src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.FeatureSettingsModelI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.ScoreModelI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.DBRefSource;
  58 import jalview.datamodel.HiddenSequences;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.FileLoader;
  69 import jalview.io.FormatAdapter;
  70 import jalview.io.HtmlSvgOutput;
  71 import jalview.io.IdentifyFile;
  72 import jalview.io.JalviewFileChooser;
  73 import jalview.io.JalviewFileView;
  74 import jalview.io.JnetAnnotationMaker;
  75 import jalview.io.NewickFile;
  76 import jalview.io.TCoffeeScoreFile;
  77 import jalview.jbgui.GAlignFrame;
  78 import jalview.schemes.Blosum62ColourScheme;
  79 import jalview.schemes.BuriedColourScheme;
  80 import jalview.schemes.ClustalxColourScheme;
  81 import jalview.schemes.ColourSchemeI;
  82 import jalview.schemes.ColourSchemeProperty;
  83 import jalview.schemes.HelixColourScheme;
  84 import jalview.schemes.HydrophobicColourScheme;
  85 import jalview.schemes.NucleotideColourScheme;
  86 import jalview.schemes.PIDColourScheme;
  87 import jalview.schemes.PurinePyrimidineColourScheme;
  88 import jalview.schemes.RNAHelicesColourChooser;
  89 import jalview.schemes.ResidueProperties;
  90 import jalview.schemes.StrandColourScheme;
  91 import jalview.schemes.TCoffeeColourScheme;
  92 import jalview.schemes.TaylorColourScheme;
  93 import jalview.schemes.TurnColourScheme;
  94 import jalview.schemes.UserColourScheme;
  95 import jalview.schemes.ZappoColourScheme;
  96 import jalview.structure.StructureSelectionManager;
  97 import jalview.util.MessageManager;
  98 import jalview.viewmodel.AlignmentViewport;
  99 import jalview.ws.DBRefFetcher;
 100 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 101 import jalview.ws.SequenceFetcher;
 102 import jalview.ws.jws1.Discoverer;
 103 import jalview.ws.jws2.Jws2Discoverer;
 104 import jalview.ws.jws2.jabaws2.Jws2Instance;
 105 import jalview.ws.seqfetcher.DbSourceProxy;
 106
 107 import java.awt.BorderLayout;
 108 import java.awt.Component;
 109 import java.awt.Rectangle;
 110 import java.awt.Toolkit;
 111 import java.awt.datatransfer.Clipboard;
 112 import java.awt.datatransfer.DataFlavor;
 113 import java.awt.datatransfer.StringSelection;
 114 import java.awt.datatransfer.Transferable;
 115 import java.awt.dnd.DnDConstants;
 116 import java.awt.dnd.DropTargetDragEvent;
 117 import java.awt.dnd.DropTargetDropEvent;
 118 import java.awt.dnd.DropTargetEvent;
 119 import java.awt.dnd.DropTargetListener;
 120 import java.awt.event.ActionEvent;
 121 import java.awt.event.ActionListener;
 122 import java.awt.event.ItemEvent;
 123 import java.awt.event.ItemListener;
 124 import java.awt.event.KeyAdapter;
 125 import java.awt.event.KeyEvent;
 126 import java.awt.event.MouseAdapter;
 127 import java.awt.event.MouseEvent;
 128 import java.awt.print.PageFormat;
 129 import java.awt.print.PrinterJob;
 130 import java.beans.PropertyChangeEvent;
 131 import java.io.File;
 132 import java.net.URL;
 133 import java.util.ArrayList;
 134 import java.util.Arrays;
 135 import java.util.Deque;
 136 import java.util.Enumeration;
 137 import java.util.Hashtable;
 138 import java.util.List;
 139 import java.util.Vector;
 140
 141 import javax.swing.JCheckBoxMenuItem;
 142 import javax.swing.JEditorPane;
 143 import javax.swing.JInternalFrame;
 144 import javax.swing.JLayeredPane;
 145 import javax.swing.JMenu;
 146 import javax.swing.JMenuItem;
 147 import javax.swing.JOptionPane;
 148 import javax.swing.JRadioButtonMenuItem;
 149 import javax.swing.JScrollPane;
 150 import javax.swing.SwingUtilities;
 151
 152 /**
 153  * DOCUMENT ME!
 154  *
 155  * @author $author$
 156  * @version $Revision$
 157  */
 158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 159         IProgressIndicator, AlignViewControllerGuiI
 160 {
 161
 162   public static final int DEFAULT_WIDTH = 700;
 163
 164   public static final int DEFAULT_HEIGHT = 500;
 165
 166   /*
 167    * The currently displayed panel (selected tabbed view if more than one)
 168    */
 169   public AlignmentPanel alignPanel;
 170
 171   AlignViewport viewport;
 172
 173   public AlignViewControllerI avc;
 174
 175   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 176
 177   /**
 178    * Last format used to load or save alignments in this window
 179    */
 180   String currentFileFormat = null;
 181
 182   /**
 183    * Current filename for this alignment
 184    */
 185   String fileName = null;
 186
 187   /**
 188    * Creates a new AlignFrame object with specific width and height.
 189    *
 190    * @param al
 191    * @param width
 192    * @param height
 193    */
 194   public AlignFrame(AlignmentI al, int width, int height)
 195   {
 196     this(al, null, width, height);
 197   }
 198
 199   /**
 200    * Creates a new AlignFrame object with specific width, height and
 201    * sequenceSetId
 202    *
 203    * @param al
 204    * @param width
 205    * @param height
 206    * @param sequenceSetId
 207    */
 208   public AlignFrame(AlignmentI al, int width, int height,
 209           String sequenceSetId)
 210   {
 211     this(al, null, width, height, sequenceSetId);
 212   }
 213
 214   /**
 215    * Creates a new AlignFrame object with specific width, height and
 216    * sequenceSetId
 217    *
 218    * @param al
 219    * @param width
 220    * @param height
 221    * @param sequenceSetId
 222    * @param viewId
 223    */
 224   public AlignFrame(AlignmentI al, int width, int height,
 225           String sequenceSetId, String viewId)
 226   {
 227     this(al, null, width, height, sequenceSetId, viewId);
 228   }
 229
 230   /**
 231    * new alignment window with hidden columns
 232    *
 233    * @param al
 234    *          AlignmentI
 235    * @param hiddenColumns
 236    *          ColumnSelection or null
 237    * @param width
 238    *          Width of alignment frame
 239    * @param height
 240    *          height of frame.
 241    */
 242   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 243           int width, int height)
 244   {
 245     this(al, hiddenColumns, width, height, null);
 246   }
 247
 248   /**
 249    * Create alignment frame for al with hiddenColumns, a specific width and
 250    * height, and specific sequenceId
 251    *
 252    * @param al
 253    * @param hiddenColumns
 254    * @param width
 255    * @param height
 256    * @param sequenceSetId
 257    *          (may be null)
 258    */
 259   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 260           int width, int height, String sequenceSetId)
 261   {
 262     this(al, hiddenColumns, width, height, sequenceSetId, null);
 263   }
 264
 265   /**
 266    * Create alignment frame for al with hiddenColumns, a specific width and
 267    * height, and specific sequenceId
 268    *
 269    * @param al
 270    * @param hiddenColumns
 271    * @param width
 272    * @param height
 273    * @param sequenceSetId
 274    *          (may be null)
 275    * @param viewId
 276    *          (may be null)
 277    */
 278   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 279           int width, int height, String sequenceSetId, String viewId)
 280   {
 281     setSize(width, height);
 282
 283     if (al.getDataset() == null)
 284     {
 285       al.setDataset(null);
 286     }
 287
 288     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 289
 290     alignPanel = new AlignmentPanel(this, viewport);
 291
 292     addAlignmentPanel(alignPanel, true);
 293     init();
 294   }
 295
 296   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 297           ColumnSelection hiddenColumns, int width, int height)
 298   {
 299     setSize(width, height);
 300
 301     if (al.getDataset() == null)
 302     {
 303       al.setDataset(null);
 304     }
 305
 306     viewport = new AlignViewport(al, hiddenColumns);
 307
 308     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 309     {
 310       viewport.hideSequence(hiddenSeqs);
 311     }
 312     alignPanel = new AlignmentPanel(this, viewport);
 313     addAlignmentPanel(alignPanel, true);
 314     init();
 315   }
 316
 317   /**
 318    * Make a new AlignFrame from existing alignmentPanels
 319    *
 320    * @param ap
 321    *          AlignmentPanel
 322    * @param av
 323    *          AlignViewport
 324    */
 325   public AlignFrame(AlignmentPanel ap)
 326   {
 327     viewport = ap.av;
 328     alignPanel = ap;
 329     addAlignmentPanel(ap, false);
 330     init();
 331   }
 332
 333   /**
 334    * initalise the alignframe from the underlying viewport data and the
 335    * configurations
 336    */
 337   void init()
 338   {
 339     if (!Jalview.isHeadlessMode())
 340     {
 341       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 342     }
 343
 344     avc = new jalview.controller.AlignViewController(this, viewport,
 345             alignPanel);
 346     if (viewport.getAlignmentConservationAnnotation() == null)
 347     {
 348       BLOSUM62Colour.setEnabled(false);
 349       conservationMenuItem.setEnabled(false);
 350       modifyConservation.setEnabled(false);
 351       // PIDColour.setEnabled(false);
 352       // abovePIDThreshold.setEnabled(false);
 353       // modifyPID.setEnabled(false);
 354     }
 355
 356     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 357             "No sort");
 358
 359     if (sortby.equals("Id"))
 360     {
 361       sortIDMenuItem_actionPerformed(null);
 362     }
 363     else if (sortby.equals("Pairwise Identity"))
 364     {
 365       sortPairwiseMenuItem_actionPerformed(null);
 366     }
 367
 368     if (Desktop.desktop != null)
 369     {
 370       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 371       addServiceListeners();
 372       setGUINucleotide(viewport.getAlignment().isNucleotide());
 373     }
 374
 375     this.alignPanel.av
 376             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 377
 378     setMenusFromViewport(viewport);
 379     buildSortByAnnotationScoresMenu();
 380     buildTreeMenu();
 381
 382     if (viewport.getWrapAlignment())
 383     {
 384       wrapMenuItem_actionPerformed(null);
 385     }
 386
 387     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 388     {
 389       this.overviewMenuItem_actionPerformed(null);
 390     }
 391
 392     addKeyListener();
 393
 394     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 395     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 396     final String menuLabel = MessageManager
 397             .getString("label.copy_format_from");
 398     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 399             new ViewSetProvider()
 400             {
 401
 402               @Override
 403               public AlignmentPanel[] getAllAlignmentPanels()
 404               {
 405                 origview.clear();
 406                 origview.add(alignPanel);
 407                 // make an array of all alignment panels except for this one
 408                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 409                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 410                 aps.remove(AlignFrame.this.alignPanel);
 411                 return aps.toArray(new AlignmentPanel[aps.size()]);
 412               }
 413             }, selviews, new ItemListener()
 414             {
 415
 416               @Override
 417               public void itemStateChanged(ItemEvent e)
 418               {
 419                 if (origview.size() > 0)
 420                 {
 421                   final AlignmentPanel ap = origview.get(0);
 422
 423                   /*
 424                    * Copy the ViewStyle of the selected panel to 'this one'.
 425                    * Don't change value of 'scaleProteinAsCdna' unless copying
 426                    * from a SplitFrame.
 427                    */
 428                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 429                           .getViewStyle();
 430                   boolean fromSplitFrame = selviews.get(0)
 431                           .getAlignViewport().getCodingComplement() != null;
 432                   if (!fromSplitFrame)
 433                   {
 434                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 435                             .getViewStyle().isScaleProteinAsCdna());
 436                   }
 437                   ap.getAlignViewport().setViewStyle(vs);
 438
 439                   /*
 440                    * Also rescale ViewStyle of SplitFrame complement if there is
 441                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 442                    * the whole ViewStyle (allow cDNA protein to have different
 443                    * fonts)
 444                    */
 445                   AlignViewportI complement = ap.getAlignViewport()
 446                           .getCodingComplement();
 447                   if (complement != null && vs.isScaleProteinAsCdna())
 448                   {
 449                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 450                     ((SplitFrame) af.getSplitViewContainer())
 451                             .adjustLayout();
 452                     af.setMenusForViewport();
 453                   }
 454
 455                   ap.updateLayout();
 456                   ap.setSelected(true);
 457                   ap.alignFrame.setMenusForViewport();
 458
 459                 }
 460               }
 461             });
 462     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 463             .indexOf("devel") > -1
 464             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 465                     .indexOf("test") > -1)
 466     {
 467       formatMenu.add(vsel);
 468     }
 469
 470   }
 471
 472   /**
 473    * Change the filename and format for the alignment, and enable the 'reload'
 474    * button functionality.
 475    *
 476    * @param file
 477    *          valid filename
 478    * @param format
 479    *          format of file
 480    */
 481   public void setFileName(String file, String format)
 482   {
 483     fileName = file;
 484     setFileFormat(format);
 485     reload.setEnabled(true);
 486   }
 487
 488   /**
 489    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 490    * events
 491    */
 492   void addKeyListener()
 493   {
 494     addKeyListener(new KeyAdapter()
 495     {
 496       @Override
 497       public void keyPressed(KeyEvent evt)
 498       {
 499         if (viewport.cursorMode
 500                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 501                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 502                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 503                 && Character.isDigit(evt.getKeyChar()))
 504         {
 505           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 506         }
 507
 508         switch (evt.getKeyCode())
 509         {
 510
 511         case 27: // escape key
 512           deselectAllSequenceMenuItem_actionPerformed(null);
 513
 514           break;
 515
 516         case KeyEvent.VK_DOWN:
 517           if (evt.isAltDown() || !viewport.cursorMode)
 518           {
 519             moveSelectedSequences(false);
 520           }
 521           if (viewport.cursorMode)
 522           {
 523             alignPanel.getSeqPanel().moveCursor(0, 1);
 524           }
 525           break;
 526
 527         case KeyEvent.VK_UP:
 528           if (evt.isAltDown() || !viewport.cursorMode)
 529           {
 530             moveSelectedSequences(true);
 531           }
 532           if (viewport.cursorMode)
 533           {
 534             alignPanel.getSeqPanel().moveCursor(0, -1);
 535           }
 536
 537           break;
 538
 539         case KeyEvent.VK_LEFT:
 540           if (evt.isAltDown() || !viewport.cursorMode)
 541           {
 542             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 543           }
 544           else
 545           {
 546             alignPanel.getSeqPanel().moveCursor(-1, 0);
 547           }
 548
 549           break;
 550
 551         case KeyEvent.VK_RIGHT:
 552           if (evt.isAltDown() || !viewport.cursorMode)
 553           {
 554             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 555           }
 556           else
 557           {
 558             alignPanel.getSeqPanel().moveCursor(1, 0);
 559           }
 560           break;
 561
 562         case KeyEvent.VK_SPACE:
 563           if (viewport.cursorMode)
 564           {
 565             alignPanel.getSeqPanel().insertGapAtCursor(
 566                     evt.isControlDown() || evt.isShiftDown()
 567                             || evt.isAltDown());
 568           }
 569           break;
 570
 571         // case KeyEvent.VK_A:
 572         // if (viewport.cursorMode)
 573         // {
 574         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 575         // //System.out.println("A");
 576         // }
 577         // break;
 578         /*
 579          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 580          * System.out.println("closing bracket"); } break;
 581          */
 582         case KeyEvent.VK_DELETE:
 583         case KeyEvent.VK_BACK_SPACE:
 584           if (!viewport.cursorMode)
 585           {
 586             cut_actionPerformed(null);
 587           }
 588           else
 589           {
 590             alignPanel.getSeqPanel().deleteGapAtCursor(
 591                     evt.isControlDown() || evt.isShiftDown()
 592                             || evt.isAltDown());
 593           }
 594
 595           break;
 596
 597         case KeyEvent.VK_S:
 598           if (viewport.cursorMode)
 599           {
 600             alignPanel.getSeqPanel().setCursorRow();
 601           }
 602           break;
 603         case KeyEvent.VK_C:
 604           if (viewport.cursorMode && !evt.isControlDown())
 605           {
 606             alignPanel.getSeqPanel().setCursorColumn();
 607           }
 608           break;
 609         case KeyEvent.VK_P:
 610           if (viewport.cursorMode)
 611           {
 612             alignPanel.getSeqPanel().setCursorPosition();
 613           }
 614           break;
 615
 616         case KeyEvent.VK_ENTER:
 617         case KeyEvent.VK_COMMA:
 618           if (viewport.cursorMode)
 619           {
 620             alignPanel.getSeqPanel().setCursorRowAndColumn();
 621           }
 622           break;
 623
 624         case KeyEvent.VK_Q:
 625           if (viewport.cursorMode)
 626           {
 627             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 628           }
 629           break;
 630         case KeyEvent.VK_M:
 631           if (viewport.cursorMode)
 632           {
 633             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 634           }
 635           break;
 636
 637         case KeyEvent.VK_F2:
 638           viewport.cursorMode = !viewport.cursorMode;
 639           statusBar.setText(MessageManager.formatMessage(
 640                   "label.keyboard_editing_mode",
 641                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 642           if (viewport.cursorMode)
 643           {
 644             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 645             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 646           }
 647           alignPanel.getSeqPanel().seqCanvas.repaint();
 648           break;
 649
 650         case KeyEvent.VK_F1:
 651           try
 652           {
 653             Help.showHelpWindow();
 654           } catch (Exception ex)
 655           {
 656             ex.printStackTrace();
 657           }
 658           break;
 659         case KeyEvent.VK_H:
 660         {
 661           boolean toggleSeqs = !evt.isControlDown();
 662           boolean toggleCols = !evt.isShiftDown();
 663           toggleHiddenRegions(toggleSeqs, toggleCols);
 664           break;
 665         }
 666         case KeyEvent.VK_PAGE_UP:
 667           if (viewport.getWrapAlignment())
 668           {
 669             alignPanel.scrollUp(true);
 670           }
 671           else
 672           {
 673             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 674                     - viewport.endSeq + viewport.startSeq);
 675           }
 676           break;
 677         case KeyEvent.VK_PAGE_DOWN:
 678           if (viewport.getWrapAlignment())
 679           {
 680             alignPanel.scrollUp(false);
 681           }
 682           else
 683           {
 684             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 685                     + viewport.endSeq - viewport.startSeq);
 686           }
 687           break;
 688         }
 689       }
 690
 691       @Override
 692       public void keyReleased(KeyEvent evt)
 693       {
 694         switch (evt.getKeyCode())
 695         {
 696         case KeyEvent.VK_LEFT:
 697           if (evt.isAltDown() || !viewport.cursorMode)
 698           {
 699             viewport.firePropertyChange("alignment", null, viewport
 700                     .getAlignment().getSequences());
 701           }
 702           break;
 703
 704         case KeyEvent.VK_RIGHT:
 705           if (evt.isAltDown() || !viewport.cursorMode)
 706           {
 707             viewport.firePropertyChange("alignment", null, viewport
 708                     .getAlignment().getSequences());
 709           }
 710           break;
 711         }
 712       }
 713     });
 714   }
 715
 716   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 717   {
 718     ap.alignFrame = this;
 719     avc = new jalview.controller.AlignViewController(this, viewport,
 720             alignPanel);
 721
 722     alignPanels.add(ap);
 723
 724     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 725
 726     int aSize = alignPanels.size();
 727
 728     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 729
 730     if (aSize == 1 && ap.av.viewName == null)
 731     {
 732       this.getContentPane().add(ap, BorderLayout.CENTER);
 733     }
 734     else
 735     {
 736       if (aSize == 2)
 737       {
 738         setInitialTabVisible();
 739       }
 740
 741       expandViews.setEnabled(true);
 742       gatherViews.setEnabled(true);
 743       tabbedPane.addTab(ap.av.viewName, ap);
 744
 745       ap.setVisible(false);
 746     }
 747
 748     if (newPanel)
 749     {
 750       if (ap.av.isPadGaps())
 751       {
 752         ap.av.getAlignment().padGaps();
 753       }
 754       ap.av.updateConservation(ap);
 755       ap.av.updateConsensus(ap);
 756       ap.av.updateStrucConsensus(ap);
 757     }
 758   }
 759
 760   public void setInitialTabVisible()
 761   {
 762     expandViews.setEnabled(true);
 763     gatherViews.setEnabled(true);
 764     tabbedPane.setVisible(true);
 765     AlignmentPanel first = alignPanels.get(0);
 766     tabbedPane.addTab(first.av.viewName, first);
 767     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 768   }
 769
 770   public AlignViewport getViewport()
 771   {
 772     return viewport;
 773   }
 774
 775   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 776   private void addServiceListeners()
 777   {
 778     final java.beans.PropertyChangeListener thisListener;
 779     Desktop.instance.addJalviewPropertyChangeListener("services",
 780             thisListener = new java.beans.PropertyChangeListener()
 781             {
 782               @Override
 783               public void propertyChange(PropertyChangeEvent evt)
 784               {
 785                 // // System.out.println("Discoverer property change.");
 786                 // if (evt.getPropertyName().equals("services"))
 787                 {
 788                   SwingUtilities.invokeLater(new Runnable()
 789                   {
 790
 791                     @Override
 792                     public void run()
 793                     {
 794                       System.err
 795                               .println("Rebuild WS Menu for service change");
 796                       BuildWebServiceMenu();
 797                     }
 798
 799                   });
 800                 }
 801               }
 802             });
 803     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 804     {
 805       @Override
 806       public void internalFrameClosed(
 807               javax.swing.event.InternalFrameEvent evt)
 808       {
 809         // System.out.println("deregistering discoverer listener");
 810         Desktop.instance.removeJalviewPropertyChangeListener("services",
 811                 thisListener);
 812         closeMenuItem_actionPerformed(true);
 813       };
 814     });
 815     // Finally, build the menu once to get current service state
 816     new Thread(new Runnable()
 817     {
 818       @Override
 819       public void run()
 820       {
 821         BuildWebServiceMenu();
 822       }
 823     }).start();
 824   }
 825
 826   /**
 827    * Configure menu items that vary according to whether the alignment is
 828    * nucleotide or protein
 829    *
 830    * @param nucleotide
 831    */
 832   public void setGUINucleotide(boolean nucleotide)
 833   {
 834     showTranslation.setVisible(nucleotide);
 835     showReverse.setVisible(nucleotide);
 836     showReverseComplement.setVisible(nucleotide);
 837     conservationMenuItem.setEnabled(!nucleotide);
 838     modifyConservation.setEnabled(!nucleotide);
 839     showGroupConservation.setEnabled(!nucleotide);
 840     rnahelicesColour.setEnabled(nucleotide);
 841     purinePyrimidineColour.setEnabled(nucleotide);
 842     showComplementMenuItem.setText(MessageManager
 843             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
 844     setColourSelected(jalview.bin.Cache.getDefault(
 845             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 846                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 847   }
 848
 849   /**
 850    * set up menus for the current viewport. This may be called after any
 851    * operation that affects the data in the current view (selection changed,
 852    * etc) to update the menus to reflect the new state.
