131   @Override
3132   protected void followHighlight_actionPerformed()
3133   {
3134     /*
3135      * Set the 'follow' flag on the Viewport (and scroll to position if now
3136      * true).
3137      */
3138     final boolean state = this.followHighlightMenuItem.getState();
3139     viewport.setFollowHighlight(state);
3140     if (state)
3141     {
3142       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3143     }
3144   }
3145
3146   /**
3147    * DOCUMENT ME!
3148    *
3149    * @param e
3150    *          DOCUMENT ME!
3151    */
3152   @Override
3153   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3154   {
3155     viewport.setColourText(colourTextMenuItem.isSelected());
3156     alignPanel.paintAlignment(true);
3157   }
3158
3159   /**
3160    * DOCUMENT ME!
3161    *
3162    * @param e
3163    *          DOCUMENT ME!
3164    */
3165   @Override
3166   public void wrapMenuItem_actionPerformed(ActionEvent e)
3167   {
3168     scaleAbove.setVisible(wrapMenuItem.isSelected());
3169     scaleLeft.setVisible(wrapMenuItem.isSelected());
3170     scaleRight.setVisible(wrapMenuItem.isSelected());
3171     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3172     alignPanel.updateLayout();
3173   }
3174
3175   @Override
3176   public void showAllSeqs_actionPerformed(ActionEvent e)
3177   {
3178     viewport.showAllHiddenSeqs();
3179   }
3180
3181   @Override
3182   public void showAllColumns_actionPerformed(ActionEvent e)
3183   {
3184     viewport.showAllHiddenColumns();
3185     alignPanel.paintAlignment(true);
3186     viewport.sendSelection();
3187   }
3188
3189   @Override
3190   public void hideSelSequences_actionPerformed(ActionEvent e)
3191   {
3192     viewport.hideAllSelectedSeqs();
3193   }
3194
3195   /**
3196    * called by key handler and the hide all/show all menu items
3197    *
3198    * @param toggleSeqs
3199    * @param toggleCols
3200    */
3201   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3202   {
3203
3204     boolean hide = false;
3205     SequenceGroup sg = viewport.getSelectionGroup();
3206     if (!toggleSeqs && !toggleCols)
3207     {
3208       // Hide everything by the current selection - this is a hack - we do the
3209       // invert and then hide
3210       // first check that there will be visible columns after the invert.
3211       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3212               && sg.getStartRes() <= sg.getEndRes()))
3213       {
3214         // now invert the sequence set, if required - empty selection implies
3215         // that no hiding is required.
3216         if (sg != null)
3217         {
3218           invertSequenceMenuItem_actionPerformed(null);
3219           sg = viewport.getSelectionGroup();
3220           toggleSeqs = true;
3221
3222         }
3223         viewport.expandColSelection(sg, true);
3224         // finally invert the column selection and get the new sequence
3225         // selection.
3226         invertColSel_actionPerformed(null);
3227         toggleCols = true;
3228       }
3229     }
3230
3231     if (toggleSeqs)
3232     {
3233       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3234       {
3235         hideSelSequences_actionPerformed(null);
3236         hide = true;
3237       }
3238       else if (!(toggleCols && viewport.hasSelectedColumns()))
3239       {
3240         showAllSeqs_actionPerformed(null);
3241       }
3242     }
3243
3244     if (toggleCols)
3245     {
3246       if (viewport.hasSelectedColumns())
3247       {
3248         hideSelColumns_actionPerformed(null);
3249         if (!toggleSeqs)
3250         {
3251           viewport.setSelectionGroup(sg);
3252         }
3253       }
3254       else if (!hide)
3255       {
3256         showAllColumns_actionPerformed(null);
3257       }
3258     }
3259   }
3260
3261   /*
3262    * (non-Javadoc)
3263    *
3264    * @see
3265    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3266    * event.ActionEvent)
3267    */
3268   @Override
3269   public void hideAllButSelection_actionPerformed(ActionEvent e)
3270   {
3271     toggleHiddenRegions(false, false);
3272     viewport.sendSelection();
3273   }
3274
3275   /*
3276    * (non-Javadoc)
3277    *
3278    * @see
3279    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3280    * .ActionEvent)
3281    */
3282   @Override
3283   public void hideAllSelection_actionPerformed(ActionEvent e)
3284   {
3285     SequenceGroup sg = viewport.getSelectionGroup();
3286     viewport.expandColSelection(sg, false);
3287     viewport.hideAllSelectedSeqs();
3288     viewport.hideSelectedColumns();
3289     alignPanel.paintAlignment(true);
3290     viewport.sendSelection();
3291   }
3292
3293   /*
3294    * (non-Javadoc)
3295    *
3296    * @see
3297    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3298    * ActionEvent)
3299    */
3300   @Override
3301   public void showAllhidden_actionPerformed(ActionEvent e)
3302   {
3303     viewport.showAllHiddenColumns();
3304     viewport.showAllHiddenSeqs();
3305     alignPanel.paintAlignment(true);
3306     viewport.sendSelection();
3307   }
3308
3309   @Override
3310   public void hideSelColumns_actionPerformed(ActionEvent e)
3311   {
3312     viewport.hideSelectedColumns();
3313     alignPanel.paintAlignment(true);
3314     viewport.sendSelection();
3315   }
3316
3317   @Override
3318   public void hiddenMarkers_actionPerformed(ActionEvent e)
3319   {
3320     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3321     repaint();
3322   }
3323
3324   /**
3325    * DOCUMENT ME!
3326    *
3327    * @param e
3328    *          DOCUMENT ME!
3329    */
3330   @Override
3331   protected void scaleAbove_actionPerformed(ActionEvent e)
3332   {
3333     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3334     alignPanel.paintAlignment(true);
3335   }
3336
3337   /**
3338    * DOCUMENT ME!
3339    *
3340    * @param e
3341    *          DOCUMENT ME!
3342    */
3343   @Override
3344   protected void scaleLeft_actionPerformed(ActionEvent e)
3345   {
3346     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3347     alignPanel.paintAlignment(true);
3348   }
3349
3350   /**
3351    * DOCUMENT ME!
3352    *
3353    * @param e
3354    *          DOCUMENT ME!
3355    */
3356   @Override
3357   protected void scaleRight_actionPerformed(ActionEvent e)
3358   {
3359     viewport.setScaleRightWrapped(scaleRight.isSelected());
3360     alignPanel.paintAlignment(true);
3361   }
3362
3363   /**
3364    * DOCUMENT ME!
3365    *
3366    * @param e
3367    *          DOCUMENT ME!
3368    */
3369   @Override
3370   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3371   {
3372     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3373     alignPanel.paintAlignment(true);
3374   }
3375
3376   /**
3377    * DOCUMENT ME!
3378    *
3379    * @param e
3380    *          DOCUMENT ME!
3381    */
3382   @Override
3383   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3384   {
3385     viewport.setShowText(viewTextMenuItem.isSelected());
3386     alignPanel.paintAlignment(true);
3387   }
3388
3389   /**
3390    * DOCUMENT ME!
3391    *
3392    * @param e
3393    *          DOCUMENT ME!
3394    */
3395   @Override
3396   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3397   {
3398     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3399     alignPanel.paintAlignment(true);
3400   }
3401
3402   public FeatureSettings featureSettings;
3403
3404   @Override
3405   public FeatureSettingsControllerI getFeatureSettingsUI()
3406   {
3407     return featureSettings;
3408   }
3409
3410   @Override
3411   public void featureSettings_actionPerformed(ActionEvent e)
3412   {
3413     if (featureSettings != null)
3414     {
3415       featureSettings.close();
3416       featureSettings = null;
3417     }
3418     if (!showSeqFeatures.isSelected())
3419     {
3420       // make sure features are actually displayed
3421       showSeqFeatures.setSelected(true);
3422       showSeqFeatures_actionPerformed(null);
3423     }
3424     featureSettings = new FeatureSettings(this);
3425   }
3426
3427   /**
3428    * Set or clear 'Show Sequence Features'
3429    *
3430    * @param evt
3431    *          DOCUMENT ME!
3432    */
3433   @Override
3434   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3435   {
3436     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3437     alignPanel.paintAlignment(true);
3438   }
3439
3440   /**
3441    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3442    * the annotations panel as a whole.
3443    *
3444    * The options to show/hide all annotations should be enabled when the panel
3445    * is shown, and disabled when the panel is hidden.
3446    *
3447    * @param e
3448    */
3449   @Override
3450   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3451   {
3452     final boolean setVisible = annotationPanelMenuItem.isSelected();
3453     viewport.setShowAnnotation(setVisible);
3454     this.showAllSeqAnnotations.setEnabled(setVisible);
3455     this.hideAllSeqAnnotations.setEnabled(setVisible);
3456     this.showAllAlAnnotations.setEnabled(setVisible);
3457     this.hideAllAlAnnotations.setEnabled(setVisible);
3458     alignPanel.updateLayout();
3459   }
3460
3461   @Override
3462   public void alignmentProperties()
3463   {
3464     JEditorPane editPane = new JEditorPane("text/html", "");
3465     editPane.setEditable(false);
3466     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3467             .formatAsHtml();
3468     editPane.setText(
3469             MessageManager.formatMessage("label.html_content", new Object[]
3470             { contents.toString() }));
3471     JInternalFrame frame = new JInternalFrame();
3472     frame.getContentPane().add(new JScrollPane(editPane));
3473
3474     Desktop.addInternalFrame(frame, MessageManager
3475             .formatMessage("label.alignment_properties", new Object[]
3476             { getTitle() }), 500, 400);
3477   }
3478
3479   /**
3480    * DOCUMENT ME!
3481    *
3482    * @param e
3483    *          DOCUMENT ME!
