src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.AAFrequency;
  24 import jalview.analysis.AlignmentSorter;
  25 import jalview.analysis.AlignmentUtils;
  26 import jalview.analysis.Conservation;
  27 import jalview.analysis.CrossRef;
  28 import jalview.analysis.NJTree;
  29 import jalview.analysis.ParseProperties;
  30 import jalview.analysis.SequenceIdMatcher;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.analysis.ScoreModelI;
  35 import jalview.bin.Cache;
  36 import jalview.commands.CommandI;
  37 import jalview.commands.EditCommand;
  38 import jalview.commands.EditCommand.Action;
  39 import jalview.commands.OrderCommand;
  40 import jalview.commands.RemoveGapColCommand;
  41 import jalview.commands.RemoveGapsCommand;
  42 import jalview.commands.SlideSequencesCommand;
  43 import jalview.commands.TrimRegionCommand;
  44 import jalview.datamodel.AlignedCodonFrame;
  45 import jalview.datamodel.Alignment;
  46 import jalview.datamodel.AlignmentAnnotation;
  47 import jalview.datamodel.AlignmentI;
  48 import jalview.datamodel.AlignmentOrder;
  49 import jalview.datamodel.AlignmentView;
  50 import jalview.datamodel.ColumnSelection;
  51 import jalview.datamodel.PDBEntry;
  52 import jalview.datamodel.SeqCigar;
  53 import jalview.datamodel.Sequence;
  54 import jalview.datamodel.SequenceGroup;
  55 import jalview.datamodel.SequenceI;
  56 import jalview.io.AlignmentProperties;
  57 import jalview.io.AnnotationFile;
  58 import jalview.io.FeaturesFile;
  59 import jalview.io.FileLoader;
  60 import jalview.io.FormatAdapter;
  61 import jalview.io.HTMLOutput;
  62 import jalview.io.IdentifyFile;
  63 import jalview.io.JalviewFileChooser;
  64 import jalview.io.JalviewFileView;
  65 import jalview.io.JnetAnnotationMaker;
  66 import jalview.io.NewickFile;
  67 import jalview.io.TCoffeeScoreFile;
  68 import jalview.jbgui.GAlignFrame;
  69 import jalview.schemes.Blosum62ColourScheme;
  70 import jalview.schemes.BuriedColourScheme;
  71 import jalview.schemes.ClustalxColourScheme;
  72 import jalview.schemes.ColourSchemeI;
  73 import jalview.schemes.ColourSchemeProperty;
  74 import jalview.schemes.HelixColourScheme;
  75 import jalview.schemes.HydrophobicColourScheme;
  76 import jalview.schemes.NucleotideColourScheme;
  77 import jalview.schemes.PIDColourScheme;
  78 import jalview.schemes.PurinePyrimidineColourScheme;
  79 import jalview.schemes.RNAHelicesColourChooser;
  80 import jalview.schemes.ResidueProperties;
  81 import jalview.schemes.StrandColourScheme;
  82 import jalview.schemes.TCoffeeColourScheme;
  83 import jalview.schemes.TaylorColourScheme;
  84 import jalview.schemes.TurnColourScheme;
  85 import jalview.schemes.UserColourScheme;
  86 import jalview.schemes.ZappoColourScheme;
  87 import jalview.structure.StructureSelectionManager;
  88 import jalview.util.MessageManager;
  89 import jalview.ws.jws1.Discoverer;
  90 import jalview.ws.jws2.Jws2Discoverer;
  91 import jalview.ws.jws2.jabaws2.Jws2Instance;
  92 import jalview.ws.seqfetcher.DbSourceProxy;
  93
  94 import java.awt.BorderLayout;
  95 import java.awt.Component;
  96 import java.awt.GridLayout;
  97 import java.awt.Rectangle;
  98 import java.awt.Toolkit;
  99 import java.awt.datatransfer.Clipboard;
 100 import java.awt.datatransfer.DataFlavor;
 101 import java.awt.datatransfer.StringSelection;
 102 import java.awt.datatransfer.Transferable;
 103 import java.awt.dnd.DnDConstants;
 104 import java.awt.dnd.DropTargetDragEvent;
 105 import java.awt.dnd.DropTargetDropEvent;
 106 import java.awt.dnd.DropTargetEvent;
 107 import java.awt.dnd.DropTargetListener;
 108 import java.awt.event.ActionEvent;
 109 import java.awt.event.ActionListener;
 110 import java.awt.event.KeyAdapter;
 111 import java.awt.event.KeyEvent;
 112 import java.awt.event.MouseAdapter;
 113 import java.awt.event.MouseEvent;
 114 import java.awt.print.PageFormat;
 115 import java.awt.print.PrinterJob;
 116 import java.beans.PropertyChangeEvent;
 117 import java.io.File;
 118 import java.net.URL;
 119 import java.util.ArrayList;
 120 import java.util.Arrays;
 121 import java.util.Enumeration;
 122 import java.util.Hashtable;
 123 import java.util.List;
 124 import java.util.Vector;
 125
 126 import javax.swing.JButton;
 127 import javax.swing.JCheckBoxMenuItem;
 128 import javax.swing.JEditorPane;
 129 import javax.swing.JInternalFrame;
 130 import javax.swing.JLabel;
 131 import javax.swing.JLayeredPane;
 132 import javax.swing.JMenu;
 133 import javax.swing.JMenuItem;
 134 import javax.swing.JOptionPane;
 135 import javax.swing.JPanel;
 136 import javax.swing.JProgressBar;
 137 import javax.swing.JRadioButtonMenuItem;
 138 import javax.swing.JScrollPane;
 139 import javax.swing.SwingUtilities;
 140
 141 /**
 142  * DOCUMENT ME!
 143  *
 144  * @author $author$
 145  * @version $Revision$
 146  */
 147 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 148         IProgressIndicator, AlignViewControllerGuiI
 149 {
 150
 151   /** DOCUMENT ME!! */
 152   public static final int DEFAULT_WIDTH = 700;
 153
 154   /** DOCUMENT ME!! */
 155   public static final int DEFAULT_HEIGHT = 500;
 156
 157   public AlignmentPanel alignPanel;
 158
 159   AlignViewport viewport;
 160
 161   public AlignViewControllerI avc;
 162
 163   Vector alignPanels = new Vector();
 164
 165   /**
 166    * Last format used to load or save alignments in this window
 167    */
 168   String currentFileFormat = null;
 169
 170   /**
 171    * Current filename for this alignment
 172    */
 173   String fileName = null;
 174
 175   /**
 176    * Creates a new AlignFrame object with specific width and height.
 177    *
 178    * @param al
 179    * @param width
 180    * @param height
 181    */
 182   public AlignFrame(AlignmentI al, int width, int height)
 183   {
 184     this(al, null, width, height);
 185   }
 186
 187   /**
 188    * Creates a new AlignFrame object with specific width, height and
 189    * sequenceSetId
 190    *
 191    * @param al
 192    * @param width
 193    * @param height
 194    * @param sequenceSetId
 195    */
 196   public AlignFrame(AlignmentI al, int width, int height,
 197           String sequenceSetId)
 198   {
 199     this(al, null, width, height, sequenceSetId);
 200   }
 201
 202   /**
 203    * Creates a new AlignFrame object with specific width, height and
 204    * sequenceSetId
 205    *
 206    * @param al
 207    * @param width
 208    * @param height
 209    * @param sequenceSetId
 210    * @param viewId
 211    */
 212   public AlignFrame(AlignmentI al, int width, int height,
 213           String sequenceSetId, String viewId)
 214   {
 215     this(al, null, width, height, sequenceSetId, viewId);
 216   }
 217
 218   /**
 219    * new alignment window with hidden columns
 220    *
 221    * @param al
 222    *          AlignmentI
 223    * @param hiddenColumns
 224    *          ColumnSelection or null
 225    * @param width
 226    *          Width of alignment frame
 227    * @param height
 228    *          height of frame.
 229    */
 230   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 231           int width, int height)
 232   {
 233     this(al, hiddenColumns, width, height, null);
 234   }
 235
 236   /**
 237    * Create alignment frame for al with hiddenColumns, a specific width and
 238    * height, and specific sequenceId
 239    *
 240    * @param al
 241    * @param hiddenColumns
 242    * @param width
 243    * @param height
 244    * @param sequenceSetId
 245    *          (may be null)
 246    */
 247   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 248           int width, int height, String sequenceSetId)
 249   {
 250     this(al, hiddenColumns, width, height, sequenceSetId, null);
 251   }
 252
 253   /**
 254    * Create alignment frame for al with hiddenColumns, a specific width and
 255    * height, and specific sequenceId
 256    *
 257    * @param al
 258    * @param hiddenColumns
 259    * @param width
 260    * @param height
 261    * @param sequenceSetId
 262    *          (may be null)
 263    * @param viewId
 264    *          (may be null)
 265    */
 266   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 267           int width, int height, String sequenceSetId, String viewId)
 268   {
 269     setSize(width, height);
 270
 271     if (al.getDataset() == null)
 272     {
 273       al.setDataset(null);
 274     }
 275
 276     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 277
 278     alignPanel = new AlignmentPanel(this, viewport);
 279
 280
 281     addAlignmentPanel(alignPanel, true);
 282     init();
 283   }
 284
 285   /**
 286    * Make a new AlignFrame from existing alignmentPanels
 287    *
 288    * @param ap
 289    *          AlignmentPanel
 290    * @param av
 291    *          AlignViewport
 292    */
 293   public AlignFrame(AlignmentPanel ap)
 294   {
 295     viewport = ap.av;
 296     alignPanel = ap;
 297     addAlignmentPanel(ap, false);
 298     init();
 299   }
 300
 301   /**
 302    * initalise the alignframe from the underlying viewport data and the
 303    * configurations
 304    */
 305   void init()
 306   {
 307     avc = new jalview.controller.AlignViewController(this, viewport,
 308             alignPanel);
 309     if (viewport.getAlignmentConservationAnnotation() == null)
 310     {
 311       BLOSUM62Colour.setEnabled(false);
 312       conservationMenuItem.setEnabled(false);
 313       modifyConservation.setEnabled(false);
 314       // PIDColour.setEnabled(false);
 315       // abovePIDThreshold.setEnabled(false);
 316       // modifyPID.setEnabled(false);
 317     }
 318
 319     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 320             "No sort");
 321
 322     if (sortby.equals("Id"))
 323     {
 324       sortIDMenuItem_actionPerformed(null);
 325     }
 326     else if (sortby.equals("Pairwise Identity"))
 327     {
 328       sortPairwiseMenuItem_actionPerformed(null);
 329     }
 330
 331     if (Desktop.desktop != null)
 332     {
 333       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 334       addServiceListeners();
 335       setGUINucleotide(viewport.getAlignment().isNucleotide());
 336     }
 337
 338     setMenusFromViewport(viewport);
 339     buildSortByAnnotationScoresMenu();
 340     buildTreeMenu();
 341
 342     if (viewport.wrapAlignment)
 343     {
 344       wrapMenuItem_actionPerformed(null);
 345     }
 346
 347     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 348     {
 349       this.overviewMenuItem_actionPerformed(null);
 350     }
 351
 352     addKeyListener();
 353
 354   }
 355
 356   /**
 357    * Change the filename and format for the alignment, and enable the 'reload'
 358    * button functionality.
 359    *
 360    * @param file
 361    *          valid filename
 362    * @param format
 363    *          format of file
 364    */
 365   public void setFileName(String file, String format)
 366   {
 367     fileName = file;
 368     currentFileFormat = format;
 369     reload.setEnabled(true);
 370   }
 371
 372   void addKeyListener()
 373   {
 374     addKeyListener(new KeyAdapter()
 375     {
 376       @Override
 377       public void keyPressed(KeyEvent evt)
 378       {
 379         if (viewport.cursorMode
 380                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 381                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 382                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 383                 && Character.isDigit(evt.getKeyChar()))
 384         {
 385           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 386         }
 387
 388         switch (evt.getKeyCode())
 389         {
 390
 391         case 27: // escape key
 392           deselectAllSequenceMenuItem_actionPerformed(null);
 393
 394           break;
 395
 396         case KeyEvent.VK_DOWN:
 397           if (evt.isAltDown() || !viewport.cursorMode)
 398           {
 399             moveSelectedSequences(false);
 400           }
 401           if (viewport.cursorMode)
 402           {
 403             alignPanel.seqPanel.moveCursor(0, 1);
 404           }
 405           break;
 406
 407         case KeyEvent.VK_UP:
 408           if (evt.isAltDown() || !viewport.cursorMode)
 409           {
 410             moveSelectedSequences(true);
 411           }
 412           if (viewport.cursorMode)
 413           {
 414             alignPanel.seqPanel.moveCursor(0, -1);
 415           }
 416
 417           break;
 418
 419         case KeyEvent.VK_LEFT:
 420           if (evt.isAltDown() || !viewport.cursorMode)
 421           {
 422             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 423           }
 424           else
 425           {
 426             alignPanel.seqPanel.moveCursor(-1, 0);
 427           }
 428
 429           break;
 430
 431         case KeyEvent.VK_RIGHT:
 432           if (evt.isAltDown() || !viewport.cursorMode)
 433           {
 434             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 435           }
 436           else
 437           {
 438             alignPanel.seqPanel.moveCursor(1, 0);
 439           }
 440           break;
 441
 442         case KeyEvent.VK_SPACE:
 443           if (viewport.cursorMode)
 444           {
 445             alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 446                     || evt.isShiftDown() || evt.isAltDown());
 447           }
 448           break;
 449
 450         // case KeyEvent.VK_A:
 451         // if (viewport.cursorMode)
 452         // {
 453         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 454         // //System.out.println("A");
 455         // }
 456         // break;
 457         /*
 458          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 459          * System.out.println("closing bracket"); } break;
 460          */
 461         case KeyEvent.VK_DELETE:
 462         case KeyEvent.VK_BACK_SPACE:
 463           if (!viewport.cursorMode)
 464           {
 465             cut_actionPerformed(null);
 466           }
 467           else
 468           {
 469             alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 470                     || evt.isShiftDown() || evt.isAltDown());
 471           }
 472
 473           break;
 474
 475         case KeyEvent.VK_S:
 476           if (viewport.cursorMode)
 477           {
 478             alignPanel.seqPanel.setCursorRow();
 479           }
 480           break;
 481         case KeyEvent.VK_C:
 482           if (viewport.cursorMode && !evt.isControlDown())
 483           {
 484             alignPanel.seqPanel.setCursorColumn();
 485           }
 486           break;
 487         case KeyEvent.VK_P:
 488           if (viewport.cursorMode)
 489           {
 490             alignPanel.seqPanel.setCursorPosition();
 491           }
 492           break;
 493
 494         case KeyEvent.VK_ENTER:
 495         case KeyEvent.VK_COMMA:
 496           if (viewport.cursorMode)
 497           {
 498             alignPanel.seqPanel.setCursorRowAndColumn();
 499           }
 500           break;
 501
 502         case KeyEvent.VK_Q:
 503           if (viewport.cursorMode)
 504           {
 505             alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 506           }
 507           break;
 508         case KeyEvent.VK_M:
 509           if (viewport.cursorMode)
 510           {
 511             alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 512           }
 513           break;
 514
 515         case KeyEvent.VK_F2:
 516           viewport.cursorMode = !viewport.cursorMode;
 517           statusBar.setText(MessageManager.formatMessage(
 518                   "label.keyboard_editing_mode", new String[]
 519                   { (viewport.cursorMode ? "on" : "off") }));
 520           if (viewport.cursorMode)
 521           {
 522             alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 523             alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 524           }
 525           alignPanel.seqPanel.seqCanvas.repaint();
 526           break;
 527
 528         case KeyEvent.VK_F1:
 529           try
 530           {
 531             Help.showHelpWindow();
 532           } catch (Exception ex)
 533           {
 534             ex.printStackTrace();
 535           }
 536           break;
 537         case KeyEvent.VK_H:
 538         {
 539           boolean toggleSeqs = !evt.isControlDown();
 540           boolean toggleCols = !evt.isShiftDown();
 541           toggleHiddenRegions(toggleSeqs, toggleCols);
 542           break;
 543         }
 544         case KeyEvent.VK_PAGE_UP:
 545           if (viewport.wrapAlignment)
 546           {
 547             alignPanel.scrollUp(true);
 548           }
 549           else
 550           {
 551             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 552                     - viewport.endSeq + viewport.startSeq);
 553           }
 554           break;
 555         case KeyEvent.VK_PAGE_DOWN:
 556           if (viewport.wrapAlignment)
 557           {
 558             alignPanel.scrollUp(false);
 559           }
 560           else
 561           {
 562             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 563                     + viewport.endSeq - viewport.startSeq);
 564           }
 565           break;
 566         }
 567       }
 568
 569       @Override
 570       public void keyReleased(KeyEvent evt)
 571       {
 572         switch (evt.getKeyCode())
 573         {
 574         case KeyEvent.VK_LEFT:
 575           if (evt.isAltDown() || !viewport.cursorMode)
 576           {
 577             viewport.firePropertyChange("alignment", null, viewport
 578                     .getAlignment().getSequences());
 579           }
 580           break;
 581
 582         case KeyEvent.VK_RIGHT:
 583           if (evt.isAltDown() || !viewport.cursorMode)
 584           {
 585             viewport.firePropertyChange("alignment", null, viewport
 586                     .getAlignment().getSequences());
 587           }
 588           break;
 589         }
 590       }
 591     });
 592   }
 593
 594   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 595   {
 596     ap.alignFrame = this;
 597     avc = new jalview.controller.AlignViewController(this, viewport,
 598             alignPanel);
 599
 600     alignPanels.addElement(ap);
 601
 602     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 603
 604     int aSize = alignPanels.size();
 605
 606     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 607
 608     if (aSize == 1 && ap.av.viewName == null)
 609     {
 610       this.getContentPane().add(ap, BorderLayout.CENTER);
 611     }
 612     else
 613     {
 614       if (aSize == 2)
 615       {
 616         setInitialTabVisible();
 617       }
 618
 619       expandViews.setEnabled(true);
 620       gatherViews.setEnabled(true);
 621       tabbedPane.addTab(ap.av.viewName, ap);
 622
 623       ap.setVisible(false);
 624     }
 625
 626     if (newPanel)
 627     {
 628       if (ap.av.isPadGaps())
 629       {
 630         ap.av.getAlignment().padGaps();
 631       }
 632       ap.av.updateConservation(ap);
 633       ap.av.updateConsensus(ap);
 634       ap.av.updateStrucConsensus(ap);
 635     }
 636   }
 637
 638   public void setInitialTabVisible()
 639   {
 640     expandViews.setEnabled(true);
 641     gatherViews.setEnabled(true);
 642     tabbedPane.setVisible(true);
 643     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
 644     tabbedPane.addTab(first.av.viewName, first);
 645     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 646   }
 647
 648   public AlignViewport getViewport()
 649   {
 650     return viewport;
 651   }
 652
 653   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 654   private void addServiceListeners()
 655   {
 656     final java.beans.PropertyChangeListener thisListener;
 657     Desktop.instance.addJalviewPropertyChangeListener("services",
 658             thisListener = new java.beans.PropertyChangeListener()
 659             {
 660               @Override
 661               public void propertyChange(PropertyChangeEvent evt)
 662               {
 663                 // // System.out.println("Discoverer property change.");
 664                 // if (evt.getPropertyName().equals("services"))
 665                 {
 666                   SwingUtilities.invokeLater(new Runnable()
 667                   {
 668
 669                     @Override
 670                     public void run()
 671                     {
 672                       System.err
 673                               .println("Rebuild WS Menu for service change");
 674                       BuildWebServiceMenu();
 675                     }
 676
 677                   });
 678                 }
 679               }
 680             });
 681     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 682     {
 683       @Override
 684       public void internalFrameClosed(
 685               javax.swing.event.InternalFrameEvent evt)
 686       {
 687         System.out.println("deregistering discoverer listener");
 688         Desktop.instance.removeJalviewPropertyChangeListener("services",
 689                 thisListener);
 690         closeMenuItem_actionPerformed(true);
 691       };
 692     });
 693     // Finally, build the menu once to get current service state
 694     new Thread(new Runnable()
 695     {
 696       @Override
 697       public void run()
 698       {
 699         BuildWebServiceMenu();
 700       }
 701     }).start();
 702   }
 703
 704   public void setGUINucleotide(boolean nucleotide)
 705   {
 706     showTranslation.setVisible(nucleotide);
 707     cdna.setVisible(!nucleotide);
 708     conservationMenuItem.setEnabled(!nucleotide);
 709     modifyConservation.setEnabled(!nucleotide);
 710     showGroupConservation.setEnabled(!nucleotide);
 711     rnahelicesColour.setEnabled(nucleotide);
 712     purinePyrimidineColour.setEnabled(nucleotide);
 713   }
 714
 715   /**
 716    * Builds codon mappings from this (protein) alignment to any compatible
 717    * nucleotide alignments. Mappings are built between sequences with the same
 718    * name and compatible lengths. Also makes the cDNA alignment a
 719    * CommandListener for the protein alignment so that edits are mirrored.