 853    */
 854   @Override
 855   public void setMenusForViewport()
 856   {
 857     setMenusFromViewport(viewport);
 858   }
 859
 860   /**
 861    * Need to call this method when tabs are selected for multiple views, or when
 862    * loading from Jalview2XML.java
 863    *
 864    * @param av
 865    *          AlignViewport
 866    */
 867   void setMenusFromViewport(AlignViewport av)
 868   {
 869     padGapsMenuitem.setSelected(av.isPadGaps());
 870     colourTextMenuItem.setSelected(av.isShowColourText());
 871     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 872     conservationMenuItem.setSelected(av.getConservationSelected());
 873     seqLimits.setSelected(av.getShowJVSuffix());
 874     idRightAlign.setSelected(av.isRightAlignIds());
 875     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 876     renderGapsMenuItem.setSelected(av.isRenderGaps());
 877     wrapMenuItem.setSelected(av.getWrapAlignment());
 878     scaleAbove.setVisible(av.getWrapAlignment());
 879     scaleLeft.setVisible(av.getWrapAlignment());
 880     scaleRight.setVisible(av.getWrapAlignment());
 881     annotationPanelMenuItem.setState(av.isShowAnnotation());
 882     /*
 883      * Show/hide annotations only enabled if annotation panel is shown
 884      */
 885     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 886     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 887     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 888     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 889     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 890     viewTextMenuItem.setSelected(av.getShowText());
 891     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 892     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 893     showGroupConservation.setSelected(av.isShowGroupConservation());
 894     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 895     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 896     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 897
 898     setColourSelected(ColourSchemeProperty.getColourName(av
 899             .getGlobalColourScheme()));
 900
 901     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 902     hiddenMarkers.setState(av.getShowHiddenMarkers());
 903     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 904     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 905     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 906     autoCalculate.setSelected(av.autoCalculateConsensus);
 907     sortByTree.setSelected(av.sortByTree);
 908     listenToViewSelections.setSelected(av.followSelection);
 909     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 910     rnahelicesColour
 911             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 912
 913     showProducts.setEnabled(canShowProducts());
 914
 915     updateEditMenuBar();
 916   }
 917
 918   private IProgressIndicator progressBar;
 919
 920   /*
 921    * (non-Javadoc)
 922    *
 923    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 924    */
 925   @Override
 926   public void setProgressBar(String message, long id)
 927   {
 928     progressBar.setProgressBar(message, id);
 929   }
 930
 931   @Override
 932   public void registerHandler(final long id,
 933           final IProgressIndicatorHandler handler)
 934   {
 935     progressBar.registerHandler(id, handler);
 936   }
 937
 938   /**
 939    *
 940    * @return true if any progress bars are still active
 941    */
 942   @Override
 943   public boolean operationInProgress()
 944   {
 945     return progressBar.operationInProgress();
 946   }
 947
 948   @Override
 949   public void setStatus(String text)
 950   {
 951     statusBar.setText(text);
 952   }
 953
 954   /*
 955    * Added so Castor Mapping file can obtain Jalview Version
 956    */
 957   public String getVersion()
 958   {
 959     return jalview.bin.Cache.getProperty("VERSION");
 960   }
 961
 962   public FeatureRenderer getFeatureRenderer()
 963   {
 964     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 965   }
 966
 967   @Override
 968   public void fetchSequence_actionPerformed(ActionEvent e)
 969   {
 970     new jalview.gui.SequenceFetcher(this);
 971   }
 972
 973   @Override
 974   public void addFromFile_actionPerformed(ActionEvent e)
 975   {
 976     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 977   }
 978
 979   @Override
 980   public void reload_actionPerformed(ActionEvent e)
 981   {
 982     if (fileName != null)
 983     {
 984       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 985       // originating file's format
 986       // TODO: work out how to recover feature settings for correct view(s) when
 987       // file is reloaded.
 988       if (currentFileFormat.equals("Jalview"))
 989       {
 990         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 991         for (int i = 0; i < frames.length; i++)
 992         {
 993           if (frames[i] instanceof AlignFrame && frames[i] != this
 994                   && ((AlignFrame) frames[i]).fileName != null
 995                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 996           {
 997             try
 998             {
 999               frames[i].setSelected(true);
1000               Desktop.instance.closeAssociatedWindows();
1001             } catch (java.beans.PropertyVetoException ex)
1002             {
1003             }
1004           }
1005
1006         }
1007         Desktop.instance.closeAssociatedWindows();
1008
1009         FileLoader loader = new FileLoader();
1010         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1011         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1012       }
1013       else
1014       {
1015         Rectangle bounds = this.getBounds();
1016
1017         FileLoader loader = new FileLoader();
1018         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1019         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1020                 protocol, currentFileFormat);
1021
1022         newframe.setBounds(bounds);
1023         if (featureSettings != null && featureSettings.isShowing())
1024         {
1025           final Rectangle fspos = featureSettings.frame.getBounds();
1026           // TODO: need a 'show feature settings' function that takes bounds -
1027           // need to refactor Desktop.addFrame
1028           newframe.featureSettings_actionPerformed(null);
1029           final FeatureSettings nfs = newframe.featureSettings;
1030           SwingUtilities.invokeLater(new Runnable()
1031           {
1032             @Override
1033             public void run()
1034             {
1035               nfs.frame.setBounds(fspos);
1036             }
1037           });
1038           this.featureSettings.close();
1039           this.featureSettings = null;
1040         }
1041         this.closeMenuItem_actionPerformed(true);
1042       }
1043     }
1044   }
1045
1046   @Override
1047   public void addFromText_actionPerformed(ActionEvent e)
1048   {
1049     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1050             .getAlignPanel());
1051   }
1052
1053   @Override
1054   public void addFromURL_actionPerformed(ActionEvent e)
1055   {
1056     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1057   }
1058
1059   @Override
1060   public void save_actionPerformed(ActionEvent e)
1061   {
1062     if (fileName == null
1063             || (currentFileFormat == null || !jalview.io.FormatAdapter
1064                     .isValidIOFormat(currentFileFormat, true))
1065             || fileName.startsWith("http"))
1066     {
1067       saveAs_actionPerformed(null);
1068     }
1069     else
1070     {
1071       saveAlignment(fileName, currentFileFormat);
1072     }
1073   }
1074
1075   /**
1076    * DOCUMENT ME!
1077    *
1078    * @param e
1079    *          DOCUMENT ME!
1080    */
1081   @Override
1082   public void saveAs_actionPerformed(ActionEvent e)
1083   {
1084     JalviewFileChooser chooser = new JalviewFileChooser(
1085             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1086             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1087             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1088             currentFileFormat, false);
1089
1090     chooser.setFileView(new JalviewFileView());
1091     chooser.setDialogTitle(MessageManager
1092             .getString("label.save_alignment_to_file"));
1093     chooser.setToolTipText(MessageManager.getString("action.save"));
1094
1095     int value = chooser.showSaveDialog(this);
1096
1097     if (value == JalviewFileChooser.APPROVE_OPTION)
1098     {
1099       currentFileFormat = chooser.getSelectedFormat();
1100       while (currentFileFormat == null)
1101       {
1102         JOptionPane
1103                 .showInternalMessageDialog(
1104                         Desktop.desktop,
1105                         MessageManager
1106                                 .getString("label.select_file_format_before_saving"),
1107                         MessageManager
1108                                 .getString("label.file_format_not_specified"),
1109                         JOptionPane.WARNING_MESSAGE);
1110         currentFileFormat = chooser.getSelectedFormat();
1111         value = chooser.showSaveDialog(this);
1112         if (value != JalviewFileChooser.APPROVE_OPTION)
1113         {
1114           return;
1115         }
1116       }
1117
1118       fileName = chooser.getSelectedFile().getPath();
1119
1120       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1121               currentFileFormat);
1122
1123       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1124       if (currentFileFormat.indexOf(" ") > -1)
1125       {
1126         currentFileFormat = currentFileFormat.substring(0,
1127                 currentFileFormat.indexOf(" "));
1128       }
1129       saveAlignment(fileName, currentFileFormat);
1130     }
1131   }
1132
1133   public boolean saveAlignment(String file, String format)
1134   {
1135     boolean success = true;
1136
1137     if (format.equalsIgnoreCase("Jalview"))
1138     {
1139       String shortName = title;
1140
1141       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1142       {
1143         shortName = shortName.substring(shortName
1144                 .lastIndexOf(java.io.File.separatorChar) + 1);
1145       }
1146
1147       success = new Jalview2XML().saveAlignment(this, file, shortName);
1148
1149       statusBar.setText(MessageManager.formatMessage(
1150               "label.successfully_saved_to_file_in_format", new Object[] {
1151                   fileName, format }));
1152
1153     }
1154     else
1155     {
1156       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1157       {
1158         warningMessage("Cannot save file " + fileName + " using format "
1159                 + format, "Alignment output format not supported");
1160         if (!Jalview.isHeadlessMode())
1161         {
1162           saveAs_actionPerformed(null);
1163         }
1164         return false;
1165       }
1166
1167       AlignmentExportData exportData = getAlignmentForExport(format,
1168               viewport, null);
1169       if (exportData.getSettings().isCancelled())
1170       {
1171         return false;
1172       }
1173       FormatAdapter f = new FormatAdapter(alignPanel,
1174               exportData.getSettings());
1175       String output = f.formatSequences(
1176               format,
1177               exportData.getAlignment(), // class cast exceptions will
1178               // occur in the distant future
1179               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180               f.getCacheSuffixDefault(format),
1181               viewport.getColumnSelection());
1182
1183       if (output == null)
1184       {
1185         success = false;
1186       }
1187       else
1188       {
1189         try
1190         {
1191           java.io.PrintWriter out = new java.io.PrintWriter(
1192                   new java.io.FileWriter(file));
1193
1194           out.print(output);
1195           out.close();
1196           this.setTitle(file);
1197           statusBar.setText(MessageManager.formatMessage(
1198                   "label.successfully_saved_to_file_in_format",
1199                   new Object[] { fileName, format }));
1200         } catch (Exception ex)
1201         {
1202           success = false;
1203           ex.printStackTrace();
1204         }
1205       }
1206     }
1207
1208     if (!success)
1209     {
1210       JOptionPane.showInternalMessageDialog(this, MessageManager
1211               .formatMessage("label.couldnt_save_file",
1212                       new Object[] { fileName }), MessageManager
1213               .getString("label.error_saving_file"),
1214               JOptionPane.WARNING_MESSAGE);
1215     }
1216
1217     return success;
1218   }
1219
1220   private void warningMessage(String warning, String title)
1221   {
1222     if (new jalview.util.Platform().isHeadless())
1223     {
1224       System.err.println("Warning: " + title + "\nWarning: " + warning);
1225
1226     }
1227     else
1228     {
1229       JOptionPane.showInternalMessageDialog(this, warning, title,
1230               JOptionPane.WARNING_MESSAGE);
1231     }
1232     return;
1233   }
1234
1235   /**
1236    * DOCUMENT ME!
1237    *
1238    * @param e
1239    *          DOCUMENT ME!
1240    */
1241   @Override
1242   protected void outputText_actionPerformed(ActionEvent e)
1243   {
1244
1245     AlignmentExportData exportData = getAlignmentForExport(
1246             e.getActionCommand(), viewport, null);
1247     if (exportData.getSettings().isCancelled())
1248     {
1249       return;
1250     }
1251     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252     cap.setForInput(null);
1253     try
1254     {
1255       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1256               .formatSequences(e.getActionCommand(),
1257                       exportData.getAlignment(),
1258                       exportData.getOmitHidden(),
1259                       exportData.getStartEndPostions(),
1260                       viewport.getColumnSelection()));
1261       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1262               "label.alignment_output_command",
1263               new Object[] { e.getActionCommand() }), 600, 500);
1264     } catch (OutOfMemoryError oom)
1265     {
1266       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1267       cap.dispose();
1268     }
1269
1270   }
1271
1272   public static AlignmentExportData getAlignmentForExport(
1273           String exportFormat, AlignViewportI viewport,
1274           AlignExportSettingI exportSettings)
1275   {
1276     AlignmentI alignmentToExport = null;
1277     AlignExportSettingI settings = exportSettings;
1278     String[] omitHidden = null;
1279     int[] alignmentStartEnd = new int[2];
1280
1281     HiddenSequences hiddenSeqs = viewport.getAlignment()
1282             .getHiddenSequences();
1283
1284     alignmentToExport = viewport.getAlignment();
1285     alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1286
1287     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1288     if (settings == null)
1289     {
1290       settings = new AlignExportSettings(hasHiddenSeqs,
1291               viewport.hasHiddenColumns(), exportFormat);
1292     }
1293     // settings.isExportAnnotations();
1294
1295     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1296     {
1297       omitHidden = viewport.getViewAsString(false);
1298     }
1299
1300     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1301     {
1302       alignmentToExport = hiddenSeqs.getFullAlignment();
1303     }
1304     else
1305     {
1306       alignmentToExport = viewport.getAlignment();
1307       alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1308               .getColumnSelection().getHiddenColumns());
1309     }
1310     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1311             omitHidden, alignmentStartEnd, settings);
1312     return ed;
1313   }
1314
1315   public static int[] getStartEnd(int[] aligmentStartEnd,
1316           List<int[]> hiddenCols)
1317   {
1318     int startPos = aligmentStartEnd[0];
1319     int endPos = aligmentStartEnd[1];
1320
1321     int[] lowestRange = new int[] { -1, -1 };
1322     int[] higestRange = new int[] { -1, -1 };
1323
1324     for (int[] hiddenCol : hiddenCols)
1325     {
1326       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1327       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1328     }
1329
1330     if (lowestRange[0] == -1 && lowestRange[1] == -1)
1331     {
1332       startPos = aligmentStartEnd[0];
1333     }
1334     else
1335     {
1336       startPos = lowestRange[1] + 1;
1337     }
1338
1339     if (higestRange[0] == -1 && higestRange[1] == -1)
1340     {
1341       endPos = aligmentStartEnd[1];
1342     }
1343     else
1344     {
1345       endPos = higestRange[0] - 1;
1346     }
1347
1348     // System.out.println("Export range : " + startPos + " - " + endPos);
1349     return new int[] { startPos, endPos };
1350   }
1351
1352   public static void main(String[] args)
1353   {
1354     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1355     hiddenCols.add(new int[] { 0, 0 });
1356     hiddenCols.add(new int[] { 6, 9 });
1357     hiddenCols.add(new int[] { 11, 12 });
1358     hiddenCols.add(new int[] { 33, 33 });
1359     hiddenCols.add(new int[] { 50, 50 });
1360
1361     int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1362     // System.out.println("Export range : " + x[0] + " - " + x[1]);
1363   }
1364
1365   /**
1366    * DOCUMENT ME!
1367    *
1368    * @param e
1369    *          DOCUMENT ME!
1370    */
1371   @Override
1372   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1373   {
1374     new HtmlSvgOutput(null, alignPanel);
1375   }
1376
1377   @Override
1378   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1379   {
1380     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1381     bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1382   }
1383
1384   public void createImageMap(File file, String image)
1385   {
1386     alignPanel.makePNGImageMap(file, image);
1387   }
1388
1389   /**
1390    * DOCUMENT ME!
1391    *
1392    * @param e
1393    *          DOCUMENT ME!
1394    */
1395   @Override
1396   public void createPNG(File f)
1397   {
1398     alignPanel.makePNG(f);
1399   }
1400
1401   /**
1402    * DOCUMENT ME!
1403    *
1404    * @param e
1405    *          DOCUMENT ME!
1406    */
1407   @Override
1408   public void createEPS(File f)
1409   {
1410     alignPanel.makeEPS(f);
1411   }
1412
1413   @Override
1414   public void createSVG(File f)
1415   {
1416     alignPanel.makeSVG(f);
1417   }
1418
1419   @Override
1420   public void pageSetup_actionPerformed(ActionEvent e)
1421   {
1422     PrinterJob printJob = PrinterJob.getPrinterJob();
1423     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1424   }
1425
1426   /**
1427    * DOCUMENT ME!
1428    *
1429    * @param e
1430    *          DOCUMENT ME!
1431    */
1432   @Override
1433   public void printMenuItem_actionPerformed(ActionEvent e)
1434   {
1435     // Putting in a thread avoids Swing painting problems
1436     PrintThread thread = new PrintThread(alignPanel);
1437     thread.start();
1438   }
1439
1440   @Override
1441   public void exportFeatures_actionPerformed(ActionEvent e)
1442   {
1443     new AnnotationExporter().exportFeatures(alignPanel);
1444   }
1445
1446   @Override
1447   public void exportAnnotations_actionPerformed(ActionEvent e)
1448   {
1449     new AnnotationExporter().exportAnnotations(alignPanel);
1450   }
1451
1452   @Override
1453   public void associatedData_actionPerformed(ActionEvent e)
1454   {
1455     // Pick the tree file
1456     JalviewFileChooser chooser = new JalviewFileChooser(
1457             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1458     chooser.setFileView(new JalviewFileView());
1459     chooser.setDialogTitle(MessageManager
1460             .getString("label.load_jalview_annotations"));
1461     chooser.setToolTipText(MessageManager
1462             .getString("label.load_jalview_annotations"));
1463
1464     int value = chooser.showOpenDialog(null);
1465
1466     if (value == JalviewFileChooser.APPROVE_OPTION)
1467     {
1468       String choice = chooser.getSelectedFile().getPath();
1469       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1470       loadJalviewDataFile(choice, null, null, null);
1471     }
1472
1473   }
1474
1475   /**
1476    * Close the current view or all views in the alignment frame. If the frame
1477    * only contains one view then the alignment will be removed from memory.
1478    *
1479    * @param closeAllTabs
1480    */
1481   @Override
1482   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1483   {
1484     if (alignPanels != null && alignPanels.size() < 2)
1485     {
1486       closeAllTabs = true;
1487     }
1488
1489     try
1490     {
1491       if (alignPanels != null)
1492       {
1493         if (closeAllTabs)
1494         {
1495           if (this.isClosed())
1496           {
1497             // really close all the windows - otherwise wait till
1498             // setClosed(true) is called
1499             for (int i = 0; i < alignPanels.size(); i++)
1500             {
1501               AlignmentPanel ap = alignPanels.get(i);
1502               ap.closePanel();
1503             }
1504           }
1505         }
1506         else
1507         {
1508           closeView(alignPanel);
1509         }
1510       }
1511
1512       if (closeAllTabs)
1513       {
1514         /*
1515          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1516          * be called recursively, with the frame now in 'closed' state
1517          */
1518         this.setClosed(true);
1519       }
1520     } catch (Exception ex)
1521     {
1522       ex.printStackTrace();
1523     }
1524   }
1525
1526   /**
1527    * Close the specified panel and close up tabs appropriately.
1528    *
1529    * @param panelToClose
1530    */
1531   public void closeView(AlignmentPanel panelToClose)
1532   {
1533     int index = tabbedPane.getSelectedIndex();
1534     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1535     alignPanels.remove(panelToClose);
1536     panelToClose.closePanel();
1537     panelToClose = null;
1538
1539     tabbedPane.removeTabAt(closedindex);
1540     tabbedPane.validate();
1541
1542     if (index > closedindex || index == tabbedPane.getTabCount())
1543     {
1544       // modify currently selected tab index if necessary.
