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