src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.gui;
  20
  21 import jalview.analysis.AAFrequency;
  22 import jalview.analysis.AlignmentSorter;
  23 import jalview.analysis.Conservation;
  24 import jalview.analysis.CrossRef;
  25 import jalview.analysis.NJTree;
  26 import jalview.analysis.ParseProperties;
  27 import jalview.analysis.SequenceIdMatcher;
  28 import jalview.api.AlignViewControllerGuiI;
  29 import jalview.api.AlignViewControllerI;
  30 import jalview.bin.Cache;
  31 import jalview.commands.CommandI;
  32 import jalview.commands.EditCommand;
  33 import jalview.commands.OrderCommand;
  34 import jalview.commands.RemoveGapColCommand;
  35 import jalview.commands.RemoveGapsCommand;
  36 import jalview.commands.SlideSequencesCommand;
  37 import jalview.commands.TrimRegionCommand;
  38 import jalview.datamodel.AlignedCodonFrame;
  39 import jalview.datamodel.Alignment;
  40 import jalview.datamodel.AlignmentAnnotation;
  41 import jalview.datamodel.AlignmentI;
  42 import jalview.datamodel.AlignmentOrder;
  43 import jalview.datamodel.AlignmentView;
  44 import jalview.datamodel.ColumnSelection;
  45 import jalview.datamodel.PDBEntry;
  46 import jalview.datamodel.SeqCigar;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AlignmentProperties;
  51 import jalview.io.AnnotationFile;
  52 import jalview.io.FeaturesFile;
  53 import jalview.io.FileLoader;
  54 import jalview.io.FormatAdapter;
  55 import jalview.io.HTMLOutput;
  56 import jalview.io.IdentifyFile;
  57 import jalview.io.JalviewFileChooser;
  58 import jalview.io.JalviewFileView;
  59 import jalview.io.JnetAnnotationMaker;
  60 import jalview.io.NewickFile;
  61 import jalview.io.TCoffeeScoreFile;
  62 import jalview.jbgui.GAlignFrame;
  63 import jalview.schemes.Blosum62ColourScheme;
  64 import jalview.schemes.BuriedColourScheme;
  65 import jalview.schemes.ClustalxColourScheme;
  66 import jalview.schemes.ColourSchemeI;
  67 import jalview.schemes.ColourSchemeProperty;
  68 import jalview.schemes.HelixColourScheme;
  69 import jalview.schemes.HydrophobicColourScheme;
  70 import jalview.schemes.NucleotideColourScheme;
  71 import jalview.schemes.PIDColourScheme;
  72 import jalview.schemes.PurinePyrimidineColourScheme;
  73 import jalview.schemes.RNAHelicesColourChooser;
  74 import jalview.schemes.ResidueProperties;
  75 import jalview.schemes.StrandColourScheme;
  76 import jalview.schemes.TCoffeeColourScheme;
  77 import jalview.schemes.TaylorColourScheme;
  78 import jalview.schemes.TurnColourScheme;
  79 import jalview.schemes.UserColourScheme;
  80 import jalview.schemes.ZappoColourScheme;
  81 import jalview.util.MessageManager;
  82 import jalview.ws.jws1.Discoverer;
  83 import jalview.ws.jws2.Jws2Discoverer;
  84 import jalview.ws.jws2.jabaws2.Jws2Instance;
  85 import jalview.ws.seqfetcher.DbSourceProxy;
  86
  87 import java.awt.BorderLayout;
  88 import java.awt.Color;
  89 import java.awt.Component;
  90 import java.awt.GridLayout;
  91 import java.awt.Rectangle;
  92 import java.awt.Toolkit;
  93 import java.awt.datatransfer.Clipboard;
  94 import java.awt.datatransfer.DataFlavor;
  95 import java.awt.datatransfer.StringSelection;
  96 import java.awt.datatransfer.Transferable;
  97 import java.awt.dnd.DnDConstants;
  98 import java.awt.dnd.DropTargetDragEvent;
  99 import java.awt.dnd.DropTargetDropEvent;
 100 import java.awt.dnd.DropTargetEvent;
 101 import java.awt.dnd.DropTargetListener;
 102 import java.awt.event.ActionEvent;
 103 import java.awt.event.ActionListener;
 104 import java.awt.event.KeyAdapter;
 105 import java.awt.event.KeyEvent;
 106 import java.awt.event.MouseAdapter;
 107 import java.awt.event.MouseEvent;
 108 import java.awt.print.PageFormat;
 109 import java.awt.print.PrinterJob;
 110 import java.beans.PropertyChangeEvent;
 111 import java.io.File;
 112 import java.net.URL;
 113 import java.util.ArrayList;
 114 import java.util.Enumeration;
 115 import java.util.Hashtable;
 116 import java.util.List;
 117 import java.util.Vector;
 118
 119 import javax.swing.JButton;
 120 import javax.swing.JEditorPane;
 121 import javax.swing.JInternalFrame;
 122 import javax.swing.JLabel;
 123 import javax.swing.JLayeredPane;
 124 import javax.swing.JMenu;
 125 import javax.swing.JMenuItem;
 126 import javax.swing.JOptionPane;
 127 import javax.swing.JPanel;
 128 import javax.swing.JProgressBar;
 129 import javax.swing.JRadioButtonMenuItem;
 130 import javax.swing.JScrollPane;
 131 import javax.swing.SwingUtilities;
 132
 133 /**
 134  * DOCUMENT ME!
 135  *
 136  * @author $author$
 137  * @version $Revision$
 138  */
 139 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 140         IProgressIndicator, AlignViewControllerGuiI
 141 {
 142
 143   /** DOCUMENT ME!! */
 144   public static final int DEFAULT_WIDTH = 700;
 145
 146   /** DOCUMENT ME!! */
 147   public static final int DEFAULT_HEIGHT = 500;
 148
 149   public AlignmentPanel alignPanel;
 150
 151   AlignViewport viewport;
 152
 153   public AlignViewControllerI avc;
 154
 155
 156   Vector alignPanels = new Vector();
 157
 158   /**
 159    * Last format used to load or save alignments in this window
 160    */
 161   String currentFileFormat = null;
 162
 163   /**
 164    * Current filename for this alignment
 165    */
 166   String fileName = null;
 167
 168   /**
 169    * Creates a new AlignFrame object with specific width and height.
 170    *
 171    * @param al
 172    * @param width
 173    * @param height
 174    */
 175   public AlignFrame(AlignmentI al, int width, int height)
 176   {
 177     this(al, null, width, height);
 178   }
 179
 180   /**
 181    * Creates a new AlignFrame object with specific width, height and
 182    * sequenceSetId
 183    *
 184    * @param al
 185    * @param width
 186    * @param height
 187    * @param sequenceSetId
 188    */
 189   public AlignFrame(AlignmentI al, int width, int height,
 190           String sequenceSetId)
 191   {
 192     this(al, null, width, height, sequenceSetId);
 193   }
 194
 195   /**
 196    * Creates a new AlignFrame object with specific width, height and
 197    * sequenceSetId
 198    *
 199    * @param al
 200    * @param width
 201    * @param height
 202    * @param sequenceSetId
 203    * @param viewId
 204    */
 205   public AlignFrame(AlignmentI al, int width, int height,
 206           String sequenceSetId, String viewId)
 207   {
 208     this(al, null, width, height, sequenceSetId, viewId);
 209   }
 210
 211   /**
 212    * new alignment window with hidden columns
 213    *
 214    * @param al
 215    *          AlignmentI
 216    * @param hiddenColumns
 217    *          ColumnSelection or null
 218    * @param width
 219    *          Width of alignment frame
 220    * @param height
 221    *          height of frame.
 222    */
 223   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 224           int width, int height)
 225   {
 226     this(al, hiddenColumns, width, height, null);
 227   }
 228
 229   /**
 230    * Create alignment frame for al with hiddenColumns, a specific width and
 231    * height, and specific sequenceId
 232    *
 233    * @param al
 234    * @param hiddenColumns
 235    * @param width
 236    * @param height
 237    * @param sequenceSetId
 238    *          (may be null)
 239    */
 240   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 241           int width, int height, String sequenceSetId)
 242   {
 243     this(al, hiddenColumns, width, height, sequenceSetId, null);
 244   }
 245
 246   /**
 247    * Create alignment frame for al with hiddenColumns, a specific width and
 248    * height, and specific sequenceId
 249    *
 250    * @param al
 251    * @param hiddenColumns
 252    * @param width
 253    * @param height
 254    * @param sequenceSetId
 255    *          (may be null)
 256    * @param viewId
 257    *          (may be null)
 258    */
 259   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 260           int width, int height, String sequenceSetId, String viewId)
 261   {
 262     setSize(width, height);
 263     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 264
 265     alignPanel = new AlignmentPanel(this, viewport);
 266
 267     if (al.getDataset() == null)
 268     {
 269       al.setDataset(null);
 270     }
 271
 272     addAlignmentPanel(alignPanel, true);
 273     init();
 274   }
 275
 276   /**
 277    * Make a new AlignFrame from exisiting alignmentPanels
 278    *
 279    * @param ap
 280    *          AlignmentPanel
 281    * @param av
 282    *          AlignViewport
 283    */
 284   public AlignFrame(AlignmentPanel ap)
 285   {
 286     viewport = ap.av;
 287     alignPanel = ap;
 288     addAlignmentPanel(ap, false);
 289     init();
 290   }
 291
 292   /**
 293    * initalise the alignframe from the underlying viewport data and the
 294    * configurations
 295    */
 296   void init()
 297   {
 298     avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
 299     if (viewport.getAlignmentConservationAnnotation() == null)
 300     {
 301       BLOSUM62Colour.setEnabled(false);
 302       conservationMenuItem.setEnabled(false);
 303       modifyConservation.setEnabled(false);
 304       // PIDColour.setEnabled(false);
 305       // abovePIDThreshold.setEnabled(false);
 306       // modifyPID.setEnabled(false);
 307     }
 308
 309     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 310             "No sort");
 311
 312     if (sortby.equals("Id"))
 313     {
 314       sortIDMenuItem_actionPerformed(null);
 315     }
 316     else if (sortby.equals("Pairwise Identity"))
 317     {
 318       sortPairwiseMenuItem_actionPerformed(null);
 319     }
 320
 321     if (Desktop.desktop != null)
 322     {
 323       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 324       addServiceListeners();
 325       setGUINucleotide(viewport.getAlignment().isNucleotide());
 326     }
 327
 328     setMenusFromViewport(viewport);
 329     buildSortByAnnotationScoresMenu();
 330     if (viewport.wrapAlignment)
 331     {
 332       wrapMenuItem_actionPerformed(null);
 333     }
 334
 335     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 336     {
 337       this.overviewMenuItem_actionPerformed(null);
 338     }
 339
 340     addKeyListener();
 341
 342   }
 343
 344   /**
 345    * Change the filename and format for the alignment, and enable the 'reload'
 346    * button functionality.