1545       index--;
1546     }
1547
1548     this.tabSelectionChanged(index);
1549   }
1550
1551   /**
1552    * DOCUMENT ME!
1553    */
1554   void updateEditMenuBar()
1555   {
1556
1557     if (viewport.getHistoryList().size() > 0)
1558     {
1559       undoMenuItem.setEnabled(true);
1560       CommandI command = viewport.getHistoryList().peek();
1561       undoMenuItem.setText(MessageManager.formatMessage(
1562               "label.undo_command",
1563               new Object[] { command.getDescription() }));
1564     }
1565     else
1566     {
1567       undoMenuItem.setEnabled(false);
1568       undoMenuItem.setText(MessageManager.getString("action.undo"));
1569     }
1570
1571     if (viewport.getRedoList().size() > 0)
1572     {
1573       redoMenuItem.setEnabled(true);
1574
1575       CommandI command = viewport.getRedoList().peek();
1576       redoMenuItem.setText(MessageManager.formatMessage(
1577               "label.redo_command",
1578               new Object[] { command.getDescription() }));
1579     }
1580     else
1581     {
1582       redoMenuItem.setEnabled(false);
1583       redoMenuItem.setText(MessageManager.getString("action.redo"));
1584     }
1585   }
1586
1587   @Override
1588   public void addHistoryItem(CommandI command)
1589   {
1590     if (command.getSize() > 0)
1591     {
1592       viewport.addToHistoryList(command);
1593       viewport.clearRedoList();
1594       updateEditMenuBar();
1595       viewport.updateHiddenColumns();
1596       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1597       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1598       // viewport.getColumnSelection()
1599       // .getHiddenColumns().size() > 0);
1600     }
1601   }
1602
1603   /**
1604    *
1605    * @return alignment objects for all views
1606    */
1607   AlignmentI[] getViewAlignments()
1608   {
1609     if (alignPanels != null)
1610     {
1611       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1612       int i = 0;
1613       for (AlignmentPanel ap : alignPanels)
1614       {
1615         als[i++] = ap.av.getAlignment();
1616       }
1617       return als;
1618     }
1619     if (viewport != null)
1620     {
1621       return new AlignmentI[] { viewport.getAlignment() };
1622     }
1623     return null;
1624   }
1625
1626   /**
1627    * DOCUMENT ME!
1628    *
1629    * @param e
1630    *          DOCUMENT ME!
1631    */
1632   @Override
1633   protected void undoMenuItem_actionPerformed(ActionEvent e)
1634   {
1635     if (viewport.getHistoryList().isEmpty())
1636     {
1637       return;
1638     }
1639     CommandI command = viewport.getHistoryList().pop();
1640     viewport.addToRedoList(command);
1641     command.undoCommand(getViewAlignments());
1642
1643     AlignmentViewport originalSource = getOriginatingSource(command);
1644     updateEditMenuBar();
1645
1646     if (originalSource != null)
1647     {
1648       if (originalSource != viewport)
1649       {
1650         Cache.log
1651                 .warn("Implementation worry: mismatch of viewport origin for undo");
1652       }
1653       originalSource.updateHiddenColumns();
1654       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1655       // null
1656       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1657       // viewport.getColumnSelection()
1658       // .getHiddenColumns().size() > 0);
1659       originalSource.firePropertyChange("alignment", null, originalSource
1660               .getAlignment().getSequences());
1661     }
1662   }
1663
1664   /**
1665    * DOCUMENT ME!
1666    *
1667    * @param e
1668    *          DOCUMENT ME!
1669    */
1670   @Override
1671   protected void redoMenuItem_actionPerformed(ActionEvent e)
1672   {
1673     if (viewport.getRedoList().size() < 1)
1674     {
1675       return;
1676     }
1677
1678     CommandI command = viewport.getRedoList().pop();
1679     viewport.addToHistoryList(command);
1680     command.doCommand(getViewAlignments());
1681
1682     AlignmentViewport originalSource = getOriginatingSource(command);
1683     updateEditMenuBar();
1684
1685     if (originalSource != null)
1686     {
1687
1688       if (originalSource != viewport)
1689       {
1690         Cache.log
1691                 .warn("Implementation worry: mismatch of viewport origin for redo");
1692       }
1693       originalSource.updateHiddenColumns();
1694       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1695       // null
1696       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1697       // viewport.getColumnSelection()
1698       // .getHiddenColumns().size() > 0);
1699       originalSource.firePropertyChange("alignment", null, originalSource
1700               .getAlignment().getSequences());
1701     }
1702   }
1703
1704   AlignmentViewport getOriginatingSource(CommandI command)
1705   {
1706     AlignmentViewport originalSource = null;
1707     // For sequence removal and addition, we need to fire
1708     // the property change event FROM the viewport where the
1709     // original alignment was altered
1710     AlignmentI al = null;
1711     if (command instanceof EditCommand)
1712     {
1713       EditCommand editCommand = (EditCommand) command;
1714       al = editCommand.getAlignment();
1715       List<Component> comps = PaintRefresher.components.get(viewport
1716               .getSequenceSetId());
1717
1718       for (Component comp : comps)
1719       {
1720         if (comp instanceof AlignmentPanel)
1721         {
1722           if (al == ((AlignmentPanel) comp).av.getAlignment())
1723           {
1724             originalSource = ((AlignmentPanel) comp).av;
1725             break;
1726           }
1727         }
1728       }
1729     }
1730
1731     if (originalSource == null)
1732     {
1733       // The original view is closed, we must validate
1734       // the current view against the closed view first
1735       if (al != null)
1736       {
1737         PaintRefresher.validateSequences(al, viewport.getAlignment());
1738       }
1739
1740       originalSource = viewport;
1741     }
1742
1743     return originalSource;
1744   }
1745
1746   /**
1747    * DOCUMENT ME!
1748    *
1749    * @param up
1750    *          DOCUMENT ME!
1751    */
1752   public void moveSelectedSequences(boolean up)
1753   {
1754     SequenceGroup sg = viewport.getSelectionGroup();
1755
1756     if (sg == null)
1757     {
1758       return;
1759     }
1760     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1761             viewport.getHiddenRepSequences(), up);
1762     alignPanel.paintAlignment(true);
1763   }
1764
1765   synchronized void slideSequences(boolean right, int size)
1766   {
1767     List<SequenceI> sg = new ArrayList<SequenceI>();
1768     if (viewport.cursorMode)
1769     {
1770       sg.add(viewport.getAlignment().getSequenceAt(
1771               alignPanel.getSeqPanel().seqCanvas.cursorY));
1772     }
1773     else if (viewport.getSelectionGroup() != null
1774             && viewport.getSelectionGroup().getSize() != viewport
1775                     .getAlignment().getHeight())
1776     {
1777       sg = viewport.getSelectionGroup().getSequences(
1778               viewport.getHiddenRepSequences());
1779     }
1780
1781     if (sg.size() < 1)
1782     {
1783       return;
1784     }
1785
1786     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1787
1788     for (SequenceI seq : viewport.getAlignment().getSequences())
1789     {
1790       if (!sg.contains(seq))
1791       {
1792         invertGroup.add(seq);
1793       }
1794     }
1795
1796     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1797
1798     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1799     for (int i = 0; i < invertGroup.size(); i++)
1800     {
1801       seqs2[i] = invertGroup.get(i);
1802     }
1803
1804     SlideSequencesCommand ssc;
1805     if (right)
1806     {
1807       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1808               size, viewport.getGapCharacter());
1809     }
1810     else
1811     {
1812       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1813               size, viewport.getGapCharacter());
1814     }
1815
1816     int groupAdjustment = 0;
1817     if (ssc.getGapsInsertedBegin() && right)
1818     {
1819       if (viewport.cursorMode)
1820       {
1821         alignPanel.getSeqPanel().moveCursor(size, 0);
1822       }
1823       else
1824       {
1825         groupAdjustment = size;
1826       }
1827     }
1828     else if (!ssc.getGapsInsertedBegin() && !right)
1829     {
1830       if (viewport.cursorMode)
1831       {
1832         alignPanel.getSeqPanel().moveCursor(-size, 0);
1833       }
1834       else
1835       {
1836         groupAdjustment = -size;
1837       }
1838     }
1839
1840     if (groupAdjustment != 0)
1841     {
1842       viewport.getSelectionGroup().setStartRes(
1843               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1844       viewport.getSelectionGroup().setEndRes(
1845               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1846     }
1847
1848     /*
1849      * just extend the last slide command if compatible; but not if in
1850      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1851      */
1852     boolean appendHistoryItem = false;
1853     Deque<CommandI> historyList = viewport.getHistoryList();
1854     boolean inSplitFrame = getSplitViewContainer() != null;
1855     if (!inSplitFrame && historyList != null && historyList.size() > 0
1856             && historyList.peek() instanceof SlideSequencesCommand)
1857     {
1858       appendHistoryItem = ssc
1859               .appendSlideCommand((SlideSequencesCommand) historyList
1860                       .peek());
1861     }
1862
1863     if (!appendHistoryItem)
1864     {
1865       addHistoryItem(ssc);
1866     }
1867
1868     repaint();
1869   }
1870
1871   /**
1872    * DOCUMENT ME!
1873    *
1874    * @param e
1875    *          DOCUMENT ME!
1876    */
1877   @Override
1878   protected void copy_actionPerformed(ActionEvent e)
1879   {
1880     System.gc();
1881     if (viewport.getSelectionGroup() == null)
1882     {
1883       return;
1884     }
1885     // TODO: preserve the ordering of displayed alignment annotation in any
1886     // internal paste (particularly sequence associated annotation)
1887     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1888     String[] omitHidden = null;
1889
1890     if (viewport.hasHiddenColumns())
1891     {
1892       omitHidden = viewport.getViewAsString(true);
1893     }
1894
1895     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1896             omitHidden, null);
1897
1898     StringSelection ss = new StringSelection(output);
1899
1900     try
1901     {
1902       jalview.gui.Desktop.internalCopy = true;
1903       // Its really worth setting the clipboard contents
1904       // to empty before setting the large StringSelection!!
1905       Toolkit.getDefaultToolkit().getSystemClipboard()
1906               .setContents(new StringSelection(""), null);
1907
1908       Toolkit.getDefaultToolkit().getSystemClipboard()
1909               .setContents(ss, Desktop.instance);
1910     } catch (OutOfMemoryError er)
1911     {
1912       new OOMWarning("copying region", er);
1913       return;
1914     }
1915
1916     ArrayList<int[]> hiddenColumns = null;
1917     if (viewport.hasHiddenColumns())
1918     {
1919       hiddenColumns = new ArrayList<int[]>();
1920       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1921               .getSelectionGroup().getEndRes();
1922       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1923       {
1924         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1925         {
1926           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1927               region[1] - hiddenOffset });
1928         }
1929       }
1930     }
1931
1932     Desktop.jalviewClipboard = new Object[] { seqs,
1933         viewport.getAlignment().getDataset(), hiddenColumns };
1934     statusBar.setText(MessageManager.formatMessage(
1935             "label.copied_sequences_to_clipboard", new Object[] { Integer
1936                     .valueOf(seqs.length).toString() }));
1937   }
1938
1939   /**
1940    * DOCUMENT ME!
1941    *
1942    * @param e
1943    *          DOCUMENT ME!
1944    */
1945   @Override
1946   protected void pasteNew_actionPerformed(ActionEvent e)
1947   {
1948     paste(true);
1949   }
1950
1951   /**
1952    * DOCUMENT ME!
1953    *
1954    * @param e
1955    *          DOCUMENT ME!
1956    */
1957   @Override
1958   protected void pasteThis_actionPerformed(ActionEvent e)
1959   {
1960     paste(false);
1961   }
1962
1963   /**
1964    * Paste contents of Jalview clipboard
1965    *
1966    * @param newAlignment
1967    *          true to paste to a new alignment, otherwise add to this.
1968    */
1969   void paste(boolean newAlignment)
1970   {
1971     boolean externalPaste = true;
1972     try
1973     {
1974       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1975       Transferable contents = c.getContents(this);
1976
1977       if (contents == null)
1978       {
1979         return;
1980       }
1981
1982       String str, format;
1983       try
1984       {
1985         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1986         if (str.length() < 1)
1987         {
1988           return;
1989         }
1990
1991         format = new IdentifyFile().identify(str, "Paste");
1992
1993       } catch (OutOfMemoryError er)
1994       {
1995         new OOMWarning("Out of memory pasting sequences!!", er);
1996         return;
1997       }
1998
1999       SequenceI[] sequences;
2000       boolean annotationAdded = false;
2001       AlignmentI alignment = null;
2002
2003       if (Desktop.jalviewClipboard != null)
2004       {
2005         // The clipboard was filled from within Jalview, we must use the
2006         // sequences
2007         // And dataset from the copied alignment
2008         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2009         // be doubly sure that we create *new* sequence objects.
2010         sequences = new SequenceI[newseq.length];
2011         for (int i = 0; i < newseq.length; i++)
2012         {
2013           sequences[i] = new Sequence(newseq[i]);
2014         }
2015         alignment = new Alignment(sequences);
2016         externalPaste = false;
2017       }
2018       else
2019       {
2020         // parse the clipboard as an alignment.
2021         alignment = new FormatAdapter().readFile(str, "Paste", format);
2022         sequences = alignment.getSequencesArray();
2023       }
2024
2025       int alwidth = 0;
2026       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2027       int fgroup = -1;
2028
2029       if (newAlignment)
2030       {
2031
2032         if (Desktop.jalviewClipboard != null)
2033         {
2034           // dataset is inherited
2035           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2036         }
2037         else
2038         {
2039           // new dataset is constructed
2040           alignment.setDataset(null);
2041         }
2042         alwidth = alignment.getWidth() + 1;
2043       }
2044       else
2045       {
2046         AlignmentI pastedal = alignment; // preserve pasted alignment object
2047         // Add pasted sequences and dataset into existing alignment.
2048         alignment = viewport.getAlignment();
2049         alwidth = alignment.getWidth() + 1;
2050         // decide if we need to import sequences from an existing dataset
2051         boolean importDs = Desktop.jalviewClipboard != null
2052                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2053         // importDs==true instructs us to copy over new dataset sequences from
2054         // an existing alignment
2055         Vector newDs = (importDs) ? new Vector() : null; // used to create
2056         // minimum dataset set
2057
2058         for (int i = 0; i < sequences.length; i++)
2059         {
2060           if (importDs)
2061           {
2062             newDs.addElement(null);
2063           }
2064           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2065           // paste
2066           if (importDs && ds != null)
2067           {
2068             if (!newDs.contains(ds))
2069             {
2070               newDs.setElementAt(ds, i);
2071               ds = new Sequence(ds);
2072               // update with new dataset sequence
2073               sequences[i].setDatasetSequence(ds);
2074             }
2075             else
2076             {
2077               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2078             }
2079           }
2080           else
2081           {
2082             // copy and derive new dataset sequence
2083             sequences[i] = sequences[i].deriveSequence();
2084             alignment.getDataset().addSequence(
2085                     sequences[i].getDatasetSequence());
2086             // TODO: avoid creation of duplicate dataset sequences with a
2087             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2088           }
2089           alignment.addSequence(sequences[i]); // merges dataset
2090         }
2091         if (newDs != null)
2092         {
2093           newDs.clear(); // tidy up
2094         }
2095         if (alignment.getAlignmentAnnotation() != null)
2096         {
2097           for (AlignmentAnnotation alan : alignment
2098                   .getAlignmentAnnotation())
2099           {
2100             if (alan.graphGroup > fgroup)
2101             {
2102               fgroup = alan.graphGroup;
2103             }
2104           }
2105         }
2106         if (pastedal.getAlignmentAnnotation() != null)
2107         {
2108           // Add any annotation attached to alignment.
2109           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2110           for (int i = 0; i < alann.length; i++)
2111           {
2112             annotationAdded = true;
2113             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2114             {
2115               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2116               if (newann.graphGroup > -1)
2117               {
2118                 if (newGraphGroups.size() <= newann.graphGroup
2119                         || newGraphGroups.get(newann.graphGroup) == null)
2120                 {
2121                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2122                   {
2123                     newGraphGroups.add(q, null);
2124                   }
2125                   newGraphGroups.set(newann.graphGroup, new Integer(
2126                           ++fgroup));
2127                 }
2128                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2129                         .intValue();
2130               }
2131
2132               newann.padAnnotation(alwidth);
2133               alignment.addAnnotation(newann);
2134             }
2135           }
2136         }
2137       }
2138       if (!newAlignment)
2139       {
2140         // /////
2141         // ADD HISTORY ITEM
2142         //
2143         addHistoryItem(new EditCommand(
2144                 MessageManager.getString("label.add_sequences"),
2145                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2146       }
2147       // Add any annotations attached to sequences
2148       for (int i = 0; i < sequences.length; i++)
2149       {
2150         if (sequences[i].getAnnotation() != null)
2151         {
2152           AlignmentAnnotation newann;
2153           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2154           {
2155             annotationAdded = true;
2156             newann = sequences[i].getAnnotation()[a];
2157             newann.adjustForAlignment();
2158             newann.padAnnotation(alwidth);
2159             if (newann.graphGroup > -1)
2160             {
2161               if (newann.graphGroup > -1)
2162               {
2163                 if (newGraphGroups.size() <= newann.graphGroup
2164                         || newGraphGroups.get(newann.graphGroup) == null)
2165                 {
2166                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2167                   {
2168                     newGraphGroups.add(q, null);
2169                   }
2170                   newGraphGroups.set(newann.graphGroup, new Integer(
2171                           ++fgroup));
2172                 }
2173                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2174                         .intValue();
2175               }
2176             }
2177             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2178             // was
2179             // duplicated
2180             // earlier
2181             alignment
2182                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2183           }
2184         }
2185       }
2186       if (!newAlignment)
2187       {
2188
2189         // propagate alignment changed.
2190         viewport.setEndSeq(alignment.getHeight());
2191         if (annotationAdded)
2192         {
2193           // Duplicate sequence annotation in all views.
2194           AlignmentI[] alview = this.getViewAlignments();
2195           for (int i = 0; i < sequences.length; i++)
2196           {
2197             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2198             if (sann == null)
2199             {
2200               continue;
2201             }
2202             for (int avnum = 0; avnum < alview.length; avnum++)
2203             {
2204               if (alview[avnum] != alignment)
2205               {
2206                 // duplicate in a view other than the one with input focus
2207                 int avwidth = alview[avnum].getWidth() + 1;
2208                 // this relies on sann being preserved after we
2209                 // modify the sequence's annotation array for each duplication
2210                 for (int a = 0; a < sann.length; a++)
2211                 {
2212                   AlignmentAnnotation newann = new AlignmentAnnotation(
2213                           sann[a]);
2214                   sequences[i].addAlignmentAnnotation(newann);
2215                   newann.padAnnotation(avwidth);
2216                   alview[avnum].addAnnotation(newann); // annotation was
2217                   // duplicated earlier
2218                   // TODO JAL-1145 graphGroups are not updated for sequence
2219                   // annotation added to several views. This may cause
2220                   // strangeness
2221                   alview[avnum].setAnnotationIndex(newann, a);
2222                 }
2223               }
2224             }
2225           }
2226           buildSortByAnnotationScoresMenu();
2227         }
2228         viewport.firePropertyChange("alignment", null,
2229                 alignment.getSequences());
2230         if (alignPanels != null)
2231         {
2232           for (AlignmentPanel ap : alignPanels)
2233           {
2234             ap.validateAnnotationDimensions(false);
2235           }
2236         }
2237         else
2238         {
2239           alignPanel.validateAnnotationDimensions(false);
2240         }
2241
2242       }
2243       else
2244       {
2245         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2246                 DEFAULT_HEIGHT);
2247         String newtitle = new String("Copied sequences");
2248
2249         if (Desktop.jalviewClipboard != null
2250                 && Desktop.jalviewClipboard[2] != null)
2251         {
2252           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2253           for (int[] region : hc)
2254           {
2255             af.viewport.hideColumns(region[0], region[1]);
2256           }
2257         }
2258
2259         // >>>This is a fix for the moment, until a better solution is
2260         // found!!<<<
2261         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2262                 .transferSettings(
2263                         alignPanel.getSeqPanel().seqCanvas
2264                                 .getFeatureRenderer());
2265
2266         // TODO: maintain provenance of an alignment, rather than just make the
2267         // title a concatenation of operations.