 720    */
 721   @Override
 722   protected void linkCdna_actionPerformed()
 723   {
 724     int linkedCount = 0;
 725     int alreadyLinkedCount = 0;
 726     final AlignmentI thisAlignment = this.alignPanel.getAlignment();
 727
 728     for (AlignFrame af : Desktop.getAlignframes())
 729     {
 730       if (af.alignPanel != null)
 731       {
 732         final AlignmentI thatAlignment = af.alignPanel.getAlignment();
 733         if (thatAlignment.isNucleotide())
 734         {
 735           // TODO exclude an AlignFrame which is already mapped to this one
 736           // temporary version: exclude if already a CommandListener (should
 737           // cover most cases but not all)
 738           final boolean alreadyMapped = this.viewport
 739                   .getStructureSelectionManager().hasCommandListener(
 740                           af.viewport);
 741           if (alreadyMapped)
 742           {
 743             alreadyLinkedCount++;
 744           }
 745           else
 746           {
 747             boolean mapped = AlignmentUtils.mapProteinToCdna(thisAlignment,
 748                     thatAlignment);
 749             if (mapped)
 750             {
 751               final StructureSelectionManager ssm = StructureSelectionManager
 752                       .getStructureSelectionManager(Desktop.instance);
 753               ssm.addMappings(thisAlignment.getCodonFrames());
 754               ssm.addCommandListener(af.getViewport());
 755               linkedCount++;
 756             }
 757           }
 758         }
 759       }
 760     }
 761     String msg = "";
 762     if (linkedCount == 0 && alreadyLinkedCount == 0)
 763     {
 764       msg = MessageManager.getString("label.no_cdna");
 765     }
 766     else if (linkedCount > 0)
 767     {
 768       msg = MessageManager.formatMessage("label.linked_cdna", linkedCount);
 769     }
 770     else
 771     {
 772       msg = MessageManager.formatMessage("label.cdna_all_linked",
 773               alreadyLinkedCount);
 774     }
 775     setStatus(msg);
 776   }
 777
 778   /**
 779    * Align any linked cDNA to match the alignment of this (protein) alignment.
 780    * Any mapped sequence regions will be realigned, unmapped sequences are not
 781    * affected.
 782    */
 783   @Override
 784   protected void alignCdna_actionPerformed()
 785   {
 786     int seqCount = 0;
 787     int alignCount = 0;
 788     final AlignmentI thisAlignment = this.alignPanel.getAlignment();
 789     for (AlignFrame af : Desktop.getAlignframes())
 790     {
 791       if (af.alignPanel != null)
 792       {
 793         final AlignmentI thatAlignment = af.alignPanel.getAlignment();
 794         if (thatAlignment.isNucleotide())
 795         {
 796           int seqsAligned = thatAlignment.alignAs(thisAlignment);
 797           seqCount += seqsAligned;
 798           if (seqsAligned > 0)
 799           {
 800             af.alignPanel.alignmentChanged();
 801             alignCount++;
 802           }
 803         }
 804       }
 805     }
 806     setStatus(MessageManager.formatMessage("label.cdna_aligned", seqCount,
 807             alignCount));
 808   }
 809   /**
 810    * set up menus for the current viewport. This may be called after any
 811    * operation that affects the data in the current view (selection changed,
 812    * etc) to update the menus to reflect the new state.
 813    */
 814   public void setMenusForViewport()
 815   {
 816     setMenusFromViewport(viewport);
 817   }
 818
 819   /**
 820    * Need to call this method when tabs are selected for multiple views, or when
 821    * loading from Jalview2XML.java
 822    *
 823    * @param av
 824    *          AlignViewport
 825    */
 826   void setMenusFromViewport(AlignViewport av)
 827   {
 828     padGapsMenuitem.setSelected(av.isPadGaps());
 829     colourTextMenuItem.setSelected(av.showColourText);
 830     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 831     conservationMenuItem.setSelected(av.getConservationSelected());
 832     seqLimits.setSelected(av.getShowJVSuffix());
 833     idRightAlign.setSelected(av.rightAlignIds);
 834     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
 835     renderGapsMenuItem.setSelected(av.renderGaps);
 836     wrapMenuItem.setSelected(av.wrapAlignment);
 837     scaleAbove.setVisible(av.wrapAlignment);
 838     scaleLeft.setVisible(av.wrapAlignment);
 839     scaleRight.setVisible(av.wrapAlignment);
 840     annotationPanelMenuItem.setState(av.showAnnotation);
 841     /*
 842      * Show/hide annotations only enabled if annotation panel is shown
 843      */
 844     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 845     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 846     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 847     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 848     viewBoxesMenuItem.setSelected(av.showBoxes);
 849     viewTextMenuItem.setSelected(av.showText);
 850     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 851     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 852     showGroupConservation.setSelected(av.isShowGroupConservation());
 853     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 854     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 855     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 856
 857     setColourSelected(ColourSchemeProperty.getColourName(av
 858             .getGlobalColourScheme()));
 859
 860     showSeqFeatures.setSelected(av.showSequenceFeatures);
 861     hiddenMarkers.setState(av.showHiddenMarkers);
 862     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 863     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
 864     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
 865     autoCalculate.setSelected(av.autoCalculateConsensus);
 866     sortByTree.setSelected(av.sortByTree);
 867     listenToViewSelections.setSelected(av.followSelection);
 868     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 869     rnahelicesColour
 870             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 871     setShowProductsEnabled();
 872     updateEditMenuBar();
 873   }
 874
 875   // methods for implementing IProgressIndicator
 876   // need to refactor to a reusable stub class
 877   Hashtable progressBars, progressBarHandlers;
 878
 879   /*
 880    * (non-Javadoc)
 881    *
 882    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 883    */
 884   @Override
 885   public void setProgressBar(String message, long id)
 886   {
 887     if (progressBars == null)
 888     {
 889       progressBars = new Hashtable();
 890       progressBarHandlers = new Hashtable();
 891     }
 892
 893     JPanel progressPanel;
 894     Long lId = new Long(id);
 895     GridLayout layout = (GridLayout) statusPanel.getLayout();
 896     if (progressBars.get(lId) != null)
 897     {
 898       progressPanel = (JPanel) progressBars.get(new Long(id));
 899       statusPanel.remove(progressPanel);
 900       progressBars.remove(lId);
 901       progressPanel = null;
 902       if (message != null)
 903       {
 904         statusBar.setText(message);
 905       }
 906       if (progressBarHandlers.contains(lId))
 907       {
 908         progressBarHandlers.remove(lId);
 909       }
 910       layout.setRows(layout.getRows() - 1);
 911     }
 912     else
 913     {
 914       progressPanel = new JPanel(new BorderLayout(10, 5));
 915
 916       JProgressBar progressBar = new JProgressBar();
 917       progressBar.setIndeterminate(true);
 918
 919       progressPanel.add(new JLabel(message), BorderLayout.WEST);
 920       progressPanel.add(progressBar, BorderLayout.CENTER);
 921
 922       layout.setRows(layout.getRows() + 1);
 923       statusPanel.add(progressPanel);
 924
 925       progressBars.put(lId, progressPanel);
 926     }
 927     // update GUI
 928     // setMenusForViewport();
 929     validate();
 930   }
 931
 932   @Override
 933   public void registerHandler(final long id,
 934           final IProgressIndicatorHandler handler)
 935   {
 936     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
 937     {
 938       throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
 939     }
 940     progressBarHandlers.put(new Long(id), handler);
 941     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
 942     if (handler.canCancel())
 943     {
 944       JButton cancel = new JButton(
 945               MessageManager.getString("action.cancel"));
 946       final IProgressIndicator us = this;
 947       cancel.addActionListener(new ActionListener()
 948       {
 949
 950         @Override
 951         public void actionPerformed(ActionEvent e)
 952         {
 953           handler.cancelActivity(id);
 954           us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
 955         }
 956       });
 957       progressPanel.add(cancel, BorderLayout.EAST);
 958     }
 959   }
 960
 961   /**
 962    *
 963    * @return true if any progress bars are still active
 964    */
 965   @Override
 966   public boolean operationInProgress()
 967   {
 968     if (progressBars != null && progressBars.size() > 0)
 969     {
 970       return true;
 971     }
 972     return false;
 973   }
 974
 975   @Override
 976   public void setStatus(String text)
 977   {
 978     statusBar.setText(text);
 979   };
 980
 981   /*
 982    * Added so Castor Mapping file can obtain Jalview Version
 983    */
 984   public String getVersion()
 985   {
 986     return jalview.bin.Cache.getProperty("VERSION");
 987   }
 988
 989   public FeatureRenderer getFeatureRenderer()
 990   {
 991     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
 992   }
 993
 994   @Override
 995   public void fetchSequence_actionPerformed(ActionEvent e)
 996   {
 997     new SequenceFetcher(this);
 998   }
 999
1000   @Override
1001   public void addFromFile_actionPerformed(ActionEvent e)
1002   {
1003     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1004   }
1005
1006   @Override
1007   public void reload_actionPerformed(ActionEvent e)
1008   {
1009     if (fileName != null)
1010     {
1011       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1012       // originating file's format
1013       // TODO: work out how to recover feature settings for correct view(s) when
1014       // file is reloaded.
1015       if (currentFileFormat.equals("Jalview"))
1016       {
1017         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1018         for (int i = 0; i < frames.length; i++)
1019         {
1020           if (frames[i] instanceof AlignFrame && frames[i] != this
1021                   && ((AlignFrame) frames[i]).fileName != null
1022                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1023           {
1024             try
1025             {
1026               frames[i].setSelected(true);
1027               Desktop.instance.closeAssociatedWindows();
1028             } catch (java.beans.PropertyVetoException ex)
1029             {
1030             }
1031           }
1032
1033         }
1034         Desktop.instance.closeAssociatedWindows();
1035
1036         FileLoader loader = new FileLoader();
1037         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1038         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1039       }
1040       else
1041       {
1042         Rectangle bounds = this.getBounds();
1043
1044         FileLoader loader = new FileLoader();
1045         String protocol = fileName.startsWith("http:") ? "URL" : "File";
1046         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1047                 protocol, currentFileFormat);
1048
1049         newframe.setBounds(bounds);
1050         if (featureSettings != null && featureSettings.isShowing())
1051         {
1052           final Rectangle fspos = featureSettings.frame.getBounds();
1053           // TODO: need a 'show feature settings' function that takes bounds -
1054           // need to refactor Desktop.addFrame
1055           newframe.featureSettings_actionPerformed(null);
1056           final FeatureSettings nfs = newframe.featureSettings;
1057           SwingUtilities.invokeLater(new Runnable()
1058           {
1059             @Override
1060             public void run()
1061             {
1062               nfs.frame.setBounds(fspos);
1063             }
1064           });
1065           this.featureSettings.close();
1066           this.featureSettings = null;
1067         }
1068         this.closeMenuItem_actionPerformed(true);
1069       }
1070     }
1071   }
1072
1073   @Override
1074   public void addFromText_actionPerformed(ActionEvent e)
1075   {
1076     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
1077   }
1078
1079   @Override
1080   public void addFromURL_actionPerformed(ActionEvent e)
1081   {
1082     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1083   }
1084
1085   @Override
1086   public void save_actionPerformed(ActionEvent e)
1087   {
1088     if (fileName == null
1089             || (currentFileFormat == null || !jalview.io.FormatAdapter
1090                     .isValidIOFormat(currentFileFormat, true))
1091             || fileName.startsWith("http"))
1092     {
1093       saveAs_actionPerformed(null);
1094     }
1095     else
1096     {
1097       saveAlignment(fileName, currentFileFormat);
1098     }
1099   }
1100
1101   /**
1102    * DOCUMENT ME!
1103    *
1104    * @param e
1105    *          DOCUMENT ME!
1106    */
1107   @Override
1108   public void saveAs_actionPerformed(ActionEvent e)
1109   {
1110     JalviewFileChooser chooser = new JalviewFileChooser(
1111             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1112             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1113             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1114             currentFileFormat, false);
1115
1116     chooser.setFileView(new JalviewFileView());
1117     chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1118     chooser.setToolTipText(MessageManager.getString("action.save"));
1119
1120     int value = chooser.showSaveDialog(this);
1121
1122     if (value == JalviewFileChooser.APPROVE_OPTION)
1123     {
1124       currentFileFormat = chooser.getSelectedFormat();
1125       while (currentFileFormat == null)
1126       {
1127         JOptionPane
1128                 .showInternalMessageDialog(
1129                         Desktop.desktop,
1130                         MessageManager
1131                                 .getString("label.select_file_format_before_saving"),
1132                         MessageManager
1133                                 .getString("label.file_format_not_specified"),
1134                         JOptionPane.WARNING_MESSAGE);
1135         currentFileFormat = chooser.getSelectedFormat();
1136         value = chooser.showSaveDialog(this);
1137         if (value != JalviewFileChooser.APPROVE_OPTION)
1138         {
1139           return;
1140         }
1141       }
1142
1143       fileName = chooser.getSelectedFile().getPath();
1144
1145       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1146               currentFileFormat);
1147
1148       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1149       if (currentFileFormat.indexOf(" ") > -1)
1150       {
1151         currentFileFormat = currentFileFormat.substring(0,
1152                 currentFileFormat.indexOf(" "));
1153       }
1154       saveAlignment(fileName, currentFileFormat);
1155     }
1156   }
1157
1158   public boolean saveAlignment(String file, String format)
1159   {
1160     boolean success = true;
1161
1162     if (format.equalsIgnoreCase("Jalview"))
1163     {
1164       String shortName = title;
1165
1166       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1167       {
1168         shortName = shortName.substring(shortName
1169                 .lastIndexOf(java.io.File.separatorChar) + 1);
1170       }
1171
1172       success = new Jalview2XML().SaveAlignment(this, file, shortName);
1173
1174       statusBar.setText(MessageManager.formatMessage(
1175               "label.successfully_saved_to_file_in_format", new String[]
1176               { fileName, format }));
1177
1178     }
1179     else
1180     {
1181       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1182       {
1183         warningMessage("Cannot save file " + fileName + " using format "
1184                 + format, "Alignment output format not supported");
1185         saveAs_actionPerformed(null);
1186         // JBPNote need to have a raise_gui flag here
1187         return false;
1188       }
1189
1190       String[] omitHidden = null;
1191
1192       if (viewport.hasHiddenColumns())
1193       {
1194         int reply = JOptionPane
1195                 .showInternalConfirmDialog(
1196                         Desktop.desktop,
1197                         MessageManager
1198                                 .getString("label.alignment_contains_hidden_columns"),
1199                         MessageManager
1200                                 .getString("action.save_omit_hidden_columns"),
1201                         JOptionPane.YES_NO_OPTION,
1202                         JOptionPane.QUESTION_MESSAGE);
1203
1204         if (reply == JOptionPane.YES_OPTION)
1205         {
1206           omitHidden = viewport.getViewAsString(false);
1207         }
1208       }
1209       FormatAdapter f = new FormatAdapter();
1210       String output = f.formatSequences(format,
1211               viewport.getAlignment(), // class cast exceptions will
1212               // occur in the distant future
1213               omitHidden, f.getCacheSuffixDefault(format),
1214               viewport.getColumnSelection());
1215
1216       if (output == null)
1217       {
1218         success = false;
1219       }
1220       else
1221       {
1222         try
1223         {
1224           java.io.PrintWriter out = new java.io.PrintWriter(
1225                   new java.io.FileWriter(file));
1226
1227           out.print(output);
1228           out.close();
1229           this.setTitle(file);
1230           statusBar.setText(MessageManager.formatMessage(
1231                   "label.successfully_saved_to_file_in_format",
1232                   new String[]
1233                   { fileName, format }));
1234         } catch (Exception ex)
1235         {
1236           success = false;
1237           ex.printStackTrace();
1238         }
1239       }
1240     }
1241
1242     if (!success)
1243     {
1244       JOptionPane.showInternalMessageDialog(this, MessageManager
1245               .formatMessage("label.couldnt_save_file", new String[]
1246               { fileName }), MessageManager
1247               .getString("label.error_saving_file"),
1248               JOptionPane.WARNING_MESSAGE);
1249     }
1250
1251     return success;
1252   }
1253
1254   private void warningMessage(String warning, String title)
1255   {
1256     if (new jalview.util.Platform().isHeadless())
1257     {
1258       System.err.println("Warning: " + title + "\nWarning: " + warning);
1259
1260     }
1261     else
1262     {
1263       JOptionPane.showInternalMessageDialog(this, warning, title,
1264               JOptionPane.WARNING_MESSAGE);
1265     }
1266     return;
1267   }
1268
1269   /**
1270    * DOCUMENT ME!
1271    *
1272    * @param e
1273    *          DOCUMENT ME!
1274    */
1275   @Override
1276   protected void outputText_actionPerformed(ActionEvent e)
1277   {
1278     String[] omitHidden = null;
1279
1280     if (viewport.hasHiddenColumns())
1281     {
1282       int reply = JOptionPane
1283               .showInternalConfirmDialog(
1284                       Desktop.desktop,
1285                       MessageManager
1286                               .getString("label.alignment_contains_hidden_columns"),
1287                       MessageManager
1288                               .getString("action.save_omit_hidden_columns"),
1289                       JOptionPane.YES_NO_OPTION,
1290                       JOptionPane.QUESTION_MESSAGE);
1291
1292       if (reply == JOptionPane.YES_OPTION)
1293       {
1294         omitHidden = viewport.getViewAsString(false);
1295       }
1296     }
1297
1298     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1299     cap.setForInput(null);
1300
1301     try
1302     {
1303       cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1304               viewport.getAlignment(), omitHidden,
1305               viewport.getColumnSelection()));
1306       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1307               "label.alignment_output_command", new String[]
1308               { e.getActionCommand() }), 600, 500);
1309     } catch (OutOfMemoryError oom)
1310     {
1311       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1312       cap.dispose();
1313     }
1314
1315   }
1316
1317   /**
1318    * DOCUMENT ME!
1319    *
1320    * @param e
1321    *          DOCUMENT ME!
1322    */
1323   @Override
1324   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1325   {
1326     new HTMLOutput(alignPanel,
1327             alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1328             alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1329   }
1330
1331   public void createImageMap(File file, String image)
1332   {
1333     alignPanel.makePNGImageMap(file, image);
1334   }
1335
1336   /**
1337    * DOCUMENT ME!
1338    *
1339    * @param e
1340    *          DOCUMENT ME!
1341    */
1342   @Override
1343   public void createPNG(File f)
1344   {
1345     alignPanel.makePNG(f);
1346   }
1347
1348   /**
1349    * DOCUMENT ME!
1350    *
1351    * @param e
1352    *          DOCUMENT ME!
1353    */
1354   @Override
1355   public void createEPS(File f)
1356   {
1357     alignPanel.makeEPS(f);
1358   }
1359
1360   public void createSVG(File f)
1361   {
1362     alignPanel.makeSVG(f);
1363   }
1364   @Override
1365   public void pageSetup_actionPerformed(ActionEvent e)
1366   {
1367     PrinterJob printJob = PrinterJob.getPrinterJob();
1368     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1369   }
1370
1371   /**
1372    * DOCUMENT ME!
1373    *
1374    * @param e
1375    *          DOCUMENT ME!
