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.trace("ALIGNFRAME making backupfiles object for " + file);
1205         BackupFiles backupfiles = new BackupFiles(file);
1206
1207         try
1208         {
1209           String tempFilePath = backupfiles.getTempFilePath();
1210           Cache.log.trace(
1211                   "ALIGNFRAME setting PrintWriter to " + tempFilePath);
1212           PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1213
1214           Cache.log.trace(
1215                   "ALIGNFRAME about to write to temp file " + tempFilePath);
1216
1217           out.print(output);
1218           Cache.log.trace("ALIGNFRAME about to close file");
1219           out.close();
1220           Cache.log.trace("ALIGNFRAME closed file");
1221           this.setTitle(file);
1222           statusBar.setText(MessageManager.formatMessage(
1223                   "label.successfully_saved_to_file_in_format", new Object[]
1224                   { file, format.getName() }));
1225         } catch (IOException e)
1226         {
1227           success = false;
1228           Cache.log.error(
1229                   "ALIGNFRAME Something happened writing the temp file");
1230           Cache.log.error(e.getMessage());
1231           Cache.log.debug(Cache.getStackTraceString(e));
1232
1233         } catch (Exception ex)
1234         {
1235           success = false;
1236           Cache.log.error(
1237                   "ALIGNFRAME Something unexpected happened writing the temp file");
1238           Cache.log.error(ex.getMessage());
1239           Cache.log.debug(Cache.getStackTraceString(ex));
1240         }
1241
1242         backupfiles.setWriteSuccess(success);
1243         Cache.log.debug("ALIGNFRAME writing temp file was "
1244                 + (success ? "" : "NOT ") + "successful");
1245         // do the backup file roll and rename the temp file to actual file
1246         Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1247         success = backupfiles.rollBackupsAndRenameTempFile();
1248         Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1249                 + (success ? "" : "un") + "successfully");
1250
1251       }
1252     }
1253
1254     if (!success)
1255     {
1256       if (!Platform.isHeadless())
1257       {
1258         JvOptionPane.showInternalMessageDialog(this, MessageManager
1259                 .formatMessage("label.couldnt_save_file", new Object[]
1260                 { file }),
1261                 MessageManager.getString("label.error_saving_file"),
1262                 JvOptionPane.WARNING_MESSAGE);
1263       }
1264     }
1265
1266     return success;
1267   }
1268
1269   private void warningMessage(String warning, String title)
1270   {
1271     if (new jalview.util.Platform().isHeadless())
1272     {
1273       System.err.println("Warning: " + title + "\nWarning: " + warning);
1274
1275     }
1276     else
1277     {
1278       JvOptionPane.showInternalMessageDialog(this, warning, title,
1279               JvOptionPane.WARNING_MESSAGE);
1280     }
1281     return;
1282   }
1283
1284   /**
1285    * DOCUMENT ME!
1286    *
1287    * @param e
1288    *          DOCUMENT ME!
1289    */
1290   @Override
1291   protected void outputText_actionPerformed(ActionEvent e)
1292   {
1293     FileFormatI fileFormat = FileFormats.getInstance()
1294             .forName(e.getActionCommand());
1295     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1296             viewport, null);
1297     if (exportData.getSettings().isCancelled())
1298     {
1299       return;
1300     }
1301     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1302     cap.setForInput(null);
1303     try
1304     {
1305       FileFormatI format = fileFormat;
1306       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1307               .formatSequences(format, exportData.getAlignment(),
1308                       exportData.getOmitHidden(),
1309                       exportData.getStartEndPostions(),
1310                       viewport.getAlignment().getHiddenColumns()));
1311       Desktop.addInternalFrame(cap, MessageManager
1312               .formatMessage("label.alignment_output_command", new Object[]
1313               { e.getActionCommand() }), 600, 500);
1314     } catch (OutOfMemoryError oom)
1315     {
1316       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1317               oom);
1318       cap.dispose();
1319     }
1320
1321   }
1322
1323   public static AlignmentExportData getAlignmentForExport(
1324           FileFormatI format, AlignViewportI viewport,
1325           AlignExportSettingI exportSettings)
1326   {
1327     AlignmentI alignmentToExport = null;
1328     AlignExportSettingI settings = exportSettings;
1329     String[] omitHidden = null;
1330
1331     HiddenSequences hiddenSeqs = viewport.getAlignment()
1332             .getHiddenSequences();
1333
1334     alignmentToExport = viewport.getAlignment();
1335
1336     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1337     if (settings == null)
1338     {
1339       settings = new AlignExportSettings(hasHiddenSeqs,
1340               viewport.hasHiddenColumns(), format);
1341     }
1342     // settings.isExportAnnotations();
1343
1344     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1345     {
1346       omitHidden = viewport.getViewAsString(false,
1347               settings.isExportHiddenSequences());
1348     }
1349
1350     int[] alignmentStartEnd = new int[2];
1351     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1352     {
1353       alignmentToExport = hiddenSeqs.getFullAlignment();
1354     }
1355     else
1356     {
1357       alignmentToExport = viewport.getAlignment();
1358     }
1359     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1360             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1361     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1362             omitHidden, alignmentStartEnd, settings);
1363     return ed;
1364   }
1365
1366   /**
1367    * DOCUMENT ME!
1368    *
1369    * @param e
1370    *          DOCUMENT ME!
1371    */
1372   @Override
1373   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1374   {
1375     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1376     htmlSVG.exportHTML(null);
1377   }
1378
1379   @Override
1380   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1381   {
1382     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1383     bjs.exportHTML(null);
1384   }
1385
1386   public void createImageMap(File file, String image)
1387   {
1388     alignPanel.makePNGImageMap(file, image);
1389   }
1390
1391   /**
1392    * DOCUMENT ME!
1393    *
1394    * @param e
1395    *          DOCUMENT ME!
1396    */
1397   @Override
1398   public void createPNG(File f)
1399   {
1400     alignPanel.makePNG(f);
1401   }
1402
1403   /**
1404    * DOCUMENT ME!
1405    *
1406    * @param e
1407    *          DOCUMENT ME!
1408    */
1409   @Override
1410   public void createEPS(File f)
1411   {
1412     alignPanel.makeEPS(f);
1413   }
1414
1415   @Override
1416   public void createSVG(File f)
1417   {
1418     alignPanel.makeSVG(f);
1419   }
1420
1421   @Override
1422   public void pageSetup_actionPerformed(ActionEvent e)
1423   {
1424     PrinterJob printJob = PrinterJob.getPrinterJob();
1425     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1426   }
1427
1428   /**
1429    * DOCUMENT ME!
1430    *
1431    * @param e
1432    *          DOCUMENT ME!
1433    */
1434   @Override
1435   public void printMenuItem_actionPerformed(ActionEvent e)
1436   {
1437     // Putting in a thread avoids Swing painting problems
1438     PrintThread thread = new PrintThread(alignPanel);
1439     thread.start();
1440   }
1441
1442   @Override
1443   public void exportFeatures_actionPerformed(ActionEvent e)
1444   {
1445     new AnnotationExporter(alignPanel).exportFeatures();
1446   }
1447
1448   @Override
1449   public void exportAnnotations_actionPerformed(ActionEvent e)
1450   {
1451     new AnnotationExporter(alignPanel).exportAnnotations();
1452   }
1453
1454   @Override
1455   public void associatedData_actionPerformed(ActionEvent e)
1456   {
1457     // Pick the tree file
1458     JalviewFileChooser chooser = new JalviewFileChooser(
1459             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1460     chooser.setFileView(new JalviewFileView());
1461     chooser.setDialogTitle(
1462             MessageManager.getString("label.load_jalview_annotations"));
1463     chooser.setToolTipText(
1464             MessageManager.getString("label.load_jalview_annotations"));
1465
1466     int value = chooser.showOpenDialog(null);
1467
1468     if (value == JalviewFileChooser.APPROVE_OPTION)
1469     {
1470       String choice = chooser.getSelectedFile().getPath();
1471       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1472       loadJalviewDataFile(choice, null, null, null);
1473     }
1474
1475   }
1476
1477   /**
1478    * Close the current view or all views in the alignment frame. If the frame
1479    * only contains one view then the alignment will be removed from memory.
1480    *
1481    * @param closeAllTabs
1482    */
1483   @Override
1484   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1485   {
1486     if (alignPanels != null && alignPanels.size() < 2)
1487     {
1488       closeAllTabs = true;
1489     }
1490
1491     try
1492     {
1493       if (alignPanels != null)
1494       {
1495         if (closeAllTabs)
1496         {
1497           if (this.isClosed())
1498           {
1499             // really close all the windows - otherwise wait till
1500             // setClosed(true) is called
1501             for (int i = 0; i < alignPanels.size(); i++)
1502             {
1503               AlignmentPanel ap = alignPanels.get(i);
1504               ap.closePanel();
1505             }
1506           }
1507         }
1508         else
1509         {
1510           closeView(alignPanel);
1511         }
1512       }
1513       if (closeAllTabs)
1514       {
1515         if (featureSettings != null && featureSettings.isOpen())
1516         {
1517           featureSettings.close();
1518           featureSettings = null;
1519         }
1520         /*
1521          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1522          * be called recursively, with the frame now in 'closed' state
1523          */
1524         this.setClosed(true);
1525       }
1526     } catch (Exception ex)
1527     {
1528       ex.printStackTrace();
1529     }
1530   }
1531
1532   /**
1533    * Close the specified panel and close up tabs appropriately.
1534    *
1535    * @param panelToClose
1536    */
1537   public void closeView(AlignmentPanel panelToClose)
1538   {
1539     int index = tabbedPane.getSelectedIndex();
1540     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1541     alignPanels.remove(panelToClose);
1542     panelToClose.closePanel();
1543     panelToClose = null;
1544
1545     tabbedPane.removeTabAt(closedindex);
1546     tabbedPane.validate();
1547
1548     if (index > closedindex || index == tabbedPane.getTabCount())
1549     {
1550       // modify currently selected tab index if necessary.
1551       index--;
1552     }
1553
1554     this.tabSelectionChanged(index);
1555   }
1556
1557   /**
1558    * DOCUMENT ME!
1559    */
1560   void updateEditMenuBar()
1561   {
1562
1563     if (viewport.getHistoryList().size() > 0)
1564     {
1565       undoMenuItem.setEnabled(true);
1566       CommandI command = viewport.getHistoryList().peek();
1567       undoMenuItem.setText(MessageManager
1568               .formatMessage("label.undo_command", new Object[]
1569               { command.getDescription() }));
1570     }
1571     else
1572     {
1573       undoMenuItem.setEnabled(false);
1574       undoMenuItem.setText(MessageManager.getString("action.undo"));
1575     }
1576
1577     if (viewport.getRedoList().size() > 0)
1578     {
1579       redoMenuItem.setEnabled(true);
1580
1581       CommandI command = viewport.getRedoList().peek();
1582       redoMenuItem.setText(MessageManager
1583               .formatMessage("label.redo_command", new Object[]
1584               { command.getDescription() }));
1585     }
1586     else
1587     {
1588       redoMenuItem.setEnabled(false);
1589       redoMenuItem.setText(MessageManager.getString("action.redo"));
1590     }
1591   }
1592
1593   @Override
1594   public void addHistoryItem(CommandI command)
1595   {
1596     if (command.getSize() > 0)
1597     {
1598       viewport.addToHistoryList(command);
1599       viewport.clearRedoList();
1600       updateEditMenuBar();
1601       viewport.updateHiddenColumns();
1602       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1603       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1604       // viewport.getColumnSelection()
1605       // .getHiddenColumns().size() > 0);
1606     }
1607   }
1608
1609   /**
1610    *
1611    * @return alignment objects for all views
1612    */
1613   AlignmentI[] getViewAlignments()
1614   {
1615     if (alignPanels != null)
1616     {
1617       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1618       int i = 0;
1619       for (AlignmentPanel ap : alignPanels)
1620       {
1621         als[i++] = ap.av.getAlignment();
1622       }
1623       return als;
1624     }
1625     if (viewport != null)
1626     {
1627       return new AlignmentI[] { viewport.getAlignment() };
1628     }
1629     return null;
1630   }
1631
1632   /**
1633    * DOCUMENT ME!
1634    *
1635    * @param e
1636    *          DOCUMENT ME!
1637    */
1638   @Override
1639   protected void undoMenuItem_actionPerformed(ActionEvent e)
1640   {
1641     if (viewport.getHistoryList().isEmpty())
1642     {
1643       return;
1644     }
1645     CommandI command = viewport.getHistoryList().pop();
1646     viewport.addToRedoList(command);
1647     command.undoCommand(getViewAlignments());
1648
1649     AlignmentViewport originalSource = getOriginatingSource(command);
1650     updateEditMenuBar();
1651
1652     if (originalSource != null)
1653     {
1654       if (originalSource != viewport)
1655       {
1656         Cache.log.warn(
1657                 "Implementation worry: mismatch of viewport origin for undo");
1658       }
1659       originalSource.updateHiddenColumns();
1660       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1661       // null
1662       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1663       // viewport.getColumnSelection()
1664       // .getHiddenColumns().size() > 0);
1665       originalSource.firePropertyChange("alignment", null,
1666               originalSource.getAlignment().getSequences());
1667     }
1668   }
1669
1670   /**
1671    * DOCUMENT ME!
1672    *
1673    * @param e
1674    *          DOCUMENT ME!
1675    */
1676   @Override
1677   protected void redoMenuItem_actionPerformed(ActionEvent e)
1678   {
1679     if (viewport.getRedoList().size() < 1)
1680     {
1681       return;
1682     }
1683
1684     CommandI command = viewport.getRedoList().pop();
1685     viewport.addToHistoryList(command);
1686     command.doCommand(getViewAlignments());
1687
1688     AlignmentViewport originalSource = getOriginatingSource(command);
1689     updateEditMenuBar();
1690
1691     if (originalSource != null)
1692     {
1693
1694       if (originalSource != viewport)
1695       {
1696         Cache.log.warn(
1697                 "Implementation worry: mismatch of viewport origin for redo");
1698       }
1699       originalSource.updateHiddenColumns();
1700       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1701       // null
1702       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1703       // viewport.getColumnSelection()
1704       // .getHiddenColumns().size() > 0);
1705       originalSource.firePropertyChange("alignment", null,
1706               originalSource.getAlignment().getSequences());
1707     }
1708   }
1709
1710   AlignmentViewport getOriginatingSource(CommandI command)
1711   {
1712     AlignmentViewport originalSource = null;
1713     // For sequence removal and addition, we need to fire
1714     // the property change event FROM the viewport where the
1715     // original alignment was altered
1716     AlignmentI al = null;
1717     if (command instanceof EditCommand)
1718     {
1719       EditCommand editCommand = (EditCommand) command;
1720       al = editCommand.getAlignment();
1721       List<Component> comps = PaintRefresher.components
1722               .get(viewport.getSequenceSetId());
1723
1724       for (Component comp : comps)
1725       {
1726         if (comp instanceof AlignmentPanel)
1727         {
1728           if (al == ((AlignmentPanel) comp).av.getAlignment())
1729           {
1730             originalSource = ((AlignmentPanel) comp).av;
1731             break;
1732           }
1733         }
1734       }
1735     }
1736
1737     if (originalSource == null)
1738     {
1739       // The original view is closed, we must validate
1740       // the current view against the closed view first
1741       if (al != null)
1742       {
1743         PaintRefresher.validateSequences(al, viewport.getAlignment());
1744       }
1745
1746       originalSource = viewport;
1747     }
1748
1749     return originalSource;
1750   }
1751
1752   /**
1753    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1754    * or the sequence under cursor in keyboard mode
1755    *
1756    * @param up
1757    *          or down (if !up)
1758    */
1759   public void moveSelectedSequences(boolean up)
1760   {
1761     SequenceGroup sg = viewport.getSelectionGroup();
1762
1763     if (sg == null)
1764     {
1765       if (viewport.cursorMode)
1766       {
1767         sg = new SequenceGroup();
1768         sg.addSequence(viewport.getAlignment().getSequenceAt(
1769                 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1770       }
1771       else
1772       {
1773         return;
1774       }
1775     }
1776
1777     if (sg.getSize() < 1)
1778     {
1779       return;
1780     }
1781
1782     // TODO: JAL-3733 - add an event to the undo buffer for this !