2268         if (!externalPaste)
2269         {
2270           if (title.startsWith("Copied sequences"))
2271           {
2272             newtitle = title;
2273           }
2274           else
2275           {
2276             newtitle = newtitle.concat("- from " + title);
2277           }
2278         }
2279         else
2280         {
2281           newtitle = new String("Pasted sequences");
2282         }
2283
2284         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2285                 DEFAULT_HEIGHT);
2286
2287       }
2288
2289     } catch (Exception ex)
2290     {
2291       ex.printStackTrace();
2292       System.out.println("Exception whilst pasting: " + ex);
2293       // could be anything being pasted in here
2294     }
2295
2296   }
2297
2298   @Override
2299   protected void expand_newalign(ActionEvent e)
2300   {
2301     try
2302     {
2303       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2304               .getAlignment(), -1);
2305       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2306               DEFAULT_HEIGHT);
2307       String newtitle = new String("Flanking alignment");
2308
2309       if (Desktop.jalviewClipboard != null
2310               && Desktop.jalviewClipboard[2] != null)
2311       {
2312         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2313         for (int region[] : hc)
2314         {
2315           af.viewport.hideColumns(region[0], region[1]);
2316         }
2317       }
2318
2319       // >>>This is a fix for the moment, until a better solution is
2320       // found!!<<<
2321       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2322               .transferSettings(
2323                       alignPanel.getSeqPanel().seqCanvas
2324                               .getFeatureRenderer());
2325
2326       // TODO: maintain provenance of an alignment, rather than just make the
2327       // title a concatenation of operations.
2328       {
2329         if (title.startsWith("Copied sequences"))
2330         {
2331           newtitle = title;
2332         }
2333         else
2334         {
2335           newtitle = newtitle.concat("- from " + title);
2336         }
2337       }
2338
2339       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2340
2341     } catch (Exception ex)
2342     {
2343       ex.printStackTrace();
2344       System.out.println("Exception whilst pasting: " + ex);
2345       // could be anything being pasted in here
2346     } catch (OutOfMemoryError oom)
2347     {
2348       new OOMWarning("Viewing flanking region of alignment", oom);
2349     }
2350   }
2351
2352   /**
2353    * DOCUMENT ME!
2354    *
2355    * @param e
2356    *          DOCUMENT ME!
2357    */
2358   @Override
2359   protected void cut_actionPerformed(ActionEvent e)
2360   {
2361     copy_actionPerformed(null);
2362     delete_actionPerformed(null);
2363   }
2364
2365   /**
2366    * DOCUMENT ME!
2367    *
2368    * @param e
2369    *          DOCUMENT ME!
2370    */
2371   @Override
2372   protected void delete_actionPerformed(ActionEvent evt)
2373   {
2374
2375     SequenceGroup sg = viewport.getSelectionGroup();
2376     if (sg == null)
2377     {
2378       return;
2379     }
2380
2381     /*
2382      * If the cut affects all sequences, warn, remove highlighted columns
2383      */
2384     if (sg.getSize() == viewport.getAlignment().getHeight())
2385     {
2386       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2387               .getAlignment().getWidth()) ? true : false;
2388       if (isEntireAlignWidth)
2389       {
2390         int confirm = JOptionPane.showConfirmDialog(this,
2391                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2392                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2393                 JOptionPane.OK_CANCEL_OPTION);
2394
2395         if (confirm == JOptionPane.CANCEL_OPTION
2396                 || confirm == JOptionPane.CLOSED_OPTION)
2397         {
2398           return;
2399         }
2400       }
2401       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2402               sg.getEndRes() + 1);
2403     }
2404     SequenceI[] cut = sg.getSequences()
2405             .toArray(new SequenceI[sg.getSize()]);
2406
2407     addHistoryItem(new EditCommand(
2408             MessageManager.getString("label.cut_sequences"), Action.CUT,
2409             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2410             viewport.getAlignment()));
2411
2412     viewport.setSelectionGroup(null);
2413     viewport.sendSelection();
2414     viewport.getAlignment().deleteGroup(sg);
2415
2416     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2417             .getSequences());
2418     if (viewport.getAlignment().getHeight() < 1)
2419     {
2420       try
2421       {
2422         this.setClosed(true);
2423       } catch (Exception ex)
2424       {
2425       }
2426     }
2427   }
2428
2429   /**
2430    * DOCUMENT ME!
2431    *
2432    * @param e
2433    *          DOCUMENT ME!
2434    */
2435   @Override
2436   protected void deleteGroups_actionPerformed(ActionEvent e)
2437   {
2438     if (avc.deleteGroups())
2439     {
2440       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2441       alignPanel.updateAnnotation();
2442       alignPanel.paintAlignment(true);
2443     }
2444   }
2445
2446   /**
2447    * DOCUMENT ME!
2448    *
2449    * @param e
2450    *          DOCUMENT ME!
2451    */
2452   @Override
2453   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2454   {
2455     SequenceGroup sg = new SequenceGroup();
2456
2457     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2458     {
2459       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2460     }
2461
2462     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2463     viewport.setSelectionGroup(sg);
2464     viewport.sendSelection();
2465     alignPanel.paintAlignment(true);
2466     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2467   }
2468
2469   /**
2470    * DOCUMENT ME!
2471    *
2472    * @param e
2473    *          DOCUMENT ME!
2474    */
2475   @Override
2476   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2477   {
2478     if (viewport.cursorMode)
2479     {
2480       alignPanel.getSeqPanel().keyboardNo1 = null;
2481       alignPanel.getSeqPanel().keyboardNo2 = null;
2482     }
2483     viewport.setSelectionGroup(null);
2484     viewport.getColumnSelection().clear();
2485     viewport.setSelectionGroup(null);
2486     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2487     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2488     alignPanel.paintAlignment(true);
2489     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2490     viewport.sendSelection();
2491   }
2492
2493   /**
2494    * DOCUMENT ME!
2495    *
2496    * @param e
2497    *          DOCUMENT ME!
2498    */
2499   @Override
2500   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2501   {
2502     SequenceGroup sg = viewport.getSelectionGroup();
2503
2504     if (sg == null)
2505     {
2506       selectAllSequenceMenuItem_actionPerformed(null);
2507
2508       return;
2509     }
2510
2511     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2512     {
2513       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2514     }
2515
2516     alignPanel.paintAlignment(true);
2517     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2518     viewport.sendSelection();
2519   }
2520
2521   @Override
2522   public void invertColSel_actionPerformed(ActionEvent e)
2523   {
2524     viewport.invertColumnSelection();
2525     alignPanel.paintAlignment(true);
2526     viewport.sendSelection();
2527   }
2528
2529   /**
2530    * DOCUMENT ME!
2531    *
2532    * @param e
2533    *          DOCUMENT ME!
2534    */
2535   @Override
2536   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2537   {
2538     trimAlignment(true);
2539   }
2540
2541   /**
2542    * DOCUMENT ME!
2543    *
2544    * @param e
2545    *          DOCUMENT ME!
2546    */
2547   @Override
2548   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2549   {
2550     trimAlignment(false);
2551   }
2552
2553   void trimAlignment(boolean trimLeft)
2554   {
2555     ColumnSelection colSel = viewport.getColumnSelection();
2556     int column;
2557
2558     if (!colSel.isEmpty())
2559     {
2560       if (trimLeft)
2561       {
2562         column = colSel.getMin();
2563       }
2564       else
2565       {
2566         column = colSel.getMax();
2567       }
2568
2569       SequenceI[] seqs;
2570       if (viewport.getSelectionGroup() != null)
2571       {
2572         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2573                 viewport.getHiddenRepSequences());
2574       }
2575       else
2576       {
2577         seqs = viewport.getAlignment().getSequencesArray();
2578       }
2579
2580       TrimRegionCommand trimRegion;
2581       if (trimLeft)
2582       {
2583         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2584                 column, viewport.getAlignment());
2585         viewport.setStartRes(0);
2586       }
2587       else
2588       {
2589         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2590                 column, viewport.getAlignment());
2591       }
2592
2593       statusBar.setText(MessageManager.formatMessage(
2594               "label.removed_columns",
2595               new String[] { Integer.valueOf(trimRegion.getSize())
2596                       .toString() }));
2597
2598       addHistoryItem(trimRegion);
2599
2600       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2601       {
2602         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2603                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2604         {
2605           viewport.getAlignment().deleteGroup(sg);
2606         }
2607       }
2608
2609       viewport.firePropertyChange("alignment", null, viewport
2610               .getAlignment().getSequences());
2611     }
2612   }
2613
2614   /**
2615    * DOCUMENT ME!
2616    *
2617    * @param e
2618    *          DOCUMENT ME!
2619    */
2620   @Override
2621   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2622   {
2623     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2624
2625     SequenceI[] seqs;
2626     if (viewport.getSelectionGroup() != null)
2627     {
2628       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2629               viewport.getHiddenRepSequences());
2630       start = viewport.getSelectionGroup().getStartRes();
2631       end = viewport.getSelectionGroup().getEndRes();
2632     }
2633     else
2634     {
2635       seqs = viewport.getAlignment().getSequencesArray();
2636     }
2637
2638     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2639             "Remove Gapped Columns", seqs, start, end,
2640             viewport.getAlignment());
2641
2642     addHistoryItem(removeGapCols);
2643
2644     statusBar.setText(MessageManager.formatMessage(
2645             "label.removed_empty_columns",
2646             new Object[] { Integer.valueOf(removeGapCols.getSize())
2647                     .toString() }));
2648
2649     // This is to maintain viewport position on first residue
2650     // of first sequence
2651     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2652     int startRes = seq.findPosition(viewport.startRes);
2653     // ShiftList shifts;
2654     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2655     // edit.alColumnChanges=shifts.getInverse();
2656     // if (viewport.hasHiddenColumns)
2657     // viewport.getColumnSelection().compensateForEdits(shifts);
2658     viewport.setStartRes(seq.findIndex(startRes) - 1);
2659     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2660             .getSequences());
2661
2662   }
2663
2664   /**
2665    * DOCUMENT ME!
2666    *
2667    * @param e
2668    *          DOCUMENT ME!
2669    */
2670   @Override
2671   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2672   {
2673     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2674
2675     SequenceI[] seqs;
2676     if (viewport.getSelectionGroup() != null)
2677     {
2678       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2679               viewport.getHiddenRepSequences());
2680       start = viewport.getSelectionGroup().getStartRes();
2681       end = viewport.getSelectionGroup().getEndRes();
2682     }
2683     else
2684     {
2685       seqs = viewport.getAlignment().getSequencesArray();
2686     }
2687
2688     // This is to maintain viewport position on first residue
2689     // of first sequence
2690     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2691     int startRes = seq.findPosition(viewport.startRes);
2692
2693     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2694             viewport.getAlignment()));
2695
2696     viewport.setStartRes(seq.findIndex(startRes) - 1);
2697
2698     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2699             .getSequences());
2700
2701   }
2702
2703   /**
2704    * DOCUMENT ME!
2705    *
2706    * @param e
2707    *          DOCUMENT ME!
2708    */
2709   @Override
2710   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2711   {
2712     viewport.setPadGaps(padGapsMenuitem.isSelected());
2713     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2714             .getSequences());
2715   }
2716
2717   /**
2718    * DOCUMENT ME!
2719    *
2720    * @param e
2721    *          DOCUMENT ME!
2722    */
2723   @Override
2724   public void findMenuItem_actionPerformed(ActionEvent e)
2725   {
2726     new Finder();
2727   }
2728
2729   /**
2730    * Create a new view of the current alignment.
2731    */
2732   @Override
2733   public void newView_actionPerformed(ActionEvent e)
2734   {
2735     newView(null, true);
2736   }
2737
2738   /**
2739    * Creates and shows a new view of the current alignment.
2740    *
2741    * @param viewTitle
2742    *          title of newly created view; if null, one will be generated
2743    * @param copyAnnotation
2744    *          if true then duplicate all annnotation, groups and settings
2745    * @return new alignment panel, already displayed.
2746    */
2747   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2748   {
2749     /*
2750      * Create a new AlignmentPanel (with its own, new Viewport)
2751      */
2752     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2753             true);
2754     if (!copyAnnotation)
2755     {
2756       /*
2757        * remove all groups and annotation except for the automatic stuff
2758        */
2759       newap.av.getAlignment().deleteAllGroups();
2760       newap.av.getAlignment().deleteAllAnnotations(false);
2761     }
2762
2763     newap.av.setGatherViewsHere(false);
2764
2765     if (viewport.viewName == null)
2766     {
2767       viewport.viewName = MessageManager
2768               .getString("label.view_name_original");
2769     }
2770
2771     /*
2772      * Views share the same edits undo and redo stacks
2773      */
2774     newap.av.setHistoryList(viewport.getHistoryList());
2775     newap.av.setRedoList(viewport.getRedoList());
2776
2777     /*
2778      * Views share the same mappings; need to deregister any new mappings
2779      * created by copyAlignPanel, and register the new reference to the shared
2780      * mappings
2781      */
2782     newap.av.replaceMappings(viewport.getAlignment());
2783
2784     newap.av.viewName = getNewViewName(viewTitle);
2785
2786     addAlignmentPanel(newap, true);
2787     newap.alignmentChanged();
2788
2789     if (alignPanels.size() == 2)
2790     {
2791       viewport.setGatherViewsHere(true);
2792     }
2793     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2794     return newap;
2795   }
2796
2797   /**
2798    * Make a new name for the view, ensuring it is unique within the current
2799    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2800    * these now use viewId. Unique view names are still desirable for usability.)
2801    *
2802    * @param viewTitle
2803    * @return
2804    */
2805   protected String getNewViewName(String viewTitle)
2806   {
2807     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2808     boolean addFirstIndex = false;
2809     if (viewTitle == null || viewTitle.trim().length() == 0)
2810     {
2811       viewTitle = MessageManager.getString("action.view");
2812       addFirstIndex = true;
2813     }
2814     else
2815     {
2816       index = 1;// we count from 1 if given a specific name
2817     }
2818     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2819
2820     List<Component> comps = PaintRefresher.components.get(viewport
2821             .getSequenceSetId());
2822
2823     List<String> existingNames = getExistingViewNames(comps);
2824
2825     while (existingNames.contains(newViewName))
2826     {
2827       newViewName = viewTitle + " " + (++index);
2828     }
2829     return newViewName;
2830   }
2831
2832   /**
2833    * Returns a list of distinct view names found in the given list of
2834    * components. View names are held on the viewport of an AlignmentPanel.
2835    *
2836    * @param comps
2837    * @return
2838    */
2839   protected List<String> getExistingViewNames(List<Component> comps)
2840   {
2841     List<String> existingNames = new ArrayList<String>();
2842     for (Component comp : comps)
2843     {
2844       if (comp instanceof AlignmentPanel)
2845       {
2846         AlignmentPanel ap = (AlignmentPanel) comp;
2847         if (!existingNames.contains(ap.av.viewName))
2848         {
2849           existingNames.add(ap.av.viewName);
2850         }
2851       }
2852     }
2853     return existingNames;
2854   }
2855
2856   /**
2857    * Explode tabbed views into separate windows.
2858    */
2859   @Override
2860   public void expandViews_actionPerformed(ActionEvent e)
2861   {
2862     Desktop.instance.explodeViews(this);
2863   }
2864
2865   /**
2866    * Gather views in separate windows back into a tabbed presentation.
2867    */
2868   @Override
2869   public void gatherViews_actionPerformed(ActionEvent e)
2870   {
2871     Desktop.instance.gatherViews(this);
2872   }
2873
2874   /**
2875    * DOCUMENT ME!
2876    *
2877    * @param e
2878    *          DOCUMENT ME!
2879    */
2880   @Override
2881   public void font_actionPerformed(ActionEvent e)
2882   {
2883     new FontChooser(alignPanel);
2884   }
2885
2886   /**
2887    * DOCUMENT ME!
2888    *
2889    * @param e
2890    *          DOCUMENT ME!
2891    */
2892   @Override
2893   protected void seqLimit_actionPerformed(ActionEvent e)
2894   {
2895     viewport.setShowJVSuffix(seqLimits.isSelected());
2896
2897     alignPanel.getIdPanel().getIdCanvas()
2898             .setPreferredSize(alignPanel.calculateIdWidth());
2899     alignPanel.paintAlignment(true);
2900   }
2901
2902   @Override
2903   public void idRightAlign_actionPerformed(ActionEvent e)
2904   {
2905     viewport.setRightAlignIds(idRightAlign.isSelected());
2906     alignPanel.paintAlignment(true);
2907   }
2908
2909   @Override
2910   public void centreColumnLabels_actionPerformed(ActionEvent e)
2911   {
2912     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2913     alignPanel.paintAlignment(true);
2914   }
2915
2916   /*
2917    * (non-Javadoc)
2918    *
2919    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2920    */
2921   @Override
2922   protected void followHighlight_actionPerformed()
2923   {
2924     /*
2925      * Set the 'follow' flag on the Viewport (and scroll to position if now
2926      * true).
2927      */
2928     final boolean state = this.followHighlightMenuItem.getState();
2929     viewport.setFollowHighlight(state);
2930     if (state)
2931     {
2932       alignPanel.scrollToPosition(
2933               alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2934     }
2935   }
2936
2937   /**
2938    * DOCUMENT ME!
2939    *
2940    * @param e
2941    *          DOCUMENT ME!
2942    */
2943   @Override
2944   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2945   {
2946     viewport.setColourText(colourTextMenuItem.isSelected());
2947     alignPanel.paintAlignment(true);
2948   }
2949
2950   /**
2951    * DOCUMENT ME!
2952    *
2953    * @param e
2954    *          DOCUMENT ME!
2955    */
2956   @Override
2957   public void wrapMenuItem_actionPerformed(ActionEvent e)
2958   {
2959     scaleAbove.setVisible(wrapMenuItem.isSelected());
2960     scaleLeft.setVisible(wrapMenuItem.isSelected());
2961     scaleRight.setVisible(wrapMenuItem.isSelected());
2962     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2963     alignPanel.updateLayout();
2964   }
2965
2966   @Override
2967   public void showAllSeqs_actionPerformed(ActionEvent e)
2968   {
2969     viewport.showAllHiddenSeqs();
2970   }
2971
2972   @Override
2973   public void showAllColumns_actionPerformed(ActionEvent e)
2974   {
2975     viewport.showAllHiddenColumns();
2976     repaint();
2977     viewport.sendSelection();
2978   }
2979
2980   @Override
2981   public void hideSelSequences_actionPerformed(ActionEvent e)
2982   {
2983     viewport.hideAllSelectedSeqs();
2984     // alignPanel.paintAlignment(true);
2985   }
2986
2987   /**
2988    * called by key handler and the hide all/show all menu items
2989    *
2990    * @param toggleSeqs
2991    * @param toggleCols
2992    */
2993   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2994   {
2995
2996     boolean hide = false;
2997     SequenceGroup sg = viewport.getSelectionGroup();
2998     if (!toggleSeqs && !toggleCols)
2999     {
3000       // Hide everything by the current selection - this is a hack - we do the
3001       // invert and then hide
3002       // first check that there will be visible columns after the invert.
3003       if ((viewport.getColumnSelection() != null
3004               && viewport.getColumnSelection().getSelected() != null && viewport
3005               .getColumnSelection().getSelected().size() > 0)
3006               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3007                       .getEndRes()))
3008       {
3009         // now invert the sequence set, if required - empty selection implies
3010         // that no hiding is required.
3011         if (sg != null)
3012         {
3013           invertSequenceMenuItem_actionPerformed(null);
3014           sg = viewport.getSelectionGroup();
3015           toggleSeqs = true;
3016
3017         }
3018         viewport.expandColSelection(sg, true);
3019         // finally invert the column selection and get the new sequence
3020         // selection.
3021         invertColSel_actionPerformed(null);
3022         toggleCols = true;
3023       }
3024     }
3025
3026     if (toggleSeqs)
3027     {
3028       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3029       {
3030         hideSelSequences_actionPerformed(null);
3031         hide = true;
3032       }
3033       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3034               .size() > 0))
3035       {
3036         showAllSeqs_actionPerformed(null);
3037       }
3038     }
3039
3040     if (toggleCols)
3041     {
3042       if (viewport.getColumnSelection().getSelected().size() > 0)
3043       {
3044         hideSelColumns_actionPerformed(null);
3045         if (!toggleSeqs)
3046         {
3047           viewport.setSelectionGroup(sg);
3048         }
3049       }
3050       else if (!hide)
3051       {
3052         showAllColumns_actionPerformed(null);
3053       }
3054     }
3055   }
3056
3057   /*
3058    * (non-Javadoc)
3059    *
3060    * @see
3061    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3062    * event.ActionEvent)
3063    */
3064   @Override
3065   public void hideAllButSelection_actionPerformed(ActionEvent e)
3066   {
3067     toggleHiddenRegions(false, false);
3068     viewport.sendSelection();
3069   }
3070
3071   /*
3072    * (non-Javadoc)
3073    *
3074    * @see
3075    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3076    * .ActionEvent)
3077    */
3078   @Override
3079   public void hideAllSelection_actionPerformed(ActionEvent e)
3080   {
3081     SequenceGroup sg = viewport.getSelectionGroup();
3082     viewport.expandColSelection(sg, false);
3083     viewport.hideAllSelectedSeqs();
3084     viewport.hideSelectedColumns();
3085     alignPanel.paintAlignment(true);
3086     viewport.sendSelection();
3087   }
3088
3089   /*
3090    * (non-Javadoc)
3091    *
3092    * @see
3093    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3094    * ActionEvent)
3095    */
3096   @Override
3097   public void showAllhidden_actionPerformed(ActionEvent e)
3098   {
3099     viewport.showAllHiddenColumns();
3100     viewport.showAllHiddenSeqs();
3101     alignPanel.paintAlignment(true);
3102     viewport.sendSelection();
3103   }
3104
3105   @Override
3106   public void hideSelColumns_actionPerformed(ActionEvent e)
3107   {
3108     viewport.hideSelectedColumns();
3109     alignPanel.paintAlignment(true);
3110     viewport.sendSelection();
3111   }
3112
3113   @Override
3114   public void hiddenMarkers_actionPerformed(ActionEvent e)
3115   {
3116     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3117     repaint();
3118   }
3119
3120   /**
3121    * DOCUMENT ME!