1376    */
1377   @Override
1378   public void printMenuItem_actionPerformed(ActionEvent e)
1379   {
1380     // Putting in a thread avoids Swing painting problems
1381     PrintThread thread = new PrintThread(alignPanel);
1382     thread.start();
1383   }
1384
1385   @Override
1386   public void exportFeatures_actionPerformed(ActionEvent e)
1387   {
1388     new AnnotationExporter().exportFeatures(alignPanel);
1389   }
1390
1391   @Override
1392   public void exportAnnotations_actionPerformed(ActionEvent e)
1393   {
1394     new AnnotationExporter().exportAnnotations(alignPanel,
1395             viewport.showAnnotation ? viewport.getAlignment()
1396                     .getAlignmentAnnotation() : null, viewport
1397                     .getAlignment().getGroups(), ((Alignment) viewport
1398                     .getAlignment()).alignmentProperties);
1399   }
1400
1401   @Override
1402   public void associatedData_actionPerformed(ActionEvent e)
1403   {
1404     // Pick the tree file
1405     JalviewFileChooser chooser = new JalviewFileChooser(
1406             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1407     chooser.setFileView(new JalviewFileView());
1408     chooser.setDialogTitle(MessageManager
1409             .getString("label.load_jalview_annotations"));
1410     chooser.setToolTipText(MessageManager
1411             .getString("label.load_jalview_annotations"));
1412
1413     int value = chooser.showOpenDialog(null);
1414
1415     if (value == JalviewFileChooser.APPROVE_OPTION)
1416     {
1417       String choice = chooser.getSelectedFile().getPath();
1418       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1419       loadJalviewDataFile(choice, null, null, null);
1420     }
1421
1422   }
1423
1424   /**
1425    * Close the current view or all views in the alignment frame. If the frame
1426    * only contains one view then the alignment will be removed from memory.
1427    *
1428    * @param closeAllTabs
1429    */
1430   @Override
1431   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1432   {
1433     if (alignPanels != null && alignPanels.size() < 2)
1434     {
1435       closeAllTabs = true;
1436     }
1437
1438     try
1439     {
1440       if (alignPanels != null)
1441       {
1442         if (closeAllTabs)
1443         {
1444           if (this.isClosed())
1445           {
1446             // really close all the windows - otherwise wait till
1447             // setClosed(true) is called
1448             for (int i = 0; i < alignPanels.size(); i++)
1449             {
1450               AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1451               ap.closePanel();
1452             }
1453           }
1454         }
1455         else
1456         {
1457           closeView(alignPanel);
1458         }
1459       }
1460
1461       if (closeAllTabs)
1462       {
1463         this.setClosed(true);
1464       }
1465     } catch (Exception ex)
1466     {
1467       ex.printStackTrace();
1468     }
1469   }
1470
1471   /**
1472    * close alignPanel2 and shuffle tabs appropriately.
1473    *
1474    * @param alignPanel2
1475    */
1476   public void closeView(AlignmentPanel alignPanel2)
1477   {
1478     int index = tabbedPane.getSelectedIndex();
1479     int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1480     alignPanels.removeElement(alignPanel2);
1481     // Unnecessary
1482     // if (viewport == alignPanel2.av)
1483     // {
1484     // viewport = null;
1485     // }
1486     alignPanel2.closePanel();
1487     alignPanel2 = null;
1488
1489     tabbedPane.removeTabAt(closedindex);
1490     tabbedPane.validate();
1491
1492     if (index > closedindex || index == tabbedPane.getTabCount())
1493     {
1494       // modify currently selected tab index if necessary.
1495       index--;
1496     }
1497
1498     this.tabSelectionChanged(index);
1499   }
1500
1501   /**
1502    * DOCUMENT ME!
1503    */
1504   void updateEditMenuBar()
1505   {
1506
1507     if (viewport.getHistoryList().size() > 0)
1508     {
1509       undoMenuItem.setEnabled(true);
1510       CommandI command = viewport.getHistoryList().peek();
1511       undoMenuItem.setText(MessageManager.formatMessage(
1512               "label.undo_command", new String[]
1513               { command.getDescription() }));
1514     }
1515     else
1516     {
1517       undoMenuItem.setEnabled(false);
1518       undoMenuItem.setText(MessageManager.getString("action.undo"));
1519     }
1520
1521     if (viewport.getRedoList().size() > 0)
1522     {
1523       redoMenuItem.setEnabled(true);
1524
1525       CommandI command = viewport.getRedoList().peek();
1526       redoMenuItem.setText(MessageManager.formatMessage(
1527               "label.redo_command", new String[]
1528               { command.getDescription() }));
1529     }
1530     else
1531     {
1532       redoMenuItem.setEnabled(false);
1533       redoMenuItem.setText(MessageManager.getString("action.redo"));
1534     }
1535   }
1536
1537   public void addHistoryItem(CommandI command)
1538   {
1539     if (command.getSize() > 0)
1540     {
1541       viewport.addToHistoryList(command);
1542       viewport.clearRedoList();
1543       updateEditMenuBar();
1544       viewport.updateHiddenColumns();
1545       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1546       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1547       // viewport.getColumnSelection()
1548       // .getHiddenColumns().size() > 0);
1549     }
1550   }
1551
1552   /**
1553    *
1554    * @return alignment objects for all views
1555    */
1556   AlignmentI[] getViewAlignments()
1557   {
1558     if (alignPanels != null)
1559     {
1560       Enumeration e = alignPanels.elements();
1561       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1562       for (int i = 0; e.hasMoreElements(); i++)
1563       {
1564         als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1565       }
1566       return als;
1567     }
1568     if (viewport != null)
1569     {
1570       return new AlignmentI[]
1571       { viewport.getAlignment() };
1572     }
1573     return null;
1574   }
1575
1576   /**
1577    * DOCUMENT ME!
1578    *
1579    * @param e
1580    *          DOCUMENT ME!
1581    */
1582   @Override
1583   protected void undoMenuItem_actionPerformed(ActionEvent e)
1584   {
1585     if (viewport.getHistoryList().isEmpty())
1586     {
1587       return;
1588     }
1589     CommandI command = viewport.getHistoryList().pop();
1590     viewport.addToRedoList(command);
1591     // TODO: execute command before adding to redo list / broadcasting?
1592     command.undoCommand(getViewAlignments());
1593
1594     AlignViewport originalSource = getOriginatingSource(command);
1595     updateEditMenuBar();
1596
1597     if (originalSource != null)
1598     {
1599       if (originalSource != viewport)
1600       {
1601         Cache.log
1602                 .warn("Implementation worry: mismatch of viewport origin for undo");
1603       }
1604       originalSource.updateHiddenColumns();
1605       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1606       // null
1607       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1608       // viewport.getColumnSelection()
1609       // .getHiddenColumns().size() > 0);
1610       originalSource.firePropertyChange("alignment", null, originalSource
1611               .getAlignment().getSequences());
1612     }
1613   }
1614
1615   /**
1616    * DOCUMENT ME!
1617    *
1618    * @param e
1619    *          DOCUMENT ME!
1620    */
1621   @Override
1622   protected void redoMenuItem_actionPerformed(ActionEvent e)
1623   {
1624     if (viewport.getRedoList().size() < 1)
1625     {
1626       return;
1627     }
1628
1629     CommandI command = viewport.getRedoList().pop();
1630     viewport.addToHistoryList(command);
1631     command.doCommand(getViewAlignments());
1632
1633     AlignViewport originalSource = getOriginatingSource(command);
1634     updateEditMenuBar();
1635
1636     if (originalSource != null)
1637     {
1638
1639       if (originalSource != viewport)
1640       {
1641         Cache.log
1642                 .warn("Implementation worry: mismatch of viewport origin for redo");
1643       }
1644       originalSource.updateHiddenColumns();
1645       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1646       // null
1647       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1648       // viewport.getColumnSelection()
1649       // .getHiddenColumns().size() > 0);
1650       originalSource.firePropertyChange("alignment", null, originalSource
1651               .getAlignment().getSequences());
1652     }
1653   }
1654
1655   AlignViewport getOriginatingSource(CommandI command)
1656   {
1657     AlignViewport originalSource = null;
1658     // For sequence removal and addition, we need to fire
1659     // the property change event FROM the viewport where the
1660     // original alignment was altered
1661     AlignmentI al = null;
1662     if (command instanceof EditCommand)
1663     {
1664       EditCommand editCommand = (EditCommand) command;
1665       al = editCommand.getAlignment();
1666       Vector comps = (Vector) PaintRefresher.components.get(viewport
1667               .getSequenceSetId());
1668
1669       for (int i = 0; i < comps.size(); i++)
1670       {
1671         if (comps.elementAt(i) instanceof AlignmentPanel)
1672         {
1673           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1674           {
1675             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1676             break;
1677           }
1678         }
1679       }
1680     }
1681
1682     if (originalSource == null)
1683     {
1684       // The original view is closed, we must validate
1685       // the current view against the closed view first
1686       if (al != null)
1687       {
1688         PaintRefresher.validateSequences(al, viewport.getAlignment());
1689       }
1690
1691       originalSource = viewport;
1692     }
1693
1694     return originalSource;
1695   }
1696
1697   /**
1698    * DOCUMENT ME!
1699    *
1700    * @param up
1701    *          DOCUMENT ME!
1702    */
1703   public void moveSelectedSequences(boolean up)
1704   {
1705     SequenceGroup sg = viewport.getSelectionGroup();
1706
1707     if (sg == null)
1708     {
1709       return;
1710     }
1711     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1712             viewport.getHiddenRepSequences(), up);
1713     alignPanel.paintAlignment(true);
1714   }
1715
1716   synchronized void slideSequences(boolean right, int size)
1717   {
1718     List<SequenceI> sg = new Vector();
1719     if (viewport.cursorMode)
1720     {
1721       sg.add(viewport.getAlignment().getSequenceAt(
1722               alignPanel.seqPanel.seqCanvas.cursorY));
1723     }
1724     else if (viewport.getSelectionGroup() != null
1725             && viewport.getSelectionGroup().getSize() != viewport
1726                     .getAlignment().getHeight())
1727     {
1728       sg = viewport.getSelectionGroup().getSequences(
1729               viewport.getHiddenRepSequences());
1730     }
1731
1732     if (sg.size() < 1)
1733     {
1734       return;
1735     }
1736
1737     Vector invertGroup = new Vector();
1738
1739     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1740     {
1741       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1742       {
1743         invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1744       }
1745     }
1746
1747     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1748
1749     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1750     for (int i = 0; i < invertGroup.size(); i++)
1751     {
1752       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1753     }
1754
1755     SlideSequencesCommand ssc;
1756     if (right)
1757     {
1758       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1759               size, viewport.getGapCharacter());
1760     }
1761     else
1762     {
1763       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1764               size, viewport.getGapCharacter());
1765     }
1766
1767     int groupAdjustment = 0;
1768     if (ssc.getGapsInsertedBegin() && right)
1769     {
1770       if (viewport.cursorMode)
1771       {
1772         alignPanel.seqPanel.moveCursor(size, 0);
1773       }
1774       else
1775       {
1776         groupAdjustment = size;
1777       }
1778     }
1779     else if (!ssc.getGapsInsertedBegin() && !right)
1780     {
1781       if (viewport.cursorMode)
1782       {
1783         alignPanel.seqPanel.moveCursor(-size, 0);
1784       }
1785       else
1786       {
1787         groupAdjustment = -size;
1788       }
1789     }
1790
1791     if (groupAdjustment != 0)
1792     {
1793       viewport.getSelectionGroup().setStartRes(
1794               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1795       viewport.getSelectionGroup().setEndRes(
1796               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1797     }
1798
1799     boolean appendHistoryItem = false;
1800     if (viewport.getHistoryList() != null
1801             && viewport.getHistoryList().size() > 0
1802             && viewport.getHistoryList().peek() instanceof SlideSequencesCommand)
1803     {
1804       appendHistoryItem = ssc
1805               .appendSlideCommand((SlideSequencesCommand) viewport
1806                       .getHistoryList()
1807                       .peek());
1808     }
1809
1810     if (!appendHistoryItem)
1811     {
1812       addHistoryItem(ssc);
1813     }
1814
1815     repaint();
1816   }
1817
1818   /**
1819    * DOCUMENT ME!
1820    *
1821    * @param e
1822    *          DOCUMENT ME!
1823    */
1824   @Override
1825   protected void copy_actionPerformed(ActionEvent e)
1826   {
1827     System.gc();
1828     if (viewport.getSelectionGroup() == null)
1829     {
1830       return;
1831     }
1832     // TODO: preserve the ordering of displayed alignment annotation in any
1833     // internal paste (particularly sequence associated annotation)
1834     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1835     String[] omitHidden = null;
1836
1837     if (viewport.hasHiddenColumns())
1838     {
1839       omitHidden = viewport.getViewAsString(true);
1840     }
1841
1842     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1843             omitHidden);
1844
1845     StringSelection ss = new StringSelection(output);
1846
1847     try
1848     {
1849       jalview.gui.Desktop.internalCopy = true;
1850       // Its really worth setting the clipboard contents
1851       // to empty before setting the large StringSelection!!
1852       Toolkit.getDefaultToolkit().getSystemClipboard()
1853               .setContents(new StringSelection(""), null);
1854
1855       Toolkit.getDefaultToolkit().getSystemClipboard()
1856               .setContents(ss, Desktop.instance);
1857     } catch (OutOfMemoryError er)
1858     {
1859       new OOMWarning("copying region", er);
1860       return;
1861     }
1862
1863     Vector hiddenColumns = null;
1864     if (viewport.hasHiddenColumns())
1865     {
1866       hiddenColumns = new Vector();
1867       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1868               .getSelectionGroup().getEndRes();
1869       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1870               .size(); i++)
1871       {
1872         int[] region = (int[]) viewport.getColumnSelection()
1873                 .getHiddenColumns().elementAt(i);
1874         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1875         {
1876           hiddenColumns.addElement(new int[]
1877           { region[0] - hiddenOffset, region[1] - hiddenOffset });
1878         }
1879       }
1880     }
1881
1882     Desktop.jalviewClipboard = new Object[]
1883     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1884     statusBar.setText(MessageManager.formatMessage(
1885             "label.copied_sequences_to_clipboard", new String[]
1886             { Integer.valueOf(seqs.length).toString() }));
1887   }
1888
1889   /**
1890    * DOCUMENT ME!
1891    *
1892    * @param e
1893    *          DOCUMENT ME!
1894    */
1895   @Override
1896   protected void pasteNew_actionPerformed(ActionEvent e)
1897   {
1898     paste(true);
1899   }
1900
1901   /**
1902    * DOCUMENT ME!
1903    *
1904    * @param e
1905    *          DOCUMENT ME!
1906    */
1907   @Override
1908   protected void pasteThis_actionPerformed(ActionEvent e)
1909   {
1910     paste(false);
1911   }
1912
1913   /**
1914    * Paste contents of Jalview clipboard
1915    *
1916    * @param newAlignment
1917    *          true to paste to a new alignment, otherwise add to this.
1918    */
1919   void paste(boolean newAlignment)
1920   {
1921     boolean externalPaste = true;
1922     try
1923     {
1924       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1925       Transferable contents = c.getContents(this);
1926
1927       if (contents == null)
1928       {
1929         return;
1930       }
1931
1932       String str, format;
1933       try
1934       {
1935         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1936         if (str.length() < 1)
1937         {
1938           return;
1939         }
1940
1941         format = new IdentifyFile().Identify(str, "Paste");
1942
1943       } catch (OutOfMemoryError er)
1944       {
1945         new OOMWarning("Out of memory pasting sequences!!", er);
1946         return;
1947       }
1948
1949       SequenceI[] sequences;
1950       boolean annotationAdded = false;
1951       AlignmentI alignment = null;
1952
1953       if (Desktop.jalviewClipboard != null)
1954       {
1955         // The clipboard was filled from within Jalview, we must use the
1956         // sequences
1957         // And dataset from the copied alignment
1958         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1959         // be doubly sure that we create *new* sequence objects.
1960         sequences = new SequenceI[newseq.length];
1961         for (int i = 0; i < newseq.length; i++)
1962         {
1963           sequences[i] = new Sequence(newseq[i]);
1964         }
1965         alignment = new Alignment(sequences);
1966         externalPaste = false;
1967       }
1968       else
1969       {
1970         // parse the clipboard as an alignment.
1971         alignment = new FormatAdapter().readFile(str, "Paste", format);
1972         sequences = alignment.getSequencesArray();
1973       }
1974
1975       int alwidth = 0;
1976       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1977       int fgroup = -1;
1978
1979       if (newAlignment)
1980       {
1981
1982         if (Desktop.jalviewClipboard != null)
1983         {
1984           // dataset is inherited
1985           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1986         }
1987         else
1988         {
1989           // new dataset is constructed
1990           alignment.setDataset(null);
1991         }
1992         alwidth = alignment.getWidth() + 1;
1993       }
1994       else
1995       {
1996         AlignmentI pastedal = alignment; // preserve pasted alignment object
1997         // Add pasted sequences and dataset into existing alignment.
1998         alignment = viewport.getAlignment();
1999         alwidth = alignment.getWidth() + 1;
2000         // decide if we need to import sequences from an existing dataset
2001         boolean importDs = Desktop.jalviewClipboard != null
2002                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2003         // importDs==true instructs us to copy over new dataset sequences from
2004         // an existing alignment
2005         Vector newDs = (importDs) ? new Vector() : null; // used to create
2006         // minimum dataset set
2007
2008         for (int i = 0; i < sequences.length; i++)
2009         {
2010           if (importDs)
2011           {
2012             newDs.addElement(null);
2013           }
2014           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2015           // paste
2016           if (importDs && ds != null)
2017           {
2018             if (!newDs.contains(ds))
2019             {
2020               newDs.setElementAt(ds, i);
2021               ds = new Sequence(ds);
2022               // update with new dataset sequence
2023               sequences[i].setDatasetSequence(ds);
2024             }
2025             else
2026             {
2027               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2028             }
2029           }
2030           else
2031           {
2032             // copy and derive new dataset sequence
2033             sequences[i] = sequences[i].deriveSequence();
2034             alignment.getDataset().addSequence(
2035                     sequences[i].getDatasetSequence());
2036             // TODO: avoid creation of duplicate dataset sequences with a
2037             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2038           }
2039           alignment.addSequence(sequences[i]); // merges dataset
2040         }
2041         if (newDs != null)
2042         {
2043           newDs.clear(); // tidy up
2044         }
2045         if (alignment.getAlignmentAnnotation() != null)
2046         {
2047           for (AlignmentAnnotation alan : alignment
2048                   .getAlignmentAnnotation())
2049           {
2050             if (alan.graphGroup > fgroup)
2051             {
2052               fgroup = alan.graphGroup;
2053             }
2054           }
2055         }
2056         if (pastedal.getAlignmentAnnotation() != null)
2057         {
2058           // Add any annotation attached to alignment.
2059           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2060           for (int i = 0; i < alann.length; i++)
2061           {
2062             annotationAdded = true;
2063             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2064             {
2065               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2066               if (newann.graphGroup > -1)
2067               {
2068                 if (newGraphGroups.size() <= newann.graphGroup
2069                         || newGraphGroups.get(newann.graphGroup) == null)
2070                 {
2071                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2072                   {
2073                     newGraphGroups.add(q, null);
2074                   }
2075                   newGraphGroups.set(newann.graphGroup, new Integer(
2076                           ++fgroup));
2077                 }
2078                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2079                         .intValue();
2080               }
2081
2082               newann.padAnnotation(alwidth);
2083               alignment.addAnnotation(newann);
2084             }
2085           }
2086         }
2087       }
2088       if (!newAlignment)
2089       {
2090         // /////
2091         // ADD HISTORY ITEM
2092         //
2093         addHistoryItem(new EditCommand(
2094                 MessageManager.getString("label.add_sequences"),
2095                 Action.PASTE,
2096                 sequences, 0, alignment.getWidth(), alignment));
2097       }
2098       // Add any annotations attached to sequences
2099       for (int i = 0; i < sequences.length; i++)
2100       {
2101         if (sequences[i].getAnnotation() != null)
2102         {
2103           AlignmentAnnotation newann;
2104           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2105           {
2106             annotationAdded = true;
2107             newann = sequences[i].getAnnotation()[a];
2108             newann.adjustForAlignment();
2109             newann.padAnnotation(alwidth);
2110             if (newann.graphGroup > -1)
2111             {
2112               if (newann.graphGroup > -1)
2113               {
2114                 if (newGraphGroups.size() <= newann.graphGroup
2115                         || newGraphGroups.get(newann.graphGroup) == null)
2116                 {
2117                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2118                   {
2119                     newGraphGroups.add(q, null);
2120                   }
2121                   newGraphGroups.set(newann.graphGroup, new Integer(
2122                           ++fgroup));
2123                 }
2124                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2125                         .intValue();
2126               }
2127             }
2128             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2129             // was
2130             // duplicated
2131             // earlier
2132             alignment
2133                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2134           }
2135         }
2136       }
2137       if (!newAlignment)
2138       {
2139
2140         // propagate alignment changed.