3484    */
3485   @Override
3486   public void overviewMenuItem_actionPerformed(ActionEvent e)
3487   {
3488     if (alignPanel.overviewPanel != null)
3489     {
3490       return;
3491     }
3492
3493     JInternalFrame frame = new JInternalFrame();
3494     final OverviewPanel overview = new OverviewPanel(alignPanel);
3495     frame.setContentPane(overview);
3496     Desktop.addInternalFrame(frame, MessageManager
3497             .formatMessage("label.overview_params", new Object[]
3498             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3499             true, true);
3500     frame.pack();
3501     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3502     frame.addInternalFrameListener(
3503             new javax.swing.event.InternalFrameAdapter()
3504             {
3505               @Override
3506               public void internalFrameClosed(
3507                       javax.swing.event.InternalFrameEvent evt)
3508               {
3509                 overview.dispose();
3510                 alignPanel.setOverviewPanel(null);
3511               };
3512             });
3513
3514     alignPanel.setOverviewPanel(overview);
3515   }
3516
3517   @Override
3518   public void textColour_actionPerformed()
3519   {
3520     new TextColourChooser().chooseColour(alignPanel, null);
3521   }
3522
3523   /*
3524    * public void covariationColour_actionPerformed() {
3525    * changeColour(new
3526    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3527    * ()[0])); }
3528    */
3529   @Override
3530   public void annotationColour_actionPerformed()
3531   {
3532     new AnnotationColourChooser(viewport, alignPanel);
3533   }
3534
3535   @Override
3536   public void annotationColumn_actionPerformed(ActionEvent e)
3537   {
3538     new AnnotationColumnChooser(viewport, alignPanel);
3539   }
3540
3541   /**
3542    * Action on the user checking or unchecking the option to apply the selected
3543    * colour scheme to all groups. If unchecked, groups may have their own
3544    * independent colour schemes.
3545    *
3546    * @param selected
3547    */
3548   @Override
3549   public void applyToAllGroups_actionPerformed(boolean selected)
3550   {
3551     viewport.setColourAppliesToAllGroups(selected);
3552   }
3553
3554   /**
3555    * Action on user selecting a colour from the colour menu
3556    *
3557    * @param name
3558    *          the name (not the menu item label!) of the colour scheme
3559    */
3560   @Override
3561   public void changeColour_actionPerformed(String name)
3562   {
3563     /*
3564      * 'User Defined' opens a panel to configure or load a
3565      * user-defined colour scheme
3566      */
3567     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3568     {
3569       new UserDefinedColours(alignPanel);
3570       return;
3571     }
3572
3573     /*
3574      * otherwise set the chosen colour scheme (or null for 'None')
3575      */
3576     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3577             viewport.getAlignment(), viewport.getHiddenRepSequences());
3578     changeColour(cs);
3579   }
3580
3581   /**
3582    * Actions on setting or changing the alignment colour scheme
3583    *
3584    * @param cs
3585    */
3586   @Override
3587   public void changeColour(ColourSchemeI cs)
3588   {
3589     // TODO: pull up to controller method
3590     ColourMenuHelper.setColourSelected(colourMenu, cs);
3591
3592     viewport.setGlobalColourScheme(cs);
3593
3594     alignPanel.paintAlignment(true);
3595   }
3596
3597   /**
3598    * Show the PID threshold slider panel
3599    */
3600   @Override
3601   protected void modifyPID_actionPerformed()
3602   {
3603     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3604             alignPanel.getViewName());
3605     SliderPanel.showPIDSlider();
3606   }
3607
3608   /**
3609    * Show the Conservation slider panel
3610    */
3611   @Override
3612   protected void modifyConservation_actionPerformed()
3613   {
3614     SliderPanel.setConservationSlider(alignPanel,
3615             viewport.getResidueShading(), alignPanel.getViewName());
3616     SliderPanel.showConservationSlider();
3617   }
3618
3619   /**
3620    * Action on selecting or deselecting (Colour) By Conservation
3621    */
3622   @Override
3623   public void conservationMenuItem_actionPerformed(boolean selected)
3624   {
3625     modifyConservation.setEnabled(selected);
3626     viewport.setConservationSelected(selected);
3627     viewport.getResidueShading().setConservationApplied(selected);
3628
3629     changeColour(viewport.getGlobalColourScheme());
3630     if (selected)
3631     {
3632       modifyConservation_actionPerformed();
3633     }
3634     else
3635     {
3636       SliderPanel.hideConservationSlider();
3637     }
3638   }
3639
3640   /**
3641    * Action on selecting or deselecting (Colour) Above PID Threshold
3642    */
3643   @Override
3644   public void abovePIDThreshold_actionPerformed(boolean selected)
3645   {
3646     modifyPID.setEnabled(selected);
3647     viewport.setAbovePIDThreshold(selected);
3648     if (!selected)
3649     {
3650       viewport.getResidueShading().setThreshold(0,
3651               viewport.isIgnoreGapsConsensus());
3652     }
3653
3654     changeColour(viewport.getGlobalColourScheme());
3655     if (selected)
3656     {
3657       modifyPID_actionPerformed();
3658     }
3659     else
3660     {
3661       SliderPanel.hidePIDSlider();
3662     }
3663   }
3664
3665   /**
3666    * DOCUMENT ME!
3667    *
3668    * @param e
3669    *          DOCUMENT ME!
3670    */
3671   @Override
3672   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3673   {
3674     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3675     AlignmentSorter.sortByPID(viewport.getAlignment(),
3676             viewport.getAlignment().getSequenceAt(0));
3677     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3678             viewport.getAlignment()));
3679     alignPanel.paintAlignment(true);
3680   }
3681
3682   /**
3683    * DOCUMENT ME!
3684    *
3685    * @param e
3686    *          DOCUMENT ME!
3687    */
3688   @Override
3689   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3690   {
3691     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3692     AlignmentSorter.sortByID(viewport.getAlignment());
3693     addHistoryItem(
3694             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3695     alignPanel.paintAlignment(true);
3696   }
3697
3698   /**
3699    * DOCUMENT ME!
3700    *
3701    * @param e
3702    *          DOCUMENT ME!
3703    */
3704   @Override
3705   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3706   {
3707     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3708     AlignmentSorter.sortByLength(viewport.getAlignment());
3709     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3710             viewport.getAlignment()));
3711     alignPanel.paintAlignment(true);
3712   }
3713
3714   /**
3715    * DOCUMENT ME!
3716    *
3717    * @param e
3718    *          DOCUMENT ME!
3719    */
3720   @Override
3721   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3722   {
3723     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3724     AlignmentSorter.sortByGroup(viewport.getAlignment());
3725     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3726             viewport.getAlignment()));
3727
3728     alignPanel.paintAlignment(true);
3729   }
3730
3731   /**
3732    * DOCUMENT ME!
3733    *
3734    * @param e
3735    *          DOCUMENT ME!
3736    */
3737   @Override
3738   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3739   {
3740     new RedundancyPanel(alignPanel, this);
3741   }
3742
3743   /**
3744    * DOCUMENT ME!
3745    *
3746    * @param e
3747    *          DOCUMENT ME!
3748    */
3749   @Override
3750   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3751   {
3752     if ((viewport.getSelectionGroup() == null)
3753             || (viewport.getSelectionGroup().getSize() < 2))
3754     {
3755       JvOptionPane.showInternalMessageDialog(this,
3756               MessageManager.getString(
3757                       "label.you_must_select_least_two_sequences"),
3758               MessageManager.getString("label.invalid_selection"),
3759               JvOptionPane.WARNING_MESSAGE);
3760     }
3761     else
3762     {
3763       JInternalFrame frame = new JInternalFrame();
3764       frame.setContentPane(new PairwiseAlignPanel(viewport));
3765       Desktop.addInternalFrame(frame,
3766               MessageManager.getString("action.pairwise_alignment"), 600,
3767               500);
3768     }
3769   }
3770
3771   @Override
3772   public void autoCalculate_actionPerformed(ActionEvent e)
3773   {
3774     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3775     if (viewport.autoCalculateConsensus)
3776     {
3777       viewport.firePropertyChange("alignment", null,
3778               viewport.getAlignment().getSequences());
3779     }
3780   }
3781
3782   @Override
3783   public void sortByTreeOption_actionPerformed(ActionEvent e)
3784   {
3785     viewport.sortByTree = sortByTree.isSelected();
3786   }
3787
3788   @Override
3789   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3790   {
3791     viewport.followSelection = listenToViewSelections.isSelected();
3792   }
3793
3794   /**
3795    * Constructs a tree panel and adds it to the desktop
3796    *
3797    * @param type
3798    *          tree type (NJ or AV)
3799    * @param modelName
3800    *          name of score model used to compute the tree
3801    * @param options
3802    *          parameters for the distance or similarity calculation
3803    */
3804   void newTreePanel(String type, String modelName,
3805           SimilarityParamsI options)
3806   {
3807     String frameTitle = "";
3808     TreePanel tp;
3809
3810     boolean onSelection = false;
3811     if (viewport.getSelectionGroup() != null
3812             && viewport.getSelectionGroup().getSize() > 0)
3813     {
3814       SequenceGroup sg = viewport.getSelectionGroup();
3815
3816       /* Decide if the selection is a column region */
3817       for (SequenceI _s : sg.getSequences())
3818       {
3819         if (_s.getLength() < sg.getEndRes())
3820         {
3821           JvOptionPane.showMessageDialog(Desktop.desktop,
3822                   MessageManager.getString(
3823                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3824                   MessageManager.getString(
3825                           "label.sequences_selection_not_aligned"),
3826                   JvOptionPane.WARNING_MESSAGE);
3827
3828           return;
3829         }
3830       }
3831       onSelection = true;
3832     }
3833     else
3834     {
3835       if (viewport.getAlignment().getHeight() < 2)
3836       {
3837         return;
3838       }
3839     }
3840
3841     tp = new TreePanel(alignPanel, type, modelName, options);
3842     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3843
3844     frameTitle += " from ";
3845
3846     if (viewport.viewName != null)
3847     {
3848       frameTitle += viewport.viewName + " of ";
3849     }
3850
3851     frameTitle += this.title;
3852
3853     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3854   }
3855
3856   /**
3857    * DOCUMENT ME!