1783
1784     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1785             viewport.getHiddenRepSequences(), up);
1786     alignPanel.paintAlignment(true, false);
1787   }
1788
1789   synchronized void slideSequences(boolean right, int size)
1790   {
1791     List<SequenceI> sg = new ArrayList<>();
1792     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
1793             .getSize() != viewport.getAlignment().getHeight())
1794     {
1795       sg = viewport.getSelectionGroup()
1796               .getSequences(viewport.getHiddenRepSequences());
1797     }
1798
1799     if (sg.size() == 0 && viewport.cursorMode)
1800     {
1801       sg.add(viewport.getAlignment()
1802               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1803     }
1804
1805     if (sg.size() < 1)
1806     {
1807       return;
1808     }
1809
1810     List<SequenceI> invertGroup = new ArrayList<>();
1811
1812     for (SequenceI seq : viewport.getAlignment().getSequences())
1813     {
1814       if (!sg.contains(seq))
1815       {
1816         invertGroup.add(seq);
1817       }
1818     }
1819
1820     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1821
1822     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1823     for (int i = 0; i < invertGroup.size(); i++)
1824     {
1825       seqs2[i] = invertGroup.get(i);
1826     }
1827
1828     SlideSequencesCommand ssc;
1829     if (right)
1830     {
1831       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1832               viewport.getGapCharacter());
1833     }
1834     else
1835     {
1836       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1837               viewport.getGapCharacter());
1838     }
1839
1840     int groupAdjustment = 0;
1841     if (ssc.getGapsInsertedBegin() && right)
1842     {
1843       if (viewport.cursorMode)
1844       {
1845         alignPanel.getSeqPanel().moveCursor(size, 0);
1846       }
1847       else
1848       {
1849         groupAdjustment = size;
1850       }
1851     }
1852     else if (!ssc.getGapsInsertedBegin() && !right)
1853     {
1854       if (viewport.cursorMode)
1855       {
1856         alignPanel.getSeqPanel().moveCursor(-size, 0);
1857       }
1858       else
1859       {
1860         groupAdjustment = -size;
1861       }
1862     }
1863
1864     if (groupAdjustment != 0)
1865     {
1866       viewport.getSelectionGroup().setStartRes(
1867               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1868       viewport.getSelectionGroup().setEndRes(
1869               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1870     }
1871
1872     /*
1873      * just extend the last slide command if compatible; but not if in
1874      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1875      */
1876     boolean appendHistoryItem = false;
1877     Deque<CommandI> historyList = viewport.getHistoryList();
1878     boolean inSplitFrame = getSplitViewContainer() != null;
1879     if (!inSplitFrame && historyList != null && historyList.size() > 0
1880             && historyList.peek() instanceof SlideSequencesCommand)
1881     {
1882       appendHistoryItem = ssc.appendSlideCommand(
1883               (SlideSequencesCommand) historyList.peek());
1884     }
1885
1886     if (!appendHistoryItem)
1887     {
1888       addHistoryItem(ssc);
1889     }
1890
1891     repaint();
1892   }
1893
1894   /**
1895    * DOCUMENT ME!
1896    *
1897    * @param e
1898    *          DOCUMENT ME!
1899    */
1900   @Override
1901   protected void copy_actionPerformed(ActionEvent e)
1902   {
1903     if (viewport.getSelectionGroup() == null)
1904     {
1905       return;
1906     }
1907     // TODO: preserve the ordering of displayed alignment annotation in any
1908     // internal paste (particularly sequence associated annotation)
1909     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1910     String[] omitHidden = null;
1911
1912     if (viewport.hasHiddenColumns())
1913     {
1914       omitHidden = viewport.getViewAsString(true);
1915     }
1916
1917     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1918             seqs, omitHidden, null);
1919
1920     StringSelection ss = new StringSelection(output);
1921
1922     try
1923     {
1924       jalview.gui.Desktop.internalCopy = true;
1925       // Its really worth setting the clipboard contents
1926       // to empty before setting the large StringSelection!!
1927       Toolkit.getDefaultToolkit().getSystemClipboard()
1928               .setContents(new StringSelection(""), null);
1929
1930       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1931               Desktop.instance);
1932     } catch (OutOfMemoryError er)
1933     {
1934       new OOMWarning("copying region", er);
1935       return;
1936     }
1937
1938     HiddenColumns hiddenColumns = null;
1939     if (viewport.hasHiddenColumns())
1940     {
1941       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1942       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1943
1944       // create new HiddenColumns object with copy of hidden regions
1945       // between startRes and endRes, offset by startRes
1946       hiddenColumns = new HiddenColumns(
1947               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1948               hiddenCutoff, hiddenOffset);
1949     }
1950
1951     Desktop.jalviewClipboard = new Object[] { seqs,
1952         viewport.getAlignment().getDataset(), hiddenColumns };
1953     statusBar.setText(MessageManager.formatMessage(
1954             "label.copied_sequences_to_clipboard", new Object[]
1955             { Integer.valueOf(seqs.length).toString() }));
1956   }
1957
1958   /**
1959    * DOCUMENT ME!
1960    *
1961    * @param e
1962    *          DOCUMENT ME!
1963    */
1964   @Override
1965   protected void pasteNew_actionPerformed(ActionEvent e)
1966   {
1967     paste(true);
1968   }
1969
1970   /**
1971    * DOCUMENT ME!
1972    *
1973    * @param e
1974    *          DOCUMENT ME!
1975    */
1976   @Override
1977   protected void pasteThis_actionPerformed(ActionEvent e)
1978   {
1979     paste(false);
1980   }
1981
1982   /**
1983    * Paste contents of Jalview clipboard
1984    *
1985    * @param newAlignment
1986    *          true to paste to a new alignment, otherwise add to this.
1987    */
1988   void paste(boolean newAlignment)
1989   {
1990     boolean externalPaste = true;
1991     try
1992     {
1993       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1994       Transferable contents = c.getContents(this);
1995
1996       if (contents == null)
1997       {
1998         return;
1999       }
2000
2001       String str;
2002       FileFormatI format;
2003       try
2004       {
2005         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2006         if (str.length() < 1)
2007         {
2008           return;
2009         }
2010
2011         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2012
2013       } catch (OutOfMemoryError er)
2014       {
2015         new OOMWarning("Out of memory pasting sequences!!", er);
2016         return;
2017       }
2018
2019       SequenceI[] sequences;
2020       boolean annotationAdded = false;
2021       AlignmentI alignment = null;
2022
2023       if (Desktop.jalviewClipboard != null)
2024       {
2025         // The clipboard was filled from within Jalview, we must use the
2026         // sequences
2027         // And dataset from the copied alignment
2028         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2029         // be doubly sure that we create *new* sequence objects.
2030         sequences = new SequenceI[newseq.length];
2031         for (int i = 0; i < newseq.length; i++)
2032         {
2033           sequences[i] = new Sequence(newseq[i]);
2034         }
2035         alignment = new Alignment(sequences);
2036         externalPaste = false;
2037       }
2038       else
2039       {
2040         // parse the clipboard as an alignment.
2041         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2042                 format);
2043         sequences = alignment.getSequencesArray();
2044       }
2045
2046       int alwidth = 0;
2047       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2048       int fgroup = -1;
2049
2050       if (newAlignment)
2051       {
2052
2053         if (Desktop.jalviewClipboard != null)
2054         {
2055           // dataset is inherited
2056           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2057         }
2058         else
2059         {
2060           // new dataset is constructed
2061           alignment.setDataset(null);
2062         }
2063         alwidth = alignment.getWidth() + 1;
2064       }
2065       else
2066       {
2067         AlignmentI pastedal = alignment; // preserve pasted alignment object
2068         // Add pasted sequences and dataset into existing alignment.
2069         alignment = viewport.getAlignment();
2070         alwidth = alignment.getWidth() + 1;
2071         // decide if we need to import sequences from an existing dataset
2072         boolean importDs = Desktop.jalviewClipboard != null
2073                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2074         // importDs==true instructs us to copy over new dataset sequences from
2075         // an existing alignment
2076         Vector newDs = (importDs) ? new Vector() : null; // used to create
2077         // minimum dataset set
2078
2079         for (int i = 0; i < sequences.length; i++)
2080         {
2081           if (importDs)
2082           {
2083             newDs.addElement(null);
2084           }
2085           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2086           // paste
2087           if (importDs && ds != null)
2088           {
2089             if (!newDs.contains(ds))
2090             {
2091               newDs.setElementAt(ds, i);
2092               ds = new Sequence(ds);
2093               // update with new dataset sequence
2094               sequences[i].setDatasetSequence(ds);
2095             }
2096             else
2097             {
2098               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2099             }
2100           }
2101           else
2102           {
2103             // copy and derive new dataset sequence
2104             sequences[i] = sequences[i].deriveSequence();
2105             alignment.getDataset()
2106                     .addSequence(sequences[i].getDatasetSequence());
2107             // TODO: avoid creation of duplicate dataset sequences with a
2108             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2109           }
2110           alignment.addSequence(sequences[i]); // merges dataset
2111         }
2112         if (newDs != null)
2113         {
2114           newDs.clear(); // tidy up
2115         }
2116         if (alignment.getAlignmentAnnotation() != null)
2117         {
2118           for (AlignmentAnnotation alan : alignment
2119                   .getAlignmentAnnotation())
2120           {
2121             if (alan.graphGroup > fgroup)
2122             {
2123               fgroup = alan.graphGroup;
2124             }
2125           }
2126         }
2127         if (pastedal.getAlignmentAnnotation() != null)
2128         {
2129           // Add any annotation attached to alignment.
2130           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2131           for (int i = 0; i < alann.length; i++)
2132           {
2133             annotationAdded = true;
2134             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2135             {
2136               AlignmentAnnotation newann = new AlignmentAnnotation(
2137                       alann[i]);
2138               if (newann.graphGroup > -1)
2139               {
2140                 if (newGraphGroups.size() <= newann.graphGroup
2141                         || newGraphGroups.get(newann.graphGroup) == null)
2142                 {
2143                   for (int q = newGraphGroups
2144                           .size(); q <= newann.graphGroup; q++)
2145                   {
2146                     newGraphGroups.add(q, null);
2147                   }
2148                   newGraphGroups.set(newann.graphGroup,
2149                           Integer.valueOf(++fgroup));
2150                 }
2151                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2152                         .intValue();
2153               }
2154
2155               newann.padAnnotation(alwidth);
2156               alignment.addAnnotation(newann);
2157             }
2158           }
2159         }
2160       }
2161       if (!newAlignment)
2162       {
2163         // /////
2164         // ADD HISTORY ITEM
2165         //
2166         addHistoryItem(new EditCommand(
2167                 MessageManager.getString("label.add_sequences"),
2168                 Action.PASTE, sequences, 0, alignment.getWidth(),
2169                 alignment));
2170       }
2171       // Add any annotations attached to sequences
2172       for (int i = 0; i < sequences.length; i++)
2173       {
2174         if (sequences[i].getAnnotation() != null)
2175         {
2176           AlignmentAnnotation newann;
2177           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2178           {
2179             annotationAdded = true;
2180             newann = sequences[i].getAnnotation()[a];
2181             newann.adjustForAlignment();
2182             newann.padAnnotation(alwidth);
2183             if (newann.graphGroup > -1)
2184             {
2185               if (newann.graphGroup > -1)
2186               {
2187                 if (newGraphGroups.size() <= newann.graphGroup
2188                         || newGraphGroups.get(newann.graphGroup) == null)
2189                 {
2190                   for (int q = newGraphGroups
2191                           .size(); q <= newann.graphGroup; q++)
2192                   {
2193                     newGraphGroups.add(q, null);
2194                   }
2195                   newGraphGroups.set(newann.graphGroup,
2196                           Integer.valueOf(++fgroup));
2197                 }
2198                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2199                         .intValue();
2200               }
2201             }
2202             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2203             // was
2204             // duplicated
2205             // earlier
2206             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2207                     a);
2208           }
2209         }
2210       }
2211       if (!newAlignment)
2212       {
2213
2214         // propagate alignment changed.
2215         viewport.getRanges().setEndSeq(alignment.getHeight());
2216         if (annotationAdded)
2217         {
2218           // Duplicate sequence annotation in all views.
2219           AlignmentI[] alview = this.getViewAlignments();
2220           for (int i = 0; i < sequences.length; i++)
2221           {
2222             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2223             if (sann == null)
2224             {
2225               continue;
2226             }
2227             for (int avnum = 0; avnum < alview.length; avnum++)
2228             {
2229               if (alview[avnum] != alignment)
2230               {
2231                 // duplicate in a view other than the one with input focus
2232                 int avwidth = alview[avnum].getWidth() + 1;
2233                 // this relies on sann being preserved after we
2234                 // modify the sequence's annotation array for each duplication
2235                 for (int a = 0; a < sann.length; a++)
2236                 {
2237                   AlignmentAnnotation newann = new AlignmentAnnotation(
2238                           sann[a]);
2239                   sequences[i].addAlignmentAnnotation(newann);
2240                   newann.padAnnotation(avwidth);
2241                   alview[avnum].addAnnotation(newann); // annotation was
2242                   // duplicated earlier
2243                   // TODO JAL-1145 graphGroups are not updated for sequence
2244                   // annotation added to several views. This may cause
2245                   // strangeness
2246                   alview[avnum].setAnnotationIndex(newann, a);
2247                 }
2248               }
2249             }
2250           }
2251           buildSortByAnnotationScoresMenu();
2252         }
2253         viewport.firePropertyChange("alignment", null,
2254                 alignment.getSequences());
2255         if (alignPanels != null)
2256         {
2257           for (AlignmentPanel ap : alignPanels)
2258           {
2259             ap.validateAnnotationDimensions(false);
2260           }
2261         }
2262         else
2263         {
2264           alignPanel.validateAnnotationDimensions(false);
2265         }
2266
2267       }
2268       else
2269       {
2270         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2271                 DEFAULT_HEIGHT);
2272         String newtitle = new String("Copied sequences");
2273
2274         if (Desktop.jalviewClipboard != null
2275                 && Desktop.jalviewClipboard[2] != null)
2276         {
2277           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2278           af.viewport.setHiddenColumns(hc);
2279         }
2280
2281         // >>>This is a fix for the moment, until a better solution is
2282         // found!!<<<
2283         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2284                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2285                         .getFeatureRenderer());
2286
2287         // TODO: maintain provenance of an alignment, rather than just make the
2288         // title a concatenation of operations.
2289         if (!externalPaste)
2290         {
2291           if (title.startsWith("Copied sequences"))
2292           {
2293             newtitle = title;
2294           }
2295           else
2296           {
2297             newtitle = newtitle.concat("- from " + title);
2298           }
2299         }
2300         else
2301         {
2302           newtitle = new String("Pasted sequences");
2303         }
2304
2305         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2306                 DEFAULT_HEIGHT);
2307
2308       }
2309
2310     } catch (Exception ex)
2311     {
2312       ex.printStackTrace();
2313       System.out.println("Exception whilst pasting: " + ex);
2314       // could be anything being pasted in here
2315     }
2316
2317   }
2318
2319   @Override
2320   protected void expand_newalign(ActionEvent e)
2321   {
2322     try
2323     {
2324       AlignmentI alignment = AlignmentUtils
2325               .expandContext(getViewport().getAlignment(), -1);
2326       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2327               DEFAULT_HEIGHT);
2328       String newtitle = new String("Flanking alignment");
2329
2330       if (Desktop.jalviewClipboard != null
2331               && Desktop.jalviewClipboard[2] != null)
2332       {
2333         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2334         af.viewport.setHiddenColumns(hc);
2335       }
2336
2337       // >>>This is a fix for the moment, until a better solution is
2338       // found!!<<<
2339       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2340               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2341                       .getFeatureRenderer());
2342
2343       // TODO: maintain provenance of an alignment, rather than just make the
2344       // title a concatenation of operations.
2345       {
2346         if (title.startsWith("Copied sequences"))
2347         {
2348           newtitle = title;
2349         }
2350         else
2351         {
2352           newtitle = newtitle.concat("- from " + title);
2353         }
2354       }
2355
2356       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2357
2358     } catch (Exception ex)
2359     {
2360       ex.printStackTrace();
2361       System.out.println("Exception whilst pasting: " + ex);
2362       // could be anything being pasted in here
2363     } catch (OutOfMemoryError oom)
2364     {
2365       new OOMWarning("Viewing flanking region of alignment", oom);
2366     }
2367   }
2368
2369   /**
2370    * DOCUMENT ME!
