src/jalview/gui/AlignFrame.java

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