3858    *
3859    * @param title
3860    *          DOCUMENT ME!
3861    * @param order
3862    *          DOCUMENT ME!
3863    */
3864   public void addSortByOrderMenuItem(String title,
3865           final AlignmentOrder order)
3866   {
3867     final JMenuItem item = new JMenuItem(MessageManager
3868             .formatMessage("action.by_title_param", new Object[]
3869             { title }));
3870     sort.add(item);
3871     item.addActionListener(new java.awt.event.ActionListener()
3872     {
3873       @Override
3874       public void actionPerformed(ActionEvent e)
3875       {
3876         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3877
3878         // TODO: JBPNote - have to map order entries to curent SequenceI
3879         // pointers
3880         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3881
3882         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3883                 viewport.getAlignment()));
3884
3885         alignPanel.paintAlignment(true);
3886       }
3887     });
3888   }
3889
3890   /**
3891    * Add a new sort by annotation score menu item
3892    *
3893    * @param sort
3894    *          the menu to add the option to
3895    * @param scoreLabel
3896    *          the label used to retrieve scores for each sequence on the
3897    *          alignment
3898    */
3899   public void addSortByAnnotScoreMenuItem(JMenu sort,
3900           final String scoreLabel)
3901   {
3902     final JMenuItem item = new JMenuItem(scoreLabel);
3903     sort.add(item);
3904     item.addActionListener(new java.awt.event.ActionListener()
3905     {
3906       @Override
3907       public void actionPerformed(ActionEvent e)
3908       {
3909         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3910         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3911                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3912         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3913                 viewport.getAlignment()));
3914         alignPanel.paintAlignment(true);
3915       }
3916     });
3917   }
3918
3919   /**
3920    * last hash for alignment's annotation array - used to minimise cost of
3921    * rebuild.
3922    */
3923   protected int _annotationScoreVectorHash;
3924
3925   /**
3926    * search the alignment and rebuild the sort by annotation score submenu the
3927    * last alignment annotation vector hash is stored to minimize cost of
3928    * rebuilding in subsequence calls.
3929    *
3930    */
3931   @Override
3932   public void buildSortByAnnotationScoresMenu()
3933   {
3934     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3935     {
3936       return;
3937     }
3938
3939     if (viewport.getAlignment().getAlignmentAnnotation()
3940             .hashCode() != _annotationScoreVectorHash)
3941     {
3942       sortByAnnotScore.removeAll();
3943       // almost certainly a quicker way to do this - but we keep it simple
3944       Hashtable scoreSorts = new Hashtable();
3945       AlignmentAnnotation aann[];
3946       for (SequenceI sqa : viewport.getAlignment().getSequences())
3947       {
3948         aann = sqa.getAnnotation();
3949         for (int i = 0; aann != null && i < aann.length; i++)
3950         {
3951           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3952           {
3953             scoreSorts.put(aann[i].label, aann[i].label);
3954           }
3955         }
3956       }
3957       Enumeration labels = scoreSorts.keys();
3958       while (labels.hasMoreElements())
3959       {
3960         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3961                 (String) labels.nextElement());
3962       }
3963       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3964       scoreSorts.clear();
3965
3966       _annotationScoreVectorHash = viewport.getAlignment()
3967               .getAlignmentAnnotation().hashCode();
3968     }
3969   }
3970
3971   /**
3972    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3973    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3974    * call. Listeners are added to remove the menu item when the treePanel is
3975    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3976    * modified.
3977    */
3978   @Override
3979   public void buildTreeSortMenu()
3980   {
3981     sortByTreeMenu.removeAll();
3982
3983     List<Component> comps = PaintRefresher.components
3984             .get(viewport.getSequenceSetId());
3985     List<TreePanel> treePanels = new ArrayList<>();
3986     for (Component comp : comps)
3987     {
3988       if (comp instanceof TreePanel)
3989       {
3990         treePanels.add((TreePanel) comp);
3991       }
3992     }
3993
3994     if (treePanels.size() < 1)
3995     {
3996       sortByTreeMenu.setVisible(false);
3997       return;
3998     }
3999
4000     sortByTreeMenu.setVisible(true);
4001
4002     for (final TreePanel tp : treePanels)
4003     {
4004       final JMenuItem item = new JMenuItem(tp.getTitle());
4005       item.addActionListener(new java.awt.event.ActionListener()
4006       {
4007         @Override
4008         public void actionPerformed(ActionEvent e)
4009         {
4010           tp.sortByTree_actionPerformed();
4011           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4012
4013         }
4014       });
4015
4016       sortByTreeMenu.add(item);
4017     }
4018   }
4019
4020   public boolean sortBy(AlignmentOrder alorder, String undoname)
4021   {
4022     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4023     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4024     if (undoname != null)
4025     {
4026       addHistoryItem(new OrderCommand(undoname, oldOrder,
4027               viewport.getAlignment()));
4028     }
4029     alignPanel.paintAlignment(true);
4030     return true;
4031   }
4032
4033   /**
4034    * Work out whether the whole set of sequences or just the selected set will
4035    * be submitted for multiple alignment.
4036    *
4037    */
4038   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4039   {
4040     // Now, check we have enough sequences
4041     AlignmentView msa = null;
4042
4043     if ((viewport.getSelectionGroup() != null)
4044             && (viewport.getSelectionGroup().getSize() > 1))
4045     {
4046       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4047       // some common interface!
4048       /*
4049        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4050        * SequenceI[sz = seqs.getSize(false)];
4051        *
4052        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4053        * seqs.getSequenceAt(i); }
4054        */
4055       msa = viewport.getAlignmentView(true);
4056     }
4057     else if (viewport.getSelectionGroup() != null
4058             && viewport.getSelectionGroup().getSize() == 1)
4059     {
4060       int option = JvOptionPane.showConfirmDialog(this,
4061               MessageManager.getString("warn.oneseq_msainput_selection"),
4062               MessageManager.getString("label.invalid_selection"),
4063               JvOptionPane.OK_CANCEL_OPTION);
4064       if (option == JvOptionPane.OK_OPTION)
4065       {
4066         msa = viewport.getAlignmentView(false);
4067       }
4068     }
4069     else
4070     {
4071       msa = viewport.getAlignmentView(false);
4072     }
4073     return msa;
4074   }
4075
4076   /**
4077    * Decides what is submitted to a secondary structure prediction service: the
4078    * first sequence in the alignment, or in the current selection, or, if the
4079    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4080    * region or the whole alignment. (where the first sequence in the set is the
4081    * one that the prediction will be for).
4082    */
4083   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4084   {
4085     AlignmentView seqs = null;
4086
4087     if ((viewport.getSelectionGroup() != null)
4088             && (viewport.getSelectionGroup().getSize() > 0))
4089     {
4090       seqs = viewport.getAlignmentView(true);
4091     }
4092     else
4093     {
4094       seqs = viewport.getAlignmentView(false);
4095     }
4096     // limit sequences - JBPNote in future - could spawn multiple prediction
4097     // jobs
4098     // TODO: viewport.getAlignment().isAligned is a global state - the local
4099     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4100     if (!viewport.getAlignment().isAligned(false))
4101     {
4102       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4103       // TODO: if seqs.getSequences().length>1 then should really have warned
4104       // user!
4105
4106     }
4107     return seqs;
4108   }
4109
4110   /**
4111    * DOCUMENT ME!
4112    *
4113    * @param e
4114    *          DOCUMENT ME!
4115    */
4116   @Override
4117   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4118   {
4119     // Pick the tree file
4120     JalviewFileChooser chooser = new JalviewFileChooser(
4121             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4122     chooser.setFileView(new JalviewFileView());
4123     chooser.setDialogTitle(
4124             MessageManager.getString("label.select_newick_like_tree_file"));
4125     chooser.setToolTipText(
4126             MessageManager.getString("label.load_tree_file"));
4127
4128     int value = chooser.showOpenDialog(null);
4129
4130     if (value == JalviewFileChooser.APPROVE_OPTION)
4131     {
4132       String filePath = chooser.getSelectedFile().getPath();
4133       Cache.setProperty("LAST_DIRECTORY", filePath);
4134       NewickFile fin = null;
4135       try
4136       {
4137         fin = new NewickFile(filePath, DataSourceType.FILE);
4138         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4139       } catch (Exception ex)
4140       {
4141         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4142                 MessageManager.getString("label.problem_reading_tree_file"),
4143                 JvOptionPane.WARNING_MESSAGE);
4144         ex.printStackTrace();
4145       }
4146       if (fin != null && fin.hasWarningMessage())
4147       {
4148         JvOptionPane.showMessageDialog(Desktop.desktop,
4149                 fin.getWarningMessage(),
4150                 MessageManager
4151                         .getString("label.possible_problem_with_tree_file"),
4152                 JvOptionPane.WARNING_MESSAGE);
4153       }
4154     }
4155   }
4156
4157   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4158   {
4159     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4160   }
4161
4162   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4163           int h, int x, int y)
4164   {
4165     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4166   }
4167
4168   /**
4169    * Add a treeviewer for the tree extracted from a Newick file object to the
4170    * current alignment view
4171    *
4172    * @param nf
4173    *          the tree
4174    * @param title
4175    *          tree viewer title
4176    * @param input
4177    *          Associated alignment input data (or null)
4178    * @param w
4179    *          width
4180    * @param h
4181    *          height
4182    * @param x
4183    *          position
4184    * @param y
4185    *          position
4186    * @return TreePanel handle
4187    */
4188   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4189           AlignmentView input, int w, int h, int x, int y)
4190   {
4191     TreePanel tp = null;
4192
4193     try
4194     {
4195       nf.parse();
4196
4197       if (nf.getTree() != null)
4198       {
4199         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4200
4201         tp.setSize(w, h);
4202
4203         if (x > 0 && y > 0)
4204         {
4205           tp.setLocation(x, y);
4206         }
4207
4208         Desktop.addInternalFrame(tp, treeTitle, w, h);
4209       }
4210     } catch (Exception ex)
4211     {
4212       ex.printStackTrace();
4213     }
4214
4215     return tp;
4216   }
4217
4218   private boolean buildingMenu = false;
4219
4220   /**
4221    * Generates menu items and listener event actions for web service clients
4222    *
4223    */
4224   public void BuildWebServiceMenu()
4225   {
4226     while (buildingMenu)
4227     {
4228       try
4229       {
4230         System.err.println("Waiting for building menu to finish.");
4231         Thread.sleep(10);
4232       } catch (Exception e)
4233       {
4234       }
4235     }
4236     final AlignFrame me = this;
4237     buildingMenu = true;
4238     new Thread(new Runnable()
4239     {
4240       @Override
4241       public void run()
4242       {
4243         final List<JMenuItem> legacyItems = new ArrayList<>();
4244         try
4245         {
4246           // System.err.println("Building ws menu again "
4247           // + Thread.currentThread());
4248           // TODO: add support for context dependent disabling of services based
4249           // on
4250           // alignment and current selection
4251           // TODO: add additional serviceHandle parameter to specify abstract
4252           // handler
4253           // class independently of AbstractName
4254           // TODO: add in rediscovery GUI function to restart discoverer
4255           // TODO: group services by location as well as function and/or
4256           // introduce
4257           // object broker mechanism.