 347    *
 348    * @param file
 349    *          valid filename
 350    * @param format
 351    *          format of file
 352    */
 353   public void setFileName(String file, String format)
 354   {
 355     fileName = file;
 356     currentFileFormat = format;
 357     reload.setEnabled(true);
 358   }
 359
 360   void addKeyListener()
 361   {
 362     addKeyListener(new KeyAdapter()
 363     {
 364       @Override
 365       public void keyPressed(KeyEvent evt)
 366       {
 367         if (viewport.cursorMode
 368                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 369                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 370                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 371                 && Character.isDigit(evt.getKeyChar()))
 372           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 373
 374         switch (evt.getKeyCode())
 375         {
 376
 377         case 27: // escape key
 378           deselectAllSequenceMenuItem_actionPerformed(null);
 379
 380           break;
 381
 382         case KeyEvent.VK_DOWN:
 383           if (evt.isAltDown() || !viewport.cursorMode)
 384             moveSelectedSequences(false);
 385           if (viewport.cursorMode)
 386             alignPanel.seqPanel.moveCursor(0, 1);
 387           break;
 388
 389         case KeyEvent.VK_UP:
 390           if (evt.isAltDown() || !viewport.cursorMode)
 391             moveSelectedSequences(true);
 392           if (viewport.cursorMode)
 393             alignPanel.seqPanel.moveCursor(0, -1);
 394
 395           break;
 396
 397         case KeyEvent.VK_LEFT:
 398           if (evt.isAltDown() || !viewport.cursorMode)
 399             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 400           else
 401             alignPanel.seqPanel.moveCursor(-1, 0);
 402
 403           break;
 404
 405         case KeyEvent.VK_RIGHT:
 406           if (evt.isAltDown() || !viewport.cursorMode)
 407             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 408           else
 409             alignPanel.seqPanel.moveCursor(1, 0);
 410           break;
 411
 412         case KeyEvent.VK_SPACE:
 413           if (viewport.cursorMode)
 414           {
 415             alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 416                     || evt.isShiftDown() || evt.isAltDown());
 417           }
 418           break;
 419
 420         // case KeyEvent.VK_A:
 421         // if (viewport.cursorMode)
 422         // {
 423         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 424         // //System.out.println("A");
 425         // }
 426         // break;
 427         /*
 428          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 429          * System.out.println("closing bracket"); } break;
 430          */
 431         case KeyEvent.VK_DELETE:
 432         case KeyEvent.VK_BACK_SPACE:
 433           if (!viewport.cursorMode)
 434           {
 435             cut_actionPerformed(null);
 436           }
 437           else
 438           {
 439             alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 440                     || evt.isShiftDown() || evt.isAltDown());
 441           }
 442
 443           break;
 444
 445         case KeyEvent.VK_S:
 446           if (viewport.cursorMode)
 447           {
 448             alignPanel.seqPanel.setCursorRow();
 449           }
 450           break;
 451         case KeyEvent.VK_C:
 452           if (viewport.cursorMode && !evt.isControlDown())
 453           {
 454             alignPanel.seqPanel.setCursorColumn();
 455           }
 456           break;
 457         case KeyEvent.VK_P:
 458           if (viewport.cursorMode)
 459           {
 460             alignPanel.seqPanel.setCursorPosition();
 461           }
 462           break;
 463
 464         case KeyEvent.VK_ENTER:
 465         case KeyEvent.VK_COMMA:
 466           if (viewport.cursorMode)
 467           {
 468             alignPanel.seqPanel.setCursorRowAndColumn();
 469           }
 470           break;
 471
 472         case KeyEvent.VK_Q:
 473           if (viewport.cursorMode)
 474           {
 475             alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 476           }
 477           break;
 478         case KeyEvent.VK_M:
 479           if (viewport.cursorMode)
 480           {
 481             alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 482           }
 483           break;
 484
 485         case KeyEvent.VK_F2:
 486           viewport.cursorMode = !viewport.cursorMode;
 487           statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
 488           if (viewport.cursorMode)
 489           {
 490             alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 491             alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 492           }
 493           alignPanel.seqPanel.seqCanvas.repaint();
 494           break;
 495
 496         case KeyEvent.VK_F1:
 497           try
 498           {
 499             ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
 500             java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
 501                     "help/help");
 502             javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
 503
 504             javax.help.HelpBroker hb = hs.createHelpBroker();
 505             hb.setCurrentID("home");
 506             hb.setDisplayed(true);
 507           } catch (Exception ex)
 508           {
 509             ex.printStackTrace();
 510           }
 511           break;
 512         case KeyEvent.VK_H:
 513         {
 514           boolean toggleSeqs = !evt.isControlDown();
 515           boolean toggleCols = !evt.isShiftDown();
 516           toggleHiddenRegions(toggleSeqs, toggleCols);
 517           break;
 518         }
 519         case KeyEvent.VK_PAGE_UP:
 520           if (viewport.wrapAlignment)
 521           {
 522             alignPanel.scrollUp(true);
 523           }
 524           else
 525           {
 526             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 527                     - viewport.endSeq + viewport.startSeq);
 528           }
 529           break;
 530         case KeyEvent.VK_PAGE_DOWN:
 531           if (viewport.wrapAlignment)
 532           {
 533             alignPanel.scrollUp(false);
 534           }
 535           else
 536           {
 537             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 538                     + viewport.endSeq - viewport.startSeq);
 539           }
 540           break;
 541         }
 542       }
 543
 544       @Override
 545       public void keyReleased(KeyEvent evt)
 546       {
 547         switch (evt.getKeyCode())
 548         {
 549         case KeyEvent.VK_LEFT:
 550           if (evt.isAltDown() || !viewport.cursorMode)
 551             viewport.firePropertyChange("alignment", null, viewport
 552                     .getAlignment().getSequences());
 553           break;
 554
 555         case KeyEvent.VK_RIGHT:
 556           if (evt.isAltDown() || !viewport.cursorMode)
 557             viewport.firePropertyChange("alignment", null, viewport
 558                     .getAlignment().getSequences());
 559           break;
 560         }
 561       }
 562     });
 563   }
 564
 565   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 566   {
 567     ap.alignFrame = this;
 568     avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
 569
 570     alignPanels.addElement(ap);
 571
 572     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 573
 574     int aSize = alignPanels.size();
 575
 576     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 577
 578     if (aSize == 1 && ap.av.viewName == null)
 579     {
 580       this.getContentPane().add(ap, BorderLayout.CENTER);
 581     }
 582     else
 583     {
 584       if (aSize == 2)
 585       {
 586         setInitialTabVisible();
 587       }
 588
 589       expandViews.setEnabled(true);
 590       gatherViews.setEnabled(true);
 591       tabbedPane.addTab(ap.av.viewName, ap);
 592
 593       ap.setVisible(false);
 594     }
 595
 596     if (newPanel)
 597     {
 598       if (ap.av.isPadGaps())
 599       {
 600         ap.av.getAlignment().padGaps();
 601       }
 602       ap.av.updateConservation(ap);
 603       ap.av.updateConsensus(ap);
 604       ap.av.updateStrucConsensus(ap);
 605     }
 606   }
 607
 608   public void setInitialTabVisible()
 609   {
 610     expandViews.setEnabled(true);
 611     gatherViews.setEnabled(true);
 612     tabbedPane.setVisible(true);
 613     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
 614     tabbedPane.addTab(first.av.viewName, first);
 615     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 616   }
 617
 618   public AlignViewport getViewport()
 619   {
 620     return viewport;
 621   }
 622
 623   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 624   private void addServiceListeners()
 625   {
 626     final java.beans.PropertyChangeListener thisListener;
 627     Desktop.instance.addJalviewPropertyChangeListener("services",
 628             thisListener = new java.beans.PropertyChangeListener()
 629             {
 630               @Override
 631               public void propertyChange(PropertyChangeEvent evt)
 632               {
 633                 // // System.out.println("Discoverer property change.");
 634                 // if (evt.getPropertyName().equals("services"))
 635                 {
 636                   SwingUtilities.invokeLater(new Runnable()
 637                   {
 638
 639                     @Override
 640                     public void run()
 641                     {
 642                       System.err
 643                               .println("Rebuild WS Menu for service change");
 644                       BuildWebServiceMenu();
 645                     }
 646
 647                   });
 648                 }
 649               }
 650             });
 651     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 652     {
 653       @Override
 654       public void internalFrameClosed(
 655               javax.swing.event.InternalFrameEvent evt)
 656       {
 657         System.out.println("deregistering discoverer listener");
 658         Desktop.instance.removeJalviewPropertyChangeListener("services",
 659                 thisListener);
 660         closeMenuItem_actionPerformed(true);
 661       };
 662     });
 663     // Finally, build the menu once to get current service state
 664     new Thread(new Runnable()
 665     {
 666       @Override
 667       public void run()
 668       {
 669         BuildWebServiceMenu();
 670       }
 671     }).start();
 672   }
 673
 674   public void setGUINucleotide(boolean nucleotide)
 675   {
 676     showTranslation.setVisible(nucleotide);
 677     conservationMenuItem.setEnabled(!nucleotide);
 678     modifyConservation.setEnabled(!nucleotide);
 679     showGroupConservation.setEnabled(!nucleotide);
 680     rnahelicesColour.setEnabled(nucleotide);
 681     purinePyrimidineColour.setEnabled(nucleotide);
 682     // Remember AlignFrame always starts as protein
 683     // if (!nucleotide)
 684     // {
 685     // showTr
 686     // calculateMenu.remove(calculateMenu.getItemCount() - 2);
 687     // }
 688   }
 689
 690   /**
 691    * set up menus for the currently viewport. This may be called after any
 692    * operation that affects the data in the current view (selection changed,
 693    * etc) to update the menus to reflect the new state.
 694    */
 695   public void setMenusForViewport()
 696   {
 697     setMenusFromViewport(viewport);
 698   }
 699
 700   /**
 701    * Need to call this method when tabs are selected for multiple views, or when
 702    * loading from Jalview2XML.java
 703    *
 704    * @param av
 705    *          AlignViewport
 706    */
 707   void setMenusFromViewport(AlignViewport av)
 708   {
 709     padGapsMenuitem.setSelected(av.isPadGaps());
 710     colourTextMenuItem.setSelected(av.showColourText);
 711     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 712     conservationMenuItem.setSelected(av.getConservationSelected());
 713     seqLimits.setSelected(av.getShowJVSuffix());
 714     idRightAlign.setSelected(av.rightAlignIds);
 715     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
 716     renderGapsMenuItem.setSelected(av.renderGaps);
 717     wrapMenuItem.setSelected(av.wrapAlignment);
 718     scaleAbove.setVisible(av.wrapAlignment);
 719     scaleLeft.setVisible(av.wrapAlignment);
 720     scaleRight.setVisible(av.wrapAlignment);
 721     annotationPanelMenuItem.setState(av.showAnnotation);
 722     viewBoxesMenuItem.setSelected(av.showBoxes);
 723     viewTextMenuItem.setSelected(av.showText);
 724     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 725     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 726     showGroupConservation.setSelected(av.isShowGroupConservation());
 727     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 728     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 729     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 730
 731     setColourSelected(ColourSchemeProperty.getColourName(av
 732             .getGlobalColourScheme()));
 733
 734     showSeqFeatures.setSelected(av.showSequenceFeatures);
 735     hiddenMarkers.setState(av.showHiddenMarkers);
 736     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 737     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
 738     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
 739     autoCalculate.setSelected(av.autoCalculateConsensus);
 740     sortByTree.setSelected(av.sortByTree);
 741     listenToViewSelections.setSelected(av.followSelection);
 742     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 743     rnahelicesColour
 744             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 745     setShowProductsEnabled();
 746     updateEditMenuBar();
 747   }
 748
 749   // methods for implementing IProgressIndicator
 750   // need to refactor to a reusable stub class
 751   Hashtable progressBars, progressBarHandlers;
 752
 753   /*
 754    * (non-Javadoc)
 755    *
 756    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 757    */
 758   @Override
 759   public void setProgressBar(String message, long id)
 760   {
 761     if (progressBars == null)
 762     {
 763       progressBars = new Hashtable();
 764       progressBarHandlers = new Hashtable();
 765     }
 766
 767     JPanel progressPanel;
 768     Long lId = new Long(id);
 769     GridLayout layout = (GridLayout) statusPanel.getLayout();
 770     if (progressBars.get(lId) != null)
 771     {
 772       progressPanel = (JPanel) progressBars.get(new Long(id));
 773       statusPanel.remove(progressPanel);
 774       progressBars.remove(lId);
 775       progressPanel = null;
 776       if (message != null)
 777       {
 778         statusBar.setText(message);
 779       }
 780       if (progressBarHandlers.contains(lId))
 781       {
 782         progressBarHandlers.remove(lId);
 783       }
 784       layout.setRows(layout.getRows() - 1);
 785     }
 786     else
 787     {
 788       progressPanel = new JPanel(new BorderLayout(10, 5));
 789
 790       JProgressBar progressBar = new JProgressBar();
 791       progressBar.setIndeterminate(true);
 792
 793       progressPanel.add(new JLabel(message), BorderLayout.WEST);
 794       progressPanel.add(progressBar, BorderLayout.CENTER);
 795
 796       layout.setRows(layout.getRows() + 1);
 797       statusPanel.add(progressPanel);
 798
 799       progressBars.put(lId, progressPanel);
 800     }
 801     // update GUI
 802     // setMenusForViewport();
 803     validate();
 804   }
 805
 806   @Override
 807   public void registerHandler(final long id,
 808           final IProgressIndicatorHandler handler)
 809   {
 810     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
 811     {
 812       throw new Error(
 813               "call setProgressBar before registering the progress bar's handler.");
 814     }
 815     progressBarHandlers.put(new Long(id), handler);
 816     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
 817     if (handler.canCancel())
 818     {
 819       JButton cancel = new JButton(MessageManager.getString("action.cancel"));
 820       final IProgressIndicator us = this;
 821       cancel.addActionListener(new ActionListener()
 822       {
 823
 824         @Override
 825         public void actionPerformed(ActionEvent e)
 826         {
 827           handler.cancelActivity(id);
 828           us.setProgressBar(
 829                   "Cancelled "
 830                           + ((JLabel) progressPanel.getComponent(0))
 831                                   .getText(), id);
 832         }
 833       });
 834       progressPanel.add(cancel, BorderLayout.EAST);
 835     }
 836   }
 837
 838   /**
 839    *
 840    * @return true if any progress bars are still active
 841    */
 842   @Override
 843   public boolean operationInProgress()
 844   {
 845     if (progressBars != null && progressBars.size() > 0)
 846     {
 847       return true;
 848     }
 849     return false;
 850   }
 851
 852   @Override
 853   public void setStatus(String text) {
 854     statusBar.setText(text);
 855   };
 856   /*
 857    * Added so Castor Mapping file can obtain Jalview Version
 858    */
 859   public String getVersion()
 860   {
 861     return jalview.bin.Cache.getProperty("VERSION");
 862   }
 863
 864   public FeatureRenderer getFeatureRenderer()
 865   {
 866     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
 867   }
 868
 869   @Override
 870   public void fetchSequence_actionPerformed(ActionEvent e)
 871   {
 872     new SequenceFetcher(this);
 873   }
 874
 875   @Override
 876   public void addFromFile_actionPerformed(ActionEvent e)
 877   {
 878     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 879   }
 880
 881   @Override
 882   public void reload_actionPerformed(ActionEvent e)
 883   {
 884     if (fileName != null)
 885     {
 886       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 887       // originating file's format
 888       // TODO: work out how to recover feature settings for correct view(s) when
 889       // file is reloaded.