2371    *
2372    * @param e
2373    *          DOCUMENT ME!
2374    */
2375   @Override
2376   protected void cut_actionPerformed(ActionEvent e)
2377   {
2378     copy_actionPerformed(null);
2379     delete_actionPerformed(null);
2380   }
2381
2382   /**
2383    * DOCUMENT ME!
2384    *
2385    * @param e
2386    *          DOCUMENT ME!
2387    */
2388   @Override
2389   protected void delete_actionPerformed(ActionEvent evt)
2390   {
2391
2392     SequenceGroup sg = viewport.getSelectionGroup();
2393     if (sg == null)
2394     {
2395       return;
2396     }
2397
2398     /*
2399      * If the cut affects all sequences, warn, remove highlighted columns
2400      */
2401     if (sg.getSize() == viewport.getAlignment().getHeight())
2402     {
2403       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2404               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2405       if (isEntireAlignWidth)
2406       {
2407         int confirm = JvOptionPane.showConfirmDialog(this,
2408                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2409                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2410                 JvOptionPane.OK_CANCEL_OPTION);
2411
2412         if (confirm == JvOptionPane.CANCEL_OPTION
2413                 || confirm == JvOptionPane.CLOSED_OPTION)
2414         {
2415           return;
2416         }
2417       }
2418       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2419               sg.getEndRes() + 1);
2420     }
2421     SequenceI[] cut = sg.getSequences()
2422             .toArray(new SequenceI[sg.getSize()]);
2423
2424     addHistoryItem(new EditCommand(
2425             MessageManager.getString("label.cut_sequences"), Action.CUT,
2426             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2427             viewport.getAlignment()));
2428
2429     viewport.setSelectionGroup(null);
2430     viewport.sendSelection();
2431     viewport.getAlignment().deleteGroup(sg);
2432
2433     viewport.firePropertyChange("alignment", null,
2434             viewport.getAlignment().getSequences());
2435     if (viewport.getAlignment().getHeight() < 1)
2436     {
2437       try
2438       {
2439         this.setClosed(true);
2440       } catch (Exception ex)
2441       {
2442       }
2443     }
2444   }
2445
2446   /**
2447    * DOCUMENT ME!
2448    *
2449    * @param e
2450    *          DOCUMENT ME!
2451    */
2452   @Override
2453   protected void deleteGroups_actionPerformed(ActionEvent e)
2454   {
2455     if (avc.deleteGroups())
2456     {
2457       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2458       alignPanel.updateAnnotation();
2459       alignPanel.paintAlignment(true, true);
2460     }
2461   }
2462
2463   /**
2464    * DOCUMENT ME!
2465    *
2466    * @param e
2467    *          DOCUMENT ME!
2468    */
2469   @Override
2470   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2471   {
2472     SequenceGroup sg = new SequenceGroup(
2473             viewport.getAlignment().getSequences());
2474
2475     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2476     viewport.setSelectionGroup(sg);
2477     viewport.isSelectionGroupChanged(true);
2478     viewport.sendSelection();
2479     // JAL-2034 - should delegate to
2480     // alignPanel to decide if overview needs
2481     // updating.
2482     alignPanel.paintAlignment(false, false);
2483     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2484   }
2485
2486   /**
2487    * DOCUMENT ME!
2488    *
2489    * @param e
2490    *          DOCUMENT ME!
2491    */
2492   @Override
2493   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2494   {
2495     if (viewport.cursorMode)
2496     {
2497       alignPanel.getSeqPanel().keyboardNo1 = null;
2498       alignPanel.getSeqPanel().keyboardNo2 = null;
2499     }
2500     viewport.setSelectionGroup(null);
2501     viewport.getColumnSelection().clear();
2502     viewport.setSearchResults(null);
2503     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2504     // JAL-2034 - should delegate to
2505     // alignPanel to decide if overview needs
2506     // updating.
2507     alignPanel.paintAlignment(false, false);
2508     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2509     viewport.sendSelection();
2510   }
2511
2512   /**
2513    * DOCUMENT ME!
2514    *
2515    * @param e
2516    *          DOCUMENT ME!
2517    */
2518   @Override
2519   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2520   {
2521     SequenceGroup sg = viewport.getSelectionGroup();
2522
2523     if (sg == null)
2524     {
2525       selectAllSequenceMenuItem_actionPerformed(null);
2526
2527       return;
2528     }
2529
2530     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2531     {
2532       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2533     }
2534     // JAL-2034 - should delegate to
2535     // alignPanel to decide if overview needs
2536     // updating.
2537
2538     alignPanel.paintAlignment(true, false);
2539     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2540     viewport.sendSelection();
2541   }
2542
2543   @Override
2544   public void invertColSel_actionPerformed(ActionEvent e)
2545   {
2546     viewport.invertColumnSelection();
2547     alignPanel.paintAlignment(true, false);
2548     viewport.sendSelection();
2549   }
2550
2551   /**
2552    * DOCUMENT ME!
2553    *
2554    * @param e
2555    *          DOCUMENT ME!
2556    */
2557   @Override
2558   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2559   {
2560     trimAlignment(true);
2561   }
2562
2563   /**
2564    * DOCUMENT ME!
2565    *
2566    * @param e
2567    *          DOCUMENT ME!
2568    */
2569   @Override
2570   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2571   {
2572     trimAlignment(false);
2573   }
2574
2575   void trimAlignment(boolean trimLeft)
2576   {
2577     ColumnSelection colSel = viewport.getColumnSelection();
2578     int column;
2579
2580     if (!colSel.isEmpty())
2581     {
2582       if (trimLeft)
2583       {
2584         column = colSel.getMin();
2585       }
2586       else
2587       {
2588         column = colSel.getMax();
2589       }
2590
2591       SequenceI[] seqs;
2592       if (viewport.getSelectionGroup() != null)
2593       {
2594         seqs = viewport.getSelectionGroup()
2595                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2596       }
2597       else
2598       {
2599         seqs = viewport.getAlignment().getSequencesArray();
2600       }
2601
2602       TrimRegionCommand trimRegion;
2603       if (trimLeft)
2604       {
2605         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2606                 column, viewport.getAlignment());
2607         viewport.getRanges().setStartRes(0);
2608       }
2609       else
2610       {
2611         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2612                 column, viewport.getAlignment());
2613       }
2614
2615       statusBar.setText(MessageManager
2616               .formatMessage("label.removed_columns", new String[]
2617               { Integer.valueOf(trimRegion.getSize()).toString() }));
2618
2619       addHistoryItem(trimRegion);
2620
2621       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2622       {
2623         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2624                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2625         {
2626           viewport.getAlignment().deleteGroup(sg);
2627         }
2628       }
2629
2630       viewport.firePropertyChange("alignment", null,
2631               viewport.getAlignment().getSequences());
2632     }
2633   }
2634
2635   /**
2636    * DOCUMENT ME!
2637    *
2638    * @param e
2639    *          DOCUMENT ME!
2640    */
2641   @Override
2642   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2643   {
2644     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2645
2646     SequenceI[] seqs;
2647     if (viewport.getSelectionGroup() != null)
2648     {
2649       seqs = viewport.getSelectionGroup()
2650               .getSequencesAsArray(viewport.getHiddenRepSequences());
2651       start = viewport.getSelectionGroup().getStartRes();
2652       end = viewport.getSelectionGroup().getEndRes();
2653     }
2654     else
2655     {
2656       seqs = viewport.getAlignment().getSequencesArray();
2657     }
2658
2659     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2660             "Remove Gapped Columns", seqs, start, end,
2661             viewport.getAlignment());
2662
2663     addHistoryItem(removeGapCols);
2664
2665     statusBar.setText(MessageManager
2666             .formatMessage("label.removed_empty_columns", new Object[]
2667             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2668
2669     // This is to maintain viewport position on first residue
2670     // of first sequence
2671     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2672     ViewportRanges ranges = viewport.getRanges();
2673     int startRes = seq.findPosition(ranges.getStartRes());
2674     // ShiftList shifts;
2675     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2676     // edit.alColumnChanges=shifts.getInverse();
2677     // if (viewport.hasHiddenColumns)
2678     // viewport.getColumnSelection().compensateForEdits(shifts);
2679     ranges.setStartRes(seq.findIndex(startRes) - 1);
2680     viewport.firePropertyChange("alignment", null,
2681             viewport.getAlignment().getSequences());
2682
2683   }
2684
2685   /**
2686    * DOCUMENT ME!
2687    *
2688    * @param e
2689    *          DOCUMENT ME!
2690    */
2691   @Override
2692   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2693   {
2694     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2695
2696     SequenceI[] seqs;
2697     if (viewport.getSelectionGroup() != null)
2698     {
2699       seqs = viewport.getSelectionGroup()
2700               .getSequencesAsArray(viewport.getHiddenRepSequences());
2701       start = viewport.getSelectionGroup().getStartRes();
2702       end = viewport.getSelectionGroup().getEndRes();
2703     }
2704     else
2705     {
2706       seqs = viewport.getAlignment().getSequencesArray();
2707     }
2708
2709     // This is to maintain viewport position on first residue
2710     // of first sequence
2711     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2712     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2713
2714     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2715             viewport.getAlignment()));
2716
2717     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2718
2719     viewport.firePropertyChange("alignment", null,
2720             viewport.getAlignment().getSequences());
2721
2722   }
2723
2724   /**
2725    * DOCUMENT ME!
2726    *
2727    * @param e
2728    *          DOCUMENT ME!
2729    */
2730   @Override
2731   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2732   {
2733     viewport.setPadGaps(padGapsMenuitem.isSelected());
2734     viewport.firePropertyChange("alignment", null,
2735             viewport.getAlignment().getSequences());
2736   }
2737
2738   /**
2739    * Opens a Finder dialog
2740    *
2741    * @param e
2742    */
2743   @Override
2744   public void findMenuItem_actionPerformed(ActionEvent e)
2745   {
2746     new Finder(alignPanel);
2747   }
2748
2749   /**
2750    * Create a new view of the current alignment.
2751    */
2752   @Override
2753   public void newView_actionPerformed(ActionEvent e)
2754   {
2755     newView(null, true);
2756   }
2757
2758   /**
2759    * Creates and shows a new view of the current alignment.
2760    *
2761    * @param viewTitle
2762    *          title of newly created view; if null, one will be generated
2763    * @param copyAnnotation
2764    *          if true then duplicate all annnotation, groups and settings
2765    * @return new alignment panel, already displayed.
2766    */
2767   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2768   {
2769     /*
2770      * Create a new AlignmentPanel (with its own, new Viewport)
2771      */
2772     AlignmentPanel newap = new jalview.project.Jalview2XML()
2773             .copyAlignPanel(alignPanel);
2774     if (!copyAnnotation)
2775     {
2776       /*
2777        * remove all groups and annotation except for the automatic stuff
2778        */
2779       newap.av.getAlignment().deleteAllGroups();
2780       newap.av.getAlignment().deleteAllAnnotations(false);
2781     }
2782
2783     newap.av.setGatherViewsHere(false);
2784
2785     if (viewport.getViewName() == null)
2786     {
2787       viewport.setViewName(
2788               MessageManager.getString("label.view_name_original"));
2789     }
2790
2791     /*
2792      * Views share the same edits undo and redo stacks
2793      */
2794     newap.av.setHistoryList(viewport.getHistoryList());
2795     newap.av.setRedoList(viewport.getRedoList());
2796
2797     /*
2798      * copy any visualisation settings that are not saved in the project
2799      */
2800     newap.av.setColourAppliesToAllGroups(
2801             viewport.getColourAppliesToAllGroups());
2802
2803     /*
2804      * Views share the same mappings; need to deregister any new mappings
2805      * created by copyAlignPanel, and register the new reference to the shared
2806      * mappings
2807      */
2808     newap.av.replaceMappings(viewport.getAlignment());
2809
2810     /*
2811      * start up cDNA consensus (if applicable) now mappings are in place
2812      */
2813     if (newap.av.initComplementConsensus())
2814     {
2815       newap.refresh(true); // adjust layout of annotations
2816     }
2817
2818     newap.av.setViewName(getNewViewName(viewTitle));
2819
2820     addAlignmentPanel(newap, true);
2821     newap.alignmentChanged();
2822
2823     if (alignPanels.size() == 2)
2824     {
2825       viewport.setGatherViewsHere(true);
2826     }
2827     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2828     return newap;
2829   }
2830
2831   /**
2832    * Make a new name for the view, ensuring it is unique within the current
2833    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2834    * these now use viewId. Unique view names are still desirable for usability.)
2835    *
2836    * @param viewTitle
2837    * @return
2838    */
2839   protected String getNewViewName(String viewTitle)
2840   {
2841     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2842     boolean addFirstIndex = false;
2843     if (viewTitle == null || viewTitle.trim().length() == 0)
2844     {
2845       viewTitle = MessageManager.getString("action.view");
2846       addFirstIndex = true;
2847     }
2848     else
2849     {
2850       index = 1;// we count from 1 if given a specific name
2851     }
2852     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2853
2854     List<Component> comps = PaintRefresher.components
2855             .get(viewport.getSequenceSetId());
2856
2857     List<String> existingNames = getExistingViewNames(comps);
2858
2859     while (existingNames.contains(newViewName))
2860     {
2861       newViewName = viewTitle + " " + (++index);
2862     }
2863     return newViewName;
2864   }
2865
2866   /**
2867    * Returns a list of distinct view names found in the given list of
2868    * components. View names are held on the viewport of an AlignmentPanel.
2869    *
2870    * @param comps
2871    * @return
2872    */
2873   protected List<String> getExistingViewNames(List<Component> comps)
2874   {
2875     List<String> existingNames = new ArrayList<>();
2876     for (Component comp : comps)
2877     {
2878       if (comp instanceof AlignmentPanel)
2879       {
2880         AlignmentPanel ap = (AlignmentPanel) comp;
2881         if (!existingNames.contains(ap.av.getViewName()))
2882         {
2883           existingNames.add(ap.av.getViewName());
2884         }
2885       }
2886     }
2887     return existingNames;
2888   }
2889
2890   /**
2891    * Explode tabbed views into separate windows.
2892    */
2893   @Override
2894   public void expandViews_actionPerformed(ActionEvent e)
2895   {
2896     Desktop.explodeViews(this);
2897   }
2898
2899   /**
2900    * Gather views in separate windows back into a tabbed presentation.
2901    */
2902   @Override
2903   public void gatherViews_actionPerformed(ActionEvent e)
2904   {
2905     Desktop.instance.gatherViews(this);
2906   }
2907
2908   /**
2909    * DOCUMENT ME!
2910    *
2911    * @param e
2912    *          DOCUMENT ME!
2913    */
2914   @Override
2915   public void font_actionPerformed(ActionEvent e)
2916   {
2917     new FontChooser(alignPanel);
2918   }
2919
2920   /**
2921    * DOCUMENT ME!
2922    *
2923    * @param e
2924    *          DOCUMENT ME!
2925    */
2926   @Override
2927   protected void seqLimit_actionPerformed(ActionEvent e)
2928   {
2929     viewport.setShowJVSuffix(seqLimits.isSelected());
2930
2931     alignPanel.getIdPanel().getIdCanvas()
2932             .setPreferredSize(alignPanel.calculateIdWidth());
2933     alignPanel.paintAlignment(true, false);
2934   }
2935
2936   @Override
2937   public void idRightAlign_actionPerformed(ActionEvent e)
2938   {
2939     viewport.setRightAlignIds(idRightAlign.isSelected());
2940     alignPanel.paintAlignment(false, false);
2941   }
2942
2943   @Override
2944   public void centreColumnLabels_actionPerformed(ActionEvent e)
2945   {
2946     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2947     alignPanel.paintAlignment(false, false);
2948   }
2949
2950   /*
2951    * (non-Javadoc)
2952    *
2953    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2954    */
2955   @Override
2956   protected void followHighlight_actionPerformed()
2957   {
2958     /*
2959      * Set the 'follow' flag on the Viewport (and scroll to position if now
2960      * true).