3122    *
3123    * @param e
3124    *          DOCUMENT ME!
3125    */
3126   @Override
3127   protected void scaleAbove_actionPerformed(ActionEvent e)
3128   {
3129     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3130     alignPanel.paintAlignment(true);
3131   }
3132
3133   /**
3134    * DOCUMENT ME!
3135    *
3136    * @param e
3137    *          DOCUMENT ME!
3138    */
3139   @Override
3140   protected void scaleLeft_actionPerformed(ActionEvent e)
3141   {
3142     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3143     alignPanel.paintAlignment(true);
3144   }
3145
3146   /**
3147    * DOCUMENT ME!
3148    *
3149    * @param e
3150    *          DOCUMENT ME!
3151    */
3152   @Override
3153   protected void scaleRight_actionPerformed(ActionEvent e)
3154   {
3155     viewport.setScaleRightWrapped(scaleRight.isSelected());
3156     alignPanel.paintAlignment(true);
3157   }
3158
3159   /**
3160    * DOCUMENT ME!
3161    *
3162    * @param e
3163    *          DOCUMENT ME!
3164    */
3165   @Override
3166   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3167   {
3168     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3169     alignPanel.paintAlignment(true);
3170   }
3171
3172   /**
3173    * DOCUMENT ME!
3174    *
3175    * @param e
3176    *          DOCUMENT ME!
3177    */
3178   @Override
3179   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3180   {
3181     viewport.setShowText(viewTextMenuItem.isSelected());
3182     alignPanel.paintAlignment(true);
3183   }
3184
3185   /**
3186    * DOCUMENT ME!
3187    *
3188    * @param e
3189    *          DOCUMENT ME!
3190    */
3191   @Override
3192   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3193   {
3194     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3195     alignPanel.paintAlignment(true);
3196   }
3197
3198   public FeatureSettings featureSettings;
3199
3200   @Override
3201   public FeatureSettingsControllerI getFeatureSettingsUI()
3202   {
3203     return featureSettings;
3204   }
3205
3206   @Override
3207   public void featureSettings_actionPerformed(ActionEvent e)
3208   {
3209     if (featureSettings != null)
3210     {
3211       featureSettings.close();
3212       featureSettings = null;
3213     }
3214     if (!showSeqFeatures.isSelected())
3215     {
3216       // make sure features are actually displayed
3217       showSeqFeatures.setSelected(true);
3218       showSeqFeatures_actionPerformed(null);
3219     }
3220     featureSettings = new FeatureSettings(this);
3221   }
3222
3223   /**
3224    * Set or clear 'Show Sequence Features'
3225    *
3226    * @param evt
3227    *          DOCUMENT ME!
3228    */
3229   @Override
3230   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3231   {
3232     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3233     alignPanel.paintAlignment(true);
3234     if (alignPanel.getOverviewPanel() != null)
3235     {
3236       alignPanel.getOverviewPanel().updateOverviewImage();
3237     }
3238   }
3239
3240   /**
3241    * Set or clear 'Show Sequence Features'
3242    *
3243    * @param evt
3244    *          DOCUMENT ME!
3245    */
3246   @Override
3247   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3248   {
3249     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3250             .isSelected());
3251     if (viewport.isShowSequenceFeaturesHeight())
3252     {
3253       // ensure we're actually displaying features
3254       viewport.setShowSequenceFeatures(true);
3255       showSeqFeatures.setSelected(true);
3256     }
3257     alignPanel.paintAlignment(true);
3258     if (alignPanel.getOverviewPanel() != null)
3259     {
3260       alignPanel.getOverviewPanel().updateOverviewImage();
3261     }
3262   }
3263
3264   /**
3265    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3266    * the annotations panel as a whole.
3267    *
3268    * The options to show/hide all annotations should be enabled when the panel
3269    * is shown, and disabled when the panel is hidden.
3270    *
3271    * @param e
3272    */
3273   @Override
3274   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3275   {
3276     final boolean setVisible = annotationPanelMenuItem.isSelected();
3277     viewport.setShowAnnotation(setVisible);
3278     this.showAllSeqAnnotations.setEnabled(setVisible);
3279     this.hideAllSeqAnnotations.setEnabled(setVisible);
3280     this.showAllAlAnnotations.setEnabled(setVisible);
3281     this.hideAllAlAnnotations.setEnabled(setVisible);
3282     alignPanel.updateLayout();
3283   }
3284
3285   @Override
3286   public void alignmentProperties()
3287   {
3288     JEditorPane editPane = new JEditorPane("text/html", "");
3289     editPane.setEditable(false);
3290     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3291             .formatAsHtml();
3292     editPane.setText(MessageManager.formatMessage("label.html_content",
3293             new Object[] { contents.toString() }));
3294     JInternalFrame frame = new JInternalFrame();
3295     frame.getContentPane().add(new JScrollPane(editPane));
3296
3297     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3298             "label.alignment_properties", new Object[] { getTitle() }),
3299             500, 400);
3300   }
3301
3302   /**
3303    * DOCUMENT ME!
3304    *
3305    * @param e
3306    *          DOCUMENT ME!
3307    */
3308   @Override
3309   public void overviewMenuItem_actionPerformed(ActionEvent e)
3310   {
3311     if (alignPanel.overviewPanel != null)
3312     {
3313       return;
3314     }
3315
3316     JInternalFrame frame = new JInternalFrame();
3317     OverviewPanel overview = new OverviewPanel(alignPanel);
3318     frame.setContentPane(overview);
3319     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3320             "label.overview_params", new Object[] { this.getTitle() }),
3321             frame.getWidth(), frame.getHeight());
3322     frame.pack();
3323     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3324     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3325     {
3326       @Override
3327       public void internalFrameClosed(
3328               javax.swing.event.InternalFrameEvent evt)
3329       {
3330         alignPanel.setOverviewPanel(null);
3331       };
3332     });
3333
3334     alignPanel.setOverviewPanel(overview);
3335   }
3336
3337   @Override
3338   public void textColour_actionPerformed(ActionEvent e)
3339   {
3340     new TextColourChooser().chooseColour(alignPanel, null);
3341   }
3342
3343   /**
3344    * DOCUMENT ME!
3345    *
3346    * @param e
3347    *          DOCUMENT ME!
3348    */
3349   @Override
3350   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3351   {
3352     changeColour(null);
3353   }
3354
3355   /**
3356    * DOCUMENT ME!
3357    *
3358    * @param e
3359    *          DOCUMENT ME!
3360    */
3361   @Override
3362   public void clustalColour_actionPerformed(ActionEvent e)
3363   {
3364     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3365             viewport.getHiddenRepSequences()));
3366   }
3367
3368   /**
3369    * DOCUMENT ME!
3370    *
3371    * @param e
3372    *          DOCUMENT ME!
3373    */
3374   @Override
3375   public void zappoColour_actionPerformed(ActionEvent e)
3376   {
3377     changeColour(new ZappoColourScheme());
3378   }
3379
3380   /**
3381    * DOCUMENT ME!
3382    *
3383    * @param e
3384    *          DOCUMENT ME!
3385    */
3386   @Override
3387   public void taylorColour_actionPerformed(ActionEvent e)
3388   {
3389     changeColour(new TaylorColourScheme());
3390   }
3391
3392   /**
3393    * DOCUMENT ME!
3394    *
3395    * @param e
3396    *          DOCUMENT ME!
3397    */
3398   @Override
3399   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3400   {
3401     changeColour(new HydrophobicColourScheme());
3402   }
3403
3404   /**
3405    * DOCUMENT ME!
3406    *
3407    * @param e
3408    *          DOCUMENT ME!
3409    */
3410   @Override
3411   public void helixColour_actionPerformed(ActionEvent e)
3412   {
3413     changeColour(new HelixColourScheme());
3414   }
3415
3416   /**
3417    * DOCUMENT ME!
3418    *
3419    * @param e
3420    *          DOCUMENT ME!
3421    */
3422   @Override
3423   public void strandColour_actionPerformed(ActionEvent e)
3424   {
3425     changeColour(new StrandColourScheme());
3426   }
3427
3428   /**
3429    * DOCUMENT ME!
3430    *
3431    * @param e
3432    *          DOCUMENT ME!
3433    */
3434   @Override
3435   public void turnColour_actionPerformed(ActionEvent e)
3436   {
3437     changeColour(new TurnColourScheme());
3438   }
3439
3440   /**
3441    * DOCUMENT ME!
3442    *
3443    * @param e
3444    *          DOCUMENT ME!
3445    */
3446   @Override
3447   public void buriedColour_actionPerformed(ActionEvent e)
3448   {
3449     changeColour(new BuriedColourScheme());
3450   }
3451
3452   /**
3453    * DOCUMENT ME!
3454    *
3455    * @param e
3456    *          DOCUMENT ME!
3457    */
3458   @Override
3459   public void nucleotideColour_actionPerformed(ActionEvent e)
3460   {
3461     changeColour(new NucleotideColourScheme());
3462   }
3463
3464   @Override
3465   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3466   {
3467     changeColour(new PurinePyrimidineColourScheme());
3468   }
3469
3470   /*
3471    * public void covariationColour_actionPerformed(ActionEvent e) {
3472    * changeColour(new
3473    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3474    * ()[0])); }
3475    */
3476   @Override
3477   public void annotationColour_actionPerformed(ActionEvent e)
3478   {
3479     new AnnotationColourChooser(viewport, alignPanel);
3480   }
3481
3482   @Override
3483   public void annotationColumn_actionPerformed(ActionEvent e)
3484   {
3485     new AnnotationColumnChooser(viewport, alignPanel);
3486   }
3487
3488   @Override
3489   public void rnahelicesColour_actionPerformed(ActionEvent e)
3490   {
3491     new RNAHelicesColourChooser(viewport, alignPanel);
3492   }
3493
3494   /**
3495    * DOCUMENT ME!
3496    *
3497    * @param e
3498    *          DOCUMENT ME!
3499    */
3500   @Override
3501   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3502   {
3503     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3504   }
3505
3506   /**
3507    * DOCUMENT ME!
3508    *
3509    * @param cs
3510    *          DOCUMENT ME!
3511    */
3512   @Override
3513   public void changeColour(ColourSchemeI cs)
3514   {
3515     // TODO: pull up to controller method
3516
3517     if (cs != null)
3518     {
3519       // Make sure viewport is up to date w.r.t. any sliders
3520       if (viewport.getAbovePIDThreshold())
3521       {
3522         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3523                 "Background");
3524         viewport.setThreshold(threshold);
3525       }
3526
3527       if (viewport.getConservationSelected())
3528       {
3529         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3530                 cs, "Background"));
3531       }
3532       if (cs instanceof TCoffeeColourScheme)
3533       {
3534         tcoffeeColour.setEnabled(true);
3535         tcoffeeColour.setSelected(true);
3536       }
3537     }
3538
3539     viewport.setGlobalColourScheme(cs);
3540
3541     alignPanel.paintAlignment(true);
3542   }
3543
3544   /**
3545    * DOCUMENT ME!
3546    *
3547    * @param e
3548    *          DOCUMENT ME!
3549    */
3550   @Override
3551   protected void modifyPID_actionPerformed(ActionEvent e)
3552   {
3553     if (viewport.getAbovePIDThreshold()
3554             && viewport.getGlobalColourScheme() != null)
3555     {
3556       SliderPanel.setPIDSliderSource(alignPanel,
3557               viewport.getGlobalColourScheme(), "Background");
3558       SliderPanel.showPIDSlider();
3559     }
3560   }
3561
3562   /**
3563    * DOCUMENT ME!
3564    *
3565    * @param e
3566    *          DOCUMENT ME!
3567    */
3568   @Override
3569   protected void modifyConservation_actionPerformed(ActionEvent e)
3570   {
3571     if (viewport.getConservationSelected()
3572             && viewport.getGlobalColourScheme() != null)
3573     {
3574       SliderPanel.setConservationSlider(alignPanel,
3575               viewport.getGlobalColourScheme(), "Background");
3576       SliderPanel.showConservationSlider();
3577     }
3578   }
3579
3580   /**
3581    * DOCUMENT ME!
3582    *
3583    * @param e
3584    *          DOCUMENT ME!
3585    */
3586   @Override
3587   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3588   {
3589     viewport.setConservationSelected(conservationMenuItem.isSelected());
3590
3591     viewport.setAbovePIDThreshold(false);
3592     abovePIDThreshold.setSelected(false);
3593
3594     changeColour(viewport.getGlobalColourScheme());
3595
3596     modifyConservation_actionPerformed(null);
3597   }
3598
3599   /**
3600    * DOCUMENT ME!
3601    *
3602    * @param e
3603    *          DOCUMENT ME!
3604    */
3605   @Override
3606   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3607   {
3608     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3609
3610     conservationMenuItem.setSelected(false);
3611     viewport.setConservationSelected(false);
3612
3613     changeColour(viewport.getGlobalColourScheme());
3614
3615     modifyPID_actionPerformed(null);
3616   }
3617
3618   /**
3619    * DOCUMENT ME!
3620    *
3621    * @param e
3622    *          DOCUMENT ME!
3623    */
3624   @Override
3625   public void userDefinedColour_actionPerformed(ActionEvent e)
3626   {
3627     if (e.getActionCommand().equals(
3628             MessageManager.getString("action.user_defined")))
3629     {
3630       new UserDefinedColours(alignPanel, null);
3631     }
3632     else
3633     {
3634       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3635               .getUserColourSchemes().get(e.getActionCommand());
3636
3637       changeColour(udc);
3638     }
3639   }
3640
3641   public void updateUserColourMenu()
3642   {
3643
3644     Component[] menuItems = colourMenu.getMenuComponents();
3645     int iSize = menuItems.length;
3646     for (int i = 0; i < iSize; i++)
3647     {
3648       if (menuItems[i].getName() != null
3649               && menuItems[i].getName().equals("USER_DEFINED"))
3650       {
3651         colourMenu.remove(menuItems[i]);
3652         iSize--;
3653       }
3654     }
3655     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3656     {
3657       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3658               .getUserColourSchemes().keys();
3659
3660       while (userColours.hasMoreElements())
3661       {
3662         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3663                 userColours.nextElement().toString());
3664         radioItem.setName("USER_DEFINED");
3665         radioItem.addMouseListener(new MouseAdapter()
3666         {
3667           @Override
3668           public void mousePressed(MouseEvent evt)
3669           {
3670             if (evt.isControlDown()
3671                     || SwingUtilities.isRightMouseButton(evt))
3672             {
3673               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3674
3675               int option = JOptionPane.showInternalConfirmDialog(
3676                       jalview.gui.Desktop.desktop,
3677                       MessageManager
3678                               .getString("label.remove_from_default_list"),
3679                       MessageManager
3680                               .getString("label.remove_user_defined_colour"),
3681                       JOptionPane.YES_NO_OPTION);
3682               if (option == JOptionPane.YES_OPTION)
3683               {
3684                 jalview.gui.UserDefinedColours
3685                         .removeColourFromDefaults(radioItem.getText());
3686                 colourMenu.remove(radioItem);
3687               }
3688               else
3689               {
3690                 radioItem.addActionListener(new ActionListener()
3691                 {
3692                   @Override
3693                   public void actionPerformed(ActionEvent evt)
3694                   {
3695                     userDefinedColour_actionPerformed(evt);
3696                   }
3697                 });
3698               }
3699             }
3700           }
3701         });
3702         radioItem.addActionListener(new ActionListener()
3703         {
3704           @Override
3705           public void actionPerformed(ActionEvent evt)
3706           {
3707             userDefinedColour_actionPerformed(evt);
3708           }
3709         });
3710
3711         colourMenu.insert(radioItem, 15);
3712         colours.add(radioItem);
3713       }
3714     }
3715   }
3716
3717   /**
3718    * DOCUMENT ME!
3719    *
3720    * @param e
3721    *          DOCUMENT ME!
3722    */
3723   @Override
3724   public void PIDColour_actionPerformed(ActionEvent e)
3725   {
3726     changeColour(new PIDColourScheme());
3727   }
3728
3729   /**
3730    * DOCUMENT ME!
3731    *
3732    * @param e
3733    *          DOCUMENT ME!
3734    */
3735   @Override
3736   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3737   {
3738     changeColour(new Blosum62ColourScheme());
3739   }
3740
3741   /**
3742    * DOCUMENT ME!
3743    *
3744    * @param e
3745    *          DOCUMENT ME!
3746    */
3747   @Override
3748   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3749   {
3750     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3752             .getAlignment().getSequenceAt(0), null);
3753     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3754             viewport.getAlignment()));
3755     alignPanel.paintAlignment(true);
3756   }
3757
3758   /**
3759    * DOCUMENT ME!
3760    *
3761    * @param e
3762    *          DOCUMENT ME!
3763    */
3764   @Override
3765   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3766   {
3767     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3768     AlignmentSorter.sortByID(viewport.getAlignment());
3769     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3770             viewport.getAlignment()));
3771     alignPanel.paintAlignment(true);
3772   }
3773
3774   /**
3775    * DOCUMENT ME!
3776    *
3777    * @param e
3778    *          DOCUMENT ME!
3779    */
3780   @Override
3781   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3782   {
3783     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3784     AlignmentSorter.sortByLength(viewport.getAlignment());
3785     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3786             viewport.getAlignment()));
3787     alignPanel.paintAlignment(true);
3788   }
3789
3790   /**
3791    * DOCUMENT ME!
3792    *
3793    * @param e
3794    *          DOCUMENT ME!
3795    */
3796   @Override
3797   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3798   {
3799     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3800     AlignmentSorter.sortByGroup(viewport.getAlignment());
3801     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3802             viewport.getAlignment()));
3803
3804     alignPanel.paintAlignment(true);
3805   }
3806
3807   /**
3808    * DOCUMENT ME!
3809    *
3810    * @param e
3811    *          DOCUMENT ME!
3812    */
3813   @Override
3814   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3815   {
3816     new RedundancyPanel(alignPanel, this);
3817   }
3818
3819   /**
3820    * DOCUMENT ME!
3821    *
3822    * @param e
3823    *          DOCUMENT ME!
3824    */
3825   @Override
3826   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3827   {
3828     if ((viewport.getSelectionGroup() == null)
3829             || (viewport.getSelectionGroup().getSize() < 2))
3830     {
3831       JOptionPane.showInternalMessageDialog(this, MessageManager
3832               .getString("label.you_must_select_least_two_sequences"),
3833               MessageManager.getString("label.invalid_selection"),
3834               JOptionPane.WARNING_MESSAGE);
3835     }
3836     else
3837     {
3838       JInternalFrame frame = new JInternalFrame();
3839       frame.setContentPane(new PairwiseAlignPanel(viewport));
3840       Desktop.addInternalFrame(frame,
3841               MessageManager.getString("action.pairwise_alignment"), 600,
3842               500);
3843     }
3844   }
3845
3846   /**
3847    * DOCUMENT ME!
3848    *
3849    * @param e
3850    *          DOCUMENT ME!
3851    */
3852   @Override
3853   public void PCAMenuItem_actionPerformed(ActionEvent e)
3854   {
3855     if (((viewport.getSelectionGroup() != null)
3856             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3857             .getSelectionGroup().getSize() > 0))
3858             || (viewport.getAlignment().getHeight() < 4))
3859     {
3860       JOptionPane
3861               .showInternalMessageDialog(
3862                       this,
3863                       MessageManager
3864                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3865                       MessageManager
3866                               .getString("label.sequence_selection_insufficient"),
3867                       JOptionPane.WARNING_MESSAGE);
3868
3869       return;
3870     }
3871
3872     new PCAPanel(alignPanel);
3873   }
3874
3875   @Override
3876   public void autoCalculate_actionPerformed(ActionEvent e)
3877   {
3878     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3879     if (viewport.autoCalculateConsensus)
3880     {
3881       viewport.firePropertyChange("alignment", null, viewport
3882               .getAlignment().getSequences());
3883     }
3884   }
3885
3886   @Override
3887   public void sortByTreeOption_actionPerformed(ActionEvent e)
3888   {
3889     viewport.sortByTree = sortByTree.isSelected();
3890   }
3891
3892   @Override
3893   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3894   {
3895     viewport.followSelection = listenToViewSelections.isSelected();
3896   }
3897
3898   /**
3899    * DOCUMENT ME!
3900    *
3901    * @param e
3902    *          DOCUMENT ME!
3903    */
3904   @Override
3905   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3906   {
3907     newTreePanel("AV", "PID", "Average distance tree using PID");
3908   }
3909
3910   /**
3911    * DOCUMENT ME!
3912    *
3913    * @param e
3914    *          DOCUMENT ME!
3915    */
3916   @Override
3917   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3918   {
3919     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3920   }
3921
3922   /**
3923    * DOCUMENT ME!