2141         viewport.setEndSeq(alignment.getHeight());
2142         if (annotationAdded)
2143         {
2144           // Duplicate sequence annotation in all views.
2145           AlignmentI[] alview = this.getViewAlignments();
2146           for (int i = 0; i < sequences.length; i++)
2147           {
2148             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2149             if (sann == null)
2150             {
2151               continue;
2152             }
2153             for (int avnum = 0; avnum < alview.length; avnum++)
2154             {
2155               if (alview[avnum] != alignment)
2156               {
2157                 // duplicate in a view other than the one with input focus
2158                 int avwidth = alview[avnum].getWidth() + 1;
2159                 // this relies on sann being preserved after we
2160                 // modify the sequence's annotation array for each duplication
2161                 for (int a = 0; a < sann.length; a++)
2162                 {
2163                   AlignmentAnnotation newann = new AlignmentAnnotation(
2164                           sann[a]);
2165                   sequences[i].addAlignmentAnnotation(newann);
2166                   newann.padAnnotation(avwidth);
2167                   alview[avnum].addAnnotation(newann); // annotation was
2168                   // duplicated earlier
2169                   // TODO JAL-1145 graphGroups are not updated for sequence
2170                   // annotation added to several views. This may cause
2171                   // strangeness
2172                   alview[avnum].setAnnotationIndex(newann, a);
2173                 }
2174               }
2175             }
2176           }
2177           buildSortByAnnotationScoresMenu();
2178         }
2179         viewport.firePropertyChange("alignment", null,
2180                 alignment.getSequences());
2181         if (alignPanels != null)
2182         {
2183           for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2184           {
2185             ap.validateAnnotationDimensions(false);
2186           }
2187         }
2188         else
2189         {
2190           alignPanel.validateAnnotationDimensions(false);
2191         }
2192
2193       }
2194       else
2195       {
2196         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2197                 DEFAULT_HEIGHT);
2198         String newtitle = new String("Copied sequences");
2199
2200         if (Desktop.jalviewClipboard != null
2201                 && Desktop.jalviewClipboard[2] != null)
2202         {
2203           Vector hc = (Vector) Desktop.jalviewClipboard[2];
2204           for (int i = 0; i < hc.size(); i++)
2205           {
2206             int[] region = (int[]) hc.elementAt(i);
2207             af.viewport.hideColumns(region[0], region[1]);
2208           }
2209         }
2210
2211         // >>>This is a fix for the moment, until a better solution is
2212         // found!!<<<
2213         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2214                 .transferSettings(
2215                         alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2216
2217         // TODO: maintain provenance of an alignment, rather than just make the
2218         // title a concatenation of operations.
2219         if (!externalPaste)
2220         {
2221           if (title.startsWith("Copied sequences"))
2222           {
2223             newtitle = title;
2224           }
2225           else
2226           {
2227             newtitle = newtitle.concat("- from " + title);
2228           }
2229         }
2230         else
2231         {
2232           newtitle = new String("Pasted sequences");
2233         }
2234
2235         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2236                 DEFAULT_HEIGHT);
2237
2238       }
2239
2240     } catch (Exception ex)
2241     {
2242       ex.printStackTrace();
2243       System.out.println("Exception whilst pasting: " + ex);
2244       // could be anything being pasted in here
2245     }
2246
2247   }
2248
2249   @Override
2250   protected void expand_newalign(ActionEvent e)
2251   {
2252     try
2253     {
2254       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2255               .getAlignment(), -1);
2256       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2257               DEFAULT_HEIGHT);
2258       String newtitle = new String("Flanking alignment");
2259
2260       if (Desktop.jalviewClipboard != null
2261               && Desktop.jalviewClipboard[2] != null)
2262       {
2263         Vector hc = (Vector) Desktop.jalviewClipboard[2];
2264         for (int i = 0; i < hc.size(); i++)
2265         {
2266           int[] region = (int[]) hc.elementAt(i);
2267           af.viewport.hideColumns(region[0], region[1]);
2268         }
2269       }
2270
2271       // >>>This is a fix for the moment, until a better solution is
2272       // found!!<<<
2273       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2274               .transferSettings(
2275                       alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2276
2277       // TODO: maintain provenance of an alignment, rather than just make the
2278       // title a concatenation of operations.
2279       {
2280         if (title.startsWith("Copied sequences"))
2281         {
2282           newtitle = title;
2283         }
2284         else
2285         {
2286           newtitle = newtitle.concat("- from " + title);
2287         }
2288       }
2289
2290       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2291
2292     } catch (Exception ex)
2293     {
2294       ex.printStackTrace();
2295       System.out.println("Exception whilst pasting: " + ex);
2296       // could be anything being pasted in here
2297     } catch (OutOfMemoryError oom)
2298     {
2299       new OOMWarning("Viewing flanking region of alignment", oom);
2300     }
2301   }
2302
2303   /**
2304    * DOCUMENT ME!
2305    *
2306    * @param e
2307    *          DOCUMENT ME!
2308    */
2309   @Override
2310   protected void cut_actionPerformed(ActionEvent e)
2311   {
2312     copy_actionPerformed(null);
2313     delete_actionPerformed(null);
2314   }
2315
2316   /**
2317    * DOCUMENT ME!
2318    *
2319    * @param e
2320    *          DOCUMENT ME!
2321    */
2322   @Override
2323   protected void delete_actionPerformed(ActionEvent evt)
2324   {
2325
2326     SequenceGroup sg = viewport.getSelectionGroup();
2327     if (sg == null)
2328     {
2329       return;
2330     }
2331
2332     List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2333     SequenceI seq;
2334     for (int i = 0; i < sg.getSize(); i++)
2335     {
2336       seq = sg.getSequenceAt(i);
2337       seqs.add(seq);
2338     }
2339
2340     // If the cut affects all sequences, warn, remove highlighted columns
2341     if (sg.getSize() == viewport.getAlignment().getHeight())
2342     {
2343       int confirm = JOptionPane.showConfirmDialog(this,
2344               MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2345               MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2346               JOptionPane.OK_CANCEL_OPTION);
2347
2348       if (confirm == JOptionPane.CANCEL_OPTION
2349               || confirm == JOptionPane.CLOSED_OPTION)
2350       {
2351         return;
2352       }
2353       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2354               sg.getEndRes() + 1);
2355     }
2356
2357     SequenceI[] cut = new SequenceI[seqs.size()];
2358     for (int i = 0; i < seqs.size(); i++)
2359     {
2360       cut[i] = seqs.get(i);
2361     }
2362
2363     /*
2364      * //ADD HISTORY ITEM
2365      */
2366     addHistoryItem(new EditCommand(
2367             MessageManager.getString("label.cut_sequences"), Action.CUT,
2368             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2369             viewport.getAlignment()));
2370
2371     viewport.setSelectionGroup(null);
2372     viewport.sendSelection();
2373     viewport.getAlignment().deleteGroup(sg);
2374
2375     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2376             .getSequences());
2377     if (viewport.getAlignment().getHeight() < 1)
2378     {
2379       try
2380       {
2381         this.setClosed(true);
2382       } catch (Exception ex)
2383       {
2384       }
2385     }
2386   }
2387
2388   /**
2389    * DOCUMENT ME!
2390    *
2391    * @param e
2392    *          DOCUMENT ME!
2393    */
2394   @Override
2395   protected void deleteGroups_actionPerformed(ActionEvent e)
2396   {
2397     if (avc.deleteGroups())
2398     {
2399       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2400       alignPanel.updateAnnotation();
2401       alignPanel.paintAlignment(true);
2402     }
2403   }
2404
2405   /**
2406    * DOCUMENT ME!
2407    *
2408    * @param e
2409    *          DOCUMENT ME!
2410    */
2411   @Override
2412   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2413   {
2414     SequenceGroup sg = new SequenceGroup();
2415
2416     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2417     {
2418       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2419     }
2420
2421     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2422     viewport.setSelectionGroup(sg);
2423     viewport.sendSelection();
2424     alignPanel.paintAlignment(true);
2425     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2426   }
2427
2428   /**
2429    * DOCUMENT ME!
2430    *
2431    * @param e
2432    *          DOCUMENT ME!
2433    */
2434   @Override
2435   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2436   {
2437     if (viewport.cursorMode)
2438     {
2439       alignPanel.seqPanel.keyboardNo1 = null;
2440       alignPanel.seqPanel.keyboardNo2 = null;
2441     }
2442     viewport.setSelectionGroup(null);
2443     viewport.getColumnSelection().clear();
2444     viewport.setSelectionGroup(null);
2445     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2446     alignPanel.idPanel.idCanvas.searchResults = null;
2447     alignPanel.paintAlignment(true);
2448     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2449     viewport.sendSelection();
2450   }
2451
2452   /**
2453    * DOCUMENT ME!
2454    *
2455    * @param e
2456    *          DOCUMENT ME!
2457    */
2458   @Override
2459   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2460   {
2461     SequenceGroup sg = viewport.getSelectionGroup();
2462
2463     if (sg == null)
2464     {
2465       selectAllSequenceMenuItem_actionPerformed(null);
2466
2467       return;
2468     }
2469
2470     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2471     {
2472       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2473     }
2474
2475     alignPanel.paintAlignment(true);
2476     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2477     viewport.sendSelection();
2478   }
2479
2480   @Override
2481   public void invertColSel_actionPerformed(ActionEvent e)
2482   {
2483     viewport.invertColumnSelection();
2484     alignPanel.paintAlignment(true);
2485     viewport.sendSelection();
2486   }
2487
2488   /**
2489    * DOCUMENT ME!
2490    *
2491    * @param e
2492    *          DOCUMENT ME!
2493    */
2494   @Override
2495   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2496   {
2497     trimAlignment(true);
2498   }
2499
2500   /**
2501    * DOCUMENT ME!
2502    *
2503    * @param e
2504    *          DOCUMENT ME!
2505    */
2506   @Override
2507   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2508   {
2509     trimAlignment(false);
2510   }
2511
2512   void trimAlignment(boolean trimLeft)
2513   {
2514     ColumnSelection colSel = viewport.getColumnSelection();
2515     int column;
2516
2517     if (colSel.size() > 0)
2518     {
2519       if (trimLeft)
2520       {
2521         column = colSel.getMin();
2522       }
2523       else
2524       {
2525         column = colSel.getMax();
2526       }
2527
2528       SequenceI[] seqs;
2529       if (viewport.getSelectionGroup() != null)
2530       {
2531         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2532                 viewport.getHiddenRepSequences());
2533       }
2534       else
2535       {
2536         seqs = viewport.getAlignment().getSequencesArray();
2537       }
2538
2539       TrimRegionCommand trimRegion;
2540       if (trimLeft)
2541       {
2542         trimRegion = new TrimRegionCommand("Remove Left",
2543                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2544                 viewport.getAlignment(), viewport.getColumnSelection(),
2545                 viewport.getSelectionGroup());
2546         viewport.setStartRes(0);
2547       }
2548       else
2549       {
2550         trimRegion = new TrimRegionCommand("Remove Right",
2551                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2552                 viewport.getAlignment(), viewport.getColumnSelection(),
2553                 viewport.getSelectionGroup());
2554       }
2555
2556       statusBar.setText(MessageManager.formatMessage(
2557               "label.removed_columns", new String[]
2558               { Integer.valueOf(trimRegion.getSize()).toString() }));
2559
2560       addHistoryItem(trimRegion);
2561
2562       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2563       {
2564         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2565                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2566         {
2567           viewport.getAlignment().deleteGroup(sg);
2568         }
2569       }
2570
2571       viewport.firePropertyChange("alignment", null, viewport
2572               .getAlignment().getSequences());
2573     }
2574   }
2575
2576   /**
2577    * DOCUMENT ME!
2578    *
2579    * @param e
2580    *          DOCUMENT ME!
2581    */
2582   @Override
2583   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2584   {
2585     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2586
2587     SequenceI[] seqs;
2588     if (viewport.getSelectionGroup() != null)
2589     {
2590       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2591               viewport.getHiddenRepSequences());
2592       start = viewport.getSelectionGroup().getStartRes();
2593       end = viewport.getSelectionGroup().getEndRes();
2594     }
2595     else
2596     {
2597       seqs = viewport.getAlignment().getSequencesArray();
2598     }
2599
2600     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2601             "Remove Gapped Columns", seqs, start, end,
2602             viewport.getAlignment());
2603
2604     addHistoryItem(removeGapCols);
2605
2606     statusBar.setText(MessageManager.formatMessage(
2607             "label.removed_empty_columns", new String[]
2608             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2609
2610     // This is to maintain viewport position on first residue
2611     // of first sequence
2612     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2613     int startRes = seq.findPosition(viewport.startRes);
2614     // ShiftList shifts;
2615     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2616     // edit.alColumnChanges=shifts.getInverse();
2617     // if (viewport.hasHiddenColumns)
2618     // viewport.getColumnSelection().compensateForEdits(shifts);
2619     viewport.setStartRes(seq.findIndex(startRes) - 1);
2620     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2621             .getSequences());
2622
2623   }
2624
2625   /**
2626    * DOCUMENT ME!
2627    *
2628    * @param e
2629    *          DOCUMENT ME!
2630    */
2631   @Override
2632   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2633   {
2634     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2635
2636     SequenceI[] seqs;
2637     if (viewport.getSelectionGroup() != null)
2638     {
2639       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2640               viewport.getHiddenRepSequences());
2641       start = viewport.getSelectionGroup().getStartRes();
2642       end = viewport.getSelectionGroup().getEndRes();
2643     }
2644     else
2645     {
2646       seqs = viewport.getAlignment().getSequencesArray();
2647     }
2648
2649     // This is to maintain viewport position on first residue
2650     // of first sequence
2651     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2652     int startRes = seq.findPosition(viewport.startRes);
2653
2654     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2655             viewport.getAlignment()));
2656
2657     viewport.setStartRes(seq.findIndex(startRes) - 1);
2658
2659     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2660             .getSequences());
2661
2662   }
2663
2664   /**
2665    * DOCUMENT ME!
2666    *
2667    * @param e
2668    *          DOCUMENT ME!
2669    */
2670   @Override
2671   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2672   {
2673     viewport.setPadGaps(padGapsMenuitem.isSelected());
2674     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2675             .getSequences());
2676   }
2677
2678   // else
2679   {
2680     // if (justifySeqs>0)
2681     {
2682       // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2683     }
2684   }
2685
2686   // }
2687
2688   /**
2689    * DOCUMENT ME!
2690    *
2691    * @param e
2692    *          DOCUMENT ME!
2693    */
2694   @Override
2695   public void findMenuItem_actionPerformed(ActionEvent e)
2696   {
2697     new Finder();
2698   }
2699
2700   /**
2701    * Create a new view of the current alignment.
2702    */
2703   @Override
2704   public void newView_actionPerformed(ActionEvent e)
2705   {
2706     newView(true);
2707   }
2708
2709   /**
2710    *
2711    * @param copyAnnotation
2712    *          if true then duplicate all annnotation, groups and settings
2713    * @return new alignment panel, already displayed.
2714    */
2715   public AlignmentPanel newView(boolean copyAnnotation)
2716   {
2717     return newView(null, copyAnnotation);
2718   }
2719
2720   /**
2721    *
2722    * @param viewTitle
2723    *          title of newly created view
2724    * @return new alignment panel, already displayed.
2725    */
2726   public AlignmentPanel newView(String viewTitle)
2727   {
2728     return newView(viewTitle, true);
2729   }
2730
2731   /**
2732    *
2733    * @param viewTitle
2734    *          title of newly created view
2735    * @param copyAnnotation
2736    *          if true then duplicate all annnotation, groups and settings
2737    * @return new alignment panel, already displayed.
2738    */
2739   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2740   {
2741     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2742             true);
2743     if (!copyAnnotation)
2744     {
2745       // just remove all the current annotation except for the automatic stuff
2746       newap.av.getAlignment().deleteAllGroups();
2747       for (AlignmentAnnotation alan : newap.av.getAlignment()
2748               .getAlignmentAnnotation())
2749       {
2750         if (!alan.autoCalculated)
2751         {
2752           newap.av.getAlignment().deleteAnnotation(alan);
2753         }
2754         ;
2755       }
2756     }
2757
2758     newap.av.gatherViewsHere = false;
2759
2760     if (viewport.viewName == null)
2761     {
2762       viewport.viewName = "Original";
2763     }
2764
2765     newap.av.setHistoryList(viewport.getHistoryList());
2766     newap.av.setRedoList(viewport.getRedoList());
2767
2768     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2769     // make sure the new view has a unique name - this is essential for Jalview
2770     // 2 archives
2771     boolean addFirstIndex = false;
2772     if (viewTitle == null || viewTitle.trim().length() == 0)
2773     {
2774       viewTitle = MessageManager.getString("action.view");
2775       addFirstIndex = true;
2776     }
2777     else
2778     {
2779       index = 1;// we count from 1 if given a specific name
2780     }
2781     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2782     Vector comps = (Vector) PaintRefresher.components.get(viewport
2783             .getSequenceSetId());
2784     Vector existingNames = new Vector();
2785     for (int i = 0; i < comps.size(); i++)
2786     {
2787       if (comps.elementAt(i) instanceof AlignmentPanel)
2788       {
2789         AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2790         if (!existingNames.contains(ap.av.viewName))
2791         {
2792           existingNames.addElement(ap.av.viewName);
2793         }
2794       }
2795     }
2796
2797     while (existingNames.contains(newViewName))
2798     {
2799       newViewName = viewTitle + " " + (++index);
2800     }
2801
2802     newap.av.viewName = newViewName;
2803
2804     addAlignmentPanel(newap, true);
2805     newap.alignmentChanged();
2806
2807     if (alignPanels.size() == 2)
2808     {
2809       viewport.gatherViewsHere = true;
2810     }
2811     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2812     return newap;
2813   }
2814
2815   @Override
2816   public void expandViews_actionPerformed(ActionEvent e)
2817   {
2818     Desktop.instance.explodeViews(this);
2819   }
2820
2821   @Override
2822   public void gatherViews_actionPerformed(ActionEvent e)
2823   {
2824     Desktop.instance.gatherViews(this);
2825   }
2826
2827   /**
2828    * DOCUMENT ME!
2829    *
2830    * @param e
2831    *          DOCUMENT ME!
2832    */
2833   @Override
2834   public void font_actionPerformed(ActionEvent e)
2835   {
2836     new FontChooser(alignPanel);
2837   }
2838
2839   /**
2840    * DOCUMENT ME!
2841    *
2842    * @param e
2843    *          DOCUMENT ME!
2844    */
2845   @Override
2846   protected void seqLimit_actionPerformed(ActionEvent e)
2847   {
2848     viewport.setShowJVSuffix(seqLimits.isSelected());
2849
2850     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2851             .calculateIdWidth());
2852     alignPanel.paintAlignment(true);
2853   }
2854
2855   @Override
2856   public void idRightAlign_actionPerformed(ActionEvent e)
2857   {
2858     viewport.rightAlignIds = idRightAlign.isSelected();
2859     alignPanel.paintAlignment(true);
2860   }
2861
2862   @Override
2863   public void centreColumnLabels_actionPerformed(ActionEvent e)
2864   {
2865     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2866     alignPanel.paintAlignment(true);
2867   }
2868
2869   /*
2870    * (non-Javadoc)
2871    *
2872    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2873    */
2874   @Override
2875   protected void followHighlight_actionPerformed()
2876   {
2877     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2878     {
2879       alignPanel.scrollToPosition(
2880               alignPanel.seqPanel.seqCanvas.searchResults, false);
2881     }
2882   }
2883
2884   /**
2885    * DOCUMENT ME!
2886    *
2887    * @param e
2888    *          DOCUMENT ME!
2889    */
2890   @Override
2891   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2892   {
2893     viewport.setColourText(colourTextMenuItem.isSelected());
2894     alignPanel.paintAlignment(true);
2895   }
2896
2897   /**
2898    * DOCUMENT ME!
2899    *
2900    * @param e
2901    *          DOCUMENT ME!