2961      */
2962     final boolean state = this.followHighlightMenuItem.getState();
2963     viewport.setFollowHighlight(state);
2964     if (state)
2965     {
2966       alignPanel.scrollToPosition(viewport.getSearchResults());
2967     }
2968   }
2969
2970   /**
2971    * DOCUMENT ME!
2972    *
2973    * @param e
2974    *          DOCUMENT ME!
2975    */
2976   @Override
2977   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2978   {
2979     viewport.setColourText(colourTextMenuItem.isSelected());
2980     alignPanel.paintAlignment(false, false);
2981   }
2982
2983   /**
2984    * DOCUMENT ME!
2985    *
2986    * @param e
2987    *          DOCUMENT ME!
2988    */
2989   @Override
2990   public void wrapMenuItem_actionPerformed(ActionEvent e)
2991   {
2992     scaleAbove.setVisible(wrapMenuItem.isSelected());
2993     scaleLeft.setVisible(wrapMenuItem.isSelected());
2994     scaleRight.setVisible(wrapMenuItem.isSelected());
2995     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2996     alignPanel.updateLayout();
2997   }
2998
2999   @Override
3000   public void showAllSeqs_actionPerformed(ActionEvent e)
3001   {
3002     viewport.showAllHiddenSeqs();
3003   }
3004
3005   @Override
3006   public void showAllColumns_actionPerformed(ActionEvent e)
3007   {
3008     viewport.showAllHiddenColumns();
3009     alignPanel.paintAlignment(true, true);
3010     viewport.sendSelection();
3011   }
3012
3013   @Override
3014   public void hideSelSequences_actionPerformed(ActionEvent e)
3015   {
3016     viewport.hideAllSelectedSeqs();
3017   }
3018
3019   /**
3020    * called by key handler and the hide all/show all menu items
3021    *
3022    * @param toggleSeqs
3023    * @param toggleCols
3024    */
3025   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3026   {
3027
3028     boolean hide = false;
3029     SequenceGroup sg = viewport.getSelectionGroup();
3030     if (!toggleSeqs && !toggleCols)
3031     {
3032       // Hide everything by the current selection - this is a hack - we do the
3033       // invert and then hide
3034       // first check that there will be visible columns after the invert.
3035       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3036               && sg.getStartRes() <= sg.getEndRes()))
3037       {
3038         // now invert the sequence set, if required - empty selection implies
3039         // that no hiding is required.
3040         if (sg != null)
3041         {
3042           invertSequenceMenuItem_actionPerformed(null);
3043           sg = viewport.getSelectionGroup();
3044           toggleSeqs = true;
3045
3046         }
3047         viewport.expandColSelection(sg, true);
3048         // finally invert the column selection and get the new sequence
3049         // selection.
3050         invertColSel_actionPerformed(null);
3051         toggleCols = true;
3052       }
3053     }
3054
3055     if (toggleSeqs)
3056     {
3057       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3058       {
3059         hideSelSequences_actionPerformed(null);
3060         hide = true;
3061       }
3062       else if (!(toggleCols && viewport.hasSelectedColumns()))
3063       {
3064         showAllSeqs_actionPerformed(null);
3065       }
3066     }
3067
3068     if (toggleCols)
3069     {
3070       if (viewport.hasSelectedColumns())
3071       {
3072         hideSelColumns_actionPerformed(null);
3073         if (!toggleSeqs)
3074         {
3075           viewport.setSelectionGroup(sg);
3076         }
3077       }
3078       else if (!hide)
3079       {
3080         showAllColumns_actionPerformed(null);
3081       }
3082     }
3083   }
3084
3085   /*
3086    * (non-Javadoc)
3087    *
3088    * @see
3089    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3090    * event.ActionEvent)
3091    */
3092   @Override
3093   public void hideAllButSelection_actionPerformed(ActionEvent e)
3094   {
3095     toggleHiddenRegions(false, false);
3096     viewport.sendSelection();
3097   }
3098
3099   /*
3100    * (non-Javadoc)
3101    *
3102    * @see
3103    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3104    * .ActionEvent)
3105    */
3106   @Override
3107   public void hideAllSelection_actionPerformed(ActionEvent e)
3108   {
3109     SequenceGroup sg = viewport.getSelectionGroup();
3110     viewport.expandColSelection(sg, false);
3111     viewport.hideAllSelectedSeqs();
3112     viewport.hideSelectedColumns();
3113     alignPanel.updateLayout();
3114     alignPanel.paintAlignment(true, true);
3115     viewport.sendSelection();
3116   }
3117
3118   /*
3119    * (non-Javadoc)
3120    *
3121    * @see
3122    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3123    * ActionEvent)
3124    */
3125   @Override
3126   public void showAllhidden_actionPerformed(ActionEvent e)
3127   {
3128     viewport.showAllHiddenColumns();
3129     viewport.showAllHiddenSeqs();
3130     alignPanel.paintAlignment(true, true);
3131     viewport.sendSelection();
3132   }
3133
3134   @Override
3135   public void hideSelColumns_actionPerformed(ActionEvent e)
3136   {
3137     viewport.hideSelectedColumns();
3138     alignPanel.updateLayout();
3139     alignPanel.paintAlignment(true, true);
3140     viewport.sendSelection();
3141   }
3142
3143   @Override
3144   public void hiddenMarkers_actionPerformed(ActionEvent e)
3145   {
3146     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3147     repaint();
3148   }
3149
3150   /**
3151    * DOCUMENT ME!
3152    *
3153    * @param e
3154    *          DOCUMENT ME!
3155    */
3156   @Override
3157   protected void scaleAbove_actionPerformed(ActionEvent e)
3158   {
3159     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3160     alignPanel.updateLayout();
3161     alignPanel.paintAlignment(true, false);
3162   }
3163
3164   /**
3165    * DOCUMENT ME!
3166    *
3167    * @param e
3168    *          DOCUMENT ME!
3169    */
3170   @Override
3171   protected void scaleLeft_actionPerformed(ActionEvent e)
3172   {
3173     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3174     alignPanel.updateLayout();
3175     alignPanel.paintAlignment(true, false);
3176   }
3177
3178   /**
3179    * DOCUMENT ME!
3180    *
3181    * @param e
3182    *          DOCUMENT ME!
3183    */
3184   @Override
3185   protected void scaleRight_actionPerformed(ActionEvent e)
3186   {
3187     viewport.setScaleRightWrapped(scaleRight.isSelected());
3188     alignPanel.updateLayout();
3189     alignPanel.paintAlignment(true, false);
3190   }
3191
3192   /**
3193    * DOCUMENT ME!
3194    *
3195    * @param e
3196    *          DOCUMENT ME!
3197    */
3198   @Override
3199   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3200   {
3201     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3202     alignPanel.paintAlignment(false, false);
3203   }
3204
3205   /**
3206    * DOCUMENT ME!
3207    *
3208    * @param e
3209    *          DOCUMENT ME!
3210    */
3211   @Override
3212   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3213   {
3214     viewport.setShowText(viewTextMenuItem.isSelected());
3215     alignPanel.paintAlignment(false, false);
3216   }
3217
3218   /**
3219    * DOCUMENT ME!
3220    *
3221    * @param e
3222    *          DOCUMENT ME!
3223    */
3224   @Override
3225   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3226   {
3227     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3228     alignPanel.paintAlignment(false, false);
3229   }
3230
3231   public FeatureSettings featureSettings;
3232
3233   @Override
3234   public FeatureSettingsControllerI getFeatureSettingsUI()
3235   {
3236     return featureSettings;
3237   }
3238
3239   @Override
3240   public void featureSettings_actionPerformed(ActionEvent e)
3241   {
3242     showFeatureSettingsUI();
3243   }
3244
3245   @Override
3246   public FeatureSettingsControllerI showFeatureSettingsUI()
3247   {
3248     if (featureSettings != null)
3249     {
3250       featureSettings.closeOldSettings();
3251       featureSettings = null;
3252     }
3253     if (!showSeqFeatures.isSelected())
3254     {
3255       // make sure features are actually displayed
3256       showSeqFeatures.setSelected(true);
3257       showSeqFeatures_actionPerformed(null);
3258     }
3259     featureSettings = new FeatureSettings(this);
3260     return featureSettings;
3261   }
3262
3263   /**
3264    * Set or clear 'Show Sequence Features'
3265    *
3266    * @param evt
3267    *          DOCUMENT ME!
3268    */
3269   @Override
3270   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3271   {
3272     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3273     alignPanel.paintAlignment(true, true);
3274   }
3275
3276   /**
3277    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3278    * the annotations panel as a whole.
3279    *
3280    * The options to show/hide all annotations should be enabled when the panel
3281    * is shown, and disabled when the panel is hidden.
3282    *
3283    * @param e
3284    */
3285   @Override
3286   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3287   {
3288     final boolean setVisible = annotationPanelMenuItem.isSelected();
3289     viewport.setShowAnnotation(setVisible);
3290     this.showAllSeqAnnotations.setEnabled(setVisible);
3291     this.hideAllSeqAnnotations.setEnabled(setVisible);
3292     this.showAllAlAnnotations.setEnabled(setVisible);
3293     this.hideAllAlAnnotations.setEnabled(setVisible);
3294     alignPanel.updateLayout();
3295   }
3296
3297   @Override
3298   public void alignmentProperties()
3299   {
3300     JEditorPane editPane = new JEditorPane("text/html", "");
3301     editPane.setEditable(false);
3302     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3303             .formatAsHtml();
3304     editPane.setText(
3305             MessageManager.formatMessage("label.html_content", new Object[]
3306             { contents.toString() }));
3307     JInternalFrame frame = new JInternalFrame();
3308     frame.getContentPane().add(new JScrollPane(editPane));
3309
3310     Desktop.addInternalFrame(frame, MessageManager
3311             .formatMessage("label.alignment_properties", new Object[]
3312             { getTitle() }), 500, 400);
3313   }
3314
3315   /**
3316    * DOCUMENT ME!
3317    *
3318    * @param e
3319    *          DOCUMENT ME!
3320    */
3321   @Override
3322   public void overviewMenuItem_actionPerformed(ActionEvent e)
3323   {
3324     if (alignPanel.overviewPanel != null)
3325     {
3326       return;
3327     }
3328
3329     JInternalFrame frame = new JInternalFrame();
3330     final OverviewPanel overview = new OverviewPanel(alignPanel);
3331     frame.setContentPane(overview);
3332     Desktop.addInternalFrame(frame, MessageManager
3333             .formatMessage("label.overview_params", new Object[]
3334             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3335             true, true);
3336     frame.pack();
3337     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3338     frame.addInternalFrameListener(
3339             new javax.swing.event.InternalFrameAdapter()
3340             {
3341               @Override
3342               public void internalFrameClosed(
3343                       javax.swing.event.InternalFrameEvent evt)
3344               {
3345                 overview.dispose();
3346                 alignPanel.setOverviewPanel(null);
3347               };
3348             });
3349     if (getKeyListeners().length > 0)
3350     {
3351       frame.addKeyListener(getKeyListeners()[0]);
3352     }
3353
3354     alignPanel.setOverviewPanel(overview);
3355   }
3356
3357   @Override
3358   public void textColour_actionPerformed()
3359   {
3360     new TextColourChooser().chooseColour(alignPanel, null);
3361   }
3362
3363   /*
3364    * public void covariationColour_actionPerformed() {
3365    * changeColour(new
3366    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3367    * ()[0])); }
3368    */
3369   @Override
3370   public void annotationColour_actionPerformed()
3371   {
3372     new AnnotationColourChooser(viewport, alignPanel);
3373   }
3374
3375   @Override
3376   public void annotationColumn_actionPerformed(ActionEvent e)
3377   {
3378     new AnnotationColumnChooser(viewport, alignPanel);
3379   }
3380
3381   /**
3382    * Action on the user checking or unchecking the option to apply the selected
3383    * colour scheme to all groups. If unchecked, groups may have their own
3384    * independent colour schemes.
3385    *
3386    * @param selected
3387    */
3388   @Override
3389   public void applyToAllGroups_actionPerformed(boolean selected)
3390   {
3391     viewport.setColourAppliesToAllGroups(selected);
3392   }
3393
3394   /**
3395    * Action on user selecting a colour from the colour menu
3396    *
3397    * @param name
3398    *          the name (not the menu item label!) of the colour scheme
3399    */
3400   @Override
3401   public void changeColour_actionPerformed(String name)
3402   {
3403     /*
3404      * 'User Defined' opens a panel to configure or load a
3405      * user-defined colour scheme
3406      */
3407     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3408     {
3409       new UserDefinedColours(alignPanel);
3410       return;
3411     }
3412
3413     /*
3414      * otherwise set the chosen colour scheme (or null for 'None')
3415      */
3416     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3417             viewport, viewport.getAlignment(),
3418             viewport.getHiddenRepSequences());
3419     changeColour(cs);
3420   }
3421
3422   /**
3423    * Actions on setting or changing the alignment colour scheme
3424    *
3425    * @param cs
3426    */
3427   @Override
3428   public void changeColour(ColourSchemeI cs)
3429   {
3430     // TODO: pull up to controller method
3431     ColourMenuHelper.setColourSelected(colourMenu, cs);
3432
3433     viewport.setGlobalColourScheme(cs);
3434
3435     alignPanel.paintAlignment(true, true);
3436   }
3437
3438   /**
3439    * Show the PID threshold slider panel
3440    */
3441   @Override
3442   protected void modifyPID_actionPerformed()
3443   {
3444     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3445             alignPanel.getViewName());
3446     SliderPanel.showPIDSlider();
3447   }
3448
3449   /**
3450    * Show the Conservation slider panel
3451    */
3452   @Override
3453   protected void modifyConservation_actionPerformed()
3454   {
3455     SliderPanel.setConservationSlider(alignPanel,
3456             viewport.getResidueShading(), alignPanel.getViewName());
3457     SliderPanel.showConservationSlider();
3458   }
3459
3460   /**
3461    * Action on selecting or deselecting (Colour) By Conservation
3462    */
3463   @Override
3464   public void conservationMenuItem_actionPerformed(boolean selected)
3465   {
3466     modifyConservation.setEnabled(selected);
3467     viewport.setConservationSelected(selected);
3468     viewport.getResidueShading().setConservationApplied(selected);
3469
3470     changeColour(viewport.getGlobalColourScheme());
3471     if (selected)
3472     {
3473       modifyConservation_actionPerformed();
3474     }
3475     else
3476     {
3477       SliderPanel.hideConservationSlider();
3478     }
3479   }
3480
3481   /**
3482    * Action on selecting or deselecting (Colour) Above PID Threshold
3483    */
3484   @Override
3485   public void abovePIDThreshold_actionPerformed(boolean selected)
3486   {
3487     modifyPID.setEnabled(selected);
3488     viewport.setAbovePIDThreshold(selected);
3489     if (!selected)
3490     {
3491       viewport.getResidueShading().setThreshold(0,
3492               viewport.isIgnoreGapsConsensus());
3493     }
3494
3495     changeColour(viewport.getGlobalColourScheme());
3496     if (selected)
3497     {
3498       modifyPID_actionPerformed();
3499     }
3500     else
3501     {
3502       SliderPanel.hidePIDSlider();
3503     }
3504   }
3505
3506   /**
3507    * DOCUMENT ME!
3508    *
3509    * @param e
3510    *          DOCUMENT ME!
3511    */
3512   @Override
3513   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3514   {
3515     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3516     AlignmentSorter.sortByPID(viewport.getAlignment(),
3517             viewport.getAlignment().getSequenceAt(0));
3518     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3519             viewport.getAlignment()));
3520     alignPanel.paintAlignment(true, false);
3521   }
3522
3523   /**
3524    * DOCUMENT ME!
3525    *
3526    * @param e
3527    *          DOCUMENT ME!
3528    */
3529   @Override
3530   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3531   {
3532     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3533     AlignmentSorter.sortByID(viewport.getAlignment());
3534     addHistoryItem(
3535             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3536     alignPanel.paintAlignment(true, false);
3537   }
3538
3539   /**
3540    * DOCUMENT ME!
3541    *
3542    * @param e
3543    *          DOCUMENT ME!