3924    *
3925    * @param e
3926    *          DOCUMENT ME!
3927    */
3928   @Override
3929   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3930   {
3931     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3932   }
3933
3934   /**
3935    * DOCUMENT ME!
3936    *
3937    * @param e
3938    *          DOCUMENT ME!
3939    */
3940   @Override
3941   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3942   {
3943     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3944   }
3945
3946   /**
3947    * DOCUMENT ME!
3948    *
3949    * @param type
3950    *          DOCUMENT ME!
3951    * @param pwType
3952    *          DOCUMENT ME!
3953    * @param title
3954    *          DOCUMENT ME!
3955    */
3956   void newTreePanel(String type, String pwType, String title)
3957   {
3958     TreePanel tp;
3959
3960     if (viewport.getSelectionGroup() != null
3961             && viewport.getSelectionGroup().getSize() > 0)
3962     {
3963       if (viewport.getSelectionGroup().getSize() < 3)
3964       {
3965         JOptionPane
3966                 .showMessageDialog(
3967                         Desktop.desktop,
3968                         MessageManager
3969                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3970                         MessageManager
3971                                 .getString("label.not_enough_sequences"),
3972                         JOptionPane.WARNING_MESSAGE);
3973         return;
3974       }
3975
3976       SequenceGroup sg = viewport.getSelectionGroup();
3977
3978       /* Decide if the selection is a column region */
3979       for (SequenceI _s : sg.getSequences())
3980       {
3981         if (_s.getLength() < sg.getEndRes())
3982         {
3983           JOptionPane
3984                   .showMessageDialog(
3985                           Desktop.desktop,
3986                           MessageManager
3987                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3988                           MessageManager
3989                                   .getString("label.sequences_selection_not_aligned"),
3990                           JOptionPane.WARNING_MESSAGE);
3991
3992           return;
3993         }
3994       }
3995
3996       title = title + " on region";
3997       tp = new TreePanel(alignPanel, type, pwType);
3998     }
3999     else
4000     {
4001       // are the visible sequences aligned?
4002       if (!viewport.getAlignment().isAligned(false))
4003       {
4004         JOptionPane
4005                 .showMessageDialog(
4006                         Desktop.desktop,
4007                         MessageManager
4008                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4009                         MessageManager
4010                                 .getString("label.sequences_not_aligned"),
4011                         JOptionPane.WARNING_MESSAGE);
4012
4013         return;
4014       }
4015
4016       if (viewport.getAlignment().getHeight() < 2)
4017       {
4018         return;
4019       }
4020
4021       tp = new TreePanel(alignPanel, type, pwType);
4022     }
4023
4024     title += " from ";
4025
4026     if (viewport.viewName != null)
4027     {
4028       title += viewport.viewName + " of ";
4029     }
4030
4031     title += this.title;
4032
4033     Desktop.addInternalFrame(tp, title, 600, 500);
4034   }
4035
4036   /**
4037    * DOCUMENT ME!
4038    *
4039    * @param title
4040    *          DOCUMENT ME!
4041    * @param order
4042    *          DOCUMENT ME!
4043    */
4044   public void addSortByOrderMenuItem(String title,
4045           final AlignmentOrder order)
4046   {
4047     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4048             "action.by_title_param", new Object[] { title }));
4049     sort.add(item);
4050     item.addActionListener(new java.awt.event.ActionListener()
4051     {
4052       @Override
4053       public void actionPerformed(ActionEvent e)
4054       {
4055         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4056
4057         // TODO: JBPNote - have to map order entries to curent SequenceI
4058         // pointers
4059         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4060
4061         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4062                 .getAlignment()));
4063
4064         alignPanel.paintAlignment(true);
4065       }
4066     });
4067   }
4068
4069   /**
4070    * Add a new sort by annotation score menu item
4071    *
4072    * @param sort
4073    *          the menu to add the option to
4074    * @param scoreLabel
4075    *          the label used to retrieve scores for each sequence on the
4076    *          alignment
4077    */
4078   public void addSortByAnnotScoreMenuItem(JMenu sort,
4079           final String scoreLabel)
4080   {
4081     final JMenuItem item = new JMenuItem(scoreLabel);
4082     sort.add(item);
4083     item.addActionListener(new java.awt.event.ActionListener()
4084     {
4085       @Override
4086       public void actionPerformed(ActionEvent e)
4087       {
4088         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4089         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4090                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4091         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4092                 viewport.getAlignment()));
4093         alignPanel.paintAlignment(true);
4094       }
4095     });
4096   }
4097
4098   /**
4099    * last hash for alignment's annotation array - used to minimise cost of
4100    * rebuild.
4101    */
4102   protected int _annotationScoreVectorHash;
4103
4104   /**
4105    * search the alignment and rebuild the sort by annotation score submenu the
4106    * last alignment annotation vector hash is stored to minimize cost of
4107    * rebuilding in subsequence calls.
4108    *
4109    */
4110   @Override
4111   public void buildSortByAnnotationScoresMenu()
4112   {
4113     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4114     {
4115       return;
4116     }
4117
4118     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4119     {
4120       sortByAnnotScore.removeAll();
4121       // almost certainly a quicker way to do this - but we keep it simple
4122       Hashtable scoreSorts = new Hashtable();
4123       AlignmentAnnotation aann[];
4124       for (SequenceI sqa : viewport.getAlignment().getSequences())
4125       {
4126         aann = sqa.getAnnotation();
4127         for (int i = 0; aann != null && i < aann.length; i++)
4128         {
4129           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4130           {
4131             scoreSorts.put(aann[i].label, aann[i].label);
4132           }
4133         }
4134       }
4135       Enumeration labels = scoreSorts.keys();
4136       while (labels.hasMoreElements())
4137       {
4138         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4139                 (String) labels.nextElement());
4140       }
4141       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4142       scoreSorts.clear();
4143
4144       _annotationScoreVectorHash = viewport.getAlignment()
4145               .getAlignmentAnnotation().hashCode();
4146     }
4147   }
4148
4149   /**
4150    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4151    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4152    * call. Listeners are added to remove the menu item when the treePanel is
4153    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4154    * modified.
4155    *
4156    * @param treePanel
4157    *          Displayed tree window.
4158    * @param title
4159    *          SortBy menu item title.
4160    */
4161   @Override
4162   public void buildTreeMenu()
4163   {
4164     calculateTree.removeAll();
4165     // build the calculate menu
4166
4167     for (final String type : new String[] { "NJ", "AV" })
4168     {
4169       String treecalcnm = MessageManager.getString("label.tree_calc_"
4170               + type.toLowerCase());
4171       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4172       {
4173         JMenuItem tm = new JMenuItem();
4174         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4175         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4176         {
4177           String smn = MessageManager.getStringOrReturn(
4178                   "label.score_model_", sm.getName());
4179           final String title = MessageManager.formatMessage(
4180                   "label.treecalc_title", treecalcnm, smn);
4181           tm.setText(title);//
4182           tm.addActionListener(new java.awt.event.ActionListener()
4183           {
4184             @Override
4185             public void actionPerformed(ActionEvent e)
4186             {
4187               newTreePanel(type, pwtype, title);
4188             }
4189           });
4190           calculateTree.add(tm);
4191         }
4192
4193       }
4194     }
4195     sortByTreeMenu.removeAll();
4196
4197     List<Component> comps = PaintRefresher.components.get(viewport
4198             .getSequenceSetId());
4199     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4200     for (Component comp : comps)
4201     {
4202       if (comp instanceof TreePanel)
4203       {
4204         treePanels.add((TreePanel) comp);
4205       }
4206     }
4207
4208     if (treePanels.size() < 1)
4209     {
4210       sortByTreeMenu.setVisible(false);
4211       return;
4212     }
4213
4214     sortByTreeMenu.setVisible(true);
4215
4216     for (final TreePanel tp : treePanels)
4217     {
4218       final JMenuItem item = new JMenuItem(tp.getTitle());
4219       item.addActionListener(new java.awt.event.ActionListener()
4220       {
4221         @Override
4222         public void actionPerformed(ActionEvent e)
4223         {
4224           tp.sortByTree_actionPerformed();
4225           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4226
4227         }
4228       });
4229
4230       sortByTreeMenu.add(item);
4231     }
4232   }
4233
4234   public boolean sortBy(AlignmentOrder alorder, String undoname)
4235   {
4236     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4237     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4238     if (undoname != null)
4239     {
4240       addHistoryItem(new OrderCommand(undoname, oldOrder,
4241               viewport.getAlignment()));
4242     }
4243     alignPanel.paintAlignment(true);
4244     return true;
4245   }
4246
4247   /**
4248    * Work out whether the whole set of sequences or just the selected set will
4249    * be submitted for multiple alignment.
4250    *
4251    */
4252   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4253   {
4254     // Now, check we have enough sequences
4255     AlignmentView msa = null;
4256
4257     if ((viewport.getSelectionGroup() != null)
4258             && (viewport.getSelectionGroup().getSize() > 1))
4259     {
4260       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4261       // some common interface!
4262       /*
4263        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4264        * SequenceI[sz = seqs.getSize(false)];
4265        *
4266        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4267        * seqs.getSequenceAt(i); }
4268        */
4269       msa = viewport.getAlignmentView(true);
4270     }
4271     else if (viewport.getSelectionGroup() != null
4272             && viewport.getSelectionGroup().getSize() == 1)
4273     {
4274       int option = JOptionPane.showConfirmDialog(this,
4275               MessageManager.getString("warn.oneseq_msainput_selection"),
4276               MessageManager.getString("label.invalid_selection"),
4277               JOptionPane.OK_CANCEL_OPTION);
4278       if (option == JOptionPane.OK_OPTION)
4279       {
4280         msa = viewport.getAlignmentView(false);
4281       }
4282     }
4283     else
4284     {
4285       msa = viewport.getAlignmentView(false);
4286     }
4287     return msa;
4288   }
4289
4290   /**
4291    * Decides what is submitted to a secondary structure prediction service: the
4292    * first sequence in the alignment, or in the current selection, or, if the
4293    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4294    * region or the whole alignment. (where the first sequence in the set is the
4295    * one that the prediction will be for).
4296    */
4297   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4298   {
4299     AlignmentView seqs = null;
4300
4301     if ((viewport.getSelectionGroup() != null)
4302             && (viewport.getSelectionGroup().getSize() > 0))
4303     {
4304       seqs = viewport.getAlignmentView(true);
4305     }
4306     else
4307     {
4308       seqs = viewport.getAlignmentView(false);
4309     }
4310     // limit sequences - JBPNote in future - could spawn multiple prediction
4311     // jobs
4312     // TODO: viewport.getAlignment().isAligned is a global state - the local
4313     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4314     if (!viewport.getAlignment().isAligned(false))
4315     {
4316       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4317       // TODO: if seqs.getSequences().length>1 then should really have warned
4318       // user!
4319
4320     }
4321     return seqs;
4322   }
4323
4324   /**
4325    * DOCUMENT ME!
4326    *
4327    * @param e
4328    *          DOCUMENT ME!
4329    */
4330   @Override
4331   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4332   {
4333     // Pick the tree file
4334     JalviewFileChooser chooser = new JalviewFileChooser(
4335             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4336     chooser.setFileView(new JalviewFileView());
4337     chooser.setDialogTitle(MessageManager
4338             .getString("label.select_newick_like_tree_file"));
4339     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4340
4341     int value = chooser.showOpenDialog(null);
4342
4343     if (value == JalviewFileChooser.APPROVE_OPTION)
4344     {
4345       String choice = chooser.getSelectedFile().getPath();
4346       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4347       jalview.io.NewickFile fin = null;
4348       try
4349       {
4350         fin = new jalview.io.NewickFile(choice, "File");
4351         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4352       } catch (Exception ex)
4353       {
4354         JOptionPane
4355                 .showMessageDialog(
4356                         Desktop.desktop,
4357                         ex.getMessage(),
4358                         MessageManager
4359                                 .getString("label.problem_reading_tree_file"),
4360                         JOptionPane.WARNING_MESSAGE);
4361         ex.printStackTrace();
4362       }
4363       if (fin != null && fin.hasWarningMessage())
4364       {
4365         JOptionPane.showMessageDialog(Desktop.desktop, fin
4366                 .getWarningMessage(), MessageManager
4367                 .getString("label.possible_problem_with_tree_file"),
4368                 JOptionPane.WARNING_MESSAGE);
4369       }
4370     }
4371   }
4372
4373   @Override
4374   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4375   {
4376     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4377   }
4378
4379   public TreePanel ShowNewickTree(NewickFile nf, String title)
4380   {
4381     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4382   }
4383
4384   public TreePanel ShowNewickTree(NewickFile nf, String title,
4385           AlignmentView input)
4386   {
4387     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4388   }
4389
4390   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4391           int h, int x, int y)
4392   {
4393     return ShowNewickTree(nf, title, null, w, h, x, y);
4394   }
4395
4396   /**
4397    * Add a treeviewer for the tree extracted from a newick file object to the
4398    * current alignment view
4399    *
4400    * @param nf
4401    *          the tree
4402    * @param title
4403    *          tree viewer title
4404    * @param input
4405    *          Associated alignment input data (or null)
4406    * @param w
4407    *          width
4408    * @param h
4409    *          height
4410    * @param x
4411    *          position
4412    * @param y
4413    *          position
4414    * @return TreePanel handle
4415    */
4416   public TreePanel ShowNewickTree(NewickFile nf, String title,
4417           AlignmentView input, int w, int h, int x, int y)
4418   {
4419     TreePanel tp = null;
4420
4421     try
4422     {
4423       nf.parse();
4424
4425       if (nf.getTree() != null)
4426       {
4427         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4428
4429         tp.setSize(w, h);
4430
4431         if (x > 0 && y > 0)
4432         {
4433           tp.setLocation(x, y);
4434         }
4435
4436         Desktop.addInternalFrame(tp, title, w, h);
4437       }
4438     } catch (Exception ex)
4439     {
4440       ex.printStackTrace();
4441     }
4442
4443     return tp;
4444   }
4445
4446   private boolean buildingMenu = false;
4447
4448   /**
4449    * Generates menu items and listener event actions for web service clients
4450    *
4451    */
4452   public void BuildWebServiceMenu()
4453   {
4454     while (buildingMenu)
4455     {
4456       try
4457       {
4458         System.err.println("Waiting for building menu to finish.");
4459         Thread.sleep(10);
4460       } catch (Exception e)
4461       {
4462       }
4463     }
4464     final AlignFrame me = this;
4465     buildingMenu = true;
4466     new Thread(new Runnable()
4467     {
4468       @Override
4469       public void run()
4470       {
4471         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4472         try
4473         {
4474           // System.err.println("Building ws menu again "
4475           // + Thread.currentThread());
4476           // TODO: add support for context dependent disabling of services based
4477           // on
4478           // alignment and current selection
4479           // TODO: add additional serviceHandle parameter to specify abstract
4480           // handler
4481           // class independently of AbstractName
4482           // TODO: add in rediscovery GUI function to restart discoverer
4483           // TODO: group services by location as well as function and/or
4484           // introduce
4485           // object broker mechanism.
4486           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4487           final IProgressIndicator af = me;
4488           final JMenu msawsmenu = new JMenu("Alignment");
4489           final JMenu secstrmenu = new JMenu(
4490                   "Secondary Structure Prediction");
4491           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4492           final JMenu analymenu = new JMenu("Analysis");
4493           final JMenu dismenu = new JMenu("Protein Disorder");
4494           // final JMenu msawsmenu = new
4495           // JMenu(MessageManager.getString("label.alignment"));
4496           // final JMenu secstrmenu = new
4497           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4498           // final JMenu seqsrchmenu = new
4499           // JMenu(MessageManager.getString("label.sequence_database_search"));
4500           // final JMenu analymenu = new
4501           // JMenu(MessageManager.getString("label.analysis"));
4502           // final JMenu dismenu = new
4503           // JMenu(MessageManager.getString("label.protein_disorder"));
4504           // JAL-940 - only show secondary structure prediction services from
4505           // the legacy server
4506           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4507               // &&
4508           Discoverer.services != null && (Discoverer.services.size() > 0))
4509           {
4510             // TODO: refactor to allow list of AbstractName/Handler bindings to
4511             // be
4512             // stored or retrieved from elsewhere
4513             // No MSAWS used any more:
4514             // Vector msaws = null; // (Vector)
4515             // Discoverer.services.get("MsaWS");
4516             Vector secstrpr = (Vector) Discoverer.services
4517                     .get("SecStrPred");
4518             if (secstrpr != null)
4519             {
4520               // Add any secondary structure prediction services
4521               for (int i = 0, j = secstrpr.size(); i < j; i++)
4522               {
4523                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4524                         .get(i);
4525                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4526                         .getServiceClient(sh);
4527                 int p = secstrmenu.getItemCount();
4528                 impl.attachWSMenuEntry(secstrmenu, me);
4529                 int q = secstrmenu.getItemCount();
4530                 for (int litm = p; litm < q; litm++)
4531                 {
4532                   legacyItems.add(secstrmenu.getItem(litm));
4533                 }
4534               }
4535             }
4536           }
4537
4538           // Add all submenus in the order they should appear on the web
4539           // services menu
4540           wsmenu.add(msawsmenu);
4541           wsmenu.add(secstrmenu);
4542           wsmenu.add(dismenu);
4543           wsmenu.add(analymenu);
4544           // No search services yet
4545           // wsmenu.add(seqsrchmenu);
4546
4547           javax.swing.SwingUtilities.invokeLater(new Runnable()
4548           {
4549             @Override
4550             public void run()
4551             {
4552               try
4553               {
4554                 webService.removeAll();
4555                 // first, add discovered services onto the webservices menu
4556                 if (wsmenu.size() > 0)
4557                 {
4558                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4559                   {
4560                     webService.add(wsmenu.get(i));
4561                   }
4562                 }
4563                 else
4564                 {
4565                   webService.add(me.webServiceNoServices);
4566                 }
4567                 // TODO: move into separate menu builder class.
4568                 boolean new_sspred = false;
4569                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4570                 {
4571                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4572                   if (jws2servs != null)
4573                   {
4574                     if (jws2servs.hasServices())
4575                     {
4576                       jws2servs.attachWSMenuEntry(webService, me);
4577                       for (Jws2Instance sv : jws2servs.getServices())
4578                       {
4579                         if (sv.description.toLowerCase().contains("jpred"))
4580                         {
4581                           for (JMenuItem jmi : legacyItems)
4582                           {
4583                             jmi.setVisible(false);
4584                           }
4585                         }
4586                       }
4587
4588                     }
4589                     if (jws2servs.isRunning())
4590                     {
4591                       JMenuItem tm = new JMenuItem(
4592                               "Still discovering JABA Services");
4593                       tm.setEnabled(false);
4594                       webService.add(tm);
4595                     }
4596                   }
4597                 }
4598                 build_urlServiceMenu(me.webService);
4599                 build_fetchdbmenu(webService);
4600                 for (JMenu item : wsmenu)
4601                 {
4602                   if (item.getItemCount() == 0)
4603                   {
4604                     item.setEnabled(false);
4605                   }
4606                   else
4607                   {
4608                     item.setEnabled(true);
4609                   }
4610                 }
4611               } catch (Exception e)
4612               {
4613                 Cache.log
4614                         .debug("Exception during web service menu building process.",
4615                                 e);
4616               }
4617             }
4618           });
4619         } catch (Exception e)
4620         {
4621         }
4622         buildingMenu = false;
4623       }
4624     }).start();
4625
4626   }
4627
4628   /**
4629    * construct any groupURL type service menu entries.
4630    *
4631    * @param webService
4632    */
4633   private void build_urlServiceMenu(JMenu webService)
4634   {
4635     // TODO: remove this code when 2.7 is released
4636     // DEBUG - alignmentView
4637     /*
4638      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4639      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4640      *
4641      * @Override public void actionPerformed(ActionEvent e) {
4642      * jalview.datamodel.AlignmentView
4643      * .testSelectionViews(af.viewport.getAlignment(),
4644      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4645      *
4646      * }); webService.add(testAlView);
4647      */
4648     // TODO: refactor to RestClient discoverer and merge menu entries for
4649     // rest-style services with other types of analysis/calculation service
4650     // SHmmr test client - still being implemented.
4651     // DEBUG - alignmentView
4652
4653     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4654             .getRestClients())
4655     {
4656       client.attachWSMenuEntry(
4657               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4658               this);
4659     }
4660   }
4661
4662   /**
4663    * Searches selected sequences for xRef products and builds the Show
4664    * Cross-References menu (formerly called Show Products)
4665    *
4666    * @return true if Show Cross-references menu should be enabled.