 890       if (currentFileFormat.equals("Jalview"))
 891       {
 892         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 893         for (int i = 0; i < frames.length; i++)
 894         {
 895           if (frames[i] instanceof AlignFrame && frames[i] != this
 896                   && ((AlignFrame) frames[i]).fileName != null
 897                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 898           {
 899             try
 900             {
 901               frames[i].setSelected(true);
 902               Desktop.instance.closeAssociatedWindows();
 903             } catch (java.beans.PropertyVetoException ex)
 904             {
 905             }
 906           }
 907
 908         }
 909         Desktop.instance.closeAssociatedWindows();
 910
 911         FileLoader loader = new FileLoader();
 912         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 913         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
 914       }
 915       else
 916       {
 917         Rectangle bounds = this.getBounds();
 918
 919         FileLoader loader = new FileLoader();
 920         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 921         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
 922                 protocol, currentFileFormat);
 923
 924         newframe.setBounds(bounds);
 925         if (featureSettings != null && featureSettings.isShowing())
 926         {
 927           final Rectangle fspos = featureSettings.frame.getBounds();
 928           // TODO: need a 'show feature settings' function that takes bounds -
 929           // need to refactor Desktop.addFrame
 930           newframe.featureSettings_actionPerformed(null);
 931           final FeatureSettings nfs = newframe.featureSettings;
 932           SwingUtilities.invokeLater(new Runnable()
 933           {
 934             @Override
 935             public void run()
 936             {
 937               nfs.frame.setBounds(fspos);
 938             }
 939           });
 940           this.featureSettings.close();
 941           this.featureSettings = null;
 942         }
 943         this.closeMenuItem_actionPerformed(true);
 944       }
 945     }
 946   }
 947
 948   @Override
 949   public void addFromText_actionPerformed(ActionEvent e)
 950   {
 951     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
 952   }
 953
 954   @Override
 955   public void addFromURL_actionPerformed(ActionEvent e)
 956   {
 957     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
 958   }
 959
 960   @Override
 961   public void save_actionPerformed(ActionEvent e)
 962   {
 963     if (fileName == null
 964             || (currentFileFormat == null || !jalview.io.FormatAdapter
 965                     .isValidIOFormat(currentFileFormat, true))
 966             || fileName.startsWith("http"))
 967     {
 968       saveAs_actionPerformed(null);
 969     }
 970     else
 971     {
 972       saveAlignment(fileName, currentFileFormat);
 973     }
 974   }
 975
 976   /**
 977    * DOCUMENT ME!
 978    *
 979    * @param e
 980    *          DOCUMENT ME!
 981    */
 982   @Override
 983   public void saveAs_actionPerformed(ActionEvent e)
 984   {
 985     JalviewFileChooser chooser = new JalviewFileChooser(
 986             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 987             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
 988             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
 989             currentFileFormat, false);
 990
 991     chooser.setFileView(new JalviewFileView());
 992     chooser.setDialogTitle("Save Alignment to file");
 993     chooser.setToolTipText(MessageManager.getString("action.save"));\r
 994
 995     int value = chooser.showSaveDialog(this);
 996
 997     if (value == JalviewFileChooser.APPROVE_OPTION)
 998     {
 999       currentFileFormat = chooser.getSelectedFormat();
1000       if (currentFileFormat == null)
1001       {
1002         JOptionPane.showInternalMessageDialog(Desktop.desktop,
1003                 MessageManager.getString("label.select_file_format_before_saving"),
1004                 MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
1005         value = chooser.showSaveDialog(this);
1006         return;
1007       }
1008
1009       fileName = chooser.getSelectedFile().getPath();
1010
1011       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1012               currentFileFormat);
1013
1014       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1015       if (currentFileFormat.indexOf(" ") > -1)
1016       {
1017         currentFileFormat = currentFileFormat.substring(0,
1018                 currentFileFormat.indexOf(" "));
1019       }
1020       saveAlignment(fileName, currentFileFormat);
1021     }
1022   }
1023
1024   public boolean saveAlignment(String file, String format)
1025   {
1026     boolean success = true;
1027
1028     if (format.equalsIgnoreCase("Jalview"))
1029     {
1030       String shortName = title;
1031
1032       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1033       {
1034         shortName = shortName.substring(shortName
1035                 .lastIndexOf(java.io.File.separatorChar) + 1);
1036       }
1037
1038       success = new Jalview2XML().SaveAlignment(this, file, shortName);
1039
1040       statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
1041
1042
1043     }
1044     else
1045     {
1046       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1047       {
1048         warningMessage("Cannot save file " + fileName + " using format "
1049                 + format, "Alignment output format not supported");
1050         saveAs_actionPerformed(null);
1051         // JBPNote need to have a raise_gui flag here
1052         return false;
1053       }
1054
1055       String[] omitHidden = null;
1056
1057       if (viewport.hasHiddenColumns())
1058       {
1059         int reply = JOptionPane
1060                 .showInternalConfirmDialog(
1061                         Desktop.desktop,
1062                         MessageManager.getString("label.alignment_contains_hidden_columns"),
1063                         MessageManager.getString("action.save_omit_hidden_columns"),
1064                         JOptionPane.YES_NO_OPTION,
1065                         JOptionPane.QUESTION_MESSAGE);
1066
1067         if (reply == JOptionPane.YES_OPTION)
1068         {
1069           omitHidden = viewport.getViewAsString(false);
1070         }
1071       }
1072       FormatAdapter f = new FormatAdapter();
1073       String output = f.formatSequences(format,
1074               viewport.getAlignment(), // class cast exceptions will
1075               // occur in the distant future
1076               omitHidden, f.getCacheSuffixDefault(format),
1077               viewport.getColumnSelection());
1078
1079       if (output == null)
1080       {
1081         success = false;
1082       }
1083       else
1084       {
1085         try
1086         {
1087           java.io.PrintWriter out = new java.io.PrintWriter(
1088                   new java.io.FileWriter(file));
1089
1090           out.print(output);
1091           out.close();
1092           this.setTitle(file);
1093           statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
1094         } catch (Exception ex)
1095         {
1096           success = false;
1097           ex.printStackTrace();
1098         }
1099       }
1100     }
1101
1102     if (!success)
1103     {
1104       JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
1105               MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
1106     }
1107
1108     return success;
1109   }
1110
1111   private void warningMessage(String warning, String title)
1112   {
1113     if (new jalview.util.Platform().isHeadless())
1114     {
1115       System.err.println("Warning: " + title + "\nWarning: " + warning);
1116
1117     }
1118     else
1119     {
1120       JOptionPane.showInternalMessageDialog(this, warning, title,
1121               JOptionPane.WARNING_MESSAGE);
1122     }
1123     return;
1124   }
1125
1126   /**
1127    * DOCUMENT ME!
1128    *
1129    * @param e
1130    *          DOCUMENT ME!
1131    */
1132   @Override
1133   protected void outputText_actionPerformed(ActionEvent e)
1134   {
1135     String[] omitHidden = null;
1136
1137     if (viewport.hasHiddenColumns())
1138     {
1139       int reply = JOptionPane
1140               .showInternalConfirmDialog(
1141                       Desktop.desktop,
1142                       MessageManager.getString("label.alignment_contains_hidden_columns"),
1143                       MessageManager.getString("action.save_omit_hidden_columns"),
1144                       JOptionPane.YES_NO_OPTION,
1145                       JOptionPane.QUESTION_MESSAGE);
1146
1147       if (reply == JOptionPane.YES_OPTION)
1148       {
1149         omitHidden = viewport.getViewAsString(false);
1150       }
1151     }
1152
1153     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1154     cap.setForInput(null);
1155
1156     try
1157     {
1158       cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1159               viewport.getAlignment(), omitHidden,
1160               viewport.getColumnSelection()));
1161       Desktop.addInternalFrame(cap,
1162               MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
1163     } catch (OutOfMemoryError oom)
1164     {
1165       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1166       cap.dispose();
1167     }
1168
1169   }
1170
1171   /**
1172    * DOCUMENT ME!
1173    *
1174    * @param e
1175    *          DOCUMENT ME!
1176    */
1177   @Override
1178   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1179   {
1180     new HTMLOutput(alignPanel,
1181             alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1182             alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1183   }
1184
1185   public void createImageMap(File file, String image)
1186   {
1187     alignPanel.makePNGImageMap(file, image);
1188   }
1189
1190   /**
1191    * DOCUMENT ME!
1192    *
1193    * @param e
1194    *          DOCUMENT ME!
1195    */
1196   @Override
1197   public void createPNG(File f)
1198   {
1199     alignPanel.makePNG(f);
1200   }
1201
1202   /**
1203    * DOCUMENT ME!
1204    *
1205    * @param e
1206    *          DOCUMENT ME!
1207    */
1208   @Override
1209   public void createEPS(File f)
1210   {
1211     alignPanel.makeEPS(f);
1212   }
1213
1214   @Override
1215   public void pageSetup_actionPerformed(ActionEvent e)
1216   {
1217     PrinterJob printJob = PrinterJob.getPrinterJob();
1218     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1219   }
1220
1221   /**
1222    * DOCUMENT ME!
1223    *
1224    * @param e
1225    *          DOCUMENT ME!
1226    */
1227   @Override
1228   public void printMenuItem_actionPerformed(ActionEvent e)
1229   {
1230     // Putting in a thread avoids Swing painting problems
1231     PrintThread thread = new PrintThread(alignPanel);
1232     thread.start();
1233   }
1234
1235   @Override
1236   public void exportFeatures_actionPerformed(ActionEvent e)
1237   {
1238     new AnnotationExporter().exportFeatures(alignPanel);
1239   }
1240
1241   @Override
1242   public void exportAnnotations_actionPerformed(ActionEvent e)
1243   {
1244     new AnnotationExporter().exportAnnotations(alignPanel,
1245             viewport.showAnnotation ? viewport.getAlignment()
1246                     .getAlignmentAnnotation() : null, viewport
1247                     .getAlignment().getGroups(), ((Alignment) viewport
1248                     .getAlignment()).alignmentProperties);
1249   }
1250
1251   @Override
1252   public void associatedData_actionPerformed(ActionEvent e)
1253   {
1254     // Pick the tree file
1255     JalviewFileChooser chooser = new JalviewFileChooser(
1256             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1257     chooser.setFileView(new JalviewFileView());
1258     chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations"));\r
1259     chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations"));\r
1260
1261     int value = chooser.showOpenDialog(null);
1262
1263     if (value == JalviewFileChooser.APPROVE_OPTION)
1264     {
1265       String choice = chooser.getSelectedFile().getPath();
1266       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1267       loadJalviewDataFile(choice, null, null, null);
1268     }
1269
1270   }
1271
1272   /**
1273    * Close the current view or all views in the alignment frame. If the frame
1274    * only contains one view then the alignment will be removed from memory.