4258           final Vector<JMenu> wsmenu = new Vector<>();
4259           final IProgressIndicator af = me;
4260
4261           /*
4262            * do not i18n these strings - they are hard-coded in class
4263            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4264            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4265            */
4266           final JMenu msawsmenu = new JMenu("Alignment");
4267           final JMenu secstrmenu = new JMenu(
4268                   "Secondary Structure Prediction");
4269           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4270           final JMenu analymenu = new JMenu("Analysis");
4271           final JMenu dismenu = new JMenu("Protein Disorder");
4272           // JAL-940 - only show secondary structure prediction services from
4273           // the legacy server
4274           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4275               // &&
4276           Discoverer.services != null && (Discoverer.services.size() > 0))
4277           {
4278             // TODO: refactor to allow list of AbstractName/Handler bindings to
4279             // be
4280             // stored or retrieved from elsewhere
4281             // No MSAWS used any more:
4282             // Vector msaws = null; // (Vector)
4283             // Discoverer.services.get("MsaWS");
4284             Vector secstrpr = (Vector) Discoverer.services
4285                     .get("SecStrPred");
4286             if (secstrpr != null)
4287             {
4288               // Add any secondary structure prediction services
4289               for (int i = 0, j = secstrpr.size(); i < j; i++)
4290               {
4291                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4292                         .get(i);
4293                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4294                         .getServiceClient(sh);
4295                 int p = secstrmenu.getItemCount();
4296                 impl.attachWSMenuEntry(secstrmenu, me);
4297                 int q = secstrmenu.getItemCount();
4298                 for (int litm = p; litm < q; litm++)
4299                 {
4300                   legacyItems.add(secstrmenu.getItem(litm));
4301                 }
4302               }
4303             }
4304           }
4305
4306           // Add all submenus in the order they should appear on the web
4307           // services menu
4308           wsmenu.add(msawsmenu);
4309           wsmenu.add(secstrmenu);
4310           wsmenu.add(dismenu);
4311           wsmenu.add(analymenu);
4312           // No search services yet
4313           // wsmenu.add(seqsrchmenu);
4314
4315           javax.swing.SwingUtilities.invokeLater(new Runnable()
4316           {
4317             @Override
4318             public void run()
4319             {
4320               try
4321               {
4322                 webService.removeAll();
4323                 // first, add discovered services onto the webservices menu
4324                 if (wsmenu.size() > 0)
4325                 {
4326                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4327                   {
4328                     webService.add(wsmenu.get(i));
4329                   }
4330                 }
4331                 else
4332                 {
4333                   webService.add(me.webServiceNoServices);
4334                 }
4335                 // TODO: move into separate menu builder class.
4336                 boolean new_sspred = false;
4337                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4338                 {
4339                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4340                   if (jws2servs != null)
4341                   {
4342                     if (jws2servs.hasServices())
4343                     {
4344                       jws2servs.attachWSMenuEntry(webService, me);
4345                       for (Jws2Instance sv : jws2servs.getServices())
4346                       {
4347                         if (sv.description.toLowerCase().contains("jpred"))
4348                         {
4349                           for (JMenuItem jmi : legacyItems)
4350                           {
4351                             jmi.setVisible(false);
4352                           }
4353                         }
4354                       }
4355
4356                     }
4357                     if (jws2servs.isRunning())
4358                     {
4359                       JMenuItem tm = new JMenuItem(
4360                               "Still discovering JABA Services");
4361                       tm.setEnabled(false);
4362                       webService.add(tm);
4363                     }
4364                   }
4365                 }
4366                 build_urlServiceMenu(me.webService);
4367                 build_fetchdbmenu(webService);
4368                 for (JMenu item : wsmenu)
4369                 {
4370                   if (item.getItemCount() == 0)
4371                   {
4372                     item.setEnabled(false);
4373                   }
4374                   else
4375                   {
4376                     item.setEnabled(true);
4377                   }
4378                 }
4379               } catch (Exception e)
4380               {
4381                 Cache.log.debug(
4382                         "Exception during web service menu building process.",
4383                         e);
4384               }
4385             }
4386           });
4387         } catch (Exception e)
4388         {
4389         }
4390         buildingMenu = false;
4391       }
4392     }).start();
4393
4394   }
4395
4396   /**
4397    * construct any groupURL type service menu entries.
4398    *
4399    * @param webService
4400    */
4401   private void build_urlServiceMenu(JMenu webService)
4402   {
4403     // TODO: remove this code when 2.7 is released
4404     // DEBUG - alignmentView
4405     /*
4406      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4407      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4408      *
4409      * @Override public void actionPerformed(ActionEvent e) {
4410      * jalview.datamodel.AlignmentView
4411      * .testSelectionViews(af.viewport.getAlignment(),
4412      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4413      *
4414      * }); webService.add(testAlView);
4415      */
4416     // TODO: refactor to RestClient discoverer and merge menu entries for
4417     // rest-style services with other types of analysis/calculation service
4418     // SHmmr test client - still being implemented.
4419     // DEBUG - alignmentView
4420
4421     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4422             .getRestClients())
4423     {
4424       client.attachWSMenuEntry(
4425               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4426               this);
4427     }
4428   }
4429
4430   /**
4431    * Searches the alignment sequences for xRefs and builds the Show
4432    * Cross-References menu (formerly called Show Products), with database
4433    * sources for which cross-references are found (protein sources for a
4434    * nucleotide alignment and vice versa)
4435    *
4436    * @return true if Show Cross-references menu should be enabled
4437    */
4438   public boolean canShowProducts()
4439   {
4440     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4441     AlignmentI dataset = viewport.getAlignment().getDataset();
4442
4443     showProducts.removeAll();
4444     final boolean dna = viewport.getAlignment().isNucleotide();
4445
4446     if (seqs == null || seqs.length == 0)
4447     {
4448       // nothing to see here.
4449       return false;
4450     }
4451
4452     boolean showp = false;
4453     try
4454     {
4455       List<String> ptypes = new CrossRef(seqs, dataset)
4456               .findXrefSourcesForSequences(dna);
4457
4458       for (final String source : ptypes)
4459       {
4460         showp = true;
4461         final AlignFrame af = this;
4462         JMenuItem xtype = new JMenuItem(source);
4463         xtype.addActionListener(new ActionListener()
4464         {
4465           @Override
4466           public void actionPerformed(ActionEvent e)
4467           {
4468             showProductsFor(af.viewport.getSequenceSelection(), dna,
4469                     source);
4470           }
4471         });
4472         showProducts.add(xtype);
4473       }
4474       showProducts.setVisible(showp);
4475       showProducts.setEnabled(showp);
4476     } catch (Exception e)
4477     {
4478       Cache.log.warn(
4479               "canShowProducts threw an exception - please report to help@jalview.org",
4480               e);
4481       return false;
4482     }
4483     return showp;
4484   }
4485
4486   /**
4487    * Finds and displays cross-references for the selected sequences (protein
4488    * products for nucleotide sequences, dna coding sequences for peptides).
4489    *
4490    * @param sel
4491    *          the sequences to show cross-references for
4492    * @param dna
4493    *          true if from a nucleotide alignment (so showing proteins)
4494    * @param source
4495    *          the database to show cross-references for
4496    */
4497   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4498           final String source)
4499   {
4500     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4501             .start();
4502   }
4503
4504   /**
4505    * Construct and display a new frame containing the translation of this
4506    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4507    */
4508   @Override
4509   public void showTranslation_actionPerformed(ActionEvent e)
4510   {
4511     AlignmentI al = null;
4512     try
4513     {
4514       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4515
4516       al = dna.translateCdna();
4517     } catch (Exception ex)
4518     {
4519       jalview.bin.Cache.log.error(
4520               "Exception during translation. Please report this !", ex);
4521       final String msg = MessageManager.getString(
4522               "label.error_when_translating_sequences_submit_bug_report");
4523       final String errorTitle = MessageManager
4524               .getString("label.implementation_error")
4525               + MessageManager.getString("label.translation_failed");
4526       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4527               JvOptionPane.ERROR_MESSAGE);
4528       return;
4529     }
4530     if (al == null || al.getHeight() == 0)
4531     {
4532       final String msg = MessageManager.getString(
4533               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4534       final String errorTitle = MessageManager
4535               .getString("label.translation_failed");
4536       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4537               JvOptionPane.WARNING_MESSAGE);
4538     }
4539     else
4540     {
4541       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4542       af.setFileFormat(this.currentFileFormat);
4543       final String newTitle = MessageManager
4544               .formatMessage("label.translation_of_params", new Object[]
4545               { this.getTitle() });
4546       af.setTitle(newTitle);
4547       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4548       {
4549         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4550         viewport.openSplitFrame(af, new Alignment(seqs));
4551       }
4552       else
4553       {
4554         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4555                 DEFAULT_HEIGHT);
4556       }
4557     }
4558   }
4559
4560   /**
4561    * Set the file format
4562    *
4563    * @param format
4564    */
4565   public void setFileFormat(FileFormatI format)
4566   {
4567     this.currentFileFormat = format;
4568   }
4569
4570   /**
4571    * Try to load a features file onto the alignment.