2902    */
2903   @Override
2904   public void wrapMenuItem_actionPerformed(ActionEvent e)
2905   {
2906     scaleAbove.setVisible(wrapMenuItem.isSelected());
2907     scaleLeft.setVisible(wrapMenuItem.isSelected());
2908     scaleRight.setVisible(wrapMenuItem.isSelected());
2909     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2910     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2911   }
2912
2913   @Override
2914   public void showAllSeqs_actionPerformed(ActionEvent e)
2915   {
2916     viewport.showAllHiddenSeqs();
2917   }
2918
2919   @Override
2920   public void showAllColumns_actionPerformed(ActionEvent e)
2921   {
2922     viewport.showAllHiddenColumns();
2923     repaint();
2924   }
2925
2926   @Override
2927   public void hideSelSequences_actionPerformed(ActionEvent e)
2928   {
2929     viewport.hideAllSelectedSeqs();
2930     alignPanel.paintAlignment(true);
2931   }
2932
2933   /**
2934    * called by key handler and the hide all/show all menu items
2935    *
2936    * @param toggleSeqs
2937    * @param toggleCols
2938    */
2939   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2940   {
2941
2942     boolean hide = false;
2943     SequenceGroup sg = viewport.getSelectionGroup();
2944     if (!toggleSeqs && !toggleCols)
2945     {
2946       // Hide everything by the current selection - this is a hack - we do the
2947       // invert and then hide
2948       // first check that there will be visible columns after the invert.
2949       if ((viewport.getColumnSelection() != null
2950               && viewport.getColumnSelection().getSelected() != null && viewport
2951               .getColumnSelection().getSelected().size() > 0)
2952               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2953                       .getEndRes()))
2954       {
2955         // now invert the sequence set, if required - empty selection implies
2956         // that no hiding is required.
2957         if (sg != null)
2958         {
2959           invertSequenceMenuItem_actionPerformed(null);
2960           sg = viewport.getSelectionGroup();
2961           toggleSeqs = true;
2962
2963         }
2964         viewport.expandColSelection(sg, true);
2965         // finally invert the column selection and get the new sequence
2966         // selection.
2967         invertColSel_actionPerformed(null);
2968         toggleCols = true;
2969       }
2970     }
2971
2972     if (toggleSeqs)
2973     {
2974       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2975       {
2976         hideSelSequences_actionPerformed(null);
2977         hide = true;
2978       }
2979       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2980               .size() > 0))
2981       {
2982         showAllSeqs_actionPerformed(null);
2983       }
2984     }
2985
2986     if (toggleCols)
2987     {
2988       if (viewport.getColumnSelection().getSelected().size() > 0)
2989       {
2990         hideSelColumns_actionPerformed(null);
2991         if (!toggleSeqs)
2992         {
2993           viewport.setSelectionGroup(sg);
2994         }
2995       }
2996       else if (!hide)
2997       {
2998         showAllColumns_actionPerformed(null);
2999       }
3000     }
3001   }
3002
3003   /*
3004    * (non-Javadoc)
3005    *
3006    * @see
3007    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3008    * event.ActionEvent)
3009    */
3010   @Override
3011   public void hideAllButSelection_actionPerformed(ActionEvent e)
3012   {
3013     toggleHiddenRegions(false, false);
3014   }
3015
3016   /*
3017    * (non-Javadoc)
3018    *
3019    * @see
3020    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3021    * .ActionEvent)
3022    */
3023   @Override
3024   public void hideAllSelection_actionPerformed(ActionEvent e)
3025   {
3026     SequenceGroup sg = viewport.getSelectionGroup();
3027     viewport.expandColSelection(sg, false);
3028     viewport.hideAllSelectedSeqs();
3029     viewport.hideSelectedColumns();
3030     alignPanel.paintAlignment(true);
3031   }
3032
3033   /*
3034    * (non-Javadoc)
3035    *
3036    * @see
3037    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3038    * ActionEvent)
3039    */
3040   @Override
3041   public void showAllhidden_actionPerformed(ActionEvent e)
3042   {
3043     viewport.showAllHiddenColumns();
3044     viewport.showAllHiddenSeqs();
3045     alignPanel.paintAlignment(true);
3046   }
3047
3048   @Override
3049   public void hideSelColumns_actionPerformed(ActionEvent e)
3050   {
3051     viewport.hideSelectedColumns();
3052     alignPanel.paintAlignment(true);
3053   }
3054
3055   @Override
3056   public void hiddenMarkers_actionPerformed(ActionEvent e)
3057   {
3058     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3059     repaint();
3060   }
3061
3062   /**
3063    * DOCUMENT ME!
3064    *
3065    * @param e
3066    *          DOCUMENT ME!
3067    */
3068   @Override
3069   protected void scaleAbove_actionPerformed(ActionEvent e)
3070   {
3071     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3072     alignPanel.paintAlignment(true);
3073   }
3074
3075   /**
3076    * DOCUMENT ME!
3077    *
3078    * @param e
3079    *          DOCUMENT ME!
3080    */
3081   @Override
3082   protected void scaleLeft_actionPerformed(ActionEvent e)
3083   {
3084     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3085     alignPanel.paintAlignment(true);
3086   }
3087
3088   /**
3089    * DOCUMENT ME!
3090    *
3091    * @param e
3092    *          DOCUMENT ME!
3093    */
3094   @Override
3095   protected void scaleRight_actionPerformed(ActionEvent e)
3096   {
3097     viewport.setScaleRightWrapped(scaleRight.isSelected());
3098     alignPanel.paintAlignment(true);
3099   }
3100
3101   /**
3102    * DOCUMENT ME!
3103    *
3104    * @param e
3105    *          DOCUMENT ME!
3106    */
3107   @Override
3108   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3109   {
3110     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3111     alignPanel.paintAlignment(true);
3112   }
3113
3114   /**
3115    * DOCUMENT ME!
3116    *
3117    * @param e
3118    *          DOCUMENT ME!
3119    */
3120   @Override
3121   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3122   {
3123     viewport.setShowText(viewTextMenuItem.isSelected());
3124     alignPanel.paintAlignment(true);
3125   }
3126
3127   /**
3128    * DOCUMENT ME!
3129    *
3130    * @param e
3131    *          DOCUMENT ME!
3132    */
3133   @Override
3134   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3135   {
3136     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3137     alignPanel.paintAlignment(true);
3138   }
3139
3140   public FeatureSettings featureSettings;
3141
3142   @Override
3143   public void featureSettings_actionPerformed(ActionEvent e)
3144   {
3145     if (featureSettings != null)
3146     {
3147       featureSettings.close();
3148       featureSettings = null;
3149     }
3150     if (!showSeqFeatures.isSelected())
3151     {
3152       // make sure features are actually displayed
3153       showSeqFeatures.setSelected(true);
3154       showSeqFeatures_actionPerformed(null);
3155     }
3156     featureSettings = new FeatureSettings(this);
3157   }
3158
3159   /**
3160    * Set or clear 'Show Sequence Features'
3161    *
3162    * @param evt
3163    *          DOCUMENT ME!
3164    */
3165   @Override
3166   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3167   {
3168     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3169     alignPanel.paintAlignment(true);
3170     if (alignPanel.getOverviewPanel() != null)
3171     {
3172       alignPanel.getOverviewPanel().updateOverviewImage();
3173     }
3174   }
3175
3176   /**
3177    * Set or clear 'Show Sequence Features'
3178    *
3179    * @param evt
3180    *          DOCUMENT ME!
3181    */
3182   @Override
3183   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3184   {
3185     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3186             .isSelected());
3187     if (viewport.getShowSequenceFeaturesHeight())
3188     {
3189       // ensure we're actually displaying features
3190       viewport.setShowSequenceFeatures(true);
3191       showSeqFeatures.setSelected(true);
3192     }
3193     alignPanel.paintAlignment(true);
3194     if (alignPanel.getOverviewPanel() != null)
3195     {
3196       alignPanel.getOverviewPanel().updateOverviewImage();
3197     }
3198   }
3199
3200   /**
3201    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3202    * the annotations panel as a whole.
3203    *
3204    * The options to show/hide all annotations should be enabled when the panel
3205    * is shown, and disabled when the panel is hidden.
3206    *
3207    * @param e
3208    */
3209   @Override
3210   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3211   {
3212     final boolean setVisible = annotationPanelMenuItem.isSelected();
3213     viewport.setShowAnnotation(setVisible);
3214     alignPanel.setAnnotationVisible(setVisible);
3215     this.showAllSeqAnnotations.setEnabled(setVisible);
3216     this.hideAllSeqAnnotations.setEnabled(setVisible);
3217     this.showAllAlAnnotations.setEnabled(setVisible);
3218     this.hideAllAlAnnotations.setEnabled(setVisible);
3219   }
3220
3221   @Override
3222   public void alignmentProperties()
3223   {
3224     JEditorPane editPane = new JEditorPane("text/html", "");
3225     editPane.setEditable(false);
3226     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3227             .formatAsHtml();
3228     editPane.setText(MessageManager.formatMessage("label.html_content",
3229             new String[]
3230             { contents.toString() }));
3231     JInternalFrame frame = new JInternalFrame();
3232     frame.getContentPane().add(new JScrollPane(editPane));
3233
3234     Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3235             "label.alignment_properties", new String[]
3236             { getTitle() }), 500, 400);
3237   }
3238
3239   /**
3240    * DOCUMENT ME!
3241    *
3242    * @param e
3243    *          DOCUMENT ME!
3244    */
3245   @Override
3246   public void overviewMenuItem_actionPerformed(ActionEvent e)
3247   {
3248     if (alignPanel.overviewPanel != null)
3249     {
3250       return;
3251     }
3252
3253     JInternalFrame frame = new JInternalFrame();
3254     OverviewPanel overview = new OverviewPanel(alignPanel);
3255     frame.setContentPane(overview);
3256     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3257             "label.overview_params", new String[]
3258             { this.getTitle() }), frame.getWidth(), frame.getHeight());
3259     frame.pack();
3260     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3261     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3262     {
3263       @Override
3264       public void internalFrameClosed(
3265               javax.swing.event.InternalFrameEvent evt)
3266       {
3267         alignPanel.setOverviewPanel(null);
3268       };
3269     });
3270
3271     alignPanel.setOverviewPanel(overview);
3272   }
3273
3274   @Override
3275   public void textColour_actionPerformed(ActionEvent e)
3276   {
3277     new TextColourChooser().chooseColour(alignPanel, null);
3278   }
3279
3280   /**
3281    * DOCUMENT ME!
3282    *
3283    * @param e
3284    *          DOCUMENT ME!
3285    */
3286   @Override
3287   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3288   {
3289     changeColour(null);
3290   }
3291
3292   /**
3293    * DOCUMENT ME!
3294    *
3295    * @param e
3296    *          DOCUMENT ME!
3297    */
3298   @Override
3299   public void clustalColour_actionPerformed(ActionEvent e)
3300   {
3301     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3302             viewport.getHiddenRepSequences()));
3303   }
3304
3305   /**
3306    * DOCUMENT ME!
3307    *
3308    * @param e
3309    *          DOCUMENT ME!
3310    */
3311   @Override
3312   public void zappoColour_actionPerformed(ActionEvent e)
3313   {
3314     changeColour(new ZappoColourScheme());
3315   }
3316
3317   /**
3318    * DOCUMENT ME!
3319    *
3320    * @param e
3321    *          DOCUMENT ME!
3322    */
3323   @Override
3324   public void taylorColour_actionPerformed(ActionEvent e)
3325   {
3326     changeColour(new TaylorColourScheme());
3327   }
3328
3329   /**
3330    * DOCUMENT ME!
3331    *
3332    * @param e
3333    *          DOCUMENT ME!
3334    */
3335   @Override
3336   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3337   {
3338     changeColour(new HydrophobicColourScheme());
3339   }
3340
3341   /**
3342    * DOCUMENT ME!
3343    *
3344    * @param e
3345    *          DOCUMENT ME!
3346    */
3347   @Override
3348   public void helixColour_actionPerformed(ActionEvent e)
3349   {
3350     changeColour(new HelixColourScheme());
3351   }
3352
3353   /**
3354    * DOCUMENT ME!
3355    *
3356    * @param e
3357    *          DOCUMENT ME!
3358    */
3359   @Override
3360   public void strandColour_actionPerformed(ActionEvent e)
3361   {
3362     changeColour(new StrandColourScheme());
3363   }
3364
3365   /**
3366    * DOCUMENT ME!
3367    *
3368    * @param e
3369    *          DOCUMENT ME!
3370    */
3371   @Override
3372   public void turnColour_actionPerformed(ActionEvent e)
3373   {
3374     changeColour(new TurnColourScheme());
3375   }
3376
3377   /**
3378    * DOCUMENT ME!
3379    *
3380    * @param e
3381    *          DOCUMENT ME!
3382    */
3383   @Override
3384   public void buriedColour_actionPerformed(ActionEvent e)
3385   {
3386     changeColour(new BuriedColourScheme());
3387   }
3388
3389   /**
3390    * DOCUMENT ME!
3391    *
3392    * @param e
3393    *          DOCUMENT ME!
3394    */
3395   @Override
3396   public void nucleotideColour_actionPerformed(ActionEvent e)
3397   {
3398     changeColour(new NucleotideColourScheme());
3399   }
3400
3401   @Override
3402   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3403   {
3404     changeColour(new PurinePyrimidineColourScheme());
3405   }
3406
3407   /*
3408    * public void covariationColour_actionPerformed(ActionEvent e) {
3409    * changeColour(new
3410    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3411    * ()[0])); }
3412    */
3413   @Override
3414   public void annotationColour_actionPerformed(ActionEvent e)
3415   {
3416     new AnnotationColourChooser(viewport, alignPanel);
3417   }
3418
3419   @Override
3420   public void rnahelicesColour_actionPerformed(ActionEvent e)
3421   {
3422     new RNAHelicesColourChooser(viewport, alignPanel);
3423   }
3424
3425   /**
3426    * DOCUMENT ME!
3427    *
3428    * @param e
3429    *          DOCUMENT ME!
3430    */
3431   @Override
3432   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3433   {
3434     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3435   }
3436
3437   /**
3438    * DOCUMENT ME!
3439    *
3440    * @param cs
3441    *          DOCUMENT ME!
3442    */
3443   public void changeColour(ColourSchemeI cs)
3444   {
3445     // TODO: compare with applet and pull up to model method
3446     int threshold = 0;
3447
3448     if (cs != null)
3449     {
3450       if (viewport.getAbovePIDThreshold())
3451       {
3452         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3453                 "Background");
3454         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3455       }
3456       else
3457       {
3458         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3459       }
3460
3461       if (viewport.getConservationSelected())
3462       {
3463
3464         Alignment al = (Alignment) viewport.getAlignment();
3465         Conservation c = new Conservation("All",
3466                 ResidueProperties.propHash, 3, al.getSequences(), 0,
3467                 al.getWidth() - 1);
3468
3469         c.calculate();
3470         c.verdict(false, viewport.getConsPercGaps());
3471
3472         cs.setConservation(c);
3473
3474         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3475                 cs, "Background"));
3476       }
3477       else
3478       {
3479         cs.setConservation(null);
3480       }
3481
3482       cs.setConsensus(viewport.getSequenceConsensusHash());
3483     }
3484
3485     viewport.setGlobalColourScheme(cs);
3486
3487     if (viewport.getColourAppliesToAllGroups())
3488     {
3489
3490       for (SequenceGroup sg : viewport.getAlignment().getGroups())
3491       {
3492         if (cs == null)
3493         {
3494           sg.cs = null;
3495           continue;
3496         }
3497
3498         if (cs instanceof ClustalxColourScheme)
3499         {
3500           sg.cs = new ClustalxColourScheme(sg,
3501                   viewport.getHiddenRepSequences());
3502         }
3503         else if (cs instanceof UserColourScheme)
3504         {
3505           sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3506         }
3507         else
3508         {
3509           try
3510           {
3511             sg.cs = cs.getClass().newInstance();
3512           } catch (Exception ex)
3513           {
3514           }
3515         }
3516
3517         if (viewport.getAbovePIDThreshold()
3518                 || cs instanceof PIDColourScheme
3519                 || cs instanceof Blosum62ColourScheme)
3520         {
3521           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3522
3523           sg.cs.setConsensus(AAFrequency.calculate(
3524                   sg.getSequences(viewport.getHiddenRepSequences()),
3525                   sg.getStartRes(), sg.getEndRes() + 1));
3526         }
3527         else
3528         {
3529           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3530         }
3531
3532         if (viewport.getConservationSelected())
3533         {
3534           Conservation c = new Conservation("Group",
3535                   ResidueProperties.propHash, 3, sg.getSequences(viewport
3536                           .getHiddenRepSequences()), sg.getStartRes(),
3537                   sg.getEndRes() + 1);
3538           c.calculate();
3539           c.verdict(false, viewport.getConsPercGaps());
3540           sg.cs.setConservation(c);
3541         }
3542         else
3543         {
3544           sg.cs.setConservation(null);
3545         }
3546       }
3547     }
3548
3549     if (alignPanel.getOverviewPanel() != null)
3550     {
3551       alignPanel.getOverviewPanel().updateOverviewImage();
3552     }
3553
3554     alignPanel.paintAlignment(true);
3555   }
3556
3557   /**
3558    * DOCUMENT ME!
3559    *
3560    * @param e
3561    *          DOCUMENT ME!
3562    */
3563   @Override
3564   protected void modifyPID_actionPerformed(ActionEvent e)
3565   {
3566     if (viewport.getAbovePIDThreshold()
3567             && viewport.getGlobalColourScheme() != null)
3568     {
3569       SliderPanel.setPIDSliderSource(alignPanel,
3570               viewport.getGlobalColourScheme(), "Background");
3571       SliderPanel.showPIDSlider();
3572     }
3573   }
3574
3575   /**
3576    * DOCUMENT ME!
3577    *
3578    * @param e
3579    *          DOCUMENT ME!
3580    */
3581   @Override
3582   protected void modifyConservation_actionPerformed(ActionEvent e)
3583   {
3584     if (viewport.getConservationSelected()
3585             && viewport.getGlobalColourScheme() != null)
3586     {
3587       SliderPanel.setConservationSlider(alignPanel,
3588               viewport.getGlobalColourScheme(), "Background");
3589       SliderPanel.showConservationSlider();
3590     }
3591   }
3592
3593   /**
3594    * DOCUMENT ME!
3595    *
3596    * @param e
3597    *          DOCUMENT ME!
3598    */
3599   @Override
3600   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3601   {
3602     viewport.setConservationSelected(conservationMenuItem.isSelected());
3603
3604     viewport.setAbovePIDThreshold(false);
3605     abovePIDThreshold.setSelected(false);
3606
3607     changeColour(viewport.getGlobalColourScheme());
3608
3609     modifyConservation_actionPerformed(null);
3610   }
3611
3612   /**
3613    * DOCUMENT ME!
3614    *
3615    * @param e
3616    *          DOCUMENT ME!
3617    */
3618   @Override
3619   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3620   {
3621     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3622
3623     conservationMenuItem.setSelected(false);
3624     viewport.setConservationSelected(false);
3625
3626     changeColour(viewport.getGlobalColourScheme());
3627
3628     modifyPID_actionPerformed(null);
3629   }
3630
3631   /**
3632    * DOCUMENT ME!
3633    *
3634    * @param e
3635    *          DOCUMENT ME!