3544    */
3545   @Override
3546   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3547   {
3548     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3549     AlignmentSorter.sortByLength(viewport.getAlignment());
3550     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3551             viewport.getAlignment()));
3552     alignPanel.paintAlignment(true, false);
3553   }
3554
3555   /**
3556    * DOCUMENT ME!
3557    *
3558    * @param e
3559    *          DOCUMENT ME!
3560    */
3561   @Override
3562   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3563   {
3564     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3565     AlignmentSorter.sortByGroup(viewport.getAlignment());
3566     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3567             viewport.getAlignment()));
3568
3569     alignPanel.paintAlignment(true, false);
3570   }
3571
3572   /**
3573    * DOCUMENT ME!
3574    *
3575    * @param e
3576    *          DOCUMENT ME!
3577    */
3578   @Override
3579   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3580   {
3581     new RedundancyPanel(alignPanel, this);
3582   }
3583
3584   /**
3585    * DOCUMENT ME!
3586    *
3587    * @param e
3588    *          DOCUMENT ME!
3589    */
3590   @Override
3591   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3592   {
3593     if ((viewport.getSelectionGroup() == null)
3594             || (viewport.getSelectionGroup().getSize() < 2))
3595     {
3596       JvOptionPane.showInternalMessageDialog(this,
3597               MessageManager.getString(
3598                       "label.you_must_select_least_two_sequences"),
3599               MessageManager.getString("label.invalid_selection"),
3600               JvOptionPane.WARNING_MESSAGE);
3601     }
3602     else
3603     {
3604       JInternalFrame frame = new JInternalFrame();
3605       frame.setContentPane(new PairwiseAlignPanel(viewport));
3606       Desktop.addInternalFrame(frame,
3607               MessageManager.getString("action.pairwise_alignment"), 600,
3608               500);
3609     }
3610   }
3611
3612   @Override
3613   public void autoCalculate_actionPerformed(ActionEvent e)
3614   {
3615     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3616     if (viewport.autoCalculateConsensus)
3617     {
3618       viewport.firePropertyChange("alignment", null,
3619               viewport.getAlignment().getSequences());
3620     }
3621   }
3622
3623   @Override
3624   public void sortByTreeOption_actionPerformed(ActionEvent e)
3625   {
3626     viewport.sortByTree = sortByTree.isSelected();
3627   }
3628
3629   @Override
3630   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3631   {
3632     viewport.followSelection = listenToViewSelections.isSelected();
3633   }
3634
3635   /**
3636    * Constructs a tree panel and adds it to the desktop
3637    *
3638    * @param type
3639    *          tree type (NJ or AV)
3640    * @param modelName
3641    *          name of score model used to compute the tree
3642    * @param options
3643    *          parameters for the distance or similarity calculation
3644    */
3645   void newTreePanel(String type, String modelName,
3646           SimilarityParamsI options)
3647   {
3648     String frameTitle = "";
3649     TreePanel tp;
3650
3651     boolean onSelection = false;
3652     if (viewport.getSelectionGroup() != null
3653             && viewport.getSelectionGroup().getSize() > 0)
3654     {
3655       SequenceGroup sg = viewport.getSelectionGroup();
3656
3657       /* Decide if the selection is a column region */
3658       for (SequenceI _s : sg.getSequences())
3659       {
3660         if (_s.getLength() < sg.getEndRes())
3661         {
3662           JvOptionPane.showMessageDialog(Desktop.desktop,
3663                   MessageManager.getString(
3664                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3665                   MessageManager.getString(
3666                           "label.sequences_selection_not_aligned"),
3667                   JvOptionPane.WARNING_MESSAGE);
3668
3669           return;
3670         }
3671       }
3672       onSelection = true;
3673     }
3674     else
3675     {
3676       if (viewport.getAlignment().getHeight() < 2)
3677       {
3678         return;
3679       }
3680     }
3681
3682     tp = new TreePanel(alignPanel, type, modelName, options);
3683     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3684
3685     frameTitle += " from ";
3686
3687     if (viewport.getViewName() != null)
3688     {
3689       frameTitle += viewport.getViewName() + " of ";
3690     }
3691
3692     frameTitle += this.title;
3693
3694     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3695   }
3696
3697   /**
3698    * DOCUMENT ME!
3699    *
3700    * @param title
3701    *          DOCUMENT ME!
3702    * @param order
3703    *          DOCUMENT ME!
3704    */
3705   public void addSortByOrderMenuItem(String title,
3706           final AlignmentOrder order)
3707   {
3708     final JMenuItem item = new JMenuItem(MessageManager
3709             .formatMessage("action.by_title_param", new Object[]
3710             { title }));
3711     sort.add(item);
3712     item.addActionListener(new java.awt.event.ActionListener()
3713     {
3714       @Override
3715       public void actionPerformed(ActionEvent e)
3716       {
3717         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3718
3719         // TODO: JBPNote - have to map order entries to curent SequenceI
3720         // pointers
3721         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3722
3723         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3724                 viewport.getAlignment()));
3725
3726         alignPanel.paintAlignment(true, false);
3727       }
3728     });
3729   }
3730
3731   /**
3732    * Add a new sort by annotation score menu item
3733    *
3734    * @param sort
3735    *          the menu to add the option to
3736    * @param scoreLabel
3737    *          the label used to retrieve scores for each sequence on the
3738    *          alignment
3739    */
3740   public void addSortByAnnotScoreMenuItem(JMenu sort,
3741           final String scoreLabel)
3742   {
3743     final JMenuItem item = new JMenuItem(scoreLabel);
3744     sort.add(item);
3745     item.addActionListener(new java.awt.event.ActionListener()
3746     {
3747       @Override
3748       public void actionPerformed(ActionEvent e)
3749       {
3750         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3752                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3753         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3754                 viewport.getAlignment()));
3755         alignPanel.paintAlignment(true, false);
3756       }
3757     });
3758   }
3759
3760   /**
3761    * last hash for alignment's annotation array - used to minimise cost of
3762    * rebuild.
3763    */
3764   protected int _annotationScoreVectorHash;
3765
3766   /**
3767    * search the alignment and rebuild the sort by annotation score submenu the
3768    * last alignment annotation vector hash is stored to minimize cost of
3769    * rebuilding in subsequence calls.
3770    *
3771    */
3772   @Override
3773   public void buildSortByAnnotationScoresMenu()
3774   {
3775     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3776     {
3777       return;
3778     }
3779
3780     if (viewport.getAlignment().getAlignmentAnnotation()
3781             .hashCode() != _annotationScoreVectorHash)
3782     {
3783       sortByAnnotScore.removeAll();
3784       // almost certainly a quicker way to do this - but we keep it simple
3785       Hashtable scoreSorts = new Hashtable();
3786       AlignmentAnnotation aann[];
3787       for (SequenceI sqa : viewport.getAlignment().getSequences())
3788       {
3789         aann = sqa.getAnnotation();
3790         for (int i = 0; aann != null && i < aann.length; i++)
3791         {
3792           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3793           {
3794             scoreSorts.put(aann[i].label, aann[i].label);
3795           }
3796         }
3797       }
3798       Enumeration labels = scoreSorts.keys();
3799       while (labels.hasMoreElements())
3800       {
3801         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3802                 (String) labels.nextElement());
3803       }
3804       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3805       scoreSorts.clear();
3806
3807       _annotationScoreVectorHash = viewport.getAlignment()
3808               .getAlignmentAnnotation().hashCode();
3809     }
3810   }
3811
3812   /**
3813    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3814    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3815    * call. Listeners are added to remove the menu item when the treePanel is
3816    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3817    * modified.
3818    */
3819   @Override
3820   public void buildTreeSortMenu()
3821   {
3822     sortByTreeMenu.removeAll();
3823
3824     List<Component> comps = PaintRefresher.components
3825             .get(viewport.getSequenceSetId());
3826     List<TreePanel> treePanels = new ArrayList<>();
3827     for (Component comp : comps)
3828     {
3829       if (comp instanceof TreePanel)
3830       {
3831         treePanels.add((TreePanel) comp);
3832       }
3833     }
3834
3835     if (treePanels.size() < 1)
3836     {
3837       sortByTreeMenu.setVisible(false);
3838       return;
3839     }
3840
3841     sortByTreeMenu.setVisible(true);
3842
3843     for (final TreePanel tp : treePanels)
3844     {
3845       final JMenuItem item = new JMenuItem(tp.getTitle());
3846       item.addActionListener(new java.awt.event.ActionListener()
3847       {
3848         @Override
3849         public void actionPerformed(ActionEvent e)
3850         {
3851           tp.sortByTree_actionPerformed();
3852           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3853
3854         }
3855       });
3856
3857       sortByTreeMenu.add(item);
3858     }
3859   }
3860
3861   public boolean sortBy(AlignmentOrder alorder, String undoname)
3862   {
3863     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3864     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3865     if (undoname != null)
3866     {
3867       addHistoryItem(new OrderCommand(undoname, oldOrder,
3868               viewport.getAlignment()));
3869     }
3870     alignPanel.paintAlignment(true, false);
3871     return true;
3872   }
3873
3874   /**
3875    * Work out whether the whole set of sequences or just the selected set will
3876    * be submitted for multiple alignment.
3877    *
3878    */
3879   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3880   {
3881     // Now, check we have enough sequences
3882     AlignmentView msa = null;
3883
3884     if ((viewport.getSelectionGroup() != null)
3885             && (viewport.getSelectionGroup().getSize() > 1))
3886     {
3887       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3888       // some common interface!
3889       /*
3890        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3891        * SequenceI[sz = seqs.getSize(false)];
3892        *
3893        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3894        * seqs.getSequenceAt(i); }
3895        */
3896       msa = viewport.getAlignmentView(true);
3897     }
3898     else if (viewport.getSelectionGroup() != null
3899             && viewport.getSelectionGroup().getSize() == 1)
3900     {
3901       int option = JvOptionPane.showConfirmDialog(this,
3902               MessageManager.getString("warn.oneseq_msainput_selection"),
3903               MessageManager.getString("label.invalid_selection"),
3904               JvOptionPane.OK_CANCEL_OPTION);
3905       if (option == JvOptionPane.OK_OPTION)
3906       {
3907         msa = viewport.getAlignmentView(false);
3908       }
3909     }
3910     else
3911     {
3912       msa = viewport.getAlignmentView(false);
3913     }
3914     return msa;
3915   }
3916
3917   /**
3918    * Decides what is submitted to a secondary structure prediction service: the
3919    * first sequence in the alignment, or in the current selection, or, if the
3920    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3921    * region or the whole alignment. (where the first sequence in the set is the
3922    * one that the prediction will be for).
3923    */
3924   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3925   {
3926     AlignmentView seqs = null;
3927
3928     if ((viewport.getSelectionGroup() != null)
3929             && (viewport.getSelectionGroup().getSize() > 0))
3930     {
3931       seqs = viewport.getAlignmentView(true);
3932     }
3933     else
3934     {
3935       seqs = viewport.getAlignmentView(false);
3936     }
3937     // limit sequences - JBPNote in future - could spawn multiple prediction
3938     // jobs
3939     // TODO: viewport.getAlignment().isAligned is a global state - the local
3940     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3941     if (!viewport.getAlignment().isAligned(false))
3942     {
3943       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3944       // TODO: if seqs.getSequences().length>1 then should really have warned
3945       // user!
3946
3947     }
3948     return seqs;
3949   }
3950
3951   /**
3952    * DOCUMENT ME!
3953    *
3954    * @param e
3955    *          DOCUMENT ME!
3956    */
3957   @Override
3958   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3959   {
3960     // Pick the tree file
3961     JalviewFileChooser chooser = new JalviewFileChooser(
3962             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3963     chooser.setFileView(new JalviewFileView());
3964     chooser.setDialogTitle(
3965             MessageManager.getString("label.select_newick_like_tree_file"));
3966     chooser.setToolTipText(
3967             MessageManager.getString("label.load_tree_file"));
3968
3969     int value = chooser.showOpenDialog(null);
3970
3971     if (value == JalviewFileChooser.APPROVE_OPTION)
3972     {
3973       String filePath = chooser.getSelectedFile().getPath();
3974       Cache.setProperty("LAST_DIRECTORY", filePath);
3975       NewickFile fin = null;
3976       try
3977       {
3978         fin = new NewickFile(filePath, DataSourceType.FILE);
3979         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3980       } catch (Exception ex)
3981       {
3982         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3983                 MessageManager.getString("label.problem_reading_tree_file"),
3984                 JvOptionPane.WARNING_MESSAGE);
3985         ex.printStackTrace();
3986       }
3987       if (fin != null && fin.hasWarningMessage())
3988       {
3989         JvOptionPane.showMessageDialog(Desktop.desktop,
3990                 fin.getWarningMessage(),
3991                 MessageManager
3992                         .getString("label.possible_problem_with_tree_file"),
3993                 JvOptionPane.WARNING_MESSAGE);
3994       }
3995     }
3996   }
3997
3998   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3999   {
4000     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4001   }
4002
4003   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4004           int h, int x, int y)
4005   {
4006     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4007   }
4008
4009   /**
4010    * Add a treeviewer for the tree extracted from a Newick file object to the
4011    * current alignment view
4012    *
4013    * @param nf
4014    *          the tree
4015    * @param title
4016    *          tree viewer title
4017    * @param input
4018    *          Associated alignment input data (or null)
4019    * @param w
4020    *          width
4021    * @param h
4022    *          height
4023    * @param x
4024    *          position
4025    * @param y
4026    *          position
4027    * @return TreePanel handle
4028    */
4029   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4030           AlignmentView input, int w, int h, int x, int y)
4031   {
4032     TreePanel tp = null;
4033
4034     try
4035     {
4036       nf.parse();
4037
4038       if (nf.getTree() != null)
4039       {
4040         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4041
4042         tp.setSize(w, h);
4043
4044         if (x > 0 && y > 0)
4045         {
4046           tp.setLocation(x, y);
4047         }
4048
4049         Desktop.addInternalFrame(tp, treeTitle, w, h);
4050       }
4051     } catch (Exception ex)
4052     {
4053       ex.printStackTrace();
4054     }
4055
4056     return tp;
4057   }
4058
4059   private boolean buildingMenu = false;
4060
4061   /**
4062    * Generates menu items and listener event actions for web service clients
4063    *
4064    */
4065   public void BuildWebServiceMenu()
4066   {
4067     while (buildingMenu)
4068     {
4069       try
4070       {
4071         System.err.println("Waiting for building menu to finish.");
4072         Thread.sleep(10);
4073       } catch (Exception e)
4074       {
4075       }
4076     }
4077     final AlignFrame me = this;
4078     buildingMenu = true;
4079     new Thread(new Runnable()
4080     {
4081       @Override
4082       public void run()
4083       {
4084         final List<JMenuItem> legacyItems = new ArrayList<>();
4085         try
4086         {
4087           // System.err.println("Building ws menu again "
4088           // + Thread.currentThread());
4089           // TODO: add support for context dependent disabling of services based
4090           // on
4091           // alignment and current selection
4092           // TODO: add additional serviceHandle parameter to specify abstract
4093           // handler
4094           // class independently of AbstractName
4095           // TODO: add in rediscovery GUI function to restart discoverer
4096           // TODO: group services by location as well as function and/or
4097           // introduce
4098           // object broker mechanism.