4572    *
4573    * @param file
4574    *          contents or path to retrieve file
4575    * @param sourceType
4576    *          access mode of file (see jalview.io.AlignFile)
4577    * @return true if features file was parsed correctly.
4578    */
4579   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4580   {
4581     return avc.parseFeaturesFile(file, sourceType,
4582             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4583
4584   }
4585
4586   @Override
4587   public void refreshFeatureUI(boolean enableIfNecessary)
4588   {
4589     // note - currently this is only still here rather than in the controller
4590     // because of the featureSettings hard reference that is yet to be
4591     // abstracted
4592     if (enableIfNecessary)
4593     {
4594       viewport.setShowSequenceFeatures(true);
4595       showSeqFeatures.setSelected(true);
4596     }
4597
4598   }
4599
4600   @Override
4601   public void dragEnter(DropTargetDragEvent evt)
4602   {
4603   }
4604
4605   @Override
4606   public void dragExit(DropTargetEvent evt)
4607   {
4608   }
4609
4610   @Override
4611   public void dragOver(DropTargetDragEvent evt)
4612   {
4613   }
4614
4615   @Override
4616   public void dropActionChanged(DropTargetDragEvent evt)
4617   {
4618   }
4619
4620   @Override
4621   public void drop(DropTargetDropEvent evt)
4622   {
4623     // JAL-1552 - acceptDrop required before getTransferable call for
4624     // Java's Transferable for native dnd
4625     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4626     Transferable t = evt.getTransferable();
4627     List<String> files = new ArrayList<>();
4628     List<DataSourceType> protocols = new ArrayList<>();
4629
4630     try
4631     {
4632       Desktop.transferFromDropTarget(files, protocols, evt, t);
4633     } catch (Exception e)
4634     {
4635       e.printStackTrace();
4636     }
4637     if (files != null)
4638     {
4639       try
4640       {
4641         // check to see if any of these files have names matching sequences in
4642         // the alignment
4643         SequenceIdMatcher idm = new SequenceIdMatcher(
4644                 viewport.getAlignment().getSequencesArray());
4645         /**
4646          * Object[] { String,SequenceI}
4647          */
4648         ArrayList<Object[]> filesmatched = new ArrayList<>();
4649         ArrayList<String> filesnotmatched = new ArrayList<>();
4650         for (int i = 0; i < files.size(); i++)
4651         {
4652           String file = files.get(i).toString();
4653           String pdbfn = "";
4654           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4655           if (protocol == DataSourceType.FILE)
4656           {
4657             File fl = new File(file);
4658             pdbfn = fl.getName();
4659           }
4660           else if (protocol == DataSourceType.URL)
4661           {
4662             URL url = new URL(file);
4663             pdbfn = url.getFile();
4664           }
4665           if (pdbfn.length() > 0)
4666           {
4667             // attempt to find a match in the alignment
4668             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4669             int l = 0, c = pdbfn.indexOf(".");
4670             while (mtch == null && c != -1)
4671             {
4672               do
4673               {
4674                 l = c;
4675               } while ((c = pdbfn.indexOf(".", l)) > l);
4676               if (l > -1)
4677               {
4678                 pdbfn = pdbfn.substring(0, l);
4679               }
4680               mtch = idm.findAllIdMatches(pdbfn);
4681             }
4682             if (mtch != null)
4683             {
4684               FileFormatI type = null;
4685               try
4686               {
4687                 type = new IdentifyFile().identify(file, protocol);
4688               } catch (Exception ex)
4689               {
4690                 type = null;
4691               }
4692               if (type != null && type.isStructureFile())
4693               {
4694                 filesmatched.add(new Object[] { file, protocol, mtch });
4695                 continue;
4696               }
4697             }
4698             // File wasn't named like one of the sequences or wasn't a PDB file.
4699             filesnotmatched.add(file);
4700           }
4701         }
4702         int assocfiles = 0;
4703         if (filesmatched.size() > 0)
4704         {
4705           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4706                   || JvOptionPane.showConfirmDialog(this,
4707                           MessageManager.formatMessage(
4708                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4709                                   new Object[]
4710                                   { Integer.valueOf(filesmatched.size())
4711                                           .toString() }),
4712                           MessageManager.getString(
4713                                   "label.automatically_associate_structure_files_by_name"),
4714                           JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4715
4716           {
4717             for (Object[] fm : filesmatched)
4718             {
4719               // try and associate
4720               // TODO: may want to set a standard ID naming formalism for
4721               // associating PDB files which have no IDs.
4722               for (SequenceI toassoc : (SequenceI[]) fm[2])
4723               {
4724                 PDBEntry pe = new AssociatePdbFileWithSeq()
4725                         .associatePdbWithSeq((String) fm[0],
4726                                 (DataSourceType) fm[1], toassoc, false,
4727                                 Desktop.instance);
4728                 if (pe != null)
4729                 {
4730                   System.err.println("Associated file : " + ((String) fm[0])
4731                           + " with " + toassoc.getDisplayId(true));
4732                   assocfiles++;
4733                 }
4734               }
4735               alignPanel.paintAlignment(true);
4736             }
4737           }
4738         }
4739         if (filesnotmatched.size() > 0)
4740         {
4741           if (assocfiles > 0 && (Cache.getDefault(
4742                   "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4743                   || JvOptionPane.showConfirmDialog(this,
4744                           "<html>" + MessageManager.formatMessage(
4745                                   "label.ignore_unmatched_dropped_files_info",
4746                                   new Object[]
4747                                   { Integer.valueOf(filesnotmatched.size())
4748                                           .toString() })
4749                                   + "</html>",
4750                           MessageManager.getString(
4751                                   "label.ignore_unmatched_dropped_files"),
4752                           JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4753           {
4754             return;
4755           }
4756           for (String fn : filesnotmatched)
4757           {
4758             loadJalviewDataFile(fn, null, null, null);
4759           }
4760
4761         }
4762       } catch (Exception ex)
4763       {
4764         ex.printStackTrace();
4765       }
4766     }
4767   }
4768
4769   /**
4770    * Attempt to load a "dropped" file or URL string, by testing in turn for
4771    * <ul>
4772    * <li>an Annotation file</li>
4773    * <li>a JNet file</li>
4774    * <li>a features file</li>
4775    * <li>else try to interpret as an alignment file</li>
4776    * </ul>
4777    *
4778    * @param file
4779    *          either a filename or a URL string.
4780    * @throws InterruptedException
4781    * @throws IOException
4782    */
4783   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4784           FileFormatI format, SequenceI assocSeq)
4785   {
4786     try
4787     {
4788       if (sourceType == null)
4789       {
4790         sourceType = FormatAdapter.checkProtocol(file);
4791       }
4792       // if the file isn't identified, or not positively identified as some
4793       // other filetype (PFAM is default unidentified alignment file type) then
4794       // try to parse as annotation.
4795       boolean isAnnotation = (format == null
4796               || FileFormat.Pfam.equals(format))
4797                       ? new AnnotationFile().annotateAlignmentView(viewport,
4798                               file, sourceType)
4799                       : false;
4800
4801       if (!isAnnotation)
4802       {
4803         // first see if its a T-COFFEE score file
4804         TCoffeeScoreFile tcf = null;
4805         try
4806         {
4807           tcf = new TCoffeeScoreFile(file, sourceType);
4808           if (tcf.isValid())
4809           {
4810             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4811             {
4812               buildColourMenu();
4813               changeColour(
4814                       new TCoffeeColourScheme(viewport.getAlignment()));
4815               isAnnotation = true;
4816               statusBar.setText(MessageManager.getString(
4817                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4818             }
4819             else
4820             {
4821               // some problem - if no warning its probable that the ID matching
4822               // process didn't work
4823               JvOptionPane.showMessageDialog(Desktop.desktop,
4824                       tcf.getWarningMessage() == null
4825                               ? MessageManager.getString(
4826                                       "label.check_file_matches_sequence_ids_alignment")
4827                               : tcf.getWarningMessage(),
4828                       MessageManager.getString(
4829                               "label.problem_reading_tcoffee_score_file"),
4830                       JvOptionPane.WARNING_MESSAGE);
4831             }
4832           }
4833           else
4834           {
4835             tcf = null;
4836           }
4837         } catch (Exception x)
4838         {
4839           Cache.log.debug(
4840                   "Exception when processing data source as T-COFFEE score file",
4841                   x);
4842           tcf = null;
4843         }
4844         if (tcf == null)
4845         {
4846           // try to see if its a JNet 'concise' style annotation file *before*
4847           // we
4848           // try to parse it as a features file
4849           if (format == null)
4850           {
4851             format = new IdentifyFile().identify(file, sourceType);
4852           }
4853           if (FileFormat.ScoreMatrix == format)
4854           {
4855             ScoreMatrixFile sm = new ScoreMatrixFile(
4856                     new FileParse(file, sourceType));
4857             sm.parse();
4858             // todo: i18n this message
4859             statusBar.setText(MessageManager.formatMessage(
4860                     "label.successfully_loaded_matrix",
4861                     sm.getMatrixName()));
4862           }
4863           else if (FileFormat.Jnet.equals(format))
4864           {
4865             JPredFile predictions = new JPredFile(file, sourceType);
4866             new JnetAnnotationMaker();
4867             JnetAnnotationMaker.add_annotation(predictions,
4868                     viewport.getAlignment(), 0, false);
4869             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4870             viewport.getAlignment().setSeqrep(repseq);
4871             HiddenColumns cs = new HiddenColumns();
4872             cs.hideInsertionsFor(repseq);
4873             viewport.getAlignment().setHiddenColumns(cs);
4874             isAnnotation = true;
4875           }
4876           // else if (IdentifyFile.FeaturesFile.equals(format))
4877           else if (FileFormat.Features.equals(format))
4878           {
4879             if (parseFeaturesFile(file, sourceType))
4880             {
4881               alignPanel.paintAlignment(true);
4882             }
4883           }
4884           else
4885           {
4886             new FileLoader().LoadFile(viewport, file, sourceType, format);
4887           }
4888         }
4889       }
4890       if (isAnnotation)
4891       {
4892         alignPanel.adjustAnnotationHeight();
4893         viewport.updateSequenceIdColours();
4894         buildSortByAnnotationScoresMenu();
4895         alignPanel.paintAlignment(true);
4896       }
4897     } catch (Exception ex)
4898     {
4899       ex.printStackTrace();
4900     } catch (OutOfMemoryError oom)
4901     {
4902       try
4903       {
4904         System.gc();
4905       } catch (Exception x)
4906       {
4907       }
4908       new OOMWarning(
4909               "loading data "
4910                       + (sourceType != null
4911                               ? (sourceType == DataSourceType.PASTE
4912                                       ? "from clipboard."