3636    */
3637   @Override
3638   public void userDefinedColour_actionPerformed(ActionEvent e)
3639   {
3640     if (e.getActionCommand().equals(
3641             MessageManager.getString("action.user_defined")))
3642     {
3643       new UserDefinedColours(alignPanel, null);
3644     }
3645     else
3646     {
3647       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3648               .getUserColourSchemes().get(e.getActionCommand());
3649
3650       changeColour(udc);
3651     }
3652   }
3653
3654   public void updateUserColourMenu()
3655   {
3656
3657     Component[] menuItems = colourMenu.getMenuComponents();
3658     int i, iSize = menuItems.length;
3659     for (i = 0; i < iSize; i++)
3660     {
3661       if (menuItems[i].getName() != null
3662               && menuItems[i].getName().equals("USER_DEFINED"))
3663       {
3664         colourMenu.remove(menuItems[i]);
3665         iSize--;
3666       }
3667     }
3668     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3669     {
3670       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3671               .getUserColourSchemes().keys();
3672
3673       while (userColours.hasMoreElements())
3674       {
3675         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3676                 userColours.nextElement().toString());
3677         radioItem.setName("USER_DEFINED");
3678         radioItem.addMouseListener(new MouseAdapter()
3679         {
3680           @Override
3681           public void mousePressed(MouseEvent evt)
3682           {
3683             if (evt.isControlDown()
3684                     || SwingUtilities.isRightMouseButton(evt))
3685             {
3686               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3687
3688               int option = JOptionPane.showInternalConfirmDialog(
3689                       jalview.gui.Desktop.desktop,
3690                       MessageManager
3691                               .getString("label.remove_from_default_list"),
3692                       MessageManager
3693                               .getString("label.remove_user_defined_colour"),
3694                       JOptionPane.YES_NO_OPTION);
3695               if (option == JOptionPane.YES_OPTION)
3696               {
3697                 jalview.gui.UserDefinedColours
3698                         .removeColourFromDefaults(radioItem.getText());
3699                 colourMenu.remove(radioItem);
3700               }
3701               else
3702               {
3703                 radioItem.addActionListener(new ActionListener()
3704                 {
3705                   @Override
3706                   public void actionPerformed(ActionEvent evt)
3707                   {
3708                     userDefinedColour_actionPerformed(evt);
3709                   }
3710                 });
3711               }
3712             }
3713           }
3714         });
3715         radioItem.addActionListener(new ActionListener()
3716         {
3717           @Override
3718           public void actionPerformed(ActionEvent evt)
3719           {
3720             userDefinedColour_actionPerformed(evt);
3721           }
3722         });
3723
3724         colourMenu.insert(radioItem, 15);
3725         colours.add(radioItem);
3726       }
3727     }
3728   }
3729
3730   /**
3731    * DOCUMENT ME!
3732    *
3733    * @param e
3734    *          DOCUMENT ME!
3735    */
3736   @Override
3737   public void PIDColour_actionPerformed(ActionEvent e)
3738   {
3739     changeColour(new PIDColourScheme());
3740   }
3741
3742   /**
3743    * DOCUMENT ME!
3744    *
3745    * @param e
3746    *          DOCUMENT ME!
3747    */
3748   @Override
3749   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3750   {
3751     changeColour(new Blosum62ColourScheme());
3752   }
3753
3754   /**
3755    * DOCUMENT ME!
3756    *
3757    * @param e
3758    *          DOCUMENT ME!
3759    */
3760   @Override
3761   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3762   {
3763     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3764     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3765             .getAlignment().getSequenceAt(0), null);
3766     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3767             viewport.getAlignment()));
3768     alignPanel.paintAlignment(true);
3769   }
3770
3771   /**
3772    * DOCUMENT ME!
3773    *
3774    * @param e
3775    *          DOCUMENT ME!
3776    */
3777   @Override
3778   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3779   {
3780     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3781     AlignmentSorter.sortByID(viewport.getAlignment());
3782     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3783             viewport.getAlignment()));
3784     alignPanel.paintAlignment(true);
3785   }
3786
3787   /**
3788    * DOCUMENT ME!
3789    *
3790    * @param e
3791    *          DOCUMENT ME!
3792    */
3793   @Override
3794   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3795   {
3796     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3797     AlignmentSorter.sortByLength(viewport.getAlignment());
3798     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3799             viewport.getAlignment()));
3800     alignPanel.paintAlignment(true);
3801   }
3802
3803   /**
3804    * DOCUMENT ME!
3805    *
3806    * @param e
3807    *          DOCUMENT ME!
3808    */
3809   @Override
3810   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3811   {
3812     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3813     AlignmentSorter.sortByGroup(viewport.getAlignment());
3814     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3815             viewport.getAlignment()));
3816
3817     alignPanel.paintAlignment(true);
3818   }
3819
3820   /**
3821    * DOCUMENT ME!
3822    *
3823    * @param e
3824    *          DOCUMENT ME!
3825    */
3826   @Override
3827   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3828   {
3829     new RedundancyPanel(alignPanel, this);
3830   }
3831
3832   /**
3833    * DOCUMENT ME!
3834    *
3835    * @param e
3836    *          DOCUMENT ME!
3837    */
3838   @Override
3839   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3840   {
3841     if ((viewport.getSelectionGroup() == null)
3842             || (viewport.getSelectionGroup().getSize() < 2))
3843     {
3844       JOptionPane.showInternalMessageDialog(this, MessageManager
3845               .getString("label.you_must_select_least_two_sequences"),
3846               MessageManager.getString("label.invalid_selection"),
3847               JOptionPane.WARNING_MESSAGE);
3848     }
3849     else
3850     {
3851       JInternalFrame frame = new JInternalFrame();
3852       frame.setContentPane(new PairwiseAlignPanel(viewport));
3853       Desktop.addInternalFrame(frame,
3854               MessageManager.getString("action.pairwise_alignment"), 600,
3855               500);
3856     }
3857   }
3858
3859   /**
3860    * DOCUMENT ME!
3861    *
3862    * @param e
3863    *          DOCUMENT ME!
3864    */
3865   @Override
3866   public void PCAMenuItem_actionPerformed(ActionEvent e)
3867   {
3868     if (((viewport.getSelectionGroup() != null)
3869             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3870             .getSelectionGroup().getSize() > 0))
3871             || (viewport.getAlignment().getHeight() < 4))
3872     {
3873       JOptionPane
3874               .showInternalMessageDialog(
3875                       this,
3876                       MessageManager
3877                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3878                       MessageManager
3879                               .getString("label.sequence_selection_insufficient"),
3880                       JOptionPane.WARNING_MESSAGE);
3881
3882       return;
3883     }
3884
3885     new PCAPanel(alignPanel);
3886   }
3887
3888   @Override
3889   public void autoCalculate_actionPerformed(ActionEvent e)
3890   {
3891     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3892     if (viewport.autoCalculateConsensus)
3893     {
3894       viewport.firePropertyChange("alignment", null, viewport
3895               .getAlignment().getSequences());
3896     }
3897   }
3898
3899   @Override
3900   public void sortByTreeOption_actionPerformed(ActionEvent e)
3901   {
3902     viewport.sortByTree = sortByTree.isSelected();
3903   }
3904
3905   @Override
3906   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3907   {
3908     viewport.followSelection = listenToViewSelections.isSelected();
3909   }
3910
3911   /**
3912    * DOCUMENT ME!
3913    *
3914    * @param e
3915    *          DOCUMENT ME!
3916    */
3917   @Override
3918   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3919   {
3920     NewTreePanel("AV", "PID", "Average distance tree using PID");
3921   }
3922
3923   /**
3924    * DOCUMENT ME!
3925    *
3926    * @param e
3927    *          DOCUMENT ME!
3928    */
3929   @Override
3930   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3931   {
3932     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3933   }
3934
3935   /**
3936    * DOCUMENT ME!
3937    *
3938    * @param e
3939    *          DOCUMENT ME!
3940    */
3941   @Override
3942   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3943   {
3944     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3945   }
3946
3947   /**
3948    * DOCUMENT ME!
3949    *
3950    * @param e
3951    *          DOCUMENT ME!
3952    */
3953   @Override
3954   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3955   {
3956     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3957   }
3958
3959   /**
3960    * DOCUMENT ME!
3961    *
3962    * @param type
3963    *          DOCUMENT ME!
3964    * @param pwType
3965    *          DOCUMENT ME!
3966    * @param title
3967    *          DOCUMENT ME!
3968    */
3969   void NewTreePanel(String type, String pwType, String title)
3970   {
3971     TreePanel tp;
3972
3973     if (viewport.getSelectionGroup() != null
3974             && viewport.getSelectionGroup().getSize() > 0)
3975     {
3976       if (viewport.getSelectionGroup().getSize() < 3)
3977       {
3978         JOptionPane
3979                 .showMessageDialog(
3980                         Desktop.desktop,
3981                         MessageManager
3982                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3983                         MessageManager
3984                                 .getString("label.not_enough_sequences"),
3985                         JOptionPane.WARNING_MESSAGE);
3986         return;
3987       }
3988
3989       SequenceGroup sg = viewport.getSelectionGroup();
3990
3991       /* Decide if the selection is a column region */
3992       for (SequenceI _s : sg.getSequences())
3993       {
3994         if (_s.getLength() < sg.getEndRes())
3995         {
3996           JOptionPane
3997                   .showMessageDialog(
3998                           Desktop.desktop,
3999                           MessageManager
4000                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
4001                           MessageManager
4002                                   .getString("label.sequences_selection_not_aligned"),
4003                           JOptionPane.WARNING_MESSAGE);
4004
4005           return;
4006         }
4007       }
4008
4009       title = title + " on region";
4010       tp = new TreePanel(alignPanel, type, pwType);
4011     }
4012     else
4013     {
4014       // are the visible sequences aligned?
4015       if (!viewport.getAlignment().isAligned(false))
4016       {
4017         JOptionPane
4018                 .showMessageDialog(
4019                         Desktop.desktop,
4020                         MessageManager
4021                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4022                         MessageManager
4023                                 .getString("label.sequences_not_aligned"),
4024                         JOptionPane.WARNING_MESSAGE);
4025
4026         return;
4027       }
4028
4029       if (viewport.getAlignment().getHeight() < 2)
4030       {
4031         return;
4032       }
4033
4034       tp = new TreePanel(alignPanel, type, pwType);
4035     }
4036
4037     title += " from ";
4038
4039     if (viewport.viewName != null)
4040     {
4041       title += viewport.viewName + " of ";
4042     }
4043
4044     title += this.title;
4045
4046     Desktop.addInternalFrame(tp, title, 600, 500);
4047   }
4048
4049   /**
4050    * DOCUMENT ME!
4051    *
4052    * @param title
4053    *          DOCUMENT ME!
4054    * @param order
4055    *          DOCUMENT ME!
4056    */
4057   public void addSortByOrderMenuItem(String title,
4058           final AlignmentOrder order)
4059   {
4060     final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
4061     sort.add(item);
4062     item.addActionListener(new java.awt.event.ActionListener()
4063     {
4064       @Override
4065       public void actionPerformed(ActionEvent e)
4066       {
4067         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4068
4069         // TODO: JBPNote - have to map order entries to curent SequenceI
4070         // pointers
4071         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4072
4073         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4074                 .getAlignment()));
4075
4076         alignPanel.paintAlignment(true);
4077       }
4078     });
4079   }
4080
4081   /**
4082    * Add a new sort by annotation score menu item
4083    *
4084    * @param sort
4085    *          the menu to add the option to
4086    * @param scoreLabel
4087    *          the label used to retrieve scores for each sequence on the
4088    *          alignment
4089    */
4090   public void addSortByAnnotScoreMenuItem(JMenu sort,
4091           final String scoreLabel)
4092   {
4093     final JMenuItem item = new JMenuItem(scoreLabel);
4094     sort.add(item);
4095     item.addActionListener(new java.awt.event.ActionListener()
4096     {
4097       @Override
4098       public void actionPerformed(ActionEvent e)
4099       {
4100         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4101         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4102                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4103         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4104                 viewport.getAlignment()));
4105         alignPanel.paintAlignment(true);
4106       }
4107     });
4108   }
4109
4110   /**
4111    * last hash for alignment's annotation array - used to minimise cost of
4112    * rebuild.
4113    */
4114   protected int _annotationScoreVectorHash;
4115
4116   /**
4117    * search the alignment and rebuild the sort by annotation score submenu the
4118    * last alignment annotation vector hash is stored to minimize cost of
4119    * rebuilding in subsequence calls.
4120    *
4121    */
4122   @Override
4123   public void buildSortByAnnotationScoresMenu()
4124   {
4125     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4126     {
4127       return;
4128     }
4129
4130     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4131     {
4132       sortByAnnotScore.removeAll();
4133       // almost certainly a quicker way to do this - but we keep it simple
4134       Hashtable scoreSorts = new Hashtable();
4135       AlignmentAnnotation aann[];
4136       for (SequenceI sqa : viewport.getAlignment().getSequences())
4137       {
4138         aann = sqa.getAnnotation();
4139         for (int i = 0; aann != null && i < aann.length; i++)
4140         {
4141           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4142           {
4143             scoreSorts.put(aann[i].label, aann[i].label);
4144           }
4145         }
4146       }
4147       Enumeration labels = scoreSorts.keys();
4148       while (labels.hasMoreElements())
4149       {
4150         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4151                 (String) labels.nextElement());
4152       }
4153       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4154       scoreSorts.clear();
4155
4156       _annotationScoreVectorHash = viewport.getAlignment()
4157               .getAlignmentAnnotation().hashCode();
4158     }
4159   }
4160
4161   /**
4162    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4163    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4164    * call. Listeners are added to remove the menu item when the treePanel is
4165    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4166    * modified.
4167    *
4168    * @param treePanel
4169    *          Displayed tree window.
4170    * @param title
4171    *          SortBy menu item title.
4172    */
4173   @Override
4174   public void buildTreeMenu()
4175   {
4176     calculateTree.removeAll();
4177     // build the calculate menu
4178
4179     for (final String type : new String[]
4180     { "NJ", "AV" })
4181     {
4182       String treecalcnm = MessageManager.getString("label.tree_calc_"
4183               + type.toLowerCase());
4184       for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4185       {
4186         JMenuItem tm = new JMenuItem();
4187         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4188         if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4189         {
4190           String smn = MessageManager.getStringOrReturn(
4191                   "label.score_model_", sm.getName());
4192           final String title = MessageManager.formatMessage(
4193                   "label.treecalc_title", treecalcnm, smn);
4194           tm.setText(title);//
4195           tm.addActionListener(new java.awt.event.ActionListener()
4196           {
4197             @Override
4198             public void actionPerformed(ActionEvent e)
4199             {
4200               NewTreePanel(type, (String) pwtype, title);
4201             }
4202           });
4203           calculateTree.add(tm);
4204         }
4205
4206       }
4207     }
4208     sortByTreeMenu.removeAll();
4209
4210     Vector comps = (Vector) PaintRefresher.components.get(viewport
4211             .getSequenceSetId());
4212     Vector treePanels = new Vector();
4213     int i, iSize = comps.size();
4214     for (i = 0; i < iSize; i++)
4215     {
4216       if (comps.elementAt(i) instanceof TreePanel)
4217       {
4218         treePanels.add(comps.elementAt(i));
4219       }
4220     }
4221
4222     iSize = treePanels.size();
4223
4224     if (iSize < 1)
4225     {
4226       sortByTreeMenu.setVisible(false);
4227       return;
4228     }
4229
4230     sortByTreeMenu.setVisible(true);
4231
4232     for (i = 0; i < treePanels.size(); i++)
4233     {
4234       final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4235       final JMenuItem item = new JMenuItem(tp.getTitle());
4236       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4237       item.addActionListener(new java.awt.event.ActionListener()
4238       {
4239         @Override
4240         public void actionPerformed(ActionEvent e)
4241         {
4242           tp.sortByTree_actionPerformed(null);
4243           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4244
4245         }
4246       });
4247
4248       sortByTreeMenu.add(item);
4249     }
4250   }
4251
4252   public boolean sortBy(AlignmentOrder alorder, String undoname)
4253   {
4254     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4255     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4256     if (undoname != null)
4257     {
4258       addHistoryItem(new OrderCommand(undoname, oldOrder,
4259               viewport.getAlignment()));
4260     }
4261     alignPanel.paintAlignment(true);
4262     return true;
4263   }
4264
4265   /**
4266    * Work out whether the whole set of sequences or just the selected set will
4267    * be submitted for multiple alignment.
4268    *
4269    */
4270   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4271   {
4272     // Now, check we have enough sequences
4273     AlignmentView msa = null;
4274
4275     if ((viewport.getSelectionGroup() != null)
4276             && (viewport.getSelectionGroup().getSize() > 1))
4277     {
4278       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4279       // some common interface!
4280       /*
4281        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4282        * SequenceI[sz = seqs.getSize(false)];
4283        *
4284        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4285        * seqs.getSequenceAt(i); }
4286        */
4287       msa = viewport.getAlignmentView(true);
4288     }
4289     else if (viewport.getSelectionGroup() != null
4290             && viewport.getSelectionGroup().getSize() == 1)
4291     {
4292       int option = JOptionPane.showConfirmDialog(this,
4293               MessageManager.getString("warn.oneseq_msainput_selection"),
4294               MessageManager.getString("label.invalid_selection"),
4295               JOptionPane.OK_CANCEL_OPTION);
4296       if (option == JOptionPane.OK_OPTION)
4297       {
4298         msa = viewport.getAlignmentView(false);
4299       }
4300     }
4301     else
4302     {
4303       msa = viewport.getAlignmentView(false);
4304     }
4305     return msa;
4306   }
4307
4308   /**
4309    * Decides what is submitted to a secondary structure prediction service: the
4310    * first sequence in the alignment, or in the current selection, or, if the
4311    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4312    * region or the whole alignment. (where the first sequence in the set is the
4313    * one that the prediction will be for).
4314    */
4315   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4316   {
4317     AlignmentView seqs = null;
4318
4319     if ((viewport.getSelectionGroup() != null)
4320             && (viewport.getSelectionGroup().getSize() > 0))
4321     {
4322       seqs = viewport.getAlignmentView(true);
4323     }
4324     else
4325     {
4326       seqs = viewport.getAlignmentView(false);
4327     }
4328     // limit sequences - JBPNote in future - could spawn multiple prediction
4329     // jobs
4330     // TODO: viewport.getAlignment().isAligned is a global state - the local
4331     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4332     if (!viewport.getAlignment().isAligned(false))
4333     {
4334       seqs.setSequences(new SeqCigar[]
4335       { seqs.getSequences()[0] });
4336       // TODO: if seqs.getSequences().length>1 then should really have warned
4337       // user!
4338
4339     }
4340     return seqs;
4341   }
4342
4343   /**
4344    * DOCUMENT ME!
4345    *
4346    * @param e
4347    *          DOCUMENT ME!
4348    */
4349   @Override
4350   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4351   {
4352     // Pick the tree file
4353     JalviewFileChooser chooser = new JalviewFileChooser(
4354             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4355     chooser.setFileView(new JalviewFileView());
4356     chooser.setDialogTitle(MessageManager
4357             .getString("label.select_newick_like_tree_file"));
4358     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4359
4360     int value = chooser.showOpenDialog(null);
4361
4362     if (value == JalviewFileChooser.APPROVE_OPTION)
4363     {
4364       String choice = chooser.getSelectedFile().getPath();
4365       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4366       jalview.io.NewickFile fin = null;
4367       try
4368       {
4369         fin = new jalview.io.NewickFile(choice, "File");
4370         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4371       } catch (Exception ex)
4372       {
4373         JOptionPane
4374                 .showMessageDialog(
4375                         Desktop.desktop,
4376                         ex.getMessage(),
4377                         MessageManager
4378                                 .getString("label.problem_reading_tree_file"),
4379                         JOptionPane.WARNING_MESSAGE);
4380         ex.printStackTrace();
4381       }
4382       if (fin != null && fin.hasWarningMessage())
4383       {
4384         JOptionPane.showMessageDialog(Desktop.desktop, fin
4385                 .getWarningMessage(), MessageManager
4386                 .getString("label.possible_problem_with_tree_file"),
4387                 JOptionPane.WARNING_MESSAGE);
4388       }
4389     }
4390   }
4391
4392   @Override
4393   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4394   {
4395     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4396   }
4397
4398   public TreePanel ShowNewickTree(NewickFile nf, String title)
4399   {
4400     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4401   }
4402
4403   public TreePanel ShowNewickTree(NewickFile nf, String title,
4404           AlignmentView input)
4405   {
4406     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4407   }
4408
4409   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4410           int h, int x, int y)
4411   {
4412     return ShowNewickTree(nf, title, null, w, h, x, y);
4413   }
4414
4415   /**
4416    * Add a treeviewer for the tree extracted from a newick file object to the
4417    * current alignment view
4418    *
4419    * @param nf
4420    *          the tree
4421    * @param title
4422    *          tree viewer title
4423    * @param input
4424    *          Associated alignment input data (or null)
4425    * @param w
4426    *          width
4427    * @param h
4428    *          height
4429    * @param x
4430    *          position
4431    * @param y
4432    *          position
4433    * @return TreePanel handle
4434    */
4435   public TreePanel ShowNewickTree(NewickFile nf, String title,
4436           AlignmentView input, int w, int h, int x, int y)
4437   {
4438     TreePanel tp = null;
4439
4440     try
4441     {
4442       nf.parse();
4443
4444       if (nf.getTree() != null)
4445       {
4446         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4447
4448         tp.setSize(w, h);
4449
4450         if (x > 0 && y > 0)
4451         {
4452           tp.setLocation(x, y);
4453         }
4454
4455         Desktop.addInternalFrame(tp, title, w, h);
4456       }
4457     } catch (Exception ex)
4458     {
4459       ex.printStackTrace();
4460     }
4461
4462     return tp;
4463   }
4464
4465   private boolean buildingMenu = false;
4466
4467   /**
4468    * Generates menu items and listener event actions for web service clients
4469    *
4470    */
4471   public void BuildWebServiceMenu()
4472   {
4473     while (buildingMenu)
4474     {
4475       try
4476       {
4477         System.err.println("Waiting for building menu to finish.");
4478         Thread.sleep(10);
4479       } catch (Exception e)
4480       {
4481       }
4482       ;
4483     }
4484     final AlignFrame me = this;
4485     buildingMenu = true;
4486     new Thread(new Runnable()
4487     {
4488       @Override
4489       public void run()
4490       {
4491         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4492         try
4493         {
4494           System.err.println("Building ws menu again "
4495                   + Thread.currentThread());
4496           // TODO: add support for context dependent disabling of services based
4497           // on
4498           // alignment and current selection
4499           // TODO: add additional serviceHandle parameter to specify abstract
4500           // handler
4501           // class independently of AbstractName
4502           // TODO: add in rediscovery GUI function to restart discoverer
4503           // TODO: group services by location as well as function and/or
4504           // introduce
4505           // object broker mechanism.
