src/jalview/gui/AlignFrame.java

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