1275    *
1276    * @param closeAllTabs
1277    */
1278   @Override
1279   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1280   {
1281     if (alignPanels != null && alignPanels.size() < 2)
1282     {
1283       closeAllTabs = true;
1284     }
1285
1286     try
1287     {
1288       if (alignPanels != null)
1289       {
1290         if (closeAllTabs)
1291         {
1292           if (this.isClosed())
1293           {
1294             // really close all the windows - otherwise wait till
1295             // setClosed(true) is called
1296             for (int i = 0; i < alignPanels.size(); i++)
1297             {
1298               AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1299               ap.closePanel();
1300             }
1301           }
1302         }
1303         else
1304         {
1305           closeView(alignPanel);
1306         }
1307       }
1308
1309       if (closeAllTabs)
1310       {
1311         this.setClosed(true);
1312       }
1313     } catch (Exception ex)
1314     {
1315       ex.printStackTrace();
1316     }
1317   }
1318
1319   /**
1320    * close alignPanel2 and shuffle tabs appropriately.
1321    *
1322    * @param alignPanel2
1323    */
1324   public void closeView(AlignmentPanel alignPanel2)
1325   {
1326     int index = tabbedPane.getSelectedIndex();
1327     int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1328     alignPanels.removeElement(alignPanel2);
1329     // Unnecessary
1330     // if (viewport == alignPanel2.av)
1331     // {
1332     // viewport = null;
1333     // }
1334     alignPanel2.closePanel();
1335     alignPanel2 = null;
1336
1337     tabbedPane.removeTabAt(closedindex);
1338     tabbedPane.validate();
1339
1340     if (index > closedindex || index == tabbedPane.getTabCount())
1341     {
1342       // modify currently selected tab index if necessary.
1343       index--;
1344     }
1345
1346     this.tabSelectionChanged(index);
1347   }
1348
1349   /**
1350    * DOCUMENT ME!
1351    */
1352   void updateEditMenuBar()
1353   {
1354
1355     if (viewport.historyList.size() > 0)
1356     {
1357       undoMenuItem.setEnabled(true);
1358       CommandI command = (CommandI) viewport.historyList.peek();
1359       undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
1360     }
1361     else
1362     {
1363       undoMenuItem.setEnabled(false);
1364       undoMenuItem.setText(MessageManager.getString("action.undo"));
1365     }
1366
1367     if (viewport.redoList.size() > 0)
1368     {
1369       redoMenuItem.setEnabled(true);
1370
1371       CommandI command = (CommandI) viewport.redoList.peek();
1372       redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
1373     }
1374     else
1375     {
1376       redoMenuItem.setEnabled(false);
1377       redoMenuItem.setText(MessageManager.getString("action.redo"));
1378     }
1379   }
1380
1381   public void addHistoryItem(CommandI command)
1382   {
1383     if (command.getSize() > 0)
1384     {
1385       viewport.historyList.push(command);
1386       viewport.redoList.clear();
1387       updateEditMenuBar();
1388       viewport.updateHiddenColumns();
1389       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1390       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1391       // viewport.getColumnSelection()
1392       // .getHiddenColumns().size() > 0);
1393     }
1394   }
1395
1396   /**
1397    *
1398    * @return alignment objects for all views
1399    */
1400   AlignmentI[] getViewAlignments()
1401   {
1402     if (alignPanels != null)
1403     {
1404       Enumeration e = alignPanels.elements();
1405       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1406       for (int i = 0; e.hasMoreElements(); i++)
1407       {
1408         als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1409       }
1410       return als;
1411     }
1412     if (viewport != null)
1413     {
1414       return new AlignmentI[]
1415       { viewport.getAlignment() };
1416     }
1417     return null;
1418   }
1419
1420   /**
1421    * DOCUMENT ME!
1422    *
1423    * @param e
1424    *          DOCUMENT ME!
1425    */
1426   @Override
1427   protected void undoMenuItem_actionPerformed(ActionEvent e)
1428   {
1429     if (viewport.historyList.empty())
1430       return;
1431     CommandI command = (CommandI) viewport.historyList.pop();
1432     viewport.redoList.push(command);
1433     command.undoCommand(getViewAlignments());
1434
1435     AlignViewport originalSource = getOriginatingSource(command);
1436     updateEditMenuBar();
1437
1438     if (originalSource != null)
1439     {
1440       if (originalSource != viewport)
1441       {
1442         Cache.log
1443                 .warn("Implementation worry: mismatch of viewport origin for undo");
1444       }
1445       originalSource.updateHiddenColumns();
1446       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1447       // null
1448       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1449       // viewport.getColumnSelection()
1450       // .getHiddenColumns().size() > 0);
1451       originalSource.firePropertyChange("alignment", null, originalSource
1452               .getAlignment().getSequences());
1453     }
1454   }
1455
1456   /**
1457    * DOCUMENT ME!
1458    *
1459    * @param e
1460    *          DOCUMENT ME!
1461    */
1462   @Override
1463   protected void redoMenuItem_actionPerformed(ActionEvent e)
1464   {
1465     if (viewport.redoList.size() < 1)
1466     {
1467       return;
1468     }
1469
1470     CommandI command = (CommandI) viewport.redoList.pop();
1471     viewport.historyList.push(command);
1472     command.doCommand(getViewAlignments());
1473
1474     AlignViewport originalSource = getOriginatingSource(command);
1475     updateEditMenuBar();
1476
1477     if (originalSource != null)
1478     {
1479
1480       if (originalSource != viewport)
1481       {
1482         Cache.log
1483                 .warn("Implementation worry: mismatch of viewport origin for redo");
1484       }
1485       originalSource.updateHiddenColumns();
1486       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1487       // null
1488       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1489       // viewport.getColumnSelection()
1490       // .getHiddenColumns().size() > 0);
1491       originalSource.firePropertyChange("alignment", null, originalSource
1492               .getAlignment().getSequences());
1493     }
1494   }
1495
1496   AlignViewport getOriginatingSource(CommandI command)
1497   {
1498     AlignViewport originalSource = null;
1499     // For sequence removal and addition, we need to fire
1500     // the property change event FROM the viewport where the
1501     // original alignment was altered
1502     AlignmentI al = null;
1503     if (command instanceof EditCommand)
1504     {
1505       EditCommand editCommand = (EditCommand) command;
1506       al = editCommand.getAlignment();
1507       Vector comps = (Vector) PaintRefresher.components.get(viewport
1508               .getSequenceSetId());
1509
1510       for (int i = 0; i < comps.size(); i++)
1511       {
1512         if (comps.elementAt(i) instanceof AlignmentPanel)
1513         {
1514           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1515           {
1516             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1517             break;
1518           }
1519         }
1520       }
1521     }
1522
1523     if (originalSource == null)
1524     {
1525       // The original view is closed, we must validate
1526       // the current view against the closed view first
1527       if (al != null)
1528       {
1529         PaintRefresher.validateSequences(al, viewport.getAlignment());
1530       }
1531
1532       originalSource = viewport;
1533     }
1534
1535     return originalSource;
1536   }
1537
1538   /**
1539    * DOCUMENT ME!
1540    *
1541    * @param up
1542    *          DOCUMENT ME!
1543    */
1544   public void moveSelectedSequences(boolean up)
1545   {
1546     SequenceGroup sg = viewport.getSelectionGroup();
1547
1548     if (sg == null)
1549     {
1550       return;
1551     }
1552     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1553             viewport.getHiddenRepSequences(), up);
1554     alignPanel.paintAlignment(true);
1555   }
1556
1557   synchronized void slideSequences(boolean right, int size)
1558   {
1559     List<SequenceI> sg = new Vector();
1560     if (viewport.cursorMode)
1561     {
1562       sg.add(viewport.getAlignment().getSequenceAt(
1563               alignPanel.seqPanel.seqCanvas.cursorY));
1564     }
1565     else if (viewport.getSelectionGroup() != null
1566             && viewport.getSelectionGroup().getSize() != viewport
1567                     .getAlignment().getHeight())
1568     {
1569       sg = viewport.getSelectionGroup().getSequences(
1570               viewport.getHiddenRepSequences());
1571     }
1572
1573     if (sg.size() < 1)
1574     {
1575       return;
1576     }
1577
1578     Vector invertGroup = new Vector();
1579
1580     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1581     {
1582       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1583         invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1584     }
1585
1586     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1587
1588     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1589     for (int i = 0; i < invertGroup.size(); i++)
1590       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1591
1592     SlideSequencesCommand ssc;
1593     if (right)
1594       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1595               size, viewport.getGapCharacter());
1596     else
1597       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1598               size, viewport.getGapCharacter());
1599
1600     int groupAdjustment = 0;
1601     if (ssc.getGapsInsertedBegin() && right)
1602     {
1603       if (viewport.cursorMode)
1604         alignPanel.seqPanel.moveCursor(size, 0);
1605       else
1606         groupAdjustment = size;
1607     }
1608     else if (!ssc.getGapsInsertedBegin() && !right)
1609     {
1610       if (viewport.cursorMode)
1611         alignPanel.seqPanel.moveCursor(-size, 0);
1612       else
1613         groupAdjustment = -size;
1614     }
1615
1616     if (groupAdjustment != 0)
1617     {
1618       viewport.getSelectionGroup().setStartRes(
1619               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1620       viewport.getSelectionGroup().setEndRes(
1621               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1622     }
1623
1624     boolean appendHistoryItem = false;
1625     if (viewport.historyList != null && viewport.historyList.size() > 0
1626             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1627     {
1628       appendHistoryItem = ssc
1629               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1630                       .peek());
1631     }
1632
1633     if (!appendHistoryItem)
1634       addHistoryItem(ssc);
1635
1636     repaint();
1637   }
1638
1639   /**
1640    * DOCUMENT ME!
1641    *
1642    * @param e
1643    *          DOCUMENT ME!
1644    */
1645   @Override
1646   protected void copy_actionPerformed(ActionEvent e)
1647   {
1648     System.gc();
1649     if (viewport.getSelectionGroup() == null)
1650     {
1651       return;
1652     }
1653     // TODO: preserve the ordering of displayed alignment annotation in any
1654     // internal paste (particularly sequence associated annotation)
1655     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1656     String[] omitHidden = null;
1657
1658     if (viewport.hasHiddenColumns())
1659     {
1660       omitHidden = viewport.getViewAsString(true);
1661     }
1662
1663     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1664             omitHidden);
1665
1666     StringSelection ss = new StringSelection(output);
1667
1668     try
1669     {
1670       jalview.gui.Desktop.internalCopy = true;
1671       // Its really worth setting the clipboard contents
1672       // to empty before setting the large StringSelection!!
1673       Toolkit.getDefaultToolkit().getSystemClipboard()
1674               .setContents(new StringSelection(""), null);
1675
1676       Toolkit.getDefaultToolkit().getSystemClipboard()
1677               .setContents(ss, Desktop.instance);
1678     } catch (OutOfMemoryError er)
1679     {
1680       new OOMWarning("copying region", er);
1681       return;
1682     }
1683
1684     Vector hiddenColumns = null;
1685     if (viewport.hasHiddenColumns())
1686     {
1687       hiddenColumns = new Vector();
1688       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1689               .getSelectionGroup().getEndRes();
1690       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1691               .size(); i++)
1692       {
1693         int[] region = (int[]) viewport.getColumnSelection()
1694                 .getHiddenColumns().elementAt(i);
1695         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1696         {
1697           hiddenColumns.addElement(new int[]
1698           { region[0] - hiddenOffset, region[1] - hiddenOffset });
1699         }
1700       }
1701     }
1702
1703     Desktop.jalviewClipboard = new Object[]
1704     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1705     statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
1706   }
1707
1708   /**
1709    * DOCUMENT ME!
1710    *
1711    * @param e
1712    *          DOCUMENT ME!
1713    */
1714   @Override
1715   protected void pasteNew_actionPerformed(ActionEvent e)
1716   {
1717     paste(true);
1718   }
1719
1720   /**
1721    * DOCUMENT ME!
1722    *
1723    * @param e
1724    *          DOCUMENT ME!
1725    */
1726   @Override
1727   protected void pasteThis_actionPerformed(ActionEvent e)
1728   {
1729     paste(false);
1730   }
1731
1732   /**
1733    * Paste contents of Jalview clipboard
1734    *
1735    * @param newAlignment
1736    *          true to paste to a new alignment, otherwise add to this.