4913                                       : "using " + sourceType + " from "
4914                                               + file)
4915                               : ".")
4916                       + (format != null
4917                               ? "(parsing as '" + format + "' file)"
4918                               : ""),
4919               oom, Desktop.desktop);
4920     }
4921   }
4922
4923   /**
4924    * Method invoked by the ChangeListener on the tabbed pane, in other words
4925    * when a different tabbed pane is selected by the user or programmatically.
4926    */
4927   @Override
4928   public void tabSelectionChanged(int index)
4929   {
4930     if (index > -1)
4931     {
4932       alignPanel = alignPanels.get(index);
4933       viewport = alignPanel.av;
4934       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4935       setMenusFromViewport(viewport);
4936     }
4937
4938     /*
4939      * 'focus' any colour slider that is open to the selected viewport
4940      */
4941     if (viewport.getConservationSelected())
4942     {
4943       SliderPanel.setConservationSlider(alignPanel,
4944               viewport.getResidueShading(), alignPanel.getViewName());
4945     }
4946     else
4947     {
4948       SliderPanel.hideConservationSlider();
4949     }
4950     if (viewport.getAbovePIDThreshold())
4951     {
4952       SliderPanel.setPIDSliderSource(alignPanel,
4953               viewport.getResidueShading(), alignPanel.getViewName());
4954     }
4955     else
4956     {
4957       SliderPanel.hidePIDSlider();
4958     }
4959
4960     /*
4961      * If there is a frame linked to this one in a SplitPane, switch it to the
4962      * same view tab index. No infinite recursion of calls should happen, since
4963      * tabSelectionChanged() should not get invoked on setting the selected
4964      * index to an unchanged value. Guard against setting an invalid index
4965      * before the new view peer tab has been created.
4966      */
4967     final AlignViewportI peer = viewport.getCodingComplement();
4968     if (peer != null)
4969     {
4970       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4971               .getAlignPanel().alignFrame;
4972       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4973       {
4974         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4975       }
4976     }
4977   }
4978
4979   /**
4980    * On right mouse click on view tab, prompt for and set new view name.
4981    */
4982   @Override
4983   public void tabbedPane_mousePressed(MouseEvent e)
4984   {
4985     if (e.isPopupTrigger())
4986     {
4987       String msg = MessageManager.getString("label.enter_view_name");
4988       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4989               JvOptionPane.QUESTION_MESSAGE);
4990
4991       if (reply != null)
4992       {
4993         viewport.viewName = reply;
4994         // TODO warn if reply is in getExistingViewNames()?
4995         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4996       }
4997     }
4998   }
4999
5000   public AlignViewport getCurrentView()
5001   {
5002     return viewport;
5003   }
5004
5005   /**
5006    * Open the dialog for regex description parsing.
5007    */
5008   @Override
5009   protected void extractScores_actionPerformed(ActionEvent e)
5010   {
5011     ParseProperties pp = new jalview.analysis.ParseProperties(
5012             viewport.getAlignment());
5013     // TODO: verify regex and introduce GUI dialog for version 2.5
5014     // if (pp.getScoresFromDescription("col", "score column ",
5015     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5016     // true)>0)
5017     if (pp.getScoresFromDescription("description column",
5018             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5019     {
5020       buildSortByAnnotationScoresMenu();
5021     }
5022   }
5023
5024   /*
5025    * (non-Javadoc)
5026    *
5027    * @see
5028    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5029    * )
5030    */
5031   @Override
5032   protected void showDbRefs_actionPerformed(ActionEvent e)
5033   {
5034     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5035   }
5036
5037   /*
5038    * (non-Javadoc)
5039    *
5040    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5041    * ActionEvent)
5042    */
5043   @Override
5044   protected void showNpFeats_actionPerformed(ActionEvent e)
5045   {
5046     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5047   }
5048
5049   /**
5050    * find the viewport amongst the tabs in this alignment frame and close that
5051    * tab
5052    *
5053    * @param av
5054    */
5055   public boolean closeView(AlignViewportI av)
5056   {
5057     if (viewport == av)
5058     {
5059       this.closeMenuItem_actionPerformed(false);
5060       return true;
5061     }
5062     Component[] comp = tabbedPane.getComponents();
5063     for (int i = 0; comp != null && i < comp.length; i++)
5064     {
5065       if (comp[i] instanceof AlignmentPanel)
5066       {
5067         if (((AlignmentPanel) comp[i]).av == av)
5068         {
5069           // close the view.
5070           closeView((AlignmentPanel) comp[i]);
5071           return true;
5072         }
5073       }
5074     }
5075     return false;
5076   }
5077
5078   protected void build_fetchdbmenu(JMenu webService)
5079   {
5080     // Temporary hack - DBRef Fetcher always top level ws entry.
5081     // TODO We probably want to store a sequence database checklist in
5082     // preferences and have checkboxes.. rather than individual sources selected
5083     // here
5084     final JMenu rfetch = new JMenu(
5085             MessageManager.getString("action.fetch_db_references"));
5086     rfetch.setToolTipText(MessageManager.getString(
5087             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5088     webService.add(rfetch);
5089
5090     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5091             MessageManager.getString("option.trim_retrieved_seqs"));
5092     trimrs.setToolTipText(
5093             MessageManager.getString("label.trim_retrieved_sequences"));
5094     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5095     trimrs.addActionListener(new ActionListener()
5096     {
5097       @Override
5098       public void actionPerformed(ActionEvent e)
5099       {
5100         trimrs.setSelected(trimrs.isSelected());
5101         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5102                 Boolean.valueOf(trimrs.isSelected()).toString());
5103       };
5104     });
5105     rfetch.add(trimrs);
5106     JMenuItem fetchr = new JMenuItem(
5107             MessageManager.getString("label.standard_databases"));
5108     fetchr.setToolTipText(
5109             MessageManager.getString("label.fetch_embl_uniprot"));
5110     fetchr.addActionListener(new ActionListener()
5111     {
5112
5113       @Override
5114       public void actionPerformed(ActionEvent e)
5115       {
5116         new Thread(new Runnable()
5117         {
5118           @Override
5119           public void run()
5120           {
5121             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5122                     .getAlignment().isNucleotide();
5123             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5124                     alignPanel.av.getSequenceSelection(),
5125                     alignPanel.alignFrame, null,
5126                     alignPanel.alignFrame.featureSettings, isNucleotide);
5127             dbRefFetcher.addListener(new FetchFinishedListenerI()
5128             {
5129               @Override
5130               public void finished()
5131               {
5132                 AlignFrame.this.setMenusForViewport();
5133               }
5134             });
5135             dbRefFetcher.fetchDBRefs(false);
5136           }
5137         }).start();
5138
5139       }
5140
5141     });
5142     rfetch.add(fetchr);
5143     final AlignFrame me = this;
5144     new Thread(new Runnable()
5145     {
5146       @Override
5147       public void run()
5148       {
5149         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5150                 .getSequenceFetcherSingleton(me);
5151         javax.swing.SwingUtilities.invokeLater(new Runnable()
5152         {
5153           @Override
5154           public void run()
5155           {
5156             String[] dbclasses = sf.getOrderedSupportedSources();
5157             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5158             // jalview.util.QuickSort.sort(otherdb, otherdb);
5159             List<DbSourceProxy> otherdb;
5160             JMenu dfetch = new JMenu();
5161             JMenu ifetch = new JMenu();
5162             JMenuItem fetchr = null;
5163             int comp = 0, icomp = 0, mcomp = 15;
5164             String mname = null;
5165             int dbi = 0;
5166             for (String dbclass : dbclasses)
5167             {
5168               otherdb = sf.getSourceProxy(dbclass);
5169               // add a single entry for this class, or submenu allowing 'fetch
5170               // all' or pick one
5171               if (otherdb == null || otherdb.size() < 1)
5172               {
5173                 continue;
5174               }
5175               // List<DbSourceProxy> dbs=otherdb;
5176               // otherdb=new ArrayList<DbSourceProxy>();
5177               // for (DbSourceProxy db:dbs)
5178               // {
5179               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5180               // }
5181               if (mname == null)
5182               {
5183                 mname = "From " + dbclass;
5184               }
5185               if (otherdb.size() == 1)
5186               {
5187                 final DbSourceProxy[] dassource = otherdb
5188                         .toArray(new DbSourceProxy[0]);
5189                 DbSourceProxy src = otherdb.get(0);
5190                 fetchr = new JMenuItem(src.getDbSource());
5191                 fetchr.addActionListener(new ActionListener()
5192                 {
5193
5194                   @Override
5195                   public void actionPerformed(ActionEvent e)
5196                   {
5197                     new Thread(new Runnable()
5198                     {
5199
5200                       @Override
5201                       public void run()
5202                       {
5203                         boolean isNucleotide = alignPanel.alignFrame
5204                                 .getViewport().getAlignment()
5205                                 .isNucleotide();
5206                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5207                                 alignPanel.av.getSequenceSelection(),
5208                                 alignPanel.alignFrame, dassource,
5209                                 alignPanel.alignFrame.featureSettings,
5210                                 isNucleotide);
5211                         dbRefFetcher
5212                                 .addListener(new FetchFinishedListenerI()
5213                                 {
5214                                   @Override
5215                                   public void finished()
5216                                   {
5217                                     AlignFrame.this.setMenusForViewport();
5218                                   }
5219                                 });
5220                         dbRefFetcher.fetchDBRefs(false);
5221                       }
5222                     }).start();
5223                   }
5224
5225                 });
5226                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5227                         MessageManager.formatMessage(
5228                                 "label.fetch_retrieve_from", new Object[]
5229                                 { src.getDbName() })));
5230                 dfetch.add(fetchr);
5231                 comp++;
5232               }
5233               else
5234               {
5235                 final DbSourceProxy[] dassource = otherdb
5236                         .toArray(new DbSourceProxy[0]);
5237                 // fetch all entry
5238                 DbSourceProxy src = otherdb.get(0);
5239                 fetchr = new JMenuItem(MessageManager
5240                         .formatMessage("label.fetch_all_param", new Object[]
5241                         { src.getDbSource() }));
5242                 fetchr.addActionListener(new ActionListener()