4099           final Vector<JMenu> wsmenu = new Vector<>();
4100           final IProgressIndicator af = me;
4101
4102           /*
4103            * do not i18n these strings - they are hard-coded in class
4104            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4105            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4106            */
4107           final JMenu msawsmenu = new JMenu("Alignment");
4108           final JMenu secstrmenu = new JMenu(
4109                   "Secondary Structure Prediction");
4110           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4111           final JMenu analymenu = new JMenu("Analysis");
4112           final JMenu dismenu = new JMenu("Protein Disorder");
4113           // JAL-940 - only show secondary structure prediction services from
4114           // the legacy server
4115           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4116               // &&
4117           Discoverer.services != null && (Discoverer.services.size() > 0))
4118           {
4119             // TODO: refactor to allow list of AbstractName/Handler bindings to
4120             // be
4121             // stored or retrieved from elsewhere
4122             // No MSAWS used any more:
4123             // Vector msaws = null; // (Vector)
4124             // Discoverer.services.get("MsaWS");
4125             Vector secstrpr = (Vector) Discoverer.services
4126                     .get("SecStrPred");
4127             if (secstrpr != null)
4128             {
4129               // Add any secondary structure prediction services
4130               for (int i = 0, j = secstrpr.size(); i < j; i++)
4131               {
4132                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4133                         .get(i);
4134                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4135                         .getServiceClient(sh);
4136                 int p = secstrmenu.getItemCount();
4137                 impl.attachWSMenuEntry(secstrmenu, me);
4138                 int q = secstrmenu.getItemCount();
4139                 for (int litm = p; litm < q; litm++)
4140                 {
4141                   legacyItems.add(secstrmenu.getItem(litm));
4142                 }
4143               }
4144             }
4145           }
4146
4147           // Add all submenus in the order they should appear on the web
4148           // services menu
4149           wsmenu.add(msawsmenu);
4150           wsmenu.add(secstrmenu);
4151           wsmenu.add(dismenu);
4152           wsmenu.add(analymenu);
4153           // No search services yet
4154           // wsmenu.add(seqsrchmenu);
4155
4156           javax.swing.SwingUtilities.invokeLater(new Runnable()
4157           {
4158             @Override
4159             public void run()
4160             {
4161               try
4162               {
4163                 webService.removeAll();
4164                 // first, add discovered services onto the webservices menu
4165                 if (wsmenu.size() > 0)
4166                 {
4167                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4168                   {
4169                     webService.add(wsmenu.get(i));
4170                   }
4171                 }
4172                 else
4173                 {
4174                   webService.add(me.webServiceNoServices);
4175                 }
4176                 // TODO: move into separate menu builder class.
4177                 {
4178                   // logic for 2.11.1.4 is
4179                   // always look to see if there is a discover. if there isn't
4180                   // we can't show any Jws2 services
4181                   // if there are services available, show them - regardless of
4182                   // the 'show JWS2 preference'
4183                   // if the discoverer is running then say so
4184                   // otherwise offer to trigger discovery if 'show JWS2' is not
4185                   // enabled
4186                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4187                   if (jws2servs != null)
4188                   {
4189                     if (jws2servs.hasServices())
4190                     {
4191                       jws2servs.attachWSMenuEntry(webService, me);
4192                       for (Jws2Instance sv : jws2servs.getServices())
4193                       {
4194                         if (sv.description.toLowerCase().contains("jpred"))
4195                         {
4196                           for (JMenuItem jmi : legacyItems)
4197                           {
4198                             jmi.setVisible(false);
4199                           }
4200                         }
4201                       }
4202                     }
4203
4204                     if (jws2servs.isRunning())
4205                     {
4206                       JMenuItem tm = new JMenuItem(
4207                               "Still discovering JABA Services");
4208                       tm.setEnabled(false);
4209                       webService.add(tm);
4210                     }
4211                     else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
4212                     {
4213                       JMenuItem enableJws2 = new JMenuItem(
4214                               "Discover Web Services");
4215                       enableJws2.setToolTipText(
4216                               "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
4217                       enableJws2.setEnabled(true);
4218                       enableJws2.addActionListener(new ActionListener()
4219                       {
4220
4221                         @Override
4222                         public void actionPerformed(ActionEvent e)
4223                         {
4224                           // start service discoverer, but ignore preference
4225                           Desktop.instance.startServiceDiscovery(false,
4226                                   true);
4227                         }
4228                       });
4229                       webService.add(enableJws2);
4230                     }
4231                   }
4232                 }
4233                 build_urlServiceMenu(me.webService);
4234                 build_fetchdbmenu(webService);
4235                 for (JMenu item : wsmenu)
4236                 {
4237                   if (item.getItemCount() == 0)
4238                   {
4239                     item.setEnabled(false);
4240                   }
4241                   else
4242                   {
4243                     item.setEnabled(true);
4244                   }
4245                 }
4246               } catch (Exception e)
4247               {
4248                 Cache.log.debug(
4249                         "Exception during web service menu building process.",
4250                         e);
4251               }
4252             }
4253           });
4254         } catch (Exception e)
4255         {
4256         }
4257         buildingMenu = false;
4258       }
4259     }).start();
4260
4261   }
4262
4263   /**
4264    * construct any groupURL type service menu entries.
4265    *
4266    * @param webService
4267    */
4268   private void build_urlServiceMenu(JMenu webService)
4269   {
4270     // TODO: remove this code when 2.7 is released
4271     // DEBUG - alignmentView
4272     /*
4273      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4274      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4275      *
4276      * @Override public void actionPerformed(ActionEvent e) {
4277      * jalview.datamodel.AlignmentView
4278      * .testSelectionViews(af.viewport.getAlignment(),
4279      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4280      *
4281      * }); webService.add(testAlView);
4282      */
4283     // TODO: refactor to RestClient discoverer and merge menu entries for
4284     // rest-style services with other types of analysis/calculation service
4285     // SHmmr test client - still being implemented.
4286     // DEBUG - alignmentView
4287
4288     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4289             .getRestClients())
4290     {
4291       client.attachWSMenuEntry(
4292               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4293               this);
4294     }
4295   }
4296
4297   /**
4298    * Searches the alignment sequences for xRefs and builds the Show
4299    * Cross-References menu (formerly called Show Products), with database
4300    * sources for which cross-references are found (protein sources for a
4301    * nucleotide alignment and vice versa)
4302    *
4303    * @return true if Show Cross-references menu should be enabled
4304    */
4305   public boolean canShowProducts()
4306   {
4307     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4308     AlignmentI dataset = viewport.getAlignment().getDataset();
4309
4310     showProducts.removeAll();
4311     final boolean dna = viewport.getAlignment().isNucleotide();
4312
4313     if (seqs == null || seqs.length == 0)
4314     {
4315       // nothing to see here.
4316       return false;
4317     }
4318
4319     boolean showp = false;
4320     try
4321     {
4322       List<String> ptypes = new CrossRef(seqs, dataset)
4323               .findXrefSourcesForSequences(dna);
4324
4325       for (final String source : ptypes)
4326       {
4327         showp = true;
4328         final AlignFrame af = this;
4329         JMenuItem xtype = new JMenuItem(source);
4330         xtype.addActionListener(new ActionListener()
4331         {
4332           @Override
4333           public void actionPerformed(ActionEvent e)
4334           {
4335             showProductsFor(af.viewport.getSequenceSelection(), dna,
4336                     source);
4337           }
4338         });
4339         showProducts.add(xtype);
4340       }
4341       showProducts.setVisible(showp);
4342       showProducts.setEnabled(showp);
4343     } catch (Exception e)
4344     {
4345       Cache.log.warn(
4346               "canShowProducts threw an exception - please report to help@jalview.org",
4347               e);
4348       return false;
4349     }
4350     return showp;
4351   }
4352
4353   /**
4354    * Finds and displays cross-references for the selected sequences (protein
4355    * products for nucleotide sequences, dna coding sequences for peptides).
4356    *
4357    * @param sel
4358    *          the sequences to show cross-references for
4359    * @param dna
4360    *          true if from a nucleotide alignment (so showing proteins)
4361    * @param source
4362    *          the database to show cross-references for
4363    */
4364   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4365           final String source)
4366   {
4367     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4368             .start();
4369   }
4370
4371   /**
4372    * Construct and display a new frame containing the translation of this
4373    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4374    */
4375   @Override
4376   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4377   {
4378     AlignmentI al = null;
4379     try
4380     {
4381       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4382
4383       al = dna.translateCdna(codeTable);
4384     } catch (Exception ex)
4385     {
4386       jalview.bin.Cache.log.error(
4387               "Exception during translation. Please report this !", ex);
4388       final String msg = MessageManager.getString(
4389               "label.error_when_translating_sequences_submit_bug_report");
4390       final String errorTitle = MessageManager
4391               .getString("label.implementation_error")
4392               + MessageManager.getString("label.translation_failed");
4393       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4394               JvOptionPane.ERROR_MESSAGE);
4395       return;
4396     }
4397     if (al == null || al.getHeight() == 0)
4398     {
4399       final String msg = MessageManager.getString(
4400               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4401       final String errorTitle = MessageManager
4402               .getString("label.translation_failed");
4403       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4404               JvOptionPane.WARNING_MESSAGE);
4405     }
4406     else
4407     {
4408       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4409       af.setFileFormat(this.currentFileFormat);
4410       final String newTitle = MessageManager
4411               .formatMessage("label.translation_of_params", new Object[]
4412               { this.getTitle(), codeTable.getId() });
4413       af.setTitle(newTitle);
4414       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4415       {
4416         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4417         viewport.openSplitFrame(af, new Alignment(seqs));
4418       }
4419       else
4420       {
4421         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4422                 DEFAULT_HEIGHT);
4423       }
4424     }
4425   }
4426
4427   /**
4428    * Set the file format
4429    *
4430    * @param format
4431    */
4432   public void setFileFormat(FileFormatI format)
4433   {
4434     this.currentFileFormat = format;
4435   }
4436
4437   /**
4438    * Try to load a features file onto the alignment.
4439    *
4440    * @param file
4441    *          contents or path to retrieve file
4442    * @param sourceType
4443    *          access mode of file (see jalview.io.AlignFile)
4444    * @return true if features file was parsed correctly.
4445    */
4446   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4447   {
4448     return avc.parseFeaturesFile(file, sourceType,
4449             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4450
4451   }
4452
4453   @Override
4454   public void refreshFeatureUI(boolean enableIfNecessary)
4455   {
4456     // note - currently this is only still here rather than in the controller
4457     // because of the featureSettings hard reference that is yet to be
4458     // abstracted
4459     if (enableIfNecessary)
4460     {
4461       viewport.setShowSequenceFeatures(true);
4462       showSeqFeatures.setSelected(true);
4463     }
4464
4465   }
4466
4467   @Override
4468   public void dragEnter(DropTargetDragEvent evt)
4469   {
4470   }
4471
4472   @Override
4473   public void dragExit(DropTargetEvent evt)
4474   {
4475   }
4476
4477   @Override
4478   public void dragOver(DropTargetDragEvent evt)
4479   {
4480   }
4481
4482   @Override
4483   public void dropActionChanged(DropTargetDragEvent evt)
4484   {
4485   }
4486
4487   @Override
4488   public void drop(DropTargetDropEvent evt)
4489   {
4490     // JAL-1552 - acceptDrop required before getTransferable call for
4491     // Java's Transferable for native dnd
4492     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4493     Transferable t = evt.getTransferable();
4494     final AlignFrame thisaf = this;
4495     final List<String> files = new ArrayList<>();
4496     List<DataSourceType> protocols = new ArrayList<>();
4497
4498     try
4499     {
4500       Desktop.transferFromDropTarget(files, protocols, evt, t);
4501     } catch (Exception e)
4502     {
4503       e.printStackTrace();
4504     }
4505     if (files != null)
4506     {
4507       new Thread(new Runnable()
4508       {
4509         @Override
4510         public void run()
4511         {
4512           try
4513           {
4514             // check to see if any of these files have names matching sequences
4515             // in
4516             // the alignment
4517             SequenceIdMatcher idm = new SequenceIdMatcher(
4518                     viewport.getAlignment().getSequencesArray());
4519             /**
4520              * Object[] { String,SequenceI}
4521              */
4522             ArrayList<Object[]> filesmatched = new ArrayList<>();
4523             ArrayList<String> filesnotmatched = new ArrayList<>();
4524             for (int i = 0; i < files.size(); i++)
4525             {
4526               String file = files.get(i).toString();
4527               String pdbfn = "";
4528               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4529               if (protocol == DataSourceType.FILE)
4530               {
4531                 File fl = new File(file);
4532                 pdbfn = fl.getName();
4533               }
4534               else if (protocol == DataSourceType.URL)
4535               {
4536                 URL url = new URL(file);
4537                 pdbfn = url.getFile();
4538               }
4539               if (pdbfn.length() > 0)
4540               {
4541                 // attempt to find a match in the alignment
4542                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4543                 int l = 0, c = pdbfn.indexOf(".");
4544                 while (mtch == null && c != -1)
4545                 {
4546                   do
4547                   {
4548                     l = c;
4549                   } while ((c = pdbfn.indexOf(".", l)) > l);
4550                   if (l > -1)
4551                   {
4552                     pdbfn = pdbfn.substring(0, l);
4553                   }
4554                   mtch = idm.findAllIdMatches(pdbfn);
4555                 }
4556                 if (mtch != null)
4557                 {
4558                   FileFormatI type = null;
4559                   try
4560                   {
4561                     type = new IdentifyFile().identify(file, protocol);
4562                   } catch (Exception ex)
4563                   {
4564                     type = null;
4565                   }
4566                   if (type != null && type.isStructureFile())
4567                   {
4568                     filesmatched.add(new Object[] { file, protocol, mtch });
4569                     continue;
4570                   }
4571                 }
4572                 // File wasn't named like one of the sequences or wasn't a PDB
4573                 // file.
4574                 filesnotmatched.add(file);
4575               }
4576             }
4577             int assocfiles = 0;
4578             if (filesmatched.size() > 0)
4579             {
4580               boolean autoAssociate = Cache
4581                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4582               if (!autoAssociate)
4583               {
4584                 String msg = MessageManager.formatMessage(
4585                         "label.automatically_associate_structure_files_with_sequences_same_name",
4586                         new Object[]
4587                         { Integer.valueOf(filesmatched.size())
4588                                 .toString() });
4589                 String ttl = MessageManager.getString(
4590                         "label.automatically_associate_structure_files_by_name");
4591                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4592                         ttl, JvOptionPane.YES_NO_OPTION);
4593                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4594               }
4595               if (autoAssociate)
4596               {
4597                 for (Object[] fm : filesmatched)
4598                 {
4599                   // try and associate
4600                   // TODO: may want to set a standard ID naming formalism for
4601                   // associating PDB files which have no IDs.
4602                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4603                   {
4604                     PDBEntry pe = new AssociatePdbFileWithSeq()
4605                             .associatePdbWithSeq((String) fm[0],
4606                                     (DataSourceType) fm[1], toassoc, false,
4607                                     Desktop.instance);
4608                     if (pe != null)
4609                     {
4610                       System.err.println("Associated file : "
4611                               + ((String) fm[0]) + " with "
4612                               + toassoc.getDisplayId(true));
4613                       assocfiles++;
4614                     }
4615                   }
4616                   // TODO: do we need to update overview ? only if features are
4617                   // shown I guess
4618                   alignPanel.paintAlignment(true, false);
4619                 }
4620               }
4621               else
4622               {
4623                 /*
4624                  * add declined structures as sequences
4625                  */
4626                 for (Object[] o : filesmatched)
4627                 {
4628                   filesnotmatched.add((String) o[0]);
4629                 }
4630               }
4631             }
4632             if (filesnotmatched.size() > 0)
4633             {
4634               if (assocfiles > 0 && (Cache.getDefault(
4635                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4636                       || JvOptionPane.showConfirmDialog(thisaf,
4637                               "<html>" + MessageManager.formatMessage(
4638                                       "label.ignore_unmatched_dropped_files_info",
4639                                       new Object[]
4640                                       { Integer.valueOf(
4641                                               filesnotmatched.size())
4642                                               .toString() })
4643                                       + "</html>",
4644                               MessageManager.getString(
4645                                       "label.ignore_unmatched_dropped_files"),
4646                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4647               {
4648                 return;
4649               }
4650               for (String fn : filesnotmatched)
4651               {
4652                 loadJalviewDataFile(fn, null, null, null);
4653               }
4654
4655             }
4656           } catch (Exception ex)
4657           {
4658             ex.printStackTrace();
4659           }
4660         }
4661       }).start();
4662     }
4663   }
4664
4665   /**
4666    * Attempt to load a "dropped" file or URL string, by testing in turn for
4667    * <ul>
4668    * <li>an Annotation file</li>
4669    * <li>a JNet file</li>
4670    * <li>a features file</li>
4671    * <li>else try to interpret as an alignment file</li>
4672    * </ul>
4673    *
4674    * @param file
4675    *          either a filename or a URL string.
4676    */
4677   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4678           FileFormatI format, SequenceI assocSeq)
4679   {
4680     try
4681     {
4682       if (sourceType == null)
4683       {
4684         sourceType = FormatAdapter.checkProtocol(file);
4685       }
4686       // if the file isn't identified, or not positively identified as some
4687       // other filetype (PFAM is default unidentified alignment file type) then
4688       // try to parse as annotation.