1737    */
1738   void paste(boolean newAlignment)
1739   {
1740     boolean externalPaste = true;
1741     try
1742     {
1743       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1744       Transferable contents = c.getContents(this);
1745
1746       if (contents == null)
1747       {
1748         return;
1749       }
1750
1751       String str, format;
1752       try
1753       {
1754         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1755         if (str.length() < 1)
1756         {
1757           return;
1758         }
1759
1760         format = new IdentifyFile().Identify(str, "Paste");
1761
1762       } catch (OutOfMemoryError er)
1763       {
1764         new OOMWarning("Out of memory pasting sequences!!", er);
1765         return;
1766       }
1767
1768       SequenceI[] sequences;
1769       boolean annotationAdded = false;
1770       AlignmentI alignment = null;
1771
1772       if (Desktop.jalviewClipboard != null)
1773       {
1774         // The clipboard was filled from within Jalview, we must use the
1775         // sequences
1776         // And dataset from the copied alignment
1777         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1778         // be doubly sure that we create *new* sequence objects.
1779         sequences = new SequenceI[newseq.length];
1780         for (int i = 0; i < newseq.length; i++)
1781         {
1782           sequences[i] = new Sequence(newseq[i]);
1783         }
1784         alignment = new Alignment(sequences);
1785         externalPaste = false;
1786       }
1787       else
1788       {
1789         // parse the clipboard as an alignment.
1790         alignment = new FormatAdapter().readFile(str, "Paste", format);
1791         sequences = alignment.getSequencesArray();
1792       }
1793
1794       int alwidth = 0;
1795       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1796       int fgroup = -1;
1797
1798       if (newAlignment)
1799       {
1800
1801         if (Desktop.jalviewClipboard != null)
1802         {
1803           // dataset is inherited
1804           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1805         }
1806         else
1807         {
1808           // new dataset is constructed
1809           alignment.setDataset(null);
1810         }
1811         alwidth = alignment.getWidth() + 1;
1812       }
1813       else
1814       {
1815         AlignmentI pastedal = alignment; // preserve pasted alignment object
1816         // Add pasted sequences and dataset into existing alignment.
1817         alignment = viewport.getAlignment();
1818         alwidth = alignment.getWidth() + 1;
1819         // decide if we need to import sequences from an existing dataset
1820         boolean importDs = Desktop.jalviewClipboard != null
1821                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1822         // importDs==true instructs us to copy over new dataset sequences from
1823         // an existing alignment
1824         Vector newDs = (importDs) ? new Vector() : null; // used to create
1825         // minimum dataset set
1826
1827         for (int i = 0; i < sequences.length; i++)
1828         {
1829           if (importDs)
1830           {
1831             newDs.addElement(null);
1832           }
1833           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1834           // paste
1835           if (importDs && ds != null)
1836           {
1837             if (!newDs.contains(ds))
1838             {
1839               newDs.setElementAt(ds, i);
1840               ds = new Sequence(ds);
1841               // update with new dataset sequence
1842               sequences[i].setDatasetSequence(ds);
1843             }
1844             else
1845             {
1846               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1847             }
1848           }
1849           else
1850           {
1851             // copy and derive new dataset sequence
1852             sequences[i] = sequences[i].deriveSequence();
1853             alignment.getDataset().addSequence(
1854                     sequences[i].getDatasetSequence());
1855             // TODO: avoid creation of duplicate dataset sequences with a
1856             // 'contains' method using SequenceI.equals()/SequenceI.contains()
1857           }
1858           alignment.addSequence(sequences[i]); // merges dataset
1859         }
1860         if (newDs != null)
1861         {
1862           newDs.clear(); // tidy up
1863         }
1864         if (alignment.getAlignmentAnnotation() != null)
1865         {
1866           for (AlignmentAnnotation alan : alignment
1867                   .getAlignmentAnnotation())
1868           {
1869             if (alan.graphGroup > fgroup)
1870             {
1871               fgroup = alan.graphGroup;
1872             }
1873           }
1874         }
1875         if (pastedal.getAlignmentAnnotation() != null)
1876         {
1877           // Add any annotation attached to alignment.
1878           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1879           for (int i = 0; i < alann.length; i++)
1880           {
1881             annotationAdded = true;
1882             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1883             {
1884               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1885               if (newann.graphGroup > -1)
1886               {
1887                 if (newGraphGroups.size() <= newann.graphGroup
1888                         || newGraphGroups.get(newann.graphGroup) == null)
1889                 {
1890                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1891                   {
1892                     newGraphGroups.add(q, null);
1893                   }
1894                   newGraphGroups.set(newann.graphGroup, new Integer(
1895                           ++fgroup));
1896                 }
1897                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1898                         .intValue();
1899               }
1900
1901               newann.padAnnotation(alwidth);
1902               alignment.addAnnotation(newann);
1903             }
1904           }
1905         }
1906       }
1907       if (!newAlignment)
1908       {
1909         // /////
1910         // ADD HISTORY ITEM
1911         //
1912         addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1913                 sequences, 0, alignment.getWidth(), alignment));
1914       }
1915       // Add any annotations attached to sequences
1916       for (int i = 0; i < sequences.length; i++)
1917       {
1918         if (sequences[i].getAnnotation() != null)
1919         {
1920           AlignmentAnnotation newann;
1921           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1922           {
1923             annotationAdded = true;
1924             newann = sequences[i].getAnnotation()[a];
1925             newann.adjustForAlignment();
1926             newann.padAnnotation(alwidth);
1927             if (newann.graphGroup > -1)
1928             {
1929               if (newann.graphGroup > -1)
1930               {
1931                 if (newGraphGroups.size() <= newann.graphGroup
1932                         || newGraphGroups.get(newann.graphGroup) == null)
1933                 {
1934                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1935                   {
1936                     newGraphGroups.add(q, null);
1937                   }
1938                   newGraphGroups.set(newann.graphGroup, new Integer(
1939                           ++fgroup));
1940                 }
1941                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1942                         .intValue();
1943               }
1944             }
1945             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1946             // was
1947             // duplicated
1948             // earlier
1949             alignment
1950                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1951           }
1952         }
1953       }
1954       if (!newAlignment)
1955       {
1956
1957         // propagate alignment changed.
1958         viewport.setEndSeq(alignment.getHeight());
1959         if (annotationAdded)
1960         {
1961           // Duplicate sequence annotation in all views.
1962           AlignmentI[] alview = this.getViewAlignments();
1963           for (int i = 0; i < sequences.length; i++)
1964           {
1965             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1966             if (sann == null)
1967               continue;
1968             for (int avnum = 0; avnum < alview.length; avnum++)
1969             {
1970               if (alview[avnum] != alignment)
1971               {
1972                 // duplicate in a view other than the one with input focus
1973                 int avwidth = alview[avnum].getWidth() + 1;
1974                 // this relies on sann being preserved after we
1975                 // modify the sequence's annotation array for each duplication
1976                 for (int a = 0; a < sann.length; a++)
1977                 {
1978                   AlignmentAnnotation newann = new AlignmentAnnotation(
1979                           sann[a]);
1980                   sequences[i].addAlignmentAnnotation(newann);
1981                   newann.padAnnotation(avwidth);
1982                   alview[avnum].addAnnotation(newann); // annotation was
1983                   // duplicated earlier
1984                   // TODO JAL-1145 graphGroups are not updated for sequence
1985                   // annotation added to several views. This may cause
1986                   // strangeness
1987                   alview[avnum].setAnnotationIndex(newann, a);
1988                 }
1989               }
1990             }
1991           }
1992           buildSortByAnnotationScoresMenu();
1993         }
1994         viewport.firePropertyChange("alignment", null,
1995                 alignment.getSequences());
1996         if (alignPanels != null)
1997         {
1998           for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
1999           {
2000             ap.validateAnnotationDimensions(false);
2001           }
2002         }
2003         else
2004         {
2005           alignPanel.validateAnnotationDimensions(false);
2006         }
2007
2008       }
2009       else
2010       {
2011         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2012                 DEFAULT_HEIGHT);
2013         String newtitle = new String("Copied sequences");
2014
2015         if (Desktop.jalviewClipboard != null
2016                 && Desktop.jalviewClipboard[2] != null)
2017         {
2018           Vector hc = (Vector) Desktop.jalviewClipboard[2];
2019           for (int i = 0; i < hc.size(); i++)
2020           {
2021             int[] region = (int[]) hc.elementAt(i);
2022             af.viewport.hideColumns(region[0], region[1]);
2023           }
2024         }
2025
2026         // >>>This is a fix for the moment, until a better solution is
2027         // found!!<<<
2028         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2029                 .transferSettings(
2030                         alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2031
2032         // TODO: maintain provenance of an alignment, rather than just make the
2033         // title a concatenation of operations.
2034         if (!externalPaste)
2035         {
2036           if (title.startsWith("Copied sequences"))
2037           {
2038             newtitle = title;
2039           }
2040           else
2041           {
2042             newtitle = newtitle.concat("- from " + title);
2043           }
2044         }
2045         else
2046         {
2047           newtitle = new String("Pasted sequences");
2048         }
2049
2050         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2051                 DEFAULT_HEIGHT);
2052
2053       }
2054
2055     } catch (Exception ex)
2056     {
2057       ex.printStackTrace();
2058       System.out.println("Exception whilst pasting: " + ex);
2059       // could be anything being pasted in here
2060     }
2061
2062   }
2063
2064   /**
2065    * DOCUMENT ME!
2066    *
2067    * @param e
2068    *          DOCUMENT ME!
2069    */
2070   @Override
2071   protected void cut_actionPerformed(ActionEvent e)
2072   {
2073     copy_actionPerformed(null);
2074     delete_actionPerformed(null);
2075   }
2076
2077   /**
2078    * DOCUMENT ME!
2079    *
2080    * @param e
2081    *          DOCUMENT ME!
2082    */
2083   @Override
2084   protected void delete_actionPerformed(ActionEvent evt)
2085   {
2086
2087     SequenceGroup sg = viewport.getSelectionGroup();
2088     if (sg == null)
2089     {
2090       return;
2091     }
2092
2093     Vector seqs = new Vector();
2094     SequenceI seq;
2095     for (int i = 0; i < sg.getSize(); i++)
2096     {
2097       seq = sg.getSequenceAt(i);
2098       seqs.addElement(seq);
2099     }
2100
2101     // If the cut affects all sequences, remove highlighted columns
2102     if (sg.getSize() == viewport.getAlignment().getHeight())
2103     {
2104       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2105               sg.getEndRes() + 1);
2106     }
2107
2108     SequenceI[] cut = new SequenceI[seqs.size()];
2109     for (int i = 0; i < seqs.size(); i++)
2110     {
2111       cut[i] = (SequenceI) seqs.elementAt(i);
2112     }
2113
2114     /*
2115      * //ADD HISTORY ITEM
2116      */
2117     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2118             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2119             viewport.getAlignment()));
2120
2121     viewport.setSelectionGroup(null);
2122     viewport.sendSelection();
2123     viewport.getAlignment().deleteGroup(sg);
2124
2125     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2126             .getSequences());
2127     if (viewport.getAlignment().getHeight() < 1)
2128     {
2129       try
2130       {
2131         this.setClosed(true);
2132       } catch (Exception ex)
2133       {
2134       }
2135     }
2136   }
2137
2138   /**
2139    * DOCUMENT ME!
2140    *
2141    * @param e
2142    *          DOCUMENT ME!
2143    */
2144   @Override
2145   protected void deleteGroups_actionPerformed(ActionEvent e)
2146   {
2147     if (avc.deleteGroups()) {
2148       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2149       alignPanel.updateAnnotation();
2150       alignPanel.paintAlignment(true);
2151     }
2152   }
2153
2154   /**
2155    * DOCUMENT ME!
2156    *
2157    * @param e
2158    *          DOCUMENT ME!
2159    */
2160   @Override
2161   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2162   {
2163     SequenceGroup sg = new SequenceGroup();
2164
2165     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2166     {
2167       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2168     }
2169
2170     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2171     viewport.setSelectionGroup(sg);
2172     viewport.sendSelection();
2173     alignPanel.paintAlignment(true);
2174     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2175   }
2176
2177   /**
2178    * DOCUMENT ME!
2179    *
2180    * @param e
2181    *          DOCUMENT ME!
2182    */
2183   @Override
2184   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2185   {
2186     if (viewport.cursorMode)
2187     {
2188       alignPanel.seqPanel.keyboardNo1 = null;
2189       alignPanel.seqPanel.keyboardNo2 = null;
2190     }
2191     viewport.setSelectionGroup(null);
2192     viewport.getColumnSelection().clear();
2193     viewport.setSelectionGroup(null);
2194     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2195     alignPanel.idPanel.idCanvas.searchResults = null;
2196     alignPanel.paintAlignment(true);
2197     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2198     viewport.sendSelection();
2199   }
2200
2201   /**
2202    * DOCUMENT ME!