5243                 {
5244                   @Override
5245                   public void actionPerformed(ActionEvent e)
5246                   {
5247                     new Thread(new Runnable()
5248                     {
5249
5250                       @Override
5251                       public void run()
5252                       {
5253                         boolean isNucleotide = alignPanel.alignFrame
5254                                 .getViewport().getAlignment()
5255                                 .isNucleotide();
5256                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5257                                 alignPanel.av.getSequenceSelection(),
5258                                 alignPanel.alignFrame, dassource,
5259                                 alignPanel.alignFrame.featureSettings,
5260                                 isNucleotide);
5261                         dbRefFetcher
5262                                 .addListener(new FetchFinishedListenerI()
5263                                 {
5264                                   @Override
5265                                   public void finished()
5266                                   {
5267                                     AlignFrame.this.setMenusForViewport();
5268                                   }
5269                                 });
5270                         dbRefFetcher.fetchDBRefs(false);
5271                       }
5272                     }).start();
5273                   }
5274                 });
5275
5276                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5277                         MessageManager.formatMessage(
5278                                 "label.fetch_retrieve_from_all_sources",
5279                                 new Object[]
5280                                 { Integer.valueOf(otherdb.size())
5281                                         .toString(),
5282                                     src.getDbSource(), src.getDbName() })));
5283                 dfetch.add(fetchr);
5284                 comp++;
5285                 // and then build the rest of the individual menus
5286                 ifetch = new JMenu(MessageManager.formatMessage(
5287                         "label.source_from_db_source", new Object[]
5288                         { src.getDbSource() }));
5289                 icomp = 0;
5290                 String imname = null;
5291                 int i = 0;
5292                 for (DbSourceProxy sproxy : otherdb)
5293                 {
5294                   String dbname = sproxy.getDbName();
5295                   String sname = dbname.length() > 5
5296                           ? dbname.substring(0, 5) + "..."
5297                           : dbname;
5298                   String msname = dbname.length() > 10
5299                           ? dbname.substring(0, 10) + "..."
5300                           : dbname;
5301                   if (imname == null)
5302                   {
5303                     imname = MessageManager
5304                             .formatMessage("label.from_msname", new Object[]
5305                             { sname });
5306                   }
5307                   fetchr = new JMenuItem(msname);
5308                   final DbSourceProxy[] dassrc = { sproxy };
5309                   fetchr.addActionListener(new ActionListener()
5310                   {
5311
5312                     @Override
5313                     public void actionPerformed(ActionEvent e)
5314                     {
5315                       new Thread(new Runnable()
5316                       {
5317
5318                         @Override
5319                         public void run()
5320                         {
5321                           boolean isNucleotide = alignPanel.alignFrame
5322                                   .getViewport().getAlignment()
5323                                   .isNucleotide();
5324                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5325                                   alignPanel.av.getSequenceSelection(),
5326                                   alignPanel.alignFrame, dassrc,
5327                                   alignPanel.alignFrame.featureSettings,
5328                                   isNucleotide);
5329                           dbRefFetcher
5330                                   .addListener(new FetchFinishedListenerI()
5331                                   {
5332                                     @Override
5333                                     public void finished()
5334                                     {
5335                                       AlignFrame.this.setMenusForViewport();
5336                                     }
5337                                   });
5338                           dbRefFetcher.fetchDBRefs(false);
5339                         }
5340                       }).start();
5341                     }
5342
5343                   });
5344                   fetchr.setToolTipText(
5345                           "<html>" + MessageManager.formatMessage(
5346                                   "label.fetch_retrieve_from", new Object[]
5347                                   { dbname }));
5348                   ifetch.add(fetchr);
5349                   ++i;
5350                   if (++icomp >= mcomp || i == (otherdb.size()))
5351                   {
5352                     ifetch.setText(MessageManager.formatMessage(
5353                             "label.source_to_target", imname, sname));
5354                     dfetch.add(ifetch);
5355                     ifetch = new JMenu();
5356                     imname = null;
5357                     icomp = 0;
5358                     comp++;
5359                   }
5360                 }
5361               }
5362               ++dbi;
5363               if (comp >= mcomp || dbi >= (dbclasses.length))
5364               {
5365                 dfetch.setText(MessageManager.formatMessage(
5366                         "label.source_to_target", mname, dbclass));
5367                 rfetch.add(dfetch);
5368                 dfetch = new JMenu();
5369                 mname = null;
5370                 comp = 0;
5371               }
5372             }
5373           }
5374         });
5375       }
5376     }).start();
5377
5378   }
5379
5380   /**
5381    * Left justify the whole alignment.
5382    */
5383   @Override
5384   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5385   {
5386     AlignmentI al = viewport.getAlignment();
5387     al.justify(false);
5388     viewport.firePropertyChange("alignment", null, al);
5389   }
5390
5391   /**
5392    * Right justify the whole alignment.
5393    */
5394   @Override
5395   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5396   {
5397     AlignmentI al = viewport.getAlignment();
5398     al.justify(true);
5399     viewport.firePropertyChange("alignment", null, al);
5400   }
5401
5402   @Override
5403   public void setShowSeqFeatures(boolean b)
5404   {
5405     showSeqFeatures.setSelected(b);
5406     viewport.setShowSequenceFeatures(b);
5407   }
5408
5409   /*
5410    * (non-Javadoc)
5411    *
5412    * @see
5413    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5414    * awt.event.ActionEvent)
5415    */
5416   @Override
5417   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5418   {
5419     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5420     alignPanel.paintAlignment(true);
5421   }
5422
5423   /*
5424    * (non-Javadoc)
5425    *
5426    * @see
5427    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5428    * .ActionEvent)
5429    */
5430   @Override
5431   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5432   {
5433     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5434     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5435
5436   }
5437
5438   /*
5439    * (non-Javadoc)
5440    *
5441    * @see
5442    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5443    * .event.ActionEvent)
5444    */
5445   @Override
5446   protected void showGroupConservation_actionPerformed(ActionEvent e)
5447   {
5448     viewport.setShowGroupConservation(showGroupConservation.getState());
5449     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5450   }
5451
5452   /*
5453    * (non-Javadoc)
5454    *
5455    * @see
5456    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5457    * .event.ActionEvent)
5458    */
5459   @Override
5460   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5461   {
5462     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5463     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5464   }
5465
5466   /*
5467    * (non-Javadoc)
5468    *
5469    * @see
5470    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5471    * .event.ActionEvent)
5472    */
5473   @Override
5474   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5475   {
5476     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5477     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5478   }
5479
5480   @Override
5481   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5482   {
5483     showSequenceLogo.setState(true);
5484     viewport.setShowSequenceLogo(true);
5485     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5486     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5487   }
5488
5489   @Override
5490   protected void showInformationHistogram_actionPerformed(ActionEvent e)
5491   {
5492     viewport.setShowInformationHistogram(
5493             showInformationHistogram.getState());
5494     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5495   }
5496
5497   @Override
5498   protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5499   {
5500     viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5501     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5502   }
5503
5504   @Override
5505   protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5506   {
5507     showHMMSequenceLogo.setState(true);
5508     viewport.setShowHMMSequenceLogo(true);
5509     viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5510     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5511   }
5512
5513   @Override
5514   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5515   {
5516     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5517   }
5518
5519   /*
5520    * (non-Javadoc)
5521    *
5522    * @see
5523    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5524    * .event.ActionEvent)
5525    */
5526   @Override
5527   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5528   {
5529     if (avc.makeGroupsFromSelection())
5530     {
5531       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5532       alignPanel.updateAnnotation();
5533       alignPanel.paintAlignment(true);
5534     }
5535   }
5536
5537   public void clearAlignmentSeqRep()
5538   {
5539     // TODO refactor alignmentseqrep to controller
5540     if (viewport.getAlignment().hasSeqrep())
5541     {
5542       viewport.getAlignment().setSeqrep(null);
5543       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5544       alignPanel.updateAnnotation();
5545       alignPanel.paintAlignment(true);
5546     }
5547   }
5548
5549   @Override
5550   protected void createGroup_actionPerformed(ActionEvent e)
5551   {
5552     if (avc.createGroup())
5553     {
5554       alignPanel.alignmentChanged();
5555     }
5556   }
5557
5558   @Override
5559   protected void unGroup_actionPerformed(ActionEvent e)
5560   {
5561     if (avc.unGroup())
5562     {
5563       alignPanel.alignmentChanged();
5564     }
5565   }
5566
5567   /**
5568    * make the given alignmentPanel the currently selected tab
5569    *
5570    * @param alignmentPanel
5571    */
5572   public void setDisplayedView(AlignmentPanel alignmentPanel)
5573   {
5574     if (!viewport.getSequenceSetId()
5575             .equals(alignmentPanel.av.getSequenceSetId()))
5576     {
5577       throw new Error(MessageManager.getString(
5578               "error.implementation_error_cannot_show_view_alignment_frame"));
5579     }
5580     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5581             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5582     {
5583       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5584     }
5585   }
5586
5587   /**
5588    * Action on selection of menu options to Show or Hide annotations.