4689       boolean isAnnotation = (format == null
4690               || FileFormat.Pfam.equals(format))
4691                       ? new AnnotationFile().annotateAlignmentView(viewport,
4692                               file, sourceType)
4693                       : false;
4694
4695       if (!isAnnotation)
4696       {
4697         // first see if its a T-COFFEE score file
4698         TCoffeeScoreFile tcf = null;
4699         try
4700         {
4701           tcf = new TCoffeeScoreFile(file, sourceType);
4702           if (tcf.isValid())
4703           {
4704             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4705             {
4706               buildColourMenu();
4707               changeColour(
4708                       new TCoffeeColourScheme(viewport.getAlignment()));
4709               isAnnotation = true;
4710               statusBar.setText(MessageManager.getString(
4711                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4712             }
4713             else
4714             {
4715               // some problem - if no warning its probable that the ID matching
4716               // process didn't work
4717               JvOptionPane.showMessageDialog(Desktop.desktop,
4718                       tcf.getWarningMessage() == null
4719                               ? MessageManager.getString(
4720                                       "label.check_file_matches_sequence_ids_alignment")
4721                               : tcf.getWarningMessage(),
4722                       MessageManager.getString(
4723                               "label.problem_reading_tcoffee_score_file"),
4724                       JvOptionPane.WARNING_MESSAGE);
4725             }
4726           }
4727           else
4728           {
4729             tcf = null;
4730           }
4731         } catch (Exception x)
4732         {
4733           Cache.log.debug(
4734                   "Exception when processing data source as T-COFFEE score file",
4735                   x);
4736           tcf = null;
4737         }
4738         if (tcf == null)
4739         {
4740           // try to see if its a JNet 'concise' style annotation file *before*
4741           // we
4742           // try to parse it as a features file
4743           if (format == null)
4744           {
4745             format = new IdentifyFile().identify(file, sourceType);
4746           }
4747           if (FileFormat.ScoreMatrix == format)
4748           {
4749             ScoreMatrixFile sm = new ScoreMatrixFile(
4750                     new FileParse(file, sourceType));
4751             sm.parse();
4752             // todo: i18n this message
4753             statusBar.setText(MessageManager.formatMessage(
4754                     "label.successfully_loaded_matrix",
4755                     sm.getMatrixName()));
4756           }
4757           else if (FileFormat.Jnet.equals(format))
4758           {
4759             JPredFile predictions = new JPredFile(file, sourceType);
4760             new JnetAnnotationMaker();
4761             JnetAnnotationMaker.add_annotation(predictions,
4762                     viewport.getAlignment(), 0, false);
4763             viewport.getAlignment().setupJPredAlignment();
4764             isAnnotation = true;
4765           }
4766           // else if (IdentifyFile.FeaturesFile.equals(format))
4767           else if (FileFormat.Features.equals(format))
4768           {
4769             if (parseFeaturesFile(file, sourceType))
4770             {
4771               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4772               if (splitFrame != null)
4773               {
4774                 splitFrame.repaint();
4775               }
4776               else
4777               {
4778                 alignPanel.paintAlignment(true, true);
4779               }
4780             }
4781           }
4782           else
4783           {
4784             new FileLoader().LoadFile(viewport, file, sourceType, format);
4785           }
4786         }
4787       }
4788       if (isAnnotation)
4789       {
4790
4791         alignPanel.adjustAnnotationHeight();
4792         viewport.updateSequenceIdColours();
4793         buildSortByAnnotationScoresMenu();
4794         alignPanel.paintAlignment(true, true);
4795       }
4796     } catch (Exception ex)
4797     {
4798       ex.printStackTrace();
4799     } catch (OutOfMemoryError oom)
4800     {
4801       try
4802       {
4803         System.gc();
4804       } catch (Exception x)
4805       {
4806       }
4807       new OOMWarning(
4808               "loading data "
4809                       + (sourceType != null
4810                               ? (sourceType == DataSourceType.PASTE
4811                                       ? "from clipboard."
4812                                       : "using " + sourceType + " from "
4813                                               + file)
4814                               : ".")
4815                       + (format != null
4816                               ? "(parsing as '" + format + "' file)"
4817                               : ""),
4818               oom, Desktop.desktop);
4819     }
4820   }
4821
4822   /**
4823    * Method invoked by the ChangeListener on the tabbed pane, in other words
4824    * when a different tabbed pane is selected by the user or programmatically.
4825    */
4826   @Override
4827   public void tabSelectionChanged(int index)
4828   {
4829     if (index > -1)
4830     {
4831       alignPanel = alignPanels.get(index);
4832       viewport = alignPanel.av;
4833       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4834       setMenusFromViewport(viewport);
4835       if (featureSettings != null && featureSettings.isOpen()
4836               && featureSettings.fr.getViewport() != viewport)
4837       {
4838         if (viewport.isShowSequenceFeatures())
4839         {
4840           // refresh the featureSettings to reflect UI change
4841           showFeatureSettingsUI();
4842         }
4843         else
4844         {
4845           // close feature settings for this view.
4846           featureSettings.close();
4847         }
4848       }
4849
4850     }
4851
4852     /*
4853      * 'focus' any colour slider that is open to the selected viewport
4854      */
4855     if (viewport.getConservationSelected())
4856     {
4857       SliderPanel.setConservationSlider(alignPanel,
4858               viewport.getResidueShading(), alignPanel.getViewName());
4859     }
4860     else
4861     {
4862       SliderPanel.hideConservationSlider();
4863     }
4864     if (viewport.getAbovePIDThreshold())
4865     {
4866       SliderPanel.setPIDSliderSource(alignPanel,
4867               viewport.getResidueShading(), alignPanel.getViewName());
4868     }
4869     else
4870     {
4871       SliderPanel.hidePIDSlider();
4872     }
4873
4874     /*
4875      * If there is a frame linked to this one in a SplitPane, switch it to the
4876      * same view tab index. No infinite recursion of calls should happen, since
4877      * tabSelectionChanged() should not get invoked on setting the selected
4878      * index to an unchanged value. Guard against setting an invalid index
4879      * before the new view peer tab has been created.
4880      */
4881     final AlignViewportI peer = viewport.getCodingComplement();
4882     if (peer != null)
4883     {
4884       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4885               .getAlignPanel().alignFrame;
4886       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4887       {
4888         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4889       }
4890     }
4891   }
4892
4893   /**
4894    * On right mouse click on view tab, prompt for and set new view name.
4895    */
4896   @Override
4897   public void tabbedPane_mousePressed(MouseEvent e)
4898   {
4899     if (e.isPopupTrigger())
4900     {
4901       String msg = MessageManager.getString("label.enter_view_name");
4902       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4903               JvOptionPane.QUESTION_MESSAGE);
4904
4905       if (reply != null)
4906       {
4907         viewport.setViewName(reply);
4908         // TODO warn if reply is in getExistingViewNames()?
4909         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4910       }
4911     }
4912   }
4913
4914   public AlignViewport getCurrentView()
4915   {
4916     return viewport;
4917   }
4918
4919   /**
4920    * Open the dialog for regex description parsing.
4921    */
4922   @Override
4923   protected void extractScores_actionPerformed(ActionEvent e)
4924   {
4925     ParseProperties pp = new jalview.analysis.ParseProperties(
4926             viewport.getAlignment());
4927     // TODO: verify regex and introduce GUI dialog for version 2.5
4928     // if (pp.getScoresFromDescription("col", "score column ",
4929     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4930     // true)>0)
4931     if (pp.getScoresFromDescription("description column",
4932             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4933     {
4934       buildSortByAnnotationScoresMenu();
4935     }
4936   }
4937
4938   /*
4939    * (non-Javadoc)
4940    *
4941    * @see
4942    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4943    * )
4944    */
4945   @Override
4946   protected void showDbRefs_actionPerformed(ActionEvent e)
4947   {
4948     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4949   }
4950
4951   /*
4952    * (non-Javadoc)
4953    *
4954    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4955    * ActionEvent)
4956    */
4957   @Override
4958   protected void showNpFeats_actionPerformed(ActionEvent e)
4959   {
4960     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4961   }
4962
4963   /**
4964    * find the viewport amongst the tabs in this alignment frame and close that
4965    * tab
4966    *
4967    * @param av
4968    */
4969   public boolean closeView(AlignViewportI av)
4970   {
4971     if (viewport == av)
4972     {
4973       this.closeMenuItem_actionPerformed(false);
4974       return true;
4975     }
4976     Component[] comp = tabbedPane.getComponents();
4977     for (int i = 0; comp != null && i < comp.length; i++)
4978     {
4979       if (comp[i] instanceof AlignmentPanel)
4980       {
4981         if (((AlignmentPanel) comp[i]).av == av)
4982         {
4983           // close the view.
4984           closeView((AlignmentPanel) comp[i]);
4985           return true;
4986         }
4987       }
4988     }
4989     return false;
4990   }
4991
4992   protected void build_fetchdbmenu(JMenu webService)
4993   {
4994     // Temporary hack - DBRef Fetcher always top level ws entry.
4995     // TODO We probably want to store a sequence database checklist in
4996     // preferences and have checkboxes.. rather than individual sources selected
4997     // here
4998     final JMenu rfetch = new JMenu(
4999             MessageManager.getString("action.fetch_db_references"));
5000     rfetch.setToolTipText(MessageManager.getString(
5001             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5002     webService.add(rfetch);
5003
5004     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5005             MessageManager.getString("option.trim_retrieved_seqs"));
5006     trimrs.setToolTipText(
5007             MessageManager.getString("label.trim_retrieved_sequences"));
5008     trimrs.setSelected(
5009             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5010     trimrs.addActionListener(new ActionListener()
5011     {
5012       @Override
5013       public void actionPerformed(ActionEvent e)
5014       {
5015         trimrs.setSelected(trimrs.isSelected());
5016         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5017                 Boolean.valueOf(trimrs.isSelected()).toString());
5018       };
5019     });
5020     rfetch.add(trimrs);
5021     JMenuItem fetchr = new JMenuItem(
5022             MessageManager.getString("label.standard_databases"));
5023     fetchr.setToolTipText(
5024             MessageManager.getString("label.fetch_embl_uniprot"));
5025     fetchr.addActionListener(new ActionListener()
5026     {
5027
5028       @Override
5029       public void actionPerformed(ActionEvent e)
5030       {
5031         new Thread(new Runnable()
5032         {
5033           @Override
5034           public void run()
5035           {
5036             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5037                     .getAlignment().isNucleotide();
5038             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5039                     alignPanel.av.getSequenceSelection(),
5040                     alignPanel.alignFrame, null,
5041                     alignPanel.alignFrame.featureSettings, isNucleotide);
5042             dbRefFetcher.addListener(new FetchFinishedListenerI()
5043             {
5044               @Override
5045               public void finished()
5046               {
5047
5048                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5049                         .getFeatureSettingsModels())
5050                 {
5051
5052                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5053                 }
5054                 AlignFrame.this.setMenusForViewport();
5055               }
5056             });
5057             dbRefFetcher.fetchDBRefs(false);
5058           }
5059         }).start();
5060
5061       }
5062
5063     });
5064     rfetch.add(fetchr);
5065     final AlignFrame me = this;
5066     new Thread(new Runnable()
5067     {
5068       @Override
5069       public void run()
5070       {
5071         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5072                 .getSequenceFetcherSingleton(me);
5073         javax.swing.SwingUtilities.invokeLater(new Runnable()
5074         {
5075           @Override
5076           public void run()
5077           {
5078             String[] dbclasses = sf.getOrderedSupportedSources();
5079             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5080             // jalview.util.QuickSort.sort(otherdb, otherdb);
5081             List<DbSourceProxy> otherdb;
5082             JMenu dfetch = new JMenu();
5083             JMenu ifetch = new JMenu();
5084             JMenuItem fetchr = null;
5085             int comp = 0, icomp = 0, mcomp = 15;
5086             String mname = null;
5087             int dbi = 0;
5088             for (String dbclass : dbclasses)
5089             {
5090               otherdb = sf.getSourceProxy(dbclass);
5091               // add a single entry for this class, or submenu allowing 'fetch
5092               // all' or pick one
5093               if (otherdb == null || otherdb.size() < 1)
5094               {
5095                 continue;
5096               }
5097               // List<DbSourceProxy> dbs=otherdb;
5098               // otherdb=new ArrayList<DbSourceProxy>();
5099               // for (DbSourceProxy db:dbs)
5100               // {
5101               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5102               // }
5103               if (mname == null)
5104               {
5105                 mname = "From " + dbclass;
5106               }
5107               if (otherdb.size() == 1)
5108               {
5109                 final DbSourceProxy[] dassource = otherdb
5110                         .toArray(new DbSourceProxy[0]);
5111                 DbSourceProxy src = otherdb.get(0);
5112                 fetchr = new JMenuItem(src.getDbSource());
5113                 fetchr.addActionListener(new ActionListener()
5114                 {
5115
5116                   @Override
5117                   public void actionPerformed(ActionEvent e)
5118                   {
5119                     new Thread(new Runnable()
5120                     {
5121
5122                       @Override
5123                       public void run()
5124                       {
5125                         boolean isNucleotide = alignPanel.alignFrame
5126                                 .getViewport().getAlignment()
5127                                 .isNucleotide();
5128                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5129                                 alignPanel.av.getSequenceSelection(),
5130                                 alignPanel.alignFrame, dassource,
5131                                 alignPanel.alignFrame.featureSettings,
5132                                 isNucleotide);
5133                         dbRefFetcher
5134                                 .addListener(new FetchFinishedListenerI()
5135                                 {
5136                                   @Override
5137                                   public void finished()
5138                                   {
5139                                     FeatureSettingsModelI srcSettings = dassource[0]
5140                                             .getFeatureColourScheme();
5141                                     alignPanel.av.mergeFeaturesStyle(
5142                                             srcSettings);
5143                                     AlignFrame.this.setMenusForViewport();
5144                                   }
5145                                 });
5146                         dbRefFetcher.fetchDBRefs(false);
5147                       }
5148                     }).start();
5149                   }
5150
5151                 });
5152                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5153                         MessageManager.formatMessage(
5154                                 "label.fetch_retrieve_from", new Object[]
5155                                 { src.getDbName() })));
5156                 dfetch.add(fetchr);
5157                 comp++;
5158               }
5159               else
5160               {
5161                 final DbSourceProxy[] dassource = otherdb
5162                         .toArray(new DbSourceProxy[0]);
5163                 // fetch all entry
5164                 DbSourceProxy src = otherdb.get(0);
5165                 fetchr = new JMenuItem(MessageManager
5166                         .formatMessage("label.fetch_all_param", new Object[]
5167                         { src.getDbSource() }));
5168                 fetchr.addActionListener(new ActionListener()
5169                 {
5170                   @Override
5171                   public void actionPerformed(ActionEvent e)
5172                   {
5173                     new Thread(new Runnable()
5174                     {
5175
5176                       @Override
5177                       public void run()
5178                       {
5179                         boolean isNucleotide = alignPanel.alignFrame
5180                                 .getViewport().getAlignment()
5181                                 .isNucleotide();
5182                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5183                                 alignPanel.av.getSequenceSelection(),
5184                                 alignPanel.alignFrame, dassource,
5185                                 alignPanel.alignFrame.featureSettings,
5186                                 isNucleotide);
5187                         dbRefFetcher
5188                                 .addListener(new FetchFinishedListenerI()
5189                                 {
5190                                   @Override
5191                                   public void finished()
5192                                   {
5193                                     AlignFrame.this.setMenusForViewport();
5194                                   }
5195                                 });
5196                         dbRefFetcher.fetchDBRefs(false);
5197                       }
5198                     }).start();
5199                   }
5200                 });
5201
5202                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5203                         MessageManager.formatMessage(
5204                                 "label.fetch_retrieve_from_all_sources",
5205                                 new Object[]
5206                                 { Integer.valueOf(otherdb.size())
5207                                         .toString(),
5208                                     src.getDbSource(), src.getDbName() })));
5209                 dfetch.add(fetchr);
5210                 comp++;
5211                 // and then build the rest of the individual menus
5212                 ifetch = new JMenu(MessageManager.formatMessage(
5213                         "label.source_from_db_source", new Object[]
5214                         { src.getDbSource() }));
5215                 icomp = 0;
5216                 String imname = null;
5217                 int i = 0;
5218                 for (DbSourceProxy sproxy : otherdb)
5219                 {
5220                   String dbname = sproxy.getDbName();
5221                   String sname = dbname.length() > 5
5222                           ? dbname.substring(0, 5) + "..."