4667    */
4668   public boolean canShowProducts()
4669   {
4670     SequenceI[] selection = viewport.getSequenceSelection();
4671     AlignmentI dataset = viewport.getAlignment().getDataset();
4672     boolean showp = false;
4673     try
4674     {
4675       showProducts.removeAll();
4676       final boolean dna = viewport.getAlignment().isNucleotide();
4677       String[] ptypes = (selection == null || selection.length == 0) ? null
4678               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4679
4680       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4681       {
4682         showp = true;
4683         final AlignFrame af = this;
4684         final String source = ptypes[t];
4685         JMenuItem xtype = new JMenuItem(ptypes[t]);
4686         xtype.addActionListener(new ActionListener()
4687         {
4688
4689           @Override
4690           public void actionPerformed(ActionEvent e)
4691           {
4692             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4693           }
4694
4695         });
4696         showProducts.add(xtype);
4697       }
4698       showProducts.setVisible(showp);
4699       showProducts.setEnabled(showp);
4700     } catch (Exception e)
4701     {
4702       jalview.bin.Cache.log
4703               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4704                       e);
4705       return false;
4706     }
4707     return showp;
4708   }
4709
4710   protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4711           final String source)
4712   {
4713     Runnable foo = new Runnable()
4714     {
4715
4716       @Override
4717       public void run()
4718       {
4719         final long sttime = System.currentTimeMillis();
4720         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4721                 "status.searching_for_sequences_from",
4722                 new Object[] { source }), sttime);
4723         try
4724         {
4725           AlignmentI alignment = AlignFrame.this.getViewport()
4726                   .getAlignment();
4727           AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4728                   alignment);
4729           if (xrefs != null)
4730           {
4731             /*
4732              * get display scheme (if any) to apply to features
4733              */
4734             FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4735                     .getFeatureColourScheme(source);
4736
4737             AlignmentI al = makeCrossReferencesAlignment(
4738                     alignment.getDataset(), xrefs);
4739
4740             AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4741                     DEFAULT_HEIGHT);
4742             String newtitle = String.format("%s %s %s",
4743                     MessageManager.getString(dna ? "label.proteins"
4744                             : "label.nucleotides"), MessageManager
4745                             .getString("label.for"), getTitle());
4746             newFrame.setTitle(newtitle);
4747
4748             if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4749             {
4750               /*
4751                * split frame display is turned off in preferences file
4752                */
4753               Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4754                       DEFAULT_HEIGHT);
4755               return; // via finally clause
4756             }
4757
4758             /*
4759              * Make a copy of this alignment (sharing the same dataset
4760              * sequences). If we are DNA, drop introns and update mappings
4761              */
4762             AlignmentI copyAlignment = null;
4763             final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4764                     .getSequenceSelection();
4765             List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4766             boolean copyAlignmentIsAligned = false;
4767             if (dna)
4768             {
4769               copyAlignment = AlignmentUtils.makeCdsAlignment(
4770                       sequenceSelection, cf, alignment);
4771               if (copyAlignment.getHeight() == 0)
4772               {
4773                 System.err.println("Failed to make CDS alignment");
4774               }
4775               al.getCodonFrames().clear();
4776               al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
4777
4778               /*
4779                * pending getting Embl transcripts to 'align',
4780                * we are only doing this for Ensembl
4781                */
4782               // TODO proper criteria for 'can align as cdna'
4783               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4784                       || AlignmentUtils.looksLikeEnsembl(alignment))
4785               {
4786                 copyAlignment.alignAs(alignment);
4787                 copyAlignmentIsAligned = true;
4788               }
4789             }
4790             else
4791             {
4792               copyAlignment = AlignmentUtils.makeCopyAlignment(
4793                       sequenceSelection, xrefs.getSequencesArray());
4794               copyAlignment.getCodonFrames().addAll(cf);
4795             }
4796             copyAlignment.setGapCharacter(AlignFrame.this.viewport
4797                     .getGapCharacter());
4798
4799             StructureSelectionManager ssm = StructureSelectionManager
4800                     .getStructureSelectionManager(Desktop.instance);
4801             ssm.registerMappings(cf);
4802
4803             if (copyAlignment.getHeight() <= 0)
4804             {
4805               System.err.println("No Sequences generated for xRef type "
4806                       + source);
4807               return;
4808             }
4809             /*
4810              * align protein to dna
4811              */
4812             if (dna && copyAlignmentIsAligned)
4813             {
4814               al.alignAs(copyAlignment);
4815             }
4816             else
4817             {
4818               /*
4819                * align cdna to protein - currently only if
4820                * fetching and aligning Ensembl transcripts!
4821                */
4822               if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4823               {
4824                 copyAlignment.alignAs(al);
4825               }
4826             }
4827
4828             AlignFrame copyThis = new AlignFrame(copyAlignment,
4829                     AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4830             copyThis.setTitle(AlignFrame.this.getTitle());
4831
4832             boolean showSequenceFeatures = viewport
4833                     .isShowSequenceFeatures();
4834             newFrame.setShowSeqFeatures(showSequenceFeatures);
4835             copyThis.setShowSeqFeatures(showSequenceFeatures);
4836             FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4837                     .getFeatureRenderer();
4838
4839             /*
4840              * copy feature rendering settings to split frame
4841              */
4842             newFrame.alignPanel.getSeqPanel().seqCanvas
4843                     .getFeatureRenderer()
4844                     .transferSettings(myFeatureStyling);
4845             copyThis.alignPanel.getSeqPanel().seqCanvas
4846                     .getFeatureRenderer()
4847                     .transferSettings(myFeatureStyling);
4848
4849             /*
4850              * apply 'database source' feature configuration
4851              * if any was found
4852              */
4853             // TODO is this the feature colouring for the original
4854             // alignment or the fetched xrefs? either could be Ensembl
4855             newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4856             copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4857
4858             SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4859                     dna ? newFrame : copyThis);
4860             newFrame.setVisible(true);
4861             copyThis.setVisible(true);
4862             String linkedTitle = MessageManager
4863                     .getString("label.linked_view_title");
4864             Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4865             sf.adjustDivider();
4866           }
4867         } catch (Exception e)
4868         {
4869           Cache.log.error(
4870                   "Exception when finding crossreferences", e);
4871         } catch (OutOfMemoryError e)
4872         {
4873           new OOMWarning("whilst fetching crossreferences", e);
4874         } catch (Throwable e)
4875         {
4876           Cache.log.error("Error when finding crossreferences",
4877                   e);
4878         } finally
4879         {
4880           AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4881                   "status.finished_searching_for_sequences_from",
4882                   new Object[] { source }), sttime);
4883         }
4884       }
4885
4886       /**
4887        * Makes an alignment containing the given sequences. If this is of the
4888        * same type as the given dataset (nucleotide/protein), then the new
4889        * alignment shares the same dataset, and its dataset sequences are added
4890        * to it. Otherwise a new dataset sequence is created for the
4891        * cross-references.
4892        *
4893        * @param dataset
4894        * @param seqs
4895        * @return
4896        */
4897       protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4898               AlignmentI seqs)
4899       {
4900         boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4901
4902         SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4903         for (int s = 0; s < sprods.length; s++)
4904         {
4905           sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4906           if (sameType)
4907           {
4908             if (dataset.getSequences() == null
4909                     || !dataset.getSequences().contains(
4910                             sprods[s].getDatasetSequence()))
4911             {
4912               dataset.addSequence(sprods[s].getDatasetSequence());
4913             }
4914           }
4915           sprods[s].updatePDBIds();
4916         }
4917         Alignment al = new Alignment(sprods);
4918         if (sameType)
4919         {
4920           al.setDataset((Alignment) dataset);
4921         }
4922         else
4923         {
4924           al.createDatasetAlignment();
4925         }
4926         return al;
4927       }
4928
4929     };
4930     Thread frunner = new Thread(foo);
4931     frunner.start();
4932   }
4933
4934   /**
4935    * Construct and display a new frame containing the translation of this
4936    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4937    */
4938   @Override
4939   public void showTranslation_actionPerformed(ActionEvent e)
4940   {
4941     AlignmentI al = null;
4942     try
4943     {
4944       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4945
4946       al = dna.translateCdna();
4947     } catch (Exception ex)
4948     {
4949       jalview.bin.Cache.log.error(
4950               "Exception during translation. Please report this !", ex);
4951       final String msg = MessageManager
4952               .getString("label.error_when_translating_sequences_submit_bug_report");
4953       final String errorTitle = MessageManager
4954               .getString("label.implementation_error")
4955               + MessageManager.getString("translation_failed");
4956       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4957               JOptionPane.ERROR_MESSAGE);
4958       return;
4959     }
4960     if (al == null || al.getHeight() == 0)
4961     {
4962       final String msg = MessageManager
4963               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4964       final String errorTitle = MessageManager
4965               .getString("label.translation_failed");
4966       JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4967               JOptionPane.WARNING_MESSAGE);
4968     }
4969     else
4970     {
4971       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4972       af.setFileFormat(this.currentFileFormat);
4973       final String newTitle = MessageManager.formatMessage(
4974               "label.translation_of_params",
4975               new Object[] { this.getTitle() });
4976       af.setTitle(newTitle);
4977       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4978       {
4979         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4980         viewport.openSplitFrame(af, new Alignment(seqs));
4981       }
4982       else
4983       {
4984         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4985                 DEFAULT_HEIGHT);
4986       }
4987     }
4988   }
4989
4990   /**
4991    * Set the file format
4992    *
4993    * @param fileFormat
4994    */
4995   public void setFileFormat(String fileFormat)
4996   {
4997     this.currentFileFormat = fileFormat;
4998   }
4999
5000   /**
5001    * Try to load a features file onto the alignment.
5002    *
5003    * @param file
5004    *          contents or path to retrieve file
5005    * @param type
5006    *          access mode of file (see jalview.io.AlignFile)
5007    * @return true if features file was parsed correctly.
5008    */
5009   public boolean parseFeaturesFile(String file, String type)
5010   {
5011     return avc.parseFeaturesFile(file, type,
5012             jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5013
5014   }
5015
5016   @Override
5017   public void refreshFeatureUI(boolean enableIfNecessary)
5018   {
5019     // note - currently this is only still here rather than in the controller
5020     // because of the featureSettings hard reference that is yet to be
5021     // abstracted
5022     if (enableIfNecessary)
5023     {
5024       viewport.setShowSequenceFeatures(true);
5025       showSeqFeatures.setSelected(true);
5026     }
5027
5028   }
5029
5030   @Override
5031   public void dragEnter(DropTargetDragEvent evt)
5032   {
5033   }
5034
5035   @Override
5036   public void dragExit(DropTargetEvent evt)
5037   {
5038   }
5039
5040   @Override
5041   public void dragOver(DropTargetDragEvent evt)
5042   {
5043   }
5044
5045   @Override
5046   public void dropActionChanged(DropTargetDragEvent evt)
5047   {
5048   }
5049
5050   @Override
5051   public void drop(DropTargetDropEvent evt)
5052   {
5053     Transferable t = evt.getTransferable();
5054     java.util.List files = null;
5055
5056     try
5057     {
5058       DataFlavor uriListFlavor = new DataFlavor(
5059               "text/uri-list;class=java.lang.String");
5060       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5061       {
5062         // Works on Windows and MacOSX
5063         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5064         files = (java.util.List) t
5065                 .getTransferData(DataFlavor.javaFileListFlavor);
5066       }
5067       else if (t.isDataFlavorSupported(uriListFlavor))
5068       {
5069         // This is used by Unix drag system
5070         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5071         String data = (String) t.getTransferData(uriListFlavor);
5072         files = new java.util.ArrayList(1);
5073         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5074                 data, "\r\n"); st.hasMoreTokens();)
5075         {
5076           String s = st.nextToken();
5077           if (s.startsWith("#"))
5078           {
5079             // the line is a comment (as per the RFC 2483)
5080             continue;
5081           }
5082
5083           java.net.URI uri = new java.net.URI(s);
5084           // check to see if we can handle this kind of URI
5085           if (uri.getScheme().toLowerCase().startsWith("http"))
5086           {
5087             files.add(uri.toString());
5088           }
5089           else
5090           {
5091             // otherwise preserve old behaviour: catch all for file objects
5092             java.io.File file = new java.io.File(uri);
5093             files.add(file.toString());
5094           }
5095         }
5096       }
5097     } catch (Exception e)
5098     {
5099       e.printStackTrace();
5100     }
5101     if (files != null)
5102     {
5103       try
5104       {
5105         // check to see if any of these files have names matching sequences in
5106         // the alignment
5107         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5108                 .getAlignment().getSequencesArray());
5109         /**
5110          * Object[] { String,SequenceI}
5111          */
5112         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5113         ArrayList<String> filesnotmatched = new ArrayList<String>();
5114         for (int i = 0; i < files.size(); i++)
5115         {
5116           String file = files.get(i).toString();
5117           String pdbfn = "";
5118           String protocol = FormatAdapter.checkProtocol(file);
5119           if (protocol == jalview.io.FormatAdapter.FILE)
5120           {
5121             File fl = new File(file);
5122             pdbfn = fl.getName();
5123           }
5124           else if (protocol == jalview.io.FormatAdapter.URL)
5125           {
5126             URL url = new URL(file);
5127             pdbfn = url.getFile();
5128           }
5129           if (pdbfn.length() > 0)
5130           {
5131             // attempt to find a match in the alignment
5132             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5133             int l = 0, c = pdbfn.indexOf(".");
5134             while (mtch == null && c != -1)
5135             {
5136               do
5137               {
5138                 l = c;
5139               } while ((c = pdbfn.indexOf(".", l)) > l);
5140               if (l > -1)
5141               {
5142                 pdbfn = pdbfn.substring(0, l);
5143               }
5144               mtch = idm.findAllIdMatches(pdbfn);
5145             }
5146             if (mtch != null)
5147             {
5148               String type = null;
5149               try
5150               {
5151                 type = new IdentifyFile().identify(file, protocol);
5152               } catch (Exception ex)
5153               {
5154                 type = null;
5155               }
5156               if (type != null)
5157               {
5158                 if (type.equalsIgnoreCase("PDB"))
5159                 {
5160                   filesmatched.add(new Object[] { file, protocol, mtch });
5161                   continue;
5162                 }
5163               }
5164             }
5165             // File wasn't named like one of the sequences or wasn't a PDB file.
5166             filesnotmatched.add(file);
5167           }
5168         }
5169         int assocfiles = 0;
5170         if (filesmatched.size() > 0)
5171         {
5172           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5173                   || JOptionPane
5174                           .showConfirmDialog(
5175                                   this,
5176                                   MessageManager
5177                                           .formatMessage(
5178                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5179                                                   new Object[] { Integer
5180                                                           .valueOf(
5181                                                                   filesmatched
5182                                                                           .size())
5183                                                           .toString() }),
5184                                   MessageManager
5185                                           .getString("label.automatically_associate_pdb_files_by_name"),
5186                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5187
5188           {
5189             for (Object[] fm : filesmatched)
5190             {
5191               // try and associate
5192               // TODO: may want to set a standard ID naming formalism for
5193               // associating PDB files which have no IDs.
5194               for (SequenceI toassoc : (SequenceI[]) fm[2])
5195               {
5196                 PDBEntry pe = new AssociatePdbFileWithSeq()
5197                         .associatePdbWithSeq((String) fm[0],
5198                                 (String) fm[1], toassoc, false,
5199                                 Desktop.instance);
5200                 if (pe != null)
5201                 {
5202                   System.err.println("Associated file : "
5203                           + ((String) fm[0]) + " with "
5204                           + toassoc.getDisplayId(true));
5205                   assocfiles++;
5206                 }
5207               }
5208               alignPanel.paintAlignment(true);
5209             }
5210           }
5211         }
5212         if (filesnotmatched.size() > 0)
5213         {
5214           if (assocfiles > 0
5215                   && (Cache.getDefault(
5216                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5217                           .showConfirmDialog(
5218                                   this,
5219                                   "<html>"
5220                                           + MessageManager
5221                                                   .formatMessage(
5222                                                           "label.ignore_unmatched_dropped_files_info",
5223                                                           new Object[] { Integer
5224                                                                   .valueOf(
5225                                                                           filesnotmatched
5226                                                                                   .size())
5227                                                                   .toString() })
5228                                           + "</html>",
5229                                   MessageManager
5230                                           .getString("label.ignore_unmatched_dropped_files"),
5231                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5232           {
5233             return;
5234           }
5235           for (String fn : filesnotmatched)
5236           {
5237             loadJalviewDataFile(fn, null, null, null);
5238           }
5239
5240         }
5241       } catch (Exception ex)
5242       {
5243         ex.printStackTrace();
5244       }
5245     }
5246   }
5247
5248   /**
5249    * Attempt to load a "dropped" file or URL string: First by testing whether
5250    * it's an Annotation file, then a JNet file, and finally a features file. If
5251    * all are false then the user may have dropped an alignment file onto this
5252    * AlignFrame.
5253    *
5254    * @param file
5255    *          either a filename or a URL string.
5256    */
5257   public void loadJalviewDataFile(String file, String protocol,
5258           String format, SequenceI assocSeq)
5259   {
5260     try
5261     {
5262       if (protocol == null)
5263       {
5264         protocol = FormatAdapter.checkProtocol(file);
5265       }
5266       // if the file isn't identified, or not positively identified as some
5267       // other filetype (PFAM is default unidentified alignment file type) then
5268       // try to parse as annotation.
5269       boolean isAnnotation = (format == null || format
5270               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5271               .annotateAlignmentView(viewport, file, protocol) : false;
5272
5273       if (!isAnnotation)
5274       {
5275         // first see if its a T-COFFEE score file
5276         TCoffeeScoreFile tcf = null;
5277         try
5278         {
5279           tcf = new TCoffeeScoreFile(file, protocol);
5280           if (tcf.isValid())
5281           {
5282             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5283             {
5284               tcoffeeColour.setEnabled(true);
5285               tcoffeeColour.setSelected(true);
5286               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5287               isAnnotation = true;
5288               statusBar
5289                       .setText(MessageManager
5290                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5291             }
5292             else
5293             {
5294               // some problem - if no warning its probable that the ID matching
5295               // process didn't work
5296               JOptionPane
5297                       .showMessageDialog(
5298                               Desktop.desktop,
5299                               tcf.getWarningMessage() == null ? MessageManager
5300                                       .getString("label.check_file_matches_sequence_ids_alignment")
5301                                       : tcf.getWarningMessage(),
5302                               MessageManager
5303                                       .getString("label.problem_reading_tcoffee_score_file"),
5304                               JOptionPane.WARNING_MESSAGE);
5305             }
5306           }
5307           else
5308           {
5309             tcf = null;
5310           }
5311         } catch (Exception x)
5312         {
5313           Cache.log
5314                   .debug("Exception when processing data source as T-COFFEE score file",
5315                           x);
5316           tcf = null;
5317         }
5318         if (tcf == null)
5319         {
5320           // try to see if its a JNet 'concise' style annotation file *before*
5321           // we
5322           // try to parse it as a features file
5323           if (format == null)
5324           {
5325             format = new IdentifyFile().identify(file, protocol);
5326           }
5327           if (format.equalsIgnoreCase("JnetFile"))
5328           {
5329             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5330                     file, protocol);
5331             new JnetAnnotationMaker();
5332             JnetAnnotationMaker.add_annotation(predictions,
5333                     viewport.getAlignment(), 0, false);
5334             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5335             viewport.getAlignment().setSeqrep(repseq);
5336             ColumnSelection cs = new ColumnSelection();
5337             cs.hideInsertionsFor(repseq);
5338             viewport.setColumnSelection(cs);
5339             isAnnotation = true;
5340           }
5341           else if (IdentifyFile.FeaturesFile.equals(format))
5342           {
5343             if (parseFeaturesFile(file, protocol))
5344             {
5345               alignPanel.paintAlignment(true);
5346             }
5347           }
5348           else
5349           {
5350             new FileLoader().LoadFile(viewport, file, protocol, format);
5351           }
5352         }
5353       }
5354       if (isAnnotation)
5355       {
5356
5357         alignPanel.adjustAnnotationHeight();
5358         viewport.updateSequenceIdColours();
5359         buildSortByAnnotationScoresMenu();
5360         alignPanel.paintAlignment(true);
5361       }
5362     } catch (Exception ex)
5363     {
5364       ex.printStackTrace();
5365     } catch (OutOfMemoryError oom)
5366     {
5367       try
5368       {
5369         System.gc();
5370       } catch (Exception x)
5371       {
5372       }
5373       new OOMWarning(
5374               "loading data "
5375                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5376                               : "using " + protocol + " from " + file)
5377                               : ".")
5378                       + (format != null ? "(parsing as '" + format
5379                               + "' file)" : ""), oom, Desktop.desktop);
5380     }
5381   }
5382
5383   /**
5384    * Method invoked by the ChangeListener on the tabbed pane, in other words
5385    * when a different tabbed pane is selected by the user or programmatically.
5386    */
5387   @Override
5388   public void tabSelectionChanged(int index)
5389   {
5390     if (index > -1)
5391     {
5392       alignPanel = alignPanels.get(index);
5393       viewport = alignPanel.av;
5394       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5395       setMenusFromViewport(viewport);
5396     }
5397
5398     /*
5399      * If there is a frame linked to this one in a SplitPane, switch it to the
5400      * same view tab index. No infinite recursion of calls should happen, since
5401      * tabSelectionChanged() should not get invoked on setting the selected
5402      * index to an unchanged value. Guard against setting an invalid index
5403      * before the new view peer tab has been created.
5404      */
5405     final AlignViewportI peer = viewport.getCodingComplement();
5406     if (peer != null)
5407     {
5408       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5409       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5410       {
5411         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5412       }
5413     }
5414   }
5415
5416   /**
5417    * On right mouse click on view tab, prompt for and set new view name.