5589    *
5590    * @param visible
5591    * @param forSequences
5592    *          update sequence-related annotations
5593    * @param forAlignment
5594    *          update non-sequence-related annotations
5595    */
5596   @Override
5597   protected void setAnnotationsVisibility(boolean visible,
5598           boolean forSequences, boolean forAlignment)
5599   {
5600     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5601             .getAlignmentAnnotation();
5602     if (anns == null)
5603     {
5604       return;
5605     }
5606     for (AlignmentAnnotation aa : anns)
5607     {
5608       /*
5609        * don't display non-positional annotations on an alignment
5610        */
5611       if (aa.annotations == null)
5612       {
5613         continue;
5614       }
5615       boolean apply = (aa.sequenceRef == null && forAlignment)
5616               || (aa.sequenceRef != null && forSequences);
5617       if (apply)
5618       {
5619         aa.visible = visible;
5620       }
5621     }
5622     alignPanel.validateAnnotationDimensions(true);
5623     alignPanel.alignmentChanged();
5624   }
5625
5626   /**
5627    * Store selected annotation sort order for the view and repaint.
5628    */
5629   @Override
5630   protected void sortAnnotations_actionPerformed()
5631   {
5632     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5633     this.alignPanel.av
5634             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5635     alignPanel.paintAlignment(true);
5636   }
5637
5638   /**
5639    *
5640    * @return alignment panels in this alignment frame
5641    */
5642   public List<? extends AlignmentViewPanel> getAlignPanels()
5643   {
5644     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5645   }
5646
5647   /**
5648    * Open a new alignment window, with the cDNA associated with this (protein)
5649    * alignment, aligned as is the protein.
5650    */
5651   protected void viewAsCdna_actionPerformed()
5652   {
5653     // TODO no longer a menu action - refactor as required
5654     final AlignmentI alignment = getViewport().getAlignment();
5655     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5656     if (mappings == null)
5657     {
5658       return;
5659     }
5660     List<SequenceI> cdnaSeqs = new ArrayList<>();
5661     for (SequenceI aaSeq : alignment.getSequences())
5662     {
5663       for (AlignedCodonFrame acf : mappings)
5664       {
5665         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5666         if (dnaSeq != null)
5667         {
5668           /*
5669            * There is a cDNA mapping for this protein sequence - add to new
5670            * alignment. It will share the same dataset sequence as other mapped
5671            * cDNA (no new mappings need to be created).
5672            */
5673           final Sequence newSeq = new Sequence(dnaSeq);
5674           newSeq.setDatasetSequence(dnaSeq);
5675           cdnaSeqs.add(newSeq);
5676         }
5677       }
5678     }
5679     if (cdnaSeqs.size() == 0)
5680     {
5681       // show a warning dialog no mapped cDNA
5682       return;
5683     }
5684     AlignmentI cdna = new Alignment(
5685             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5686     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5687             AlignFrame.DEFAULT_HEIGHT);
5688     cdna.alignAs(alignment);
5689     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5690             + this.title;
5691     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5692             AlignFrame.DEFAULT_HEIGHT);
5693   }
5694
5695   /**
5696    * Set visibility of dna/protein complement view (available when shown in a
5697    * split frame).
5698    *
5699    * @param show
5700    */
5701   @Override
5702   protected void showComplement_actionPerformed(boolean show)
5703   {
5704     SplitContainerI sf = getSplitViewContainer();
5705     if (sf != null)
5706     {
5707       sf.setComplementVisible(this, show);
5708     }
5709   }
5710
5711   /**
5712    * Generate the reverse (optionally complemented) of the selected sequences,
5713    * and add them to the alignment
5714    */
5715   @Override
5716   protected void showReverse_actionPerformed(boolean complement)
5717   {
5718     AlignmentI al = null;
5719     try
5720     {
5721       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5722       al = dna.reverseCdna(complement);
5723       viewport.addAlignment(al, "");
5724       addHistoryItem(new EditCommand(
5725               MessageManager.getString("label.add_sequences"), Action.PASTE,
5726               al.getSequencesArray(), 0, al.getWidth(),
5727               viewport.getAlignment()));
5728     } catch (Exception ex)
5729     {
5730       System.err.println(ex.getMessage());
5731       return;
5732     }
5733   }
5734
5735   /**
5736    * Try to run a script in the Groovy console, having first ensured that this
5737    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5738    * be targeted at this alignment.
5739    */
5740   @Override
5741   protected void runGroovy_actionPerformed()
5742   {
5743     Jalview.setCurrentAlignFrame(this);
5744     groovy.ui.Console console = Desktop.getGroovyConsole();
5745     if (console != null)
5746     {
5747       try
5748       {
5749         console.runScript();
5750       } catch (Exception ex)
5751       {
5752         System.err.println((ex.toString()));
5753         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5754                 MessageManager.getString("label.couldnt_run_groovy_script"),
5755                 MessageManager.getString("label.groovy_support_failed"),
5756                 JvOptionPane.ERROR_MESSAGE);
5757       }
5758     }
5759     else
5760     {
5761       System.err.println("Can't run Groovy script as console not found");
5762     }
5763   }
5764
5765   /**
5766    * Hides columns containing (or not containing) a specified feature, provided
5767    * that would not leave all columns hidden
5768    *
5769    * @param featureType
5770    * @param columnsContaining
5771    * @return
5772    */
5773   public boolean hideFeatureColumns(String featureType,
5774           boolean columnsContaining)
5775   {
5776     boolean notForHiding = avc.markColumnsContainingFeatures(
5777             columnsContaining, false, false, featureType);
5778     if (notForHiding)
5779     {
5780       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5781               false, featureType))
5782       {
5783         getViewport().hideSelectedColumns();
5784         return true;
5785       }
5786     }
5787     return false;
5788   }
5789
5790   @Override
5791   protected void selectHighlightedColumns_actionPerformed(
5792           ActionEvent actionEvent)
5793   {
5794     // include key modifier check in case user selects from menu
5795     avc.markHighlightedColumns(
5796             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5797             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5798                     | ActionEvent.CTRL_MASK)) != 0);
5799   }
5800
5801   /**
5802    * Rebuilds the Colour menu, including any user-defined colours which have
5803    * been loaded either on startup or during the session
5804    */
5805   public void buildColourMenu()
5806   {
5807     colourMenu.removeAll();
5808
5809     colourMenu.add(applyToAllGroups);
5810     colourMenu.add(textColour);
5811     colourMenu.addSeparator();
5812
5813     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5814             false);
5815
5816     colourMenu.addSeparator();
5817     colourMenu.add(conservationMenuItem);
5818     colourMenu.add(modifyConservation);
5819     colourMenu.add(abovePIDThreshold);
5820     colourMenu.add(modifyPID);
5821     colourMenu.add(annotationColour);
5822
5823     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5824     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5825   }
5826
5827   /**
5828    * Open a dialog (if not already open) that allows the user to select and
5829    * calculate PCA or Tree analysis
5830    */
5831   protected void openTreePcaDialog()
5832   {
5833     if (alignPanel.getCalculationDialog() == null)
5834     {
5835       new CalculationChooser(AlignFrame.this);
5836     }
5837   }
5838
5839   /**
5840    * Sets the status of the HMMER menu
5841    */
5842   public void updateHMMERStatus()
5843   {
5844     hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
5845   }
5846
5847   /**
5848    * Returns the selected hidden Markov model.
5849    *
5850    * @return
5851    */
5852   public HiddenMarkovModel getSelectedHMM()
5853   {
5854     if (selectedHMMSequence == null)
5855     {
5856       return null;
5857     }
5858     return selectedHMMSequence.getHMM();
5859   }
5860
5861   /**
5862    * Returns the selected hidden Markov model.
5863    *
5864    * @return
5865    */
5866   public SequenceI getSelectedHMMSequence()
5867   {
5868     return selectedHMMSequence;
5869   }
5870
5871   /**
5872    * Sets the selected hidden Markov model
5873    *
5874    * @param selectedHMM
5875    */
5876   public void setSelectedHMMSequence(SequenceI selectedHMM)
5877   {
5878     this.selectedHMMSequence = selectedHMM;
5879     hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
5880             + selectedHMM.getHMM().getName());
5881     hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
5882             + selectedHMM.getHMM().getName());
5883   }
5884
5885   @Override
5886   public void hmmerMenu_actionPerformed(ActionEvent e)
5887   {
5888     SequenceGroup grp = getViewport().getSelectionGroup();
5889     if (grp != null)
5890     {
5891       hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
5892               + grp.getName());
5893     }
5894     else
5895     {
5896       hmmBuild.setText(MessageManager.getString("label.hmmbuild")
5897               + " from Alignment");
5898     }
5899   }
5900
5901 }
5902
5903 class PrintThread extends Thread
5904 {
5905   AlignmentPanel ap;
5906
5907   public PrintThread(AlignmentPanel ap)
5908   {
5909     this.ap = ap;
5910   }
5911
5912   static PageFormat pf;
5913
5914   @Override
5915   public void run()
5916   {
5917     PrinterJob printJob = PrinterJob.getPrinterJob();
5918
5919     if (pf != null)
5920     {
5921       printJob.setPrintable(ap, pf);
5922     }
5923     else
5924     {
5925       printJob.setPrintable(ap);
5926     }
5927
5928     if (printJob.printDialog())
5929     {
5930       try
5931       {
5932         printJob.print();
5933       } catch (Exception PrintException)
5934       {
5935         PrintException.printStackTrace();
5936       }
5937     }
5938   }
5939 }