5223                           : dbname;
5224                   String msname = dbname.length() > 10
5225                           ? dbname.substring(0, 10) + "..."
5226                           : dbname;
5227                   if (imname == null)
5228                   {
5229                     imname = MessageManager
5230                             .formatMessage("label.from_msname", new Object[]
5231                             { sname });
5232                   }
5233                   fetchr = new JMenuItem(msname);
5234                   final DbSourceProxy[] dassrc = { sproxy };
5235                   fetchr.addActionListener(new ActionListener()
5236                   {
5237
5238                     @Override
5239                     public void actionPerformed(ActionEvent e)
5240                     {
5241                       new Thread(new Runnable()
5242                       {
5243
5244                         @Override
5245                         public void run()
5246                         {
5247                           boolean isNucleotide = alignPanel.alignFrame
5248                                   .getViewport().getAlignment()
5249                                   .isNucleotide();
5250                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5251                                   alignPanel.av.getSequenceSelection(),
5252                                   alignPanel.alignFrame, dassrc,
5253                                   alignPanel.alignFrame.featureSettings,
5254                                   isNucleotide);
5255                           dbRefFetcher
5256                                   .addListener(new FetchFinishedListenerI()
5257                                   {
5258                                     @Override
5259                                     public void finished()
5260                                     {
5261                                       AlignFrame.this.setMenusForViewport();
5262                                     }
5263                                   });
5264                           dbRefFetcher.fetchDBRefs(false);
5265                         }
5266                       }).start();
5267                     }
5268
5269                   });
5270                   fetchr.setToolTipText(
5271                           "<html>" + MessageManager.formatMessage(
5272                                   "label.fetch_retrieve_from", new Object[]
5273                                   { dbname }));
5274                   ifetch.add(fetchr);
5275                   ++i;
5276                   if (++icomp >= mcomp || i == (otherdb.size()))
5277                   {
5278                     ifetch.setText(MessageManager.formatMessage(
5279                             "label.source_to_target", imname, sname));
5280                     dfetch.add(ifetch);
5281                     ifetch = new JMenu();
5282                     imname = null;
5283                     icomp = 0;
5284                     comp++;
5285                   }
5286                 }
5287               }
5288               ++dbi;
5289               if (comp >= mcomp || dbi >= (dbclasses.length))
5290               {
5291                 dfetch.setText(MessageManager.formatMessage(
5292                         "label.source_to_target", mname, dbclass));
5293                 rfetch.add(dfetch);
5294                 dfetch = new JMenu();
5295                 mname = null;
5296                 comp = 0;
5297               }
5298             }
5299           }
5300         });
5301       }
5302     }).start();
5303
5304   }
5305
5306   /**
5307    * Left justify the whole alignment.
5308    */
5309   @Override
5310   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5311   {
5312     AlignmentI al = viewport.getAlignment();
5313     al.justify(false);
5314     viewport.firePropertyChange("alignment", null, al);
5315   }
5316
5317   /**
5318    * Right justify the whole alignment.
5319    */
5320   @Override
5321   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5322   {
5323     AlignmentI al = viewport.getAlignment();
5324     al.justify(true);
5325     viewport.firePropertyChange("alignment", null, al);
5326   }
5327
5328   @Override
5329   public void setShowSeqFeatures(boolean b)
5330   {
5331     showSeqFeatures.setSelected(b);
5332     viewport.setShowSequenceFeatures(b);
5333   }
5334
5335   /*
5336    * (non-Javadoc)
5337    *
5338    * @see
5339    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5340    * awt.event.ActionEvent)
5341    */
5342   @Override
5343   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5344   {
5345     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5346     alignPanel.paintAlignment(false, false);
5347   }
5348
5349   /*
5350    * (non-Javadoc)
5351    *
5352    * @see
5353    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5354    * .ActionEvent)
5355    */
5356   @Override
5357   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5358   {
5359     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5360     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5361
5362   }
5363
5364   /*
5365    * (non-Javadoc)
5366    *
5367    * @see
5368    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5369    * .event.ActionEvent)
5370    */
5371   @Override
5372   protected void showGroupConservation_actionPerformed(ActionEvent e)
5373   {
5374     viewport.setShowGroupConservation(showGroupConservation.getState());
5375     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5376   }
5377
5378   /*
5379    * (non-Javadoc)
5380    *
5381    * @see
5382    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5383    * .event.ActionEvent)
5384    */
5385   @Override
5386   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5387   {
5388     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5389     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5390   }
5391
5392   /*
5393    * (non-Javadoc)
5394    *
5395    * @see
5396    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5397    * .event.ActionEvent)
5398    */
5399   @Override
5400   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5401   {
5402     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5403     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5404   }
5405
5406   @Override
5407   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5408   {
5409     showSequenceLogo.setState(true);
5410     viewport.setShowSequenceLogo(true);
5411     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5412     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5413   }
5414
5415   @Override
5416   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5417   {
5418     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5419   }
5420
5421   /*
5422    * (non-Javadoc)
5423    *
5424    * @see
5425    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5426    * .event.ActionEvent)
5427    */
5428   @Override
5429   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5430   {
5431     if (avc.makeGroupsFromSelection())
5432     {
5433       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5434       alignPanel.updateAnnotation();
5435       alignPanel.paintAlignment(true,
5436               viewport.needToUpdateStructureViews());
5437     }
5438   }
5439
5440   public void clearAlignmentSeqRep()
5441   {
5442     // TODO refactor alignmentseqrep to controller
5443     if (viewport.getAlignment().hasSeqrep())
5444     {
5445       viewport.getAlignment().setSeqrep(null);
5446       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5447       alignPanel.updateAnnotation();
5448       alignPanel.paintAlignment(true, true);
5449     }
5450   }
5451
5452   @Override
5453   protected void createGroup_actionPerformed(ActionEvent e)
5454   {
5455     if (avc.createGroup())
5456     {
5457       if (applyAutoAnnotationSettings.isSelected())
5458       {
5459         alignPanel.updateAnnotation(true, false);
5460       }
5461       alignPanel.alignmentChanged();
5462     }
5463   }
5464
5465   @Override
5466   protected void unGroup_actionPerformed(ActionEvent e)
5467   {
5468     if (avc.unGroup())
5469     {
5470       alignPanel.alignmentChanged();
5471     }
5472   }
5473
5474   /**
5475    * make the given alignmentPanel the currently selected tab
5476    *
5477    * @param alignmentPanel
5478    */
5479   public void setDisplayedView(AlignmentPanel alignmentPanel)
5480   {
5481     if (!viewport.getSequenceSetId()
5482             .equals(alignmentPanel.av.getSequenceSetId()))
5483     {
5484       throw new Error(MessageManager.getString(
5485               "error.implementation_error_cannot_show_view_alignment_frame"));
5486     }
5487     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5488             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5489     {
5490       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5491     }
5492   }
5493
5494   /**
5495    * Action on selection of menu options to Show or Hide annotations.
5496    *
5497    * @param visible
5498    * @param forSequences
5499    *          update sequence-related annotations
5500    * @param forAlignment
5501    *          update non-sequence-related annotations
5502    */
5503   @Override
5504   protected void setAnnotationsVisibility(boolean visible,
5505           boolean forSequences, boolean forAlignment)
5506   {
5507     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5508             .getAlignmentAnnotation();
5509     if (anns == null)
5510     {
5511       return;
5512     }
5513     for (AlignmentAnnotation aa : anns)
5514     {
5515       /*
5516        * don't display non-positional annotations on an alignment
5517        */
5518       if (aa.annotations == null)
5519       {
5520         continue;
5521       }
5522       boolean apply = (aa.sequenceRef == null && forAlignment)
5523               || (aa.sequenceRef != null && forSequences);
5524       if (apply)
5525       {
5526         aa.visible = visible;
5527       }
5528     }
5529     alignPanel.validateAnnotationDimensions(true);
5530     alignPanel.alignmentChanged();
5531   }
5532
5533   /**
5534    * Store selected annotation sort order for the view and repaint.
5535    */
5536   @Override
5537   protected void sortAnnotations_actionPerformed()
5538   {
5539     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5540     this.alignPanel.av
5541             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5542     alignPanel.paintAlignment(false, false);
5543   }
5544
5545   /**
5546    *
5547    * @return alignment panels in this alignment frame
5548    */
5549   public List<? extends AlignmentViewPanel> getAlignPanels()
5550   {
5551     // alignPanels is never null
5552     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5553     return alignPanels;
5554   }
5555
5556   /**
5557    * Open a new alignment window, with the cDNA associated with this (protein)
5558    * alignment, aligned as is the protein.
5559    */
5560   protected void viewAsCdna_actionPerformed()
5561   {
5562     // TODO no longer a menu action - refactor as required
5563     final AlignmentI alignment = getViewport().getAlignment();
5564     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5565     if (mappings == null)
5566     {
5567       return;
5568     }
5569     List<SequenceI> cdnaSeqs = new ArrayList<>();
5570     for (SequenceI aaSeq : alignment.getSequences())
5571     {
5572       for (AlignedCodonFrame acf : mappings)
5573       {
5574         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5575         if (dnaSeq != null)
5576         {
5577           /*
5578            * There is a cDNA mapping for this protein sequence - add to new
5579            * alignment. It will share the same dataset sequence as other mapped
5580            * cDNA (no new mappings need to be created).
5581            */
5582           final Sequence newSeq = new Sequence(dnaSeq);
5583           newSeq.setDatasetSequence(dnaSeq);
5584           cdnaSeqs.add(newSeq);
5585         }
5586       }
5587     }
5588     if (cdnaSeqs.size() == 0)
5589     {
5590       // show a warning dialog no mapped cDNA
5591       return;
5592     }
5593     AlignmentI cdna = new Alignment(
5594             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5595     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5596             AlignFrame.DEFAULT_HEIGHT);
5597     cdna.alignAs(alignment);
5598     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5599             + this.title;
5600     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5601             AlignFrame.DEFAULT_HEIGHT);
5602   }
5603
5604   /**
5605    * Set visibility of dna/protein complement view (available when shown in a
5606    * split frame).
5607    *
5608    * @param show
5609    */
5610   @Override
5611   protected void showComplement_actionPerformed(boolean show)
5612   {
5613     SplitContainerI sf = getSplitViewContainer();
5614     if (sf != null)
5615     {
5616       sf.setComplementVisible(this, show);
5617     }
5618   }
5619
5620   /**
5621    * Generate the reverse (optionally complemented) of the selected sequences,
5622    * and add them to the alignment
5623    */
5624   @Override
5625   protected void showReverse_actionPerformed(boolean complement)
5626   {
5627     AlignmentI al = null;
5628     try
5629     {
5630       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5631       al = dna.reverseCdna(complement);
5632       viewport.addAlignment(al, "");
5633       addHistoryItem(new EditCommand(
5634               MessageManager.getString("label.add_sequences"), Action.PASTE,
5635               al.getSequencesArray(), 0, al.getWidth(),
5636               viewport.getAlignment()));
5637     } catch (Exception ex)
5638     {
5639       System.err.println(ex.getMessage());
5640       return;
5641     }
5642   }
5643
5644   /**
5645    * Try to run a script in the Groovy console, having first ensured that this
5646    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5647    * be targeted at this alignment.
5648    */
5649   @Override
5650   protected void runGroovy_actionPerformed()
5651   {
5652     Jalview.setCurrentAlignFrame(this);
5653     groovy.ui.Console console = Desktop.getGroovyConsole();
5654     if (console != null)
5655     {
5656       try
5657       {
5658         console.runScript();
5659       } catch (Exception ex)
5660       {
5661         System.err.println((ex.toString()));
5662         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5663                 MessageManager.getString("label.couldnt_run_groovy_script"),
5664                 MessageManager.getString("label.groovy_support_failed"),
5665                 JvOptionPane.ERROR_MESSAGE);
5666       }
5667     }
5668     else
5669     {
5670       System.err.println("Can't run Groovy script as console not found");
5671     }
5672   }
5673
5674   /**
5675    * Hides columns containing (or not containing) a specified feature, provided
5676    * that would not leave all columns hidden
5677    *
5678    * @param featureType
5679    * @param columnsContaining
5680    * @return
5681    */
5682   public boolean hideFeatureColumns(String featureType,
5683           boolean columnsContaining)
5684   {
5685     boolean notForHiding = avc.markColumnsContainingFeatures(
5686             columnsContaining, false, false, featureType);
5687     if (notForHiding)
5688     {
5689       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5690               false, featureType))
5691       {
5692         getViewport().hideSelectedColumns();
5693         return true;
5694       }
5695     }
5696     return false;
5697   }
5698
5699   @Override
5700   protected void selectHighlightedColumns_actionPerformed(
5701           ActionEvent actionEvent)
5702   {
5703     // include key modifier check in case user selects from menu
5704     avc.markHighlightedColumns(
5705             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5706             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5707                     | ActionEvent.CTRL_MASK)) != 0);
5708   }
5709
5710   /**
5711    * Rebuilds the Colour menu, including any user-defined colours which have
5712    * been loaded either on startup or during the session
5713    */
5714   public void buildColourMenu()
5715   {
5716     colourMenu.removeAll();
5717
5718     colourMenu.add(applyToAllGroups);
5719     colourMenu.add(textColour);
5720     colourMenu.addSeparator();
5721
5722     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5723             viewport.getAlignment(), false);
5724
5725     colourMenu.add(annotationColour);
5726     bg.add(annotationColour);
5727     colourMenu.addSeparator();
5728     colourMenu.add(conservationMenuItem);
5729     colourMenu.add(modifyConservation);
5730     colourMenu.add(abovePIDThreshold);
5731     colourMenu.add(modifyPID);
5732
5733     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5734     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5735   }
5736
5737   /**
5738    * Open a dialog (if not already open) that allows the user to select and
5739    * calculate PCA or Tree analysis
5740    */
5741   protected void openTreePcaDialog()
5742   {
5743     if (alignPanel.getCalculationDialog() == null)
5744     {
5745       new CalculationChooser(AlignFrame.this);
5746     }
5747   }
5748
5749   @Override
5750   protected void loadVcf_actionPerformed()
5751   {
5752     JalviewFileChooser chooser = new JalviewFileChooser(
5753             Cache.getProperty("LAST_DIRECTORY"));
5754     chooser.setFileView(new JalviewFileView());
5755     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5756     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5757
5758     int value = chooser.showOpenDialog(null);
5759
5760     if (value == JalviewFileChooser.APPROVE_OPTION)
5761     {
5762       String choice = chooser.getSelectedFile().getPath();
5763       Cache.setProperty("LAST_DIRECTORY", choice);
5764       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5765       new VCFLoader(choice).loadVCF(seqs, this);
5766     }
5767
5768   }
5769
5770   private Rectangle lastFeatureSettingsBounds = null;
5771
5772   @Override
5773   public void setFeatureSettingsGeometry(Rectangle bounds)
5774   {
5775     lastFeatureSettingsBounds = bounds;
5776   }
5777
5778   @Override
5779   public Rectangle getFeatureSettingsGeometry()
5780   {
5781     return lastFeatureSettingsBounds;
5782   }
5783 }
5784
5785 class PrintThread extends Thread
5786 {
5787   AlignmentPanel ap;
5788
5789   public PrintThread(AlignmentPanel ap)
5790   {
5791     this.ap = ap;
5792   }
5793
5794   static PageFormat pf;
5795
5796   @Override
5797   public void run()
5798   {
5799     PrinterJob printJob = PrinterJob.getPrinterJob();
5800
5801     if (pf != null)
5802     {
5803       printJob.setPrintable(ap, pf);
5804     }
5805     else
5806     {
5807       printJob.setPrintable(ap);
5808     }
5809
5810     if (printJob.printDialog())
5811     {
5812       try
5813       {
5814         printJob.print();
5815       } catch (Exception PrintException)
5816       {
5817         PrintException.printStackTrace();
5818       }
5819     }
5820   }
5821 }