2203    *
2204    * @param e
2205    *          DOCUMENT ME!
2206    */
2207   @Override
2208   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2209   {
2210     SequenceGroup sg = viewport.getSelectionGroup();
2211
2212     if (sg == null)
2213     {
2214       selectAllSequenceMenuItem_actionPerformed(null);
2215
2216       return;
2217     }
2218
2219     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2220     {
2221       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2222     }
2223
2224     alignPanel.paintAlignment(true);
2225     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2226     viewport.sendSelection();
2227   }
2228
2229   @Override
2230   public void invertColSel_actionPerformed(ActionEvent e)
2231   {
2232     viewport.invertColumnSelection();
2233     alignPanel.paintAlignment(true);
2234     viewport.sendSelection();
2235   }
2236
2237   /**
2238    * DOCUMENT ME!
2239    *
2240    * @param e
2241    *          DOCUMENT ME!
2242    */
2243   @Override
2244   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2245   {
2246     trimAlignment(true);
2247   }
2248
2249   /**
2250    * DOCUMENT ME!
2251    *
2252    * @param e
2253    *          DOCUMENT ME!
2254    */
2255   @Override
2256   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2257   {
2258     trimAlignment(false);
2259   }
2260
2261   void trimAlignment(boolean trimLeft)
2262   {
2263     ColumnSelection colSel = viewport.getColumnSelection();
2264     int column;
2265
2266     if (colSel.size() > 0)
2267     {
2268       if (trimLeft)
2269       {
2270         column = colSel.getMin();
2271       }
2272       else
2273       {
2274         column = colSel.getMax();
2275       }
2276
2277       SequenceI[] seqs;
2278       if (viewport.getSelectionGroup() != null)
2279       {
2280         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2281                 viewport.getHiddenRepSequences());
2282       }
2283       else
2284       {
2285         seqs = viewport.getAlignment().getSequencesArray();
2286       }
2287
2288       TrimRegionCommand trimRegion;
2289       if (trimLeft)
2290       {
2291         trimRegion = new TrimRegionCommand("Remove Left",
2292                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2293                 viewport.getAlignment(), viewport.getColumnSelection(),
2294                 viewport.getSelectionGroup());
2295         viewport.setStartRes(0);
2296       }
2297       else
2298       {
2299         trimRegion = new TrimRegionCommand("Remove Right",
2300                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2301                 viewport.getAlignment(), viewport.getColumnSelection(),
2302                 viewport.getSelectionGroup());
2303       }
2304
2305       statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
2306
2307       addHistoryItem(trimRegion);
2308
2309       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2310       {
2311         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2312                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2313         {
2314           viewport.getAlignment().deleteGroup(sg);
2315         }
2316       }
2317
2318       viewport.firePropertyChange("alignment", null, viewport
2319               .getAlignment().getSequences());
2320     }
2321   }
2322
2323   /**
2324    * DOCUMENT ME!
2325    *
2326    * @param e
2327    *          DOCUMENT ME!
2328    */
2329   @Override
2330   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2331   {
2332     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2333
2334     SequenceI[] seqs;
2335     if (viewport.getSelectionGroup() != null)
2336     {
2337       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2338               viewport.getHiddenRepSequences());
2339       start = viewport.getSelectionGroup().getStartRes();
2340       end = viewport.getSelectionGroup().getEndRes();
2341     }
2342     else
2343     {
2344       seqs = viewport.getAlignment().getSequencesArray();
2345     }
2346
2347     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2348             "Remove Gapped Columns", seqs, start, end,
2349             viewport.getAlignment());
2350
2351     addHistoryItem(removeGapCols);
2352
2353     statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
2354
2355     // This is to maintain viewport position on first residue
2356     // of first sequence
2357     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2358     int startRes = seq.findPosition(viewport.startRes);
2359     // ShiftList shifts;
2360     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2361     // edit.alColumnChanges=shifts.getInverse();
2362     // if (viewport.hasHiddenColumns)
2363     // viewport.getColumnSelection().compensateForEdits(shifts);
2364     viewport.setStartRes(seq.findIndex(startRes) - 1);
2365     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2366             .getSequences());
2367
2368   }
2369
2370   /**
2371    * DOCUMENT ME!
2372    *
2373    * @param e
2374    *          DOCUMENT ME!
2375    */
2376   @Override
2377   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2378   {
2379     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2380
2381     SequenceI[] seqs;
2382     if (viewport.getSelectionGroup() != null)
2383     {
2384       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2385               viewport.getHiddenRepSequences());
2386       start = viewport.getSelectionGroup().getStartRes();
2387       end = viewport.getSelectionGroup().getEndRes();
2388     }
2389     else
2390     {
2391       seqs = viewport.getAlignment().getSequencesArray();
2392     }
2393
2394     // This is to maintain viewport position on first residue
2395     // of first sequence
2396     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2397     int startRes = seq.findPosition(viewport.startRes);
2398
2399     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2400             viewport.getAlignment()));
2401
2402     viewport.setStartRes(seq.findIndex(startRes) - 1);
2403
2404     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2405             .getSequences());
2406
2407   }
2408
2409   /**
2410    * DOCUMENT ME!
2411    *
2412    * @param e
2413    *          DOCUMENT ME!
2414    */
2415   @Override
2416   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2417   {
2418     viewport.setPadGaps(padGapsMenuitem.isSelected());
2419     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2420             .getSequences());
2421   }
2422
2423   // else
2424   {
2425     // if (justifySeqs>0)
2426     {
2427       // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2428     }
2429   }
2430
2431   // }
2432
2433   /**
2434    * DOCUMENT ME!
2435    *
2436    * @param e
2437    *          DOCUMENT ME!
2438    */
2439   @Override
2440   public void findMenuItem_actionPerformed(ActionEvent e)
2441   {
2442     new Finder();
2443   }
2444
2445   @Override
2446   public void newView_actionPerformed(ActionEvent e)
2447   {
2448     newView(true);
2449   }
2450
2451   /**
2452    *
2453    * @param copyAnnotation
2454    *          if true then duplicate all annnotation, groups and settings
2455    * @return new alignment panel, already displayed.
2456    */
2457   public AlignmentPanel newView(boolean copyAnnotation)
2458   {
2459     return newView(null, copyAnnotation);
2460   }
2461
2462   /**
2463    *
2464    * @param viewTitle
2465    *          title of newly created view
2466    * @return new alignment panel, already displayed.
2467    */
2468   public AlignmentPanel newView(String viewTitle)
2469   {
2470     return newView(viewTitle, true);
2471   }
2472
2473   /**
2474    *
2475    * @param viewTitle
2476    *          title of newly created view
2477    * @param copyAnnotation
2478    *          if true then duplicate all annnotation, groups and settings
2479    * @return new alignment panel, already displayed.
2480    */
2481   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2482   {
2483     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2484             true);
2485     if (!copyAnnotation)
2486     {
2487       // just remove all the current annotation except for the automatic stuff
2488       newap.av.getAlignment().deleteAllGroups();
2489       for (AlignmentAnnotation alan : newap.av.getAlignment()
2490               .getAlignmentAnnotation())
2491       {
2492         if (!alan.autoCalculated)
2493         {
2494           newap.av.getAlignment().deleteAnnotation(alan);
2495         }
2496         ;
2497       }
2498     }
2499
2500     newap.av.gatherViewsHere = false;
2501
2502     if (viewport.viewName == null)
2503     {
2504       viewport.viewName = "Original";
2505     }
2506
2507     newap.av.historyList = viewport.historyList;
2508     newap.av.redoList = viewport.redoList;
2509
2510     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2511     // make sure the new view has a unique name - this is essential for Jalview
2512     // 2 archives
2513     boolean addFirstIndex = false;
2514     if (viewTitle == null || viewTitle.trim().length() == 0)
2515     {
2516       viewTitle = "View";
2517       addFirstIndex = true;
2518     }
2519     else
2520     {
2521       index = 1;// we count from 1 if given a specific name
2522     }
2523     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2524     Vector comps = (Vector) PaintRefresher.components.get(viewport
2525             .getSequenceSetId());
2526     Vector existingNames = new Vector();
2527     for (int i = 0; i < comps.size(); i++)
2528     {
2529       if (comps.elementAt(i) instanceof AlignmentPanel)
2530       {
2531         AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2532         if (!existingNames.contains(ap.av.viewName))
2533         {
2534           existingNames.addElement(ap.av.viewName);
2535         }
2536       }
2537     }
2538
2539     while (existingNames.contains(newViewName))
2540     {
2541       newViewName = viewTitle + " " + (++index);
2542     }
2543
2544     newap.av.viewName = newViewName;
2545
2546     addAlignmentPanel(newap, true);
2547     newap.alignmentChanged();
2548
2549     if (alignPanels.size() == 2)
2550     {
2551       viewport.gatherViewsHere = true;
2552     }
2553     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2554     return newap;
2555   }
2556
2557   @Override
2558   public void expandViews_actionPerformed(ActionEvent e)
2559   {
2560     Desktop.instance.explodeViews(this);
2561   }
2562
2563   @Override
2564   public void gatherViews_actionPerformed(ActionEvent e)
2565   {
2566     Desktop.instance.gatherViews(this);
2567   }
2568
2569   /**
2570    * DOCUMENT ME!
2571    *
2572    * @param e
2573    *          DOCUMENT ME!
2574    */
2575   @Override
2576   public void font_actionPerformed(ActionEvent e)
2577   {
2578     new FontChooser(alignPanel);
2579   }
2580
2581   /**
2582    * DOCUMENT ME!
2583    *
2584    * @param e
2585    *          DOCUMENT ME!
2586    */
2587   @Override
2588   protected void seqLimit_actionPerformed(ActionEvent e)
2589   {
2590     viewport.setShowJVSuffix(seqLimits.isSelected());
2591
2592     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2593             .calculateIdWidth());
2594     alignPanel.paintAlignment(true);
2595   }
2596
2597   @Override
2598   public void idRightAlign_actionPerformed(ActionEvent e)
2599   {
2600     viewport.rightAlignIds = idRightAlign.isSelected();
2601     alignPanel.paintAlignment(true);
2602   }
2603
2604   @Override
2605   public void centreColumnLabels_actionPerformed(ActionEvent e)
2606   {
2607     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2608     alignPanel.paintAlignment(true);
2609   }
2610
2611   /*
2612    * (non-Javadoc)
2613    *
2614    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2615    */
2616   @Override
2617   protected void followHighlight_actionPerformed()
2618   {
2619     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2620     {
2621       alignPanel.scrollToPosition(
2622               alignPanel.seqPanel.seqCanvas.searchResults, false);
2623     }
2624   }
2625
2626   /**
2627    * DOCUMENT ME!
2628    *
2629    * @param e
2630    *          DOCUMENT ME!
2631    */
2632   @Override
2633   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2634   {
2635     viewport.setColourText(colourTextMenuItem.isSelected());
2636     alignPanel.paintAlignment(true);
2637   }
2638
2639   /**
2640    * DOCUMENT ME!
2641    *
2642    * @param e
2643    *          DOCUMENT ME!
2644    */
2645   @Override
2646   public void wrapMenuItem_actionPerformed(ActionEvent e)
2647   {
2648     scaleAbove.setVisible(wrapMenuItem.isSelected());
2649     scaleLeft.setVisible(wrapMenuItem.isSelected());
2650     scaleRight.setVisible(wrapMenuItem.isSelected());
2651     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2652     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2653   }
2654
2655   @Override
2656   public void showAllSeqs_actionPerformed(ActionEvent e)
2657   {
2658     viewport.showAllHiddenSeqs();
2659   }
2660
2661   @Override
2662   public void showAllColumns_actionPerformed(ActionEvent e)
2663   {
2664     viewport.showAllHiddenColumns();
2665     repaint();
2666   }
2667
2668   @Override
2669   public void hideSelSequences_actionPerformed(ActionEvent e)
2670   {
2671     viewport.hideAllSelectedSeqs();
2672     alignPanel.paintAlignment(true);
2673   }
2674
2675   /**
2676    * called by key handler and the hide all/show all menu items
2677    *
2678    * @param toggleSeqs
2679    * @param toggleCols
2680    */
2681   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2682   {
2683
2684     boolean hide = false;
2685     SequenceGroup sg = viewport.getSelectionGroup();
2686     if (!toggleSeqs && !toggleCols)
2687     {
2688       // Hide everything by the current selection - this is a hack - we do the
2689       // invert and then hide
2690       // first check that there will be visible columns after the invert.