5418    */
5419   @Override
5420   public void tabbedPane_mousePressed(MouseEvent e)
5421   {
5422     if (SwingUtilities.isRightMouseButton(e))
5423     {
5424       String msg = MessageManager.getString("label.enter_view_name");
5425       String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5426               JOptionPane.QUESTION_MESSAGE);
5427
5428       if (reply != null)
5429       {
5430         viewport.viewName = reply;
5431         // TODO warn if reply is in getExistingViewNames()?
5432         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5433       }
5434     }
5435   }
5436
5437   public AlignViewport getCurrentView()
5438   {
5439     return viewport;
5440   }
5441
5442   /**
5443    * Open the dialog for regex description parsing.
5444    */
5445   @Override
5446   protected void extractScores_actionPerformed(ActionEvent e)
5447   {
5448     ParseProperties pp = new jalview.analysis.ParseProperties(
5449             viewport.getAlignment());
5450     // TODO: verify regex and introduce GUI dialog for version 2.5
5451     // if (pp.getScoresFromDescription("col", "score column ",
5452     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5453     // true)>0)
5454     if (pp.getScoresFromDescription("description column",
5455             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5456     {
5457       buildSortByAnnotationScoresMenu();
5458     }
5459   }
5460
5461   /*
5462    * (non-Javadoc)
5463    *
5464    * @see
5465    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5466    * )
5467    */
5468   @Override
5469   protected void showDbRefs_actionPerformed(ActionEvent e)
5470   {
5471     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5472   }
5473
5474   /*
5475    * (non-Javadoc)
5476    *
5477    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5478    * ActionEvent)
5479    */
5480   @Override
5481   protected void showNpFeats_actionPerformed(ActionEvent e)
5482   {
5483     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5484   }
5485
5486   /**
5487    * find the viewport amongst the tabs in this alignment frame and close that
5488    * tab
5489    *
5490    * @param av
5491    */
5492   public boolean closeView(AlignViewportI av)
5493   {
5494     if (viewport == av)
5495     {
5496       this.closeMenuItem_actionPerformed(false);
5497       return true;
5498     }
5499     Component[] comp = tabbedPane.getComponents();
5500     for (int i = 0; comp != null && i < comp.length; i++)
5501     {
5502       if (comp[i] instanceof AlignmentPanel)
5503       {
5504         if (((AlignmentPanel) comp[i]).av == av)
5505         {
5506           // close the view.
5507           closeView((AlignmentPanel) comp[i]);
5508           return true;
5509         }
5510       }
5511     }
5512     return false;
5513   }
5514
5515   protected void build_fetchdbmenu(JMenu webService)
5516   {
5517     // Temporary hack - DBRef Fetcher always top level ws entry.
5518     // TODO We probably want to store a sequence database checklist in
5519     // preferences and have checkboxes.. rather than individual sources selected
5520     // here
5521     final JMenu rfetch = new JMenu(
5522             MessageManager.getString("action.fetch_db_references"));
5523     rfetch.setToolTipText(MessageManager
5524             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5525     webService.add(rfetch);
5526
5527     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5528             MessageManager.getString("option.trim_retrieved_seqs"));
5529     trimrs.setToolTipText(MessageManager
5530             .getString("label.trim_retrieved_sequences"));
5531     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5532     trimrs.addActionListener(new ActionListener()
5533     {
5534       @Override
5535       public void actionPerformed(ActionEvent e)
5536       {
5537         trimrs.setSelected(trimrs.isSelected());
5538         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5539                 Boolean.valueOf(trimrs.isSelected()).toString());
5540       };
5541     });
5542     rfetch.add(trimrs);
5543     JMenuItem fetchr = new JMenuItem(
5544             MessageManager.getString("label.standard_databases"));
5545     fetchr.setToolTipText(MessageManager
5546             .getString("label.fetch_embl_uniprot"));
5547     fetchr.addActionListener(new ActionListener()
5548     {
5549
5550       @Override
5551       public void actionPerformed(ActionEvent e)
5552       {
5553         new Thread(new Runnable()
5554         {
5555           @Override
5556           public void run()
5557           {
5558             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5559                     .getAlignment().isNucleotide();
5560             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5561                     .getSequenceSelection(), alignPanel.alignFrame, null,
5562                     alignPanel.alignFrame.featureSettings, isNucleotide);
5563             dbRefFetcher.addListener(new FetchFinishedListenerI()
5564             {
5565               @Override
5566               public void finished()
5567               {
5568                 AlignFrame.this.setMenusForViewport();
5569               }
5570             });
5571             dbRefFetcher
5572                     .fetchDBRefs(false);
5573           }
5574         }).start();
5575
5576       }
5577
5578     });
5579     rfetch.add(fetchr);
5580     final AlignFrame me = this;
5581     new Thread(new Runnable()
5582     {
5583       @Override
5584       public void run()
5585       {
5586         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5587                 .getSequenceFetcherSingleton(me);
5588         javax.swing.SwingUtilities.invokeLater(new Runnable()
5589         {
5590           @Override
5591           public void run()
5592           {
5593             String[] dbclasses = sf.getOrderedSupportedSources();
5594             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5595             // jalview.util.QuickSort.sort(otherdb, otherdb);
5596             List<DbSourceProxy> otherdb;
5597             JMenu dfetch = new JMenu();
5598             JMenu ifetch = new JMenu();
5599             JMenuItem fetchr = null;
5600             int comp = 0, icomp = 0, mcomp = 15;
5601             String mname = null;
5602             int dbi = 0;
5603             for (String dbclass : dbclasses)
5604             {
5605               otherdb = sf.getSourceProxy(dbclass);
5606               // add a single entry for this class, or submenu allowing 'fetch
5607               // all' or pick one
5608               if (otherdb == null || otherdb.size() < 1)
5609               {
5610                 continue;
5611               }
5612               // List<DbSourceProxy> dbs=otherdb;
5613               // otherdb=new ArrayList<DbSourceProxy>();
5614               // for (DbSourceProxy db:dbs)
5615               // {
5616               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5617               // }
5618               if (mname == null)
5619               {
5620                 mname = "From " + dbclass;
5621               }
5622               if (otherdb.size() == 1)
5623               {
5624                 final DbSourceProxy[] dassource = otherdb
5625                         .toArray(new DbSourceProxy[0]);
5626                 DbSourceProxy src = otherdb.get(0);
5627                 fetchr = new JMenuItem(src.getDbSource());
5628                 fetchr.addActionListener(new ActionListener()
5629                 {
5630
5631                   @Override
5632                   public void actionPerformed(ActionEvent e)
5633                   {
5634                     new Thread(new Runnable()
5635                     {
5636
5637                       @Override
5638                       public void run()
5639                       {
5640                         boolean isNucleotide = alignPanel.alignFrame
5641                                 .getViewport().getAlignment()
5642                                 .isNucleotide();
5643                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5644                                 alignPanel.av.getSequenceSelection(),
5645                                 alignPanel.alignFrame, dassource,
5646                                 alignPanel.alignFrame.featureSettings,
5647                                 isNucleotide);
5648                         dbRefFetcher
5649                                 .addListener(new FetchFinishedListenerI()
5650                                 {
5651                                   @Override
5652                                   public void finished()
5653                                   {
5654                                     AlignFrame.this.setMenusForViewport();
5655                                   }
5656                                 });
5657                         dbRefFetcher.fetchDBRefs(false);
5658                       }
5659                     }).start();
5660                   }
5661
5662                 });
5663                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5664                         MessageManager.formatMessage(
5665                                 "label.fetch_retrieve_from",
5666                                 new Object[] { src.getDbName() })));
5667                 dfetch.add(fetchr);
5668                 comp++;
5669               }
5670               else
5671               {
5672                 final DbSourceProxy[] dassource = otherdb
5673                         .toArray(new DbSourceProxy[0]);
5674                 // fetch all entry
5675                 DbSourceProxy src = otherdb.get(0);
5676                 fetchr = new JMenuItem(MessageManager.formatMessage(
5677                         "label.fetch_all_param",
5678                         new Object[] { src.getDbSource() }));
5679                 fetchr.addActionListener(new ActionListener()
5680                 {
5681                   @Override
5682                   public void actionPerformed(ActionEvent e)
5683                   {
5684                     new Thread(new Runnable()
5685                     {
5686
5687                       @Override
5688                       public void run()
5689                       {
5690                         boolean isNucleotide = alignPanel.alignFrame
5691                                 .getViewport().getAlignment()
5692                                 .isNucleotide();
5693                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5694                                 alignPanel.av.getSequenceSelection(),
5695                                 alignPanel.alignFrame, dassource,
5696                                 alignPanel.alignFrame.featureSettings,
5697                                 isNucleotide);
5698                         dbRefFetcher
5699                                 .addListener(new FetchFinishedListenerI()
5700                                 {
5701                                   @Override
5702                                   public void finished()
5703                                   {
5704                                     AlignFrame.this.setMenusForViewport();
5705                                   }
5706                                 });
5707                         dbRefFetcher.fetchDBRefs(false);
5708                       }
5709                     }).start();
5710                   }
5711                 });
5712
5713                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5714                         MessageManager.formatMessage(
5715                                 "label.fetch_retrieve_from_all_sources",
5716                                 new Object[] {
5717                                     Integer.valueOf(otherdb.size())
5718                                             .toString(), src.getDbSource(),
5719                                     src.getDbName() })));
5720                 dfetch.add(fetchr);
5721                 comp++;
5722                 // and then build the rest of the individual menus
5723                 ifetch = new JMenu(MessageManager.formatMessage(
5724                         "label.source_from_db_source",
5725                         new Object[] { src.getDbSource() }));
5726                 icomp = 0;
5727                 String imname = null;
5728                 int i = 0;
5729                 for (DbSourceProxy sproxy : otherdb)
5730                 {
5731                   String dbname = sproxy.getDbName();
5732                   String sname = dbname.length() > 5 ? dbname.substring(0,
5733                           5) + "..." : dbname;
5734                   String msname = dbname.length() > 10 ? dbname.substring(
5735                           0, 10) + "..." : dbname;
5736                   if (imname == null)
5737                   {
5738                     imname = MessageManager.formatMessage(
5739                             "label.from_msname", new Object[] { sname });
5740                   }
5741                   fetchr = new JMenuItem(msname);
5742                   final DbSourceProxy[] dassrc = { sproxy };
5743                   fetchr.addActionListener(new ActionListener()
5744                   {
5745
5746                     @Override
5747                     public void actionPerformed(ActionEvent e)
5748                     {
5749                       new Thread(new Runnable()
5750                       {
5751
5752                         @Override
5753                         public void run()
5754                         {
5755                           boolean isNucleotide = alignPanel.alignFrame
5756                                   .getViewport().getAlignment()
5757                                   .isNucleotide();
5758                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5759                                   alignPanel.av.getSequenceSelection(),
5760                                   alignPanel.alignFrame, dassrc,
5761                                   alignPanel.alignFrame.featureSettings,
5762                                   isNucleotide);
5763                           dbRefFetcher
5764                                   .addListener(new FetchFinishedListenerI()
5765                                   {
5766                                     @Override
5767                                     public void finished()
5768                                     {
5769                                       AlignFrame.this.setMenusForViewport();
5770                                     }
5771                                   });
5772                           dbRefFetcher.fetchDBRefs(false);
5773                         }
5774                       }).start();
5775                     }
5776
5777                   });
5778                   fetchr.setToolTipText("<html>"
5779                           + MessageManager.formatMessage(
5780                                   "label.fetch_retrieve_from", new Object[]
5781                                   { dbname }));
5782                   ifetch.add(fetchr);
5783                   ++i;
5784                   if (++icomp >= mcomp || i == (otherdb.size()))
5785                   {
5786                     ifetch.setText(MessageManager.formatMessage(
5787                             "label.source_to_target", imname, sname));
5788                     dfetch.add(ifetch);
5789                     ifetch = new JMenu();
5790                     imname = null;
5791                     icomp = 0;
5792                     comp++;
5793                   }
5794                 }
5795               }
5796               ++dbi;
5797               if (comp >= mcomp || dbi >= (dbclasses.length))
5798               {
5799                 dfetch.setText(MessageManager.formatMessage(
5800                         "label.source_to_target", mname, dbclass));
5801                 rfetch.add(dfetch);
5802                 dfetch = new JMenu();
5803                 mname = null;
5804                 comp = 0;
5805               }
5806             }
5807           }
5808         });
5809       }
5810     }).start();
5811
5812   }
5813
5814   /**
5815    * Left justify the whole alignment.
5816    */
5817   @Override
5818   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5819   {
5820     AlignmentI al = viewport.getAlignment();
5821     al.justify(false);
5822     viewport.firePropertyChange("alignment", null, al);
5823   }
5824
5825   /**
5826    * Right justify the whole alignment.
5827    */
5828   @Override
5829   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5830   {
5831     AlignmentI al = viewport.getAlignment();
5832     al.justify(true);
5833     viewport.firePropertyChange("alignment", null, al);
5834   }
5835
5836   @Override
5837   public void setShowSeqFeatures(boolean b)
5838   {
5839     showSeqFeatures.setSelected(b);
5840     viewport.setShowSequenceFeatures(b);
5841   }
5842
5843   /*
5844    * (non-Javadoc)
5845    *
5846    * @see
5847    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5848    * awt.event.ActionEvent)
5849    */
5850   @Override
5851   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5852   {
5853     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5854     alignPanel.paintAlignment(true);
5855   }
5856
5857   /*
5858    * (non-Javadoc)
5859    *
5860    * @see
5861    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5862    * .ActionEvent)
5863    */
5864   @Override
5865   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5866   {
5867     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5868     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5869
5870   }
5871
5872   /*
5873    * (non-Javadoc)
5874    *
5875    * @see
5876    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5877    * .event.ActionEvent)
5878    */
5879   @Override
5880   protected void showGroupConservation_actionPerformed(ActionEvent e)
5881   {
5882     viewport.setShowGroupConservation(showGroupConservation.getState());
5883     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5884   }
5885
5886   /*
5887    * (non-Javadoc)
5888    *
5889    * @see
5890    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5891    * .event.ActionEvent)
5892    */
5893   @Override
5894   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5895   {
5896     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5897     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5898   }
5899
5900   /*
5901    * (non-Javadoc)
5902    *
5903    * @see
5904    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5905    * .event.ActionEvent)
5906    */
5907   @Override
5908   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5909   {
5910     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5911     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5912   }
5913
5914   @Override
5915   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5916   {
5917     showSequenceLogo.setState(true);
5918     viewport.setShowSequenceLogo(true);
5919     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5920     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5921   }
5922
5923   @Override
5924   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5925   {
5926     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5927   }
5928
5929   /*
5930    * (non-Javadoc)
5931    *
5932    * @see
5933    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5934    * .event.ActionEvent)
5935    */
5936   @Override
5937   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5938   {
5939     if (avc.makeGroupsFromSelection())
5940     {
5941       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5942       alignPanel.updateAnnotation();
5943       alignPanel.paintAlignment(true);
5944     }
5945   }
5946
5947   public void clearAlignmentSeqRep()
5948   {
5949     // TODO refactor alignmentseqrep to controller
5950     if (viewport.getAlignment().hasSeqrep())
5951     {
5952       viewport.getAlignment().setSeqrep(null);
5953       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5954       alignPanel.updateAnnotation();
5955       alignPanel.paintAlignment(true);
5956     }
5957   }
5958
5959   @Override
5960   protected void createGroup_actionPerformed(ActionEvent e)
5961   {
5962     if (avc.createGroup())
5963     {
5964       alignPanel.alignmentChanged();
5965     }
5966   }
5967
5968   @Override
5969   protected void unGroup_actionPerformed(ActionEvent e)
5970   {
5971     if (avc.unGroup())
5972     {
5973       alignPanel.alignmentChanged();
5974     }
5975   }
5976
5977   /**
5978    * make the given alignmentPanel the currently selected tab
5979    *
5980    * @param alignmentPanel
5981    */
5982   public void setDisplayedView(AlignmentPanel alignmentPanel)
5983   {
5984     if (!viewport.getSequenceSetId().equals(
5985             alignmentPanel.av.getSequenceSetId()))
5986     {
5987       throw new Error(
5988               MessageManager
5989                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5990     }
5991     if (tabbedPane != null
5992             && tabbedPane.getTabCount() > 0
5993             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5994                     .getSelectedIndex())
5995     {
5996       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5997     }
5998   }
5999
6000   /**
6001    * Action on selection of menu options to Show or Hide annotations.
6002    *
6003    * @param visible
6004    * @param forSequences
6005    *          update sequence-related annotations
6006    * @param forAlignment
6007    *          update non-sequence-related annotations
6008    */
6009   @Override
6010   protected void setAnnotationsVisibility(boolean visible,
6011           boolean forSequences, boolean forAlignment)
6012   {
6013     for (AlignmentAnnotation aa : alignPanel.getAlignment()
6014             .getAlignmentAnnotation())
6015     {
6016       /*
6017        * don't display non-positional annotations on an alignment
6018        */
6019       if (aa.annotations == null)
6020       {
6021         continue;
6022       }
6023       boolean apply = (aa.sequenceRef == null && forAlignment)
6024               || (aa.sequenceRef != null && forSequences);
6025       if (apply)
6026       {
6027         aa.visible = visible;
6028       }
6029     }
6030     alignPanel.validateAnnotationDimensions(true);
6031     alignPanel.alignmentChanged();
6032   }
6033
6034   /**
6035    * Store selected annotation sort order for the view and repaint.
6036    */
6037   @Override
6038   protected void sortAnnotations_actionPerformed()
6039   {
6040     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6041     this.alignPanel.av
6042             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6043     alignPanel.paintAlignment(true);
6044   }
6045
6046   /**
6047    *
6048    * @return alignment panels in this alignment frame
6049    */
6050   public List<? extends AlignmentViewPanel> getAlignPanels()
6051   {
6052     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6053   }
6054
6055   /**
6056    * Open a new alignment window, with the cDNA associated with this (protein)
6057    * alignment, aligned as is the protein.
6058    */
6059   protected void viewAsCdna_actionPerformed()
6060   {
6061     // TODO no longer a menu action - refactor as required
6062     final AlignmentI alignment = getViewport().getAlignment();
6063     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6064     if (mappings == null)
6065     {
6066       return;
6067     }
6068     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6069     for (SequenceI aaSeq : alignment.getSequences())
6070     {
6071       for (AlignedCodonFrame acf : mappings)
6072       {
6073         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6074         if (dnaSeq != null)
6075         {
6076           /*
6077            * There is a cDNA mapping for this protein sequence - add to new
6078            * alignment. It will share the same dataset sequence as other mapped
6079            * cDNA (no new mappings need to be created).
6080            */
6081           final Sequence newSeq = new Sequence(dnaSeq);
6082           newSeq.setDatasetSequence(dnaSeq);
6083           cdnaSeqs.add(newSeq);
6084         }
6085       }
6086     }
6087     if (cdnaSeqs.size() == 0)
6088     {
6089       // show a warning dialog no mapped cDNA
6090       return;
6091     }
6092     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6093             .size()]));
6094     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6095             AlignFrame.DEFAULT_HEIGHT);
6096     cdna.alignAs(alignment);
6097     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6098             + this.title;
6099     Desktop.addInternalFrame(alignFrame, newtitle,
6100             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6101   }
6102
6103   /**
6104    * Set visibility of dna/protein complement view (available when shown in a
6105    * split frame).
6106    *
6107    * @param show
6108    */
6109   @Override
6110   protected void showComplement_actionPerformed(boolean show)
6111   {
6112     SplitContainerI sf = getSplitViewContainer();
6113     if (sf != null)
6114     {
6115       sf.setComplementVisible(this, show);
6116     }
6117   }
6118
6119   /**
6120    * Generate the reverse (optionally complemented) of the selected sequences,
6121    * and add them to the alignment
6122    */
6123   @Override
6124   protected void showReverse_actionPerformed(boolean complement)
6125   {
6126     AlignmentI al = null;
6127     try
6128     {
6129       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6130
6131       al = dna.reverseCdna(complement);
6132       viewport.addAlignment(al, "");
6133     } catch (Exception ex)
6134     {
6135       System.err.println(ex.getMessage());
6136       return;
6137     }
6138   }
6139 }
6140
6141 class PrintThread extends Thread
6142 {
6143   AlignmentPanel ap;
6144
6145   public PrintThread(AlignmentPanel ap)
6146   {
6147     this.ap = ap;
6148   }
6149
6150   static PageFormat pf;
6151
6152   @Override
6153   public void run()
6154   {
6155     PrinterJob printJob = PrinterJob.getPrinterJob();
6156
6157     if (pf != null)
6158     {
6159       printJob.setPrintable(ap, pf);
6160     }
6161     else
6162     {
6163       printJob.setPrintable(ap);
6164     }
6165
6166     if (printJob.printDialog())
6167     {
6168       try
6169       {
6170         printJob.print();
6171       } catch (Exception PrintException)
6172       {
6173         PrintException.printStackTrace();
6174       }
6175     }
6176   }
6177 }