4506           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4507           final IProgressIndicator af = me;
4508           final JMenu msawsmenu = new JMenu("Alignment");
4509           final JMenu secstrmenu = new JMenu(
4510                   "Secondary Structure Prediction");
4511           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4512           final JMenu analymenu = new JMenu("Analysis");
4513           final JMenu dismenu = new JMenu("Protein Disorder");
4514           // final JMenu msawsmenu = new
4515           // JMenu(MessageManager.getString("label.alignment"));
4516           // final JMenu secstrmenu = new
4517           // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4518           // final JMenu seqsrchmenu = new
4519           // JMenu(MessageManager.getString("label.sequence_database_search"));
4520           // final JMenu analymenu = new
4521           // JMenu(MessageManager.getString("label.analysis"));
4522           // final JMenu dismenu = new
4523           // JMenu(MessageManager.getString("label.protein_disorder"));
4524           // JAL-940 - only show secondary structure prediction services from
4525           // the legacy server
4526           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4527               // &&
4528           Discoverer.services != null && (Discoverer.services.size() > 0))
4529           {
4530             // TODO: refactor to allow list of AbstractName/Handler bindings to
4531             // be
4532             // stored or retrieved from elsewhere
4533             // No MSAWS used any more:
4534             // Vector msaws = null; // (Vector)
4535             // Discoverer.services.get("MsaWS");
4536             Vector secstrpr = (Vector) Discoverer.services
4537                     .get("SecStrPred");
4538             if (secstrpr != null)
4539             {
4540               // Add any secondary structure prediction services
4541               for (int i = 0, j = secstrpr.size(); i < j; i++)
4542               {
4543                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4544                         .get(i);
4545                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4546                         .getServiceClient(sh);
4547                 int p = secstrmenu.getItemCount();
4548                 impl.attachWSMenuEntry(secstrmenu, me);
4549                 int q = secstrmenu.getItemCount();
4550                 for (int litm = p; litm < q; litm++)
4551                 {
4552                   legacyItems.add(secstrmenu.getItem(litm));
4553                 }
4554               }
4555             }
4556           }
4557
4558           // Add all submenus in the order they should appear on the web
4559           // services menu
4560           wsmenu.add(msawsmenu);
4561           wsmenu.add(secstrmenu);
4562           wsmenu.add(dismenu);
4563           wsmenu.add(analymenu);
4564           // No search services yet
4565           // wsmenu.add(seqsrchmenu);
4566
4567           javax.swing.SwingUtilities.invokeLater(new Runnable()
4568           {
4569             @Override
4570             public void run()
4571             {
4572               try
4573               {
4574                 webService.removeAll();
4575                 // first, add discovered services onto the webservices menu
4576                 if (wsmenu.size() > 0)
4577                 {
4578                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4579                   {
4580                     webService.add(wsmenu.get(i));
4581                   }
4582                 }
4583                 else
4584                 {
4585                   webService.add(me.webServiceNoServices);
4586                 }
4587                 // TODO: move into separate menu builder class.
4588                 boolean new_sspred = false;
4589                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4590                 {
4591                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4592                   if (jws2servs != null)
4593                   {
4594                     if (jws2servs.hasServices())
4595                     {
4596                       jws2servs.attachWSMenuEntry(webService, me);
4597                       for (Jws2Instance sv : jws2servs.getServices())
4598                       {
4599                         if (sv.description.toLowerCase().contains("jpred"))
4600                         {
4601                           for (JMenuItem jmi : legacyItems)
4602                           {
4603                             jmi.setVisible(false);
4604                           }
4605                         }
4606                       }
4607
4608                     }
4609                     if (jws2servs.isRunning())
4610                     {
4611                       JMenuItem tm = new JMenuItem(
4612                               "Still discovering JABA Services");
4613                       tm.setEnabled(false);
4614                       webService.add(tm);
4615                     }
4616                   }
4617                 }
4618                 build_urlServiceMenu(me.webService);
4619                 build_fetchdbmenu(webService);
4620                 for (JMenu item : wsmenu)
4621                 {
4622                   if (item.getItemCount() == 0)
4623                   {
4624                     item.setEnabled(false);
4625                   }
4626                   else
4627                   {
4628                     item.setEnabled(true);
4629                   }
4630                 }
4631               } catch (Exception e)
4632               {
4633                 Cache.log
4634                         .debug("Exception during web service menu building process.",
4635                                 e);
4636               }
4637               ;
4638             }
4639           });
4640         } catch (Exception e)
4641         {
4642         }
4643         ;
4644
4645         buildingMenu = false;
4646       }
4647     }).start();
4648
4649   }
4650
4651   /**
4652    * construct any groupURL type service menu entries.
4653    *
4654    * @param webService
4655    */
4656   private void build_urlServiceMenu(JMenu webService)
4657   {
4658     // TODO: remove this code when 2.7 is released
4659     // DEBUG - alignmentView
4660     /*
4661      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4662      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4663      *
4664      * @Override public void actionPerformed(ActionEvent e) {
4665      * jalview.datamodel.AlignmentView
4666      * .testSelectionViews(af.viewport.getAlignment(),
4667      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4668      *
4669      * }); webService.add(testAlView);
4670      */
4671     // TODO: refactor to RestClient discoverer and merge menu entries for
4672     // rest-style services with other types of analysis/calculation service
4673     // SHmmr test client - still being implemented.
4674     // DEBUG - alignmentView
4675
4676     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4677             .getRestClients())
4678     {
4679       client.attachWSMenuEntry(
4680               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4681               this);
4682     }
4683   }
4684
4685   /*
4686    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4687    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4688    * getProperty("LAST_DIRECTORY"));
4689    *
4690    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4691    * to Vamsas file"); chooser.setToolTipText("Export");
4692    *
4693    * int value = chooser.showSaveDialog(this);
4694    *
4695    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4696    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4697    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4698    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4699    */
4700   /**
4701    * prototype of an automatically enabled/disabled analysis function
4702    *
4703    */
4704   protected void setShowProductsEnabled()
4705   {
4706     SequenceI[] selection = viewport.getSequenceSelection();
4707     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4708             viewport.getAlignment().getDataset()))
4709     {
4710       showProducts.setEnabled(true);
4711
4712     }
4713     else
4714     {
4715       showProducts.setEnabled(false);
4716     }
4717   }
4718
4719   /**
4720    * search selection for sequence xRef products and build the show products
4721    * menu.
4722    *
4723    * @param selection
4724    * @param dataset
4725    * @return true if showProducts menu should be enabled.
4726    */
4727   public boolean canShowProducts(SequenceI[] selection,
4728           boolean isRegionSelection, Alignment dataset)
4729   {
4730     boolean showp = false;
4731     try
4732     {
4733       showProducts.removeAll();
4734       final boolean dna = viewport.getAlignment().isNucleotide();
4735       final Alignment ds = dataset;
4736       String[] ptypes = (selection == null || selection.length == 0) ? null
4737               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4738       // Object[] prods =
4739       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4740       // selection, dataset, true);
4741       final SequenceI[] sel = selection;
4742       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4743       {
4744         showp = true;
4745         final boolean isRegSel = isRegionSelection;
4746         final AlignFrame af = this;
4747         final String source = ptypes[t];
4748         JMenuItem xtype = new JMenuItem(ptypes[t]);
4749         xtype.addActionListener(new ActionListener()
4750         {
4751
4752           @Override
4753           public void actionPerformed(ActionEvent e)
4754           {
4755             // TODO: new thread for this call with vis-delay
4756             af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4757                     isRegSel, dna, source);
4758           }
4759
4760         });
4761         showProducts.add(xtype);
4762       }
4763       showProducts.setVisible(showp);
4764       showProducts.setEnabled(showp);
4765     } catch (Exception e)
4766     {
4767       jalview.bin.Cache.log
4768               .warn("canTranslate threw an exception - please report to help@jalview.org",
4769                       e);
4770       return false;
4771     }
4772     return showp;
4773   }
4774
4775   protected void showProductsFor(SequenceI[] sel, Alignment ds,
4776           boolean isRegSel, boolean dna, String source)
4777   {
4778     final boolean fisRegSel = isRegSel;
4779     final boolean fdna = dna;
4780     final String fsrc = source;
4781     final AlignFrame ths = this;
4782     final SequenceI[] fsel = sel;
4783     Runnable foo = new Runnable()
4784     {
4785
4786       @Override
4787       public void run()
4788       {
4789         final long sttime = System.currentTimeMillis();
4790         ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4791         try
4792         {
4793           Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4794           // our local
4795           // dataset
4796           // reference
4797           Alignment prods = CrossRef
4798                   .findXrefSequences(fsel, fdna, fsrc, ds);
4799           if (prods != null)
4800           {
4801             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4802             for (int s = 0; s < sprods.length; s++)
4803             {
4804               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4805               if (ds.getSequences() == null
4806                       || !ds.getSequences().contains(
4807                               sprods[s].getDatasetSequence()))
4808               {
4809                 ds.addSequence(sprods[s].getDatasetSequence());
4810               }
4811               sprods[s].updatePDBIds();
4812             }
4813             Alignment al = new Alignment(sprods);
4814             AlignedCodonFrame[] cf = prods.getCodonFrames();
4815             al.setDataset(ds);
4816             for (int s = 0; cf != null && s < cf.length; s++)
4817             {
4818               al.addCodonFrame(cf[s]);
4819               cf[s] = null;
4820             }
4821             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4822                     DEFAULT_HEIGHT);
4823             String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4824                     + " for " + ((fisRegSel) ? "selected region of " : "")
4825                     + getTitle();
4826             Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4827                     DEFAULT_HEIGHT);
4828           }
4829           else
4830           {
4831             System.err.println("No Sequences generated for xRef type "
4832                     + fsrc);
4833           }
4834         } catch (Exception e)
4835         {
4836           jalview.bin.Cache.log.error(
4837                   "Exception when finding crossreferences", e);
4838         } catch (OutOfMemoryError e)
4839         {
4840           new OOMWarning("whilst fetching crossreferences", e);
4841         } catch (Error e)
4842         {
4843           jalview.bin.Cache.log.error("Error when finding crossreferences",
4844                   e);
4845         }
4846         ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4847                 sttime);
4848       }
4849
4850     };
4851     Thread frunner = new Thread(foo);
4852     frunner.start();
4853   }
4854
4855   public boolean canShowTranslationProducts(SequenceI[] selection,
4856           AlignmentI alignment)
4857   {
4858     // old way
4859     try
4860     {
4861       return (jalview.analysis.Dna.canTranslate(selection,
4862               viewport.getViewAsVisibleContigs(true)));
4863     } catch (Exception e)
4864     {
4865       jalview.bin.Cache.log
4866               .warn("canTranslate threw an exception - please report to help@jalview.org",
4867                       e);
4868       return false;
4869     }
4870   }
4871
4872   /**
4873    * Construct and display a new frame containing the translation of this
4874    * frame's cDNA sequences to their protein (amino acid) equivalents.
4875    */
4876   @Override
4877   public void showTranslation_actionPerformed(ActionEvent e)
4878   {
4879     // /////////////////////////////
4880     // Collect Data to be translated/transferred
4881
4882     SequenceI[] selection = viewport.getSequenceSelection();
4883     String[] seqstring = viewport.getViewAsString(true);
4884     AlignmentI al = null;
4885     try
4886     {
4887       al = jalview.analysis.Dna.cdnaTranslate(selection, seqstring,
4888               viewport.getViewAsVisibleContigs(true), viewport
4889                       .getGapCharacter(), viewport.getAlignment()
4890                       .getAlignmentAnnotation(), viewport.getAlignment()
4891                       .getWidth(), viewport.getAlignment().getDataset());
4892     } catch (Exception ex)
4893     {
4894       al = null;
4895       jalview.bin.Cache.log.error(
4896               "Exception during translation. Please report this !", ex);
4897       JOptionPane
4898               .showMessageDialog(
4899                       Desktop.desktop,
4900                       MessageManager
4901                               .getString("label.error_when_translating_sequences_submit_bug_report"),
4902                       MessageManager
4903                               .getString("label.implementation_error")
4904                               + MessageManager
4905                                       .getString("translation_failed"),
4906                       JOptionPane.ERROR_MESSAGE);
4907       return;
4908     }
4909     if (al == null)
4910     {
4911       JOptionPane
4912               .showMessageDialog(
4913                       Desktop.desktop,
4914                       MessageManager
4915                               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4916                       MessageManager.getString("label.translation_failed"),
4917                       JOptionPane.WARNING_MESSAGE);
4918     }
4919     else
4920     {
4921       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4922       Desktop.addInternalFrame(af, MessageManager.formatMessage(
4923               "label.translation_of_params", new String[]
4924               { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4925       viewport.getStructureSelectionManager().addCommandListener(viewport);
4926     }
4927   }
4928
4929   /**
4930    * Try to load a features file onto the alignment.
4931    *
4932    * @param file
4933    *          contents or path to retrieve file
4934    * @param type
4935    *          access mode of file (see jalview.io.AlignFile)
4936    * @return true if features file was parsed corectly.
4937    */
4938   public boolean parseFeaturesFile(String file, String type)
4939   {
4940     boolean featuresFile = false;
4941     try
4942     {
4943       featuresFile = new FeaturesFile(file, type).parse(viewport
4944               .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4945               .getFeatureRenderer().featureColours, false,
4946               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4947     } catch (Exception ex)
4948     {
4949       ex.printStackTrace();
4950     }
4951
4952     if (featuresFile)
4953     {
4954       viewport.showSequenceFeatures = true;
4955       showSeqFeatures.setSelected(true);
4956       if (alignPanel.seqPanel.seqCanvas.fr != null)
4957       {
4958         // update the min/max ranges where necessary
4959         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4960       }
4961       if (featureSettings != null)
4962       {
4963         featureSettings.setTableData();
4964       }
4965       alignPanel.paintAlignment(true);
4966     }
4967
4968     return featuresFile;
4969   }
4970
4971   @Override
4972   public void dragEnter(DropTargetDragEvent evt)
4973   {
4974   }
4975
4976   @Override
4977   public void dragExit(DropTargetEvent evt)
4978   {
4979   }
4980
4981   @Override
4982   public void dragOver(DropTargetDragEvent evt)
4983   {
4984   }
4985
4986   @Override
4987   public void dropActionChanged(DropTargetDragEvent evt)
4988   {
4989   }
4990
4991   @Override
4992   public void drop(DropTargetDropEvent evt)
4993   {
4994     Transferable t = evt.getTransferable();
4995     java.util.List files = null;
4996
4997     try
4998     {
4999       DataFlavor uriListFlavor = new DataFlavor(
5000               "text/uri-list;class=java.lang.String");
5001       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5002       {
5003         // Works on Windows and MacOSX
5004         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5005         files = (java.util.List) t
5006                 .getTransferData(DataFlavor.javaFileListFlavor);
5007       }
5008       else if (t.isDataFlavorSupported(uriListFlavor))
5009       {
5010         // This is used by Unix drag system
5011         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5012         String data = (String) t.getTransferData(uriListFlavor);
5013         files = new java.util.ArrayList(1);
5014         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5015                 data, "\r\n"); st.hasMoreTokens();)
5016         {
5017           String s = st.nextToken();
5018           if (s.startsWith("#"))
5019           {
5020             // the line is a comment (as per the RFC 2483)
5021             continue;
5022           }
5023
5024           java.net.URI uri = new java.net.URI(s);
5025           // check to see if we can handle this kind of URI
5026           if (uri.getScheme().toLowerCase().startsWith("http"))
5027           {
5028             files.add(uri.toString());
5029           }
5030           else
5031           {
5032             // otherwise preserve old behaviour: catch all for file objects
5033             java.io.File file = new java.io.File(uri);
5034             files.add(file.toString());
5035           }
5036         }
5037       }
5038     } catch (Exception e)
5039     {
5040       e.printStackTrace();
5041     }
5042     if (files != null)
5043     {
5044       try
5045       {
5046         // check to see if any of these files have names matching sequences in
5047         // the alignment
5048         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5049                 .getAlignment().getSequencesArray());
5050         /**
5051          * Object[] { String,SequenceI}
5052          */
5053         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5054         ArrayList<String> filesnotmatched = new ArrayList<String>();
5055         for (int i = 0; i < files.size(); i++)
5056         {
5057           String file = files.get(i).toString();
5058           String pdbfn = "";
5059           String protocol = FormatAdapter.checkProtocol(file);
5060           if (protocol == jalview.io.FormatAdapter.FILE)
5061           {
5062             File fl = new File(file);
5063             pdbfn = fl.getName();
5064           }
5065           else if (protocol == jalview.io.FormatAdapter.URL)
5066           {
5067             URL url = new URL(file);
5068             pdbfn = url.getFile();
5069           }
5070           if (pdbfn.length() > 0)
5071           {
5072             // attempt to find a match in the alignment
5073             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5074             int l = 0, c = pdbfn.indexOf(".");
5075             while (mtch == null && c != -1)
5076             {
5077               do
5078               {
5079                 l = c;
5080               } while ((c = pdbfn.indexOf(".", l)) > l);
5081               if (l > -1)
5082               {
5083                 pdbfn = pdbfn.substring(0, l);
5084               }
5085               mtch = idm.findAllIdMatches(pdbfn);
5086             }
5087             if (mtch != null)
5088             {
5089               String type = null;
5090               try
5091               {
5092                 type = new IdentifyFile().Identify(file, protocol);
5093               } catch (Exception ex)
5094               {
5095                 type = null;
5096               }
5097               if (type != null)
5098               {
5099                 if (type.equalsIgnoreCase("PDB"))
5100                 {
5101                   filesmatched.add(new Object[]
5102                   { file, protocol, mtch });
5103                   continue;
5104                 }
5105               }
5106             }
5107             // File wasn't named like one of the sequences or wasn't a PDB file.
5108             filesnotmatched.add(file);
5109           }
5110         }
5111         int assocfiles = 0;
5112         if (filesmatched.size() > 0)
5113         {
5114           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5115                   || JOptionPane
5116                           .showConfirmDialog(
5117                                   this,
5118                                   MessageManager
5119                                           .formatMessage(
5120                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
5121                                                   new String[]
5122                                                   { Integer.valueOf(
5123                                                           filesmatched
5124                                                                   .size())
5125                                                           .toString() }),
5126                                   MessageManager
5127                                           .getString("label.automatically_associate_pdb_files_by_name"),
5128                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5129
5130           {
5131             for (Object[] fm : filesmatched)
5132             {
5133               // try and associate
5134               // TODO: may want to set a standard ID naming formalism for
5135               // associating PDB files which have no IDs.