2691       if ((viewport.getColumnSelection() != null
2692               && viewport.getColumnSelection().getSelected() != null && viewport
2693               .getColumnSelection().getSelected().size() > 0)
2694               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2695                       .getEndRes()))
2696       {
2697         // now invert the sequence set, if required - empty selection implies
2698         // that no hiding is required.
2699         if (sg != null)
2700         {
2701           invertSequenceMenuItem_actionPerformed(null);
2702           sg = viewport.getSelectionGroup();
2703           toggleSeqs = true;
2704
2705         }
2706         viewport.expandColSelection(sg, true);
2707         // finally invert the column selection and get the new sequence
2708         // selection.
2709         invertColSel_actionPerformed(null);
2710         toggleCols = true;
2711       }
2712     }
2713
2714     if (toggleSeqs)
2715     {
2716       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2717       {
2718         hideSelSequences_actionPerformed(null);
2719         hide = true;
2720       }
2721       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2722               .size() > 0))
2723       {
2724         showAllSeqs_actionPerformed(null);
2725       }
2726     }
2727
2728     if (toggleCols)
2729     {
2730       if (viewport.getColumnSelection().getSelected().size() > 0)
2731       {
2732         hideSelColumns_actionPerformed(null);
2733         if (!toggleSeqs)
2734         {
2735           viewport.setSelectionGroup(sg);
2736         }
2737       }
2738       else if (!hide)
2739       {
2740         showAllColumns_actionPerformed(null);
2741       }
2742     }
2743   }
2744
2745   /*
2746    * (non-Javadoc)
2747    *
2748    * @see
2749    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2750    * event.ActionEvent)
2751    */
2752   @Override
2753   public void hideAllButSelection_actionPerformed(ActionEvent e)
2754   {
2755     toggleHiddenRegions(false, false);
2756   }
2757
2758   /*
2759    * (non-Javadoc)
2760    *
2761    * @see
2762    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2763    * .ActionEvent)
2764    */
2765   @Override
2766   public void hideAllSelection_actionPerformed(ActionEvent e)
2767   {
2768     SequenceGroup sg = viewport.getSelectionGroup();
2769     viewport.expandColSelection(sg, false);
2770     viewport.hideAllSelectedSeqs();
2771     viewport.hideSelectedColumns();
2772     alignPanel.paintAlignment(true);
2773   }
2774
2775   /*
2776    * (non-Javadoc)
2777    *
2778    * @see
2779    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2780    * ActionEvent)
2781    */
2782   @Override
2783   public void showAllhidden_actionPerformed(ActionEvent e)
2784   {
2785     viewport.showAllHiddenColumns();
2786     viewport.showAllHiddenSeqs();
2787     alignPanel.paintAlignment(true);
2788   }
2789
2790   @Override
2791   public void hideSelColumns_actionPerformed(ActionEvent e)
2792   {
2793     viewport.hideSelectedColumns();
2794     alignPanel.paintAlignment(true);
2795   }
2796
2797   @Override
2798   public void hiddenMarkers_actionPerformed(ActionEvent e)
2799   {
2800     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2801     repaint();
2802   }
2803
2804   /**
2805    * DOCUMENT ME!
2806    *
2807    * @param e
2808    *          DOCUMENT ME!
2809    */
2810   @Override
2811   protected void scaleAbove_actionPerformed(ActionEvent e)
2812   {
2813     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2814     alignPanel.paintAlignment(true);
2815   }
2816
2817   /**
2818    * DOCUMENT ME!
2819    *
2820    * @param e
2821    *          DOCUMENT ME!
2822    */
2823   @Override
2824   protected void scaleLeft_actionPerformed(ActionEvent e)
2825   {
2826     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2827     alignPanel.paintAlignment(true);
2828   }
2829
2830   /**
2831    * DOCUMENT ME!
2832    *
2833    * @param e
2834    *          DOCUMENT ME!
2835    */
2836   @Override
2837   protected void scaleRight_actionPerformed(ActionEvent e)
2838   {
2839     viewport.setScaleRightWrapped(scaleRight.isSelected());
2840     alignPanel.paintAlignment(true);
2841   }
2842
2843   /**
2844    * DOCUMENT ME!
2845    *
2846    * @param e
2847    *          DOCUMENT ME!
2848    */
2849   @Override
2850   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2851   {
2852     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2853     alignPanel.paintAlignment(true);
2854   }
2855
2856   /**
2857    * DOCUMENT ME!
2858    *
2859    * @param e
2860    *          DOCUMENT ME!
2861    */
2862   @Override
2863   public void viewTextMenuItem_actionPerformed(ActionEvent e)
2864   {
2865     viewport.setShowText(viewTextMenuItem.isSelected());
2866     alignPanel.paintAlignment(true);
2867   }
2868
2869   /**
2870    * DOCUMENT ME!
2871    *
2872    * @param e
2873    *          DOCUMENT ME!
2874    */
2875   @Override
2876   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2877   {
2878     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2879     alignPanel.paintAlignment(true);
2880   }
2881
2882   public FeatureSettings featureSettings;
2883
2884   @Override
2885   public void featureSettings_actionPerformed(ActionEvent e)
2886   {
2887     if (featureSettings != null)
2888     {
2889       featureSettings.close();
2890       featureSettings = null;
2891     }
2892     if (!showSeqFeatures.isSelected())
2893     {
2894       // make sure features are actually displayed
2895       showSeqFeatures.setSelected(true);
2896       showSeqFeatures_actionPerformed(null);
2897     }
2898     featureSettings = new FeatureSettings(this);
2899   }
2900
2901   /**
2902    * Set or clear 'Show Sequence Features'
2903    *
2904    * @param evt
2905    *          DOCUMENT ME!
2906    */
2907   @Override
2908   public void showSeqFeatures_actionPerformed(ActionEvent evt)
2909   {
2910     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2911     alignPanel.paintAlignment(true);
2912     if (alignPanel.getOverviewPanel() != null)
2913     {
2914       alignPanel.getOverviewPanel().updateOverviewImage();
2915     }
2916   }
2917
2918   /**
2919    * Set or clear 'Show Sequence Features'
2920    *
2921    * @param evt
2922    *          DOCUMENT ME!
2923    */
2924   @Override
2925   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2926   {
2927     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2928             .isSelected());
2929     if (viewport.getShowSequenceFeaturesHeight())
2930     {
2931       // ensure we're actually displaying features
2932       viewport.setShowSequenceFeatures(true);
2933       showSeqFeatures.setSelected(true);
2934     }
2935     alignPanel.paintAlignment(true);
2936     if (alignPanel.getOverviewPanel() != null)
2937     {
2938       alignPanel.getOverviewPanel().updateOverviewImage();
2939     }
2940   }
2941
2942   /**
2943    * DOCUMENT ME!
2944    *
2945    * @param e
2946    *          DOCUMENT ME!
2947    */
2948   @Override
2949   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2950   {
2951     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2952     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2953   }
2954
2955   @Override
2956   public void alignmentProperties()
2957   {
2958     JEditorPane editPane = new JEditorPane("text/html", "");
2959     editPane.setEditable(false);
2960     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2961             .formatAsHtml();
2962     editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
2963     JInternalFrame frame = new JInternalFrame();
2964     frame.getContentPane().add(new JScrollPane(editPane));
2965
2966     Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400);\r
2967   }
2968
2969   /**
2970    * DOCUMENT ME!
2971    *
2972    * @param e
2973    *          DOCUMENT ME!
2974    */
2975   @Override
2976   public void overviewMenuItem_actionPerformed(ActionEvent e)
2977   {
2978     if (alignPanel.overviewPanel != null)
2979     {
2980       return;
2981     }
2982
2983     JInternalFrame frame = new JInternalFrame();
2984     OverviewPanel overview = new OverviewPanel(alignPanel);
2985     frame.setContentPane(overview);
2986     Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),\r
2987             frame.getWidth(), frame.getHeight());
2988     frame.pack();
2989     frame.setLayer(JLayeredPane.PALETTE_LAYER);
2990     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2991     {
2992       @Override
2993       public void internalFrameClosed(
2994               javax.swing.event.InternalFrameEvent evt)
2995       {
2996         alignPanel.setOverviewPanel(null);
2997       };
2998     });
2999
3000     alignPanel.setOverviewPanel(overview);
3001   }
3002
3003   @Override
3004   public void textColour_actionPerformed(ActionEvent e)
3005   {
3006     new TextColourChooser().chooseColour(alignPanel, null);
3007   }
3008
3009   /**
3010    * DOCUMENT ME!
3011    *
3012    * @param e
3013    *          DOCUMENT ME!
3014    */
3015   @Override
3016   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3017   {
3018     changeColour(null);
3019   }
3020
3021   /**
3022    * DOCUMENT ME!
3023    *
3024    * @param e
3025    *          DOCUMENT ME!
3026    */
3027   @Override
3028   public void clustalColour_actionPerformed(ActionEvent e)
3029   {
3030     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3031             viewport.getHiddenRepSequences()));
3032   }
3033
3034   /**
3035    * DOCUMENT ME!
3036    *
3037    * @param e
3038    *          DOCUMENT ME!
3039    */
3040   @Override
3041   public void zappoColour_actionPerformed(ActionEvent e)
3042   {
3043     changeColour(new ZappoColourScheme());
3044   }
3045
3046   /**
3047    * DOCUMENT ME!
3048    *
3049    * @param e
3050    *          DOCUMENT ME!
3051    */
3052   @Override
3053   public void taylorColour_actionPerformed(ActionEvent e)
3054   {
3055     changeColour(new TaylorColourScheme());
3056   }
3057
3058   /**
3059    * DOCUMENT ME!
3060    *
3061    * @param e
3062    *          DOCUMENT ME!
3063    */
3064   @Override
3065   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3066   {
3067     changeColour(new HydrophobicColourScheme());
3068   }
3069
3070   /**
3071    * DOCUMENT ME!
3072    *
3073    * @param e
3074    *          DOCUMENT ME!
3075    */
3076   @Override
3077   public void helixColour_actionPerformed(ActionEvent e)
3078   {
3079     changeColour(new HelixColourScheme());
3080   }
3081
3082   /**
3083    * DOCUMENT ME!
3084    *
3085    * @param e
3086    *          DOCUMENT ME!
3087    */
3088   @Override
3089   public void strandColour_actionPerformed(ActionEvent e)
3090   {
3091     changeColour(new StrandColourScheme());
3092   }
3093
3094   /**
3095    * DOCUMENT ME!
3096    *
3097    * @param e
3098    *          DOCUMENT ME!
3099    */
3100   @Override
3101   public void turnColour_actionPerformed(ActionEvent e)
3102   {
3103     changeColour(new TurnColourScheme());
3104   }
3105
3106   /**
3107    * DOCUMENT ME!
3108    *
3109    * @param e
3110    *          DOCUMENT ME!
3111    */
3112   @Override
3113   public void buriedColour_actionPerformed(ActionEvent e)
3114   {
3115     changeColour(new BuriedColourScheme());
3116   }
3117
3118   /**
3119    * DOCUMENT ME!
3120    *
3121    * @param e
3122    *          DOCUMENT ME!
3123    */
3124   @Override
3125   public void nucleotideColour_actionPerformed(ActionEvent e)
3126   {
3127     changeColour(new NucleotideColourScheme());
3128   }
3129
3130   @Override
3131   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3132   {
3133     changeColour(new PurinePyrimidineColourScheme());
3134   }
3135
3136   /*
3137    * public void covariationColour_actionPerformed(ActionEvent e) {
3138    * changeColour(new
3139    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3140    * ()[0])); }
3141    */
3142   @Override
3143   public void annotationColour_actionPerformed(ActionEvent e)
3144   {
3145     new AnnotationColourChooser(viewport, alignPanel);
3146   }
3147
3148   @Override
3149   public void rnahelicesColour_actionPerformed(ActionEvent e)
3150   {
3151     new RNAHelicesColourChooser(viewport, alignPanel);
3152   }
3153
3154   /**
3155    * DOCUMENT ME!
3156    *
3157    * @param e
3158    *          DOCUMENT ME!
3159    */
3160   @Override
3161   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3162   {
3163     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3164   }
3165
3166   /**
3167    * DOCUMENT ME!
3168    *
3169    * @param cs
3170    *          DOCUMENT ME!