5136               for (SequenceI toassoc : (SequenceI[]) fm[2])
5137               {
5138                 PDBEntry pe = new AssociatePdbFileWithSeq()
5139                         .associatePdbWithSeq((String) fm[0],
5140                                 (String) fm[1], toassoc, false,
5141                                 Desktop.instance);
5142                 if (pe != null)
5143                 {
5144                   System.err.println("Associated file : "
5145                           + ((String) fm[0]) + " with "
5146                           + toassoc.getDisplayId(true));
5147                   assocfiles++;
5148                 }
5149               }
5150               alignPanel.paintAlignment(true);
5151             }
5152           }
5153         }
5154         if (filesnotmatched.size() > 0)
5155         {
5156           if (assocfiles > 0
5157                   && (Cache.getDefault(
5158                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5159                           .showConfirmDialog(
5160                                   this,
5161                                   "<html>"+MessageManager
5162                                           .formatMessage(
5163                                                   "label.ignore_unmatched_dropped_files_info",
5164                                                   new String[]
5165                                                   { Integer.valueOf(
5166                                                           filesnotmatched
5167                                                                   .size())
5168                                                           .toString() })+"</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               .readAnnotationFile(viewport.getAlignment(), file, protocol)
5212               : false;
5213
5214       if (!isAnnotation)
5215       {
5216         // first see if its a T-COFFEE score file
5217         TCoffeeScoreFile tcf = null;
5218         try
5219         {
5220           tcf = new TCoffeeScoreFile(file, protocol);
5221           if (tcf.isValid())
5222           {
5223             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5224             {
5225               tcoffeeColour.setEnabled(true);
5226               tcoffeeColour.setSelected(true);
5227               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5228               isAnnotation = true;
5229               statusBar
5230                       .setText(MessageManager
5231                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5232             }
5233             else
5234             {
5235               // some problem - if no warning its probable that the ID matching
5236               // process didn't work
5237               JOptionPane
5238                       .showMessageDialog(
5239                               Desktop.desktop,
5240                               tcf.getWarningMessage() == null ? MessageManager
5241                                       .getString("label.check_file_matches_sequence_ids_alignment")
5242                                       : tcf.getWarningMessage(),
5243                               MessageManager
5244                                       .getString("label.problem_reading_tcoffee_score_file"),
5245                               JOptionPane.WARNING_MESSAGE);
5246             }
5247           }
5248           else
5249           {
5250             tcf = null;
5251           }
5252         } catch (Exception x)
5253         {
5254           Cache.log
5255                   .debug("Exception when processing data source as T-COFFEE score file",
5256                           x);
5257           tcf = null;
5258         }
5259         if (tcf == null)
5260         {
5261           // try to see if its a JNet 'concise' style annotation file *before*
5262           // we
5263           // try to parse it as a features file
5264           if (format == null)
5265           {
5266             format = new IdentifyFile().Identify(file, protocol);
5267           }
5268           if (format.equalsIgnoreCase("JnetFile"))
5269           {
5270             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5271                     file, protocol);
5272             new JnetAnnotationMaker().add_annotation(predictions,
5273                     viewport.getAlignment(), 0, false);
5274             isAnnotation = true;
5275           }
5276           else
5277           {
5278             /*
5279              * if (format.equalsIgnoreCase("PDB")) {
5280              *
5281              * String pdbfn = ""; // try to match up filename with sequence id
5282              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5283              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5284              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5285              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5286              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5287              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5288              * // attempt to find a match in the alignment SequenceI mtch =
5289              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5290              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5291              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5292              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5293              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5294              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5295              * { System.err.println("Associated file : " + file + " with " +
5296              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5297              * TODO: maybe need to load as normal otherwise return; } }
5298              */
5299             // try to parse it as a features file
5300             boolean isGroupsFile = parseFeaturesFile(file, protocol);
5301             // if it wasn't a features file then we just treat it as a general
5302             // alignment file to load into the current view.
5303             if (!isGroupsFile)
5304             {
5305               new FileLoader().LoadFile(viewport, file, protocol, format);
5306             }
5307             else
5308             {
5309               alignPanel.paintAlignment(true);
5310             }
5311           }
5312         }
5313       }
5314       if (isAnnotation)
5315       {
5316
5317         alignPanel.adjustAnnotationHeight();
5318         viewport.updateSequenceIdColours();
5319         buildSortByAnnotationScoresMenu();
5320         alignPanel.paintAlignment(true);
5321       }
5322     } catch (Exception ex)
5323     {
5324       ex.printStackTrace();
5325     } catch (OutOfMemoryError oom)
5326     {
5327       try
5328       {
5329         System.gc();
5330       } catch (Exception x)
5331       {
5332       }
5333       ;
5334       new OOMWarning(
5335               "loading data "
5336                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5337                               : "using " + protocol + " from " + file)
5338                               : ".")
5339                       + (format != null ? "(parsing as '" + format
5340                               + "' file)" : ""), oom, Desktop.desktop);
5341     }
5342   }
5343
5344   @Override
5345   public void tabSelectionChanged(int index)
5346   {
5347     if (index > -1)
5348     {
5349       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5350       viewport = alignPanel.av;
5351       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5352       setMenusFromViewport(viewport);
5353     }
5354   }
5355
5356   @Override
5357   public void tabbedPane_mousePressed(MouseEvent e)
5358   {
5359     if (SwingUtilities.isRightMouseButton(e))
5360     {
5361       String reply = JOptionPane.showInternalInputDialog(this,
5362               MessageManager.getString("label.enter_view_name"),
5363               MessageManager.getString("label.enter_view_name"),
5364               JOptionPane.QUESTION_MESSAGE);
5365
5366       if (reply != null)
5367       {
5368         viewport.viewName = reply;
5369         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5370       }
5371     }
5372   }
5373
5374   public AlignViewport getCurrentView()
5375   {
5376     return viewport;
5377   }
5378
5379   /**
5380    * Open the dialog for regex description parsing.
5381    */
5382   @Override
5383   protected void extractScores_actionPerformed(ActionEvent e)
5384   {
5385     ParseProperties pp = new jalview.analysis.ParseProperties(
5386             viewport.getAlignment());
5387     // TODO: verify regex and introduce GUI dialog for version 2.5
5388     // if (pp.getScoresFromDescription("col", "score column ",
5389     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5390     // true)>0)
5391     if (pp.getScoresFromDescription("description column",
5392             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5393     {
5394       buildSortByAnnotationScoresMenu();
5395     }
5396   }
5397
5398   /*
5399    * (non-Javadoc)
5400    *
5401    * @see
5402    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5403    * )
5404    */
5405   @Override
5406   protected void showDbRefs_actionPerformed(ActionEvent e)
5407   {
5408     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5409   }
5410
5411   /*
5412    * (non-Javadoc)
5413    *
5414    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5415    * ActionEvent)
5416    */
5417   @Override
5418   protected void showNpFeats_actionPerformed(ActionEvent e)
5419   {
5420     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5421   }
5422
5423   /**
5424    * find the viewport amongst the tabs in this alignment frame and close that
5425    * tab
5426    *
5427    * @param av
5428    */
5429   public boolean closeView(AlignViewport av)
5430   {
5431     if (viewport == av)
5432     {
5433       this.closeMenuItem_actionPerformed(false);
5434       return true;
5435     }
5436     Component[] comp = tabbedPane.getComponents();
5437     for (int i = 0; comp != null && i < comp.length; i++)
5438     {
5439       if (comp[i] instanceof AlignmentPanel)
5440       {
5441         if (((AlignmentPanel) comp[i]).av == av)
5442         {
5443           // close the view.
5444           closeView((AlignmentPanel) comp[i]);
5445           return true;
5446         }
5447       }
5448     }
5449     return false;
5450   }
5451
5452   protected void build_fetchdbmenu(JMenu webService)
5453   {
5454     // Temporary hack - DBRef Fetcher always top level ws entry.
5455     // TODO We probably want to store a sequence database checklist in
5456     // preferences and have checkboxes.. rather than individual sources selected
5457     // here
5458     final JMenu rfetch = new JMenu(
5459             MessageManager.getString("action.fetch_db_references"));
5460     rfetch.setToolTipText(MessageManager
5461             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5462     webService.add(rfetch);
5463
5464     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5465             MessageManager.getString("option.trim_retrieved_seqs"));
5466     trimrs.setToolTipText(MessageManager
5467             .getString("label.trim_retrieved_sequences"));
5468     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5469     trimrs.addActionListener(new ActionListener()
5470     {
5471       @Override
5472       public void actionPerformed(ActionEvent e)
5473       {
5474         trimrs.setSelected(trimrs.isSelected());
5475         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5476                 Boolean.valueOf(trimrs.isSelected()).toString());
5477       };
5478     });
5479     rfetch.add(trimrs);
5480     JMenuItem fetchr = new JMenuItem(
5481             MessageManager.getString("label.standard_databases"));
5482     fetchr.setToolTipText(MessageManager
5483             .getString("label.fetch_embl_uniprot"));
5484     fetchr.addActionListener(new ActionListener()
5485     {
5486
5487       @Override
5488       public void actionPerformed(ActionEvent e)
5489       {
5490         new Thread(new Runnable()
5491         {
5492
5493           @Override
5494           public void run()
5495           {
5496             new jalview.ws.DBRefFetcher(alignPanel.av
5497                     .getSequenceSelection(), alignPanel.alignFrame)
5498                     .fetchDBRefs(false);
5499           }
5500         }).start();
5501
5502       }
5503
5504     });
5505     rfetch.add(fetchr);
5506     final AlignFrame me = this;
5507     new Thread(new Runnable()
5508     {
5509       @Override
5510       public void run()
5511       {
5512         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5513                 .getSequenceFetcherSingleton(me);
5514         javax.swing.SwingUtilities.invokeLater(new Runnable()
5515         {
5516           @Override
5517           public void run()
5518           {
5519             String[] dbclasses = sf.getOrderedSupportedSources();
5520             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5521             // jalview.util.QuickSort.sort(otherdb, otherdb);
5522             List<DbSourceProxy> otherdb;
5523             JMenu dfetch = new JMenu();
5524             JMenu ifetch = new JMenu();
5525             JMenuItem fetchr = null;
5526             int comp = 0, icomp = 0, mcomp = 15;
5527             String mname = null;
5528             int dbi = 0;
5529             for (String dbclass : dbclasses)
5530             {
5531               otherdb = sf.getSourceProxy(dbclass);
5532               // add a single entry for this class, or submenu allowing 'fetch
5533               // all' or pick one
5534               if (otherdb == null || otherdb.size() < 1)
5535               {
5536                 continue;
5537               }
5538               // List<DbSourceProxy> dbs=otherdb;
5539               // otherdb=new ArrayList<DbSourceProxy>();
5540               // for (DbSourceProxy db:dbs)
5541               // {
5542               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5543               // }
5544               if (mname == null)
5545               {
5546                 mname = "From " + dbclass;
5547               }
5548               if (otherdb.size() == 1)
5549               {
5550                 final DbSourceProxy[] dassource = otherdb
5551                         .toArray(new DbSourceProxy[0]);
5552                 DbSourceProxy src = otherdb.get(0);
5553                 fetchr = new JMenuItem(src.getDbSource());
5554                 fetchr.addActionListener(new ActionListener()
5555                 {
5556
5557                   @Override
5558                   public void actionPerformed(ActionEvent e)
5559                   {
5560                     new Thread(new Runnable()
5561                     {
5562
5563                       @Override
5564                       public void run()
5565                       {
5566                         new jalview.ws.DBRefFetcher(alignPanel.av
5567                                 .getSequenceSelection(),
5568                                 alignPanel.alignFrame, dassource)
5569                                 .fetchDBRefs(false);
5570                       }
5571                     }).start();
5572                   }
5573
5574                 });
5575                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5576                 dfetch.add(fetchr);
5577                 comp++;
5578               }
5579               else
5580               {
5581                 final DbSourceProxy[] dassource = otherdb
5582                         .toArray(new DbSourceProxy[0]);
5583                 // fetch all entry
5584                 DbSourceProxy src = otherdb.get(0);
5585                 fetchr = new JMenuItem(MessageManager.formatMessage(
5586                         "label.fetch_all_param", new String[]
5587                         { src.getDbSource() }));
5588                 fetchr.addActionListener(new ActionListener()
5589                 {
5590                   @Override
5591                   public void actionPerformed(ActionEvent e)
5592                   {
5593                     new Thread(new Runnable()
5594                     {
5595
5596                       @Override
5597                       public void run()
5598                       {
5599                         new jalview.ws.DBRefFetcher(alignPanel.av
5600                                 .getSequenceSelection(),
5601                                 alignPanel.alignFrame, dassource)
5602                                 .fetchDBRefs(false);
5603                       }
5604                     }).start();
5605                   }
5606                 });
5607
5608                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5609                 dfetch.add(fetchr);
5610                 comp++;
5611                 // and then build the rest of the individual menus
5612                 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5613                 icomp = 0;
5614                 String imname = null;
5615                 int i = 0;
5616                 for (DbSourceProxy sproxy : otherdb)
5617                 {
5618                   String dbname = sproxy.getDbName();
5619                   String sname = dbname.length() > 5 ? dbname.substring(0,
5620                           5) + "..." : dbname;
5621                   String msname = dbname.length() > 10 ? dbname.substring(
5622                           0, 10) + "..." : dbname;
5623                   if (imname == null)
5624                   {
5625                     imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5626                   }
5627                   fetchr = new JMenuItem(msname);
5628                   final DbSourceProxy[] dassrc =
5629                   { sproxy };
5630                   fetchr.addActionListener(new ActionListener()
5631                   {
5632
5633                     @Override
5634                     public void actionPerformed(ActionEvent e)
5635                     {
5636                       new Thread(new Runnable()
5637                       {
5638
5639                         @Override
5640                         public void run()
5641                         {
5642                           new jalview.ws.DBRefFetcher(alignPanel.av
5643                                   .getSequenceSelection(),
5644                                   alignPanel.alignFrame, dassrc)
5645                                   .fetchDBRefs(false);
5646                         }
5647                       }).start();
5648                     }
5649
5650                   });
5651                   fetchr.setToolTipText("<html>"
5652                           + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5653                   ifetch.add(fetchr);
5654                   ++i;
5655                   if (++icomp >= mcomp || i == (otherdb.size()))
5656                   {
5657                     ifetch.setText(MessageManager.formatMessage(
5658                             "label.source_to_target", imname, sname));
5659                     dfetch.add(ifetch);
5660                     ifetch = new JMenu();
5661                     imname = null;
5662                     icomp = 0;
5663                     comp++;
5664                   }
5665                 }
5666               }
5667               ++dbi;
5668               if (comp >= mcomp || dbi >= (dbclasses.length))
5669               {
5670                 dfetch.setText(MessageManager.formatMessage(
5671                         "label.source_to_target", mname, dbclass));
5672                 rfetch.add(dfetch);
5673                 dfetch = new JMenu();
5674                 mname = null;
5675                 comp = 0;
5676               }
5677             }
5678           }
5679         });
5680       }
5681     }).start();
5682
5683   }
5684
5685   /**
5686    * Left justify the whole alignment.
5687    */
5688   @Override
5689   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5690   {
5691     AlignmentI al = viewport.getAlignment();
5692     al.justify(false);
5693     viewport.firePropertyChange("alignment", null, al);
5694   }
5695
5696   /**
5697    * Right justify the whole alignment.
5698    */
5699   @Override
5700   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5701   {
5702     AlignmentI al = viewport.getAlignment();
5703     al.justify(true);
5704     viewport.firePropertyChange("alignment", null, al);
5705   }
5706
5707   public void setShowSeqFeatures(boolean b)
5708   {
5709     showSeqFeatures.setSelected(true);
5710     viewport.setShowSequenceFeatures(true);
5711   }
5712
5713   /*
5714    * (non-Javadoc)
5715    *
5716    * @see
5717    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5718    * awt.event.ActionEvent)
5719    */
5720   @Override
5721   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5722   {
5723     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5724     alignPanel.paintAlignment(true);
5725   }
5726
5727   /*
5728    * (non-Javadoc)
5729    *
5730    * @see
5731    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5732    * .ActionEvent)
5733    */
5734   @Override
5735   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5736   {
5737     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5738     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5739
5740   }
5741
5742   /*
5743    * (non-Javadoc)
5744    *
5745    * @see
5746    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5747    * .event.ActionEvent)
5748    */
5749   @Override
5750   protected void showGroupConservation_actionPerformed(ActionEvent e)
5751   {
5752     viewport.setShowGroupConservation(showGroupConservation.getState());
5753     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5754   }
5755
5756   /*
5757    * (non-Javadoc)
5758    *
5759    * @see
5760    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5761    * .event.ActionEvent)
5762    */
5763   @Override
5764   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5765   {
5766     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5767     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5768   }
5769
5770   /*
5771    * (non-Javadoc)
5772    *
5773    * @see
5774    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5775    * .event.ActionEvent)
5776    */
5777   @Override
5778   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5779   {
5780     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5781     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5782   }
5783
5784   @Override
5785   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5786   {
5787     showSequenceLogo.setState(true);
5788     viewport.setShowSequenceLogo(true);
5789     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5790     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5791   }
5792
5793   @Override
5794   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5795   {
5796     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5797   }
5798
5799   /*
5800    * (non-Javadoc)
5801    *
5802    * @see
5803    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5804    * .event.ActionEvent)
5805    */
5806   @Override
5807   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5808   {
5809     if (avc.makeGroupsFromSelection())
5810     {
5811       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5812       alignPanel.updateAnnotation();
5813       alignPanel.paintAlignment(true);
5814     }
5815   }
5816
5817   @Override
5818   protected void createGroup_actionPerformed(ActionEvent e)
5819   {
5820     if (avc.createGroup())
5821     {
5822       alignPanel.alignmentChanged();
5823     }
5824   }
5825
5826   @Override
5827   protected void unGroup_actionPerformed(ActionEvent e)
5828   {
5829     if (avc.unGroup())
5830     {
5831       alignPanel.alignmentChanged();
5832     }
5833   }
5834
5835   /**
5836    * make the given alignmentPanel the currently selected tab
5837    *
5838    * @param alignmentPanel
5839    */
5840   public void setDisplayedView(AlignmentPanel alignmentPanel)
5841   {
5842     if (!viewport.getSequenceSetId().equals(
5843             alignmentPanel.av.getSequenceSetId()))
5844     {
5845       throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5846     }
5847     if (tabbedPane != null
5848             & alignPanels.indexOf(alignmentPanel) != tabbedPane
5849                     .getSelectedIndex())
5850     {
5851       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5852     }
5853   }
5854
5855   /**
5856    * Action on selection of menu options to Show or Hide annotations.
5857    *
5858    * @param visible
5859    * @param forSequences
5860    *          update sequence-related annotations
5861    * @param forAlignment
5862    *          update non-sequence-related annotations
5863    */
5864   @Override
5865   protected void setAnnotationsVisibility(boolean visible,
5866           boolean forSequences, boolean forAlignment)
5867   {
5868     for (AlignmentAnnotation aa : alignPanel.getAlignment()
5869             .getAlignmentAnnotation())
5870     {
5871       boolean apply = (aa.sequenceRef == null && forAlignment)
5872               || (aa.sequenceRef != null && forSequences);
5873       if (apply)
5874       {
5875         aa.visible = visible;
5876       }
5877     }
5878     alignPanel.validateAnnotationDimensions(false);
5879     alignPanel.alignmentChanged();
5880   }
5881
5882   /**
5883    * Store selected annotation sort order for the view and repaint.
5884    */
5885   @Override
5886   protected void sortAnnotations_actionPerformed()
5887   {
5888     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5889     this.alignPanel.av
5890             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5891     alignPanel.paintAlignment(true);
5892   }
5893
5894   /**
5895    *
5896    * @return alignment panels in this alignemnt frame
5897    */
5898   public List<AlignmentViewPanel> getAlignPanels()
5899   {
5900     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5901   }
5902 }
5903
5904 class PrintThread extends Thread
5905 {
5906   AlignmentPanel ap;
5907
5908   public PrintThread(AlignmentPanel ap)
5909   {
5910     this.ap = ap;
5911   }
5912
5913   static PageFormat pf;
5914
5915   @Override
5916   public void run()
5917   {
5918     PrinterJob printJob = PrinterJob.getPrinterJob();
5919
5920     if (pf != null)
5921     {
5922       printJob.setPrintable(ap, pf);
5923     }
5924     else
5925     {
5926       printJob.setPrintable(ap);
5927     }
5928
5929     if (printJob.printDialog())
5930     {
5931       try
5932       {
5933         printJob.print();
5934       } catch (Exception PrintException)
5935       {
5936         PrintException.printStackTrace();
5937       }
5938     }
5939   }
5940 }