3171    */
3172   public void changeColour(ColourSchemeI cs)
3173   {
3174     // TODO: compare with applet and pull up to model method
3175     int threshold = 0;
3176
3177     if (cs != null)
3178     {
3179       if (viewport.getAbovePIDThreshold())
3180       {
3181         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3182                 "Background");
3183
3184         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3185
3186         viewport.setGlobalColourScheme(cs);
3187       }
3188       else
3189       {
3190         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3191       }
3192
3193       if (viewport.getConservationSelected())
3194       {
3195
3196         Alignment al = (Alignment) viewport.getAlignment();
3197         Conservation c = new Conservation("All",
3198                 ResidueProperties.propHash, 3, al.getSequences(), 0,
3199                 al.getWidth() - 1);
3200
3201         c.calculate();
3202         c.verdict(false, viewport.getConsPercGaps());
3203
3204         cs.setConservation(c);
3205
3206         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3207                 cs, "Background"));
3208       }
3209       else
3210       {
3211         cs.setConservation(null);
3212       }
3213
3214       cs.setConsensus(viewport.getSequenceConsensusHash());
3215     }
3216
3217     viewport.setGlobalColourScheme(cs);
3218
3219     if (viewport.getColourAppliesToAllGroups())
3220     {
3221
3222       for (SequenceGroup sg : viewport.getAlignment().getGroups())
3223       {
3224         if (cs == null)
3225         {
3226           sg.cs = null;
3227           continue;
3228         }
3229
3230         if (cs instanceof ClustalxColourScheme)
3231         {
3232           sg.cs = new ClustalxColourScheme(sg,
3233                   viewport.getHiddenRepSequences());
3234         }
3235         else if (cs instanceof UserColourScheme)
3236         {
3237           sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3238         }
3239         else
3240         {
3241           try
3242           {
3243             sg.cs = cs.getClass().newInstance();
3244           } catch (Exception ex)
3245           {
3246           }
3247         }
3248
3249         if (viewport.getAbovePIDThreshold()
3250                 || cs instanceof PIDColourScheme
3251                 || cs instanceof Blosum62ColourScheme)
3252         {
3253           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3254
3255           sg.cs.setConsensus(AAFrequency.calculate(
3256                   sg.getSequences(viewport.getHiddenRepSequences()),
3257                   sg.getStartRes(), sg.getEndRes() + 1));
3258         }
3259         else
3260         {
3261           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3262         }
3263
3264         if (viewport.getConservationSelected())
3265         {
3266           Conservation c = new Conservation("Group",
3267                   ResidueProperties.propHash, 3, sg.getSequences(viewport
3268                           .getHiddenRepSequences()), sg.getStartRes(),
3269                   sg.getEndRes() + 1);
3270           c.calculate();
3271           c.verdict(false, viewport.getConsPercGaps());
3272           sg.cs.setConservation(c);
3273         }
3274         else
3275         {
3276           sg.cs.setConservation(null);
3277         }
3278       }
3279     }
3280
3281     if (alignPanel.getOverviewPanel() != null)
3282     {
3283       alignPanel.getOverviewPanel().updateOverviewImage();
3284     }
3285
3286     alignPanel.paintAlignment(true);
3287   }
3288
3289   /**
3290    * DOCUMENT ME!
3291    *
3292    * @param e
3293    *          DOCUMENT ME!
3294    */
3295   @Override
3296   protected void modifyPID_actionPerformed(ActionEvent e)
3297   {
3298     if (viewport.getAbovePIDThreshold()
3299             && viewport.getGlobalColourScheme() != null)
3300     {
3301       SliderPanel.setPIDSliderSource(alignPanel,
3302               viewport.getGlobalColourScheme(), "Background");
3303       SliderPanel.showPIDSlider();
3304     }
3305   }
3306
3307   /**
3308    * DOCUMENT ME!
3309    *
3310    * @param e
3311    *          DOCUMENT ME!
3312    */
3313   @Override
3314   protected void modifyConservation_actionPerformed(ActionEvent e)
3315   {
3316     if (viewport.getConservationSelected()
3317             && viewport.getGlobalColourScheme() != null)
3318     {
3319       SliderPanel.setConservationSlider(alignPanel,
3320               viewport.getGlobalColourScheme(), "Background");
3321       SliderPanel.showConservationSlider();
3322     }
3323   }
3324
3325   /**
3326    * DOCUMENT ME!
3327    *
3328    * @param e
3329    *          DOCUMENT ME!
3330    */
3331   @Override
3332   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3333   {
3334     viewport.setConservationSelected(conservationMenuItem.isSelected());
3335
3336     viewport.setAbovePIDThreshold(false);
3337     abovePIDThreshold.setSelected(false);
3338
3339     changeColour(viewport.getGlobalColourScheme());
3340
3341     modifyConservation_actionPerformed(null);
3342   }
3343
3344   /**
3345    * DOCUMENT ME!
3346    *
3347    * @param e
3348    *          DOCUMENT ME!
3349    */
3350   @Override
3351   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3352   {
3353     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3354
3355     conservationMenuItem.setSelected(false);
3356     viewport.setConservationSelected(false);
3357
3358     changeColour(viewport.getGlobalColourScheme());
3359
3360     modifyPID_actionPerformed(null);
3361   }
3362
3363   /**
3364    * DOCUMENT ME!
3365    *
3366    * @param e
3367    *          DOCUMENT ME!
3368    */
3369   @Override
3370   public void userDefinedColour_actionPerformed(ActionEvent e)
3371   {
3372     if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))\r
3373     {
3374       new UserDefinedColours(alignPanel, null);
3375     }
3376     else
3377     {
3378       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3379               .getUserColourSchemes().get(e.getActionCommand());
3380
3381       changeColour(udc);
3382     }
3383   }
3384
3385   public void updateUserColourMenu()
3386   {
3387
3388     Component[] menuItems = colourMenu.getMenuComponents();
3389     int i, iSize = menuItems.length;
3390     for (i = 0; i < iSize; i++)
3391     {
3392       if (menuItems[i].getName() != null
3393               && menuItems[i].getName().equals("USER_DEFINED"))
3394       {
3395         colourMenu.remove(menuItems[i]);
3396         iSize--;
3397       }
3398     }
3399     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3400     {
3401       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3402               .getUserColourSchemes().keys();
3403
3404       while (userColours.hasMoreElements())
3405       {
3406         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3407                 userColours.nextElement().toString());
3408         radioItem.setName("USER_DEFINED");
3409         radioItem.addMouseListener(new MouseAdapter()
3410         {
3411           @Override
3412           public void mousePressed(MouseEvent evt)
3413           {
3414             if (evt.isControlDown()
3415                     || SwingUtilities.isRightMouseButton(evt))
3416             {
3417               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3418
3419               int option = JOptionPane.showInternalConfirmDialog(
3420                       jalview.gui.Desktop.desktop,
3421                       MessageManager.getString("label.remove_from_default_list"),
3422                       MessageManager.getString("label.remove_user_defined_colour"),
3423                       JOptionPane.YES_NO_OPTION);
3424               if (option == JOptionPane.YES_OPTION)
3425               {
3426                 jalview.gui.UserDefinedColours
3427                         .removeColourFromDefaults(radioItem.getText());
3428                 colourMenu.remove(radioItem);
3429               }
3430               else
3431               {
3432                 radioItem.addActionListener(new ActionListener()
3433                 {
3434                   @Override
3435                   public void actionPerformed(ActionEvent evt)
3436                   {
3437                     userDefinedColour_actionPerformed(evt);
3438                   }
3439                 });
3440               }
3441             }
3442           }
3443         });
3444         radioItem.addActionListener(new ActionListener()
3445         {
3446           @Override
3447           public void actionPerformed(ActionEvent evt)
3448           {
3449             userDefinedColour_actionPerformed(evt);
3450           }
3451         });
3452
3453         colourMenu.insert(radioItem, 15);
3454         colours.add(radioItem);
3455       }
3456     }
3457   }
3458
3459   /**
3460    * DOCUMENT ME!
3461    *
3462    * @param e
3463    *          DOCUMENT ME!
3464    */
3465   @Override
3466   public void PIDColour_actionPerformed(ActionEvent e)
3467   {
3468     changeColour(new PIDColourScheme());
3469   }
3470
3471   /**
3472    * DOCUMENT ME!
3473    *
3474    * @param e
3475    *          DOCUMENT ME!
3476    */
3477   @Override
3478   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3479   {
3480     changeColour(new Blosum62ColourScheme());
3481   }
3482
3483   /**
3484    * DOCUMENT ME!
3485    *
3486    * @param e
3487    *          DOCUMENT ME!
3488    */
3489   @Override
3490   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3491   {
3492     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3493     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3494             .getAlignment().getSequenceAt(0), null);
3495     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3496             viewport.getAlignment()));
3497     alignPanel.paintAlignment(true);
3498   }
3499
3500   /**
3501    * DOCUMENT ME!
3502    *
3503    * @param e
3504    *          DOCUMENT ME!
3505    */
3506   @Override
3507   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3508   {
3509     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3510     AlignmentSorter.sortByID(viewport.getAlignment());
3511     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3512             viewport.getAlignment()));
3513     alignPanel.paintAlignment(true);
3514   }
3515
3516   /**
3517    * DOCUMENT ME!
3518    *
3519    * @param e
3520    *          DOCUMENT ME!
3521    */
3522   @Override
3523   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3524   {
3525     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3526     AlignmentSorter.sortByLength(viewport.getAlignment());
3527     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3528             viewport.getAlignment()));
3529     alignPanel.paintAlignment(true);
3530   }
3531
3532   /**
3533    * DOCUMENT ME!
3534    *
3535    * @param e
3536    *          DOCUMENT ME!
3537    */
3538   @Override
3539   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3540   {
3541     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3542     AlignmentSorter.sortByGroup(viewport.getAlignment());
3543     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3544             viewport.getAlignment()));
3545
3546     alignPanel.paintAlignment(true);
3547   }
3548
3549   /**
3550    * DOCUMENT ME!
3551    *
3552    * @param e
3553    *          DOCUMENT ME!
3554    */
3555   @Override
3556   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3557   {
3558     new RedundancyPanel(alignPanel, this);
3559   }
3560
3561   /**
3562    * DOCUMENT ME!
3563    *
3564    * @param e
3565    *          DOCUMENT ME!
3566    */
3567   @Override
3568   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3569   {
3570     if ((viewport.getSelectionGroup() == null)
3571             || (viewport.getSelectionGroup().getSize() < 2))
3572     {
3573       JOptionPane.showInternalMessageDialog(this,
3574               MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
3575               JOptionPane.WARNING_MESSAGE);
3576     }
3577     else
3578     {
3579       JInternalFrame frame = new JInternalFrame();
3580       frame.setContentPane(new PairwiseAlignPanel(viewport));
3581       Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500);\r
3582     }
3583   }
3584
3585   /**
3586    * DOCUMENT ME!
3587    *
3588    * @param e
3589    *          DOCUMENT ME!
3590    */
3591   @Override
3592   public void PCAMenuItem_actionPerformed(ActionEvent e)
3593   {
3594     if (((viewport.getSelectionGroup() != null)
3595             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3596             .getSelectionGroup().getSize() > 0))
3597             || (viewport.getAlignment().getHeight() < 4))
3598     {
3599       JOptionPane.showInternalMessageDialog(this,
3600               MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3601               MessageManager.getString("label.sequence_selection_insufficient"),
3602               JOptionPane.WARNING_MESSAGE);
3603
3604       return;
3605     }
3606
3607     new PCAPanel(alignPanel);
3608   }
3609
3610   @Override
3611   public void autoCalculate_actionPerformed(ActionEvent e)
3612   {
3613     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3614     if (viewport.autoCalculateConsensus)
3615     {
3616       viewport.firePropertyChange("alignment", null, viewport
3617               .getAlignment().getSequences());
3618     }
3619   }
3620
3621   @Override
3622   public void sortByTreeOption_actionPerformed(ActionEvent e)
3623   {
3624     viewport.sortByTree = sortByTree.isSelected();
3625   }
3626
3627   @Override
3628   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3629   {
3630     viewport.followSelection = listenToViewSelections.isSelected();
3631   }
3632
3633   /**
3634    * DOCUMENT ME!
3635    *
3636    * @param e
3637    *          DOCUMENT ME!
3638    */
3639   @Override
3640   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3641   {
3642     NewTreePanel("AV", "PID", "Average distance tree using PID");
3643   }
3644
3645   /**
3646    * DOCUMENT ME!
3647    *
3648    * @param e
3649    *          DOCUMENT ME!
3650    */
3651   @Override
3652   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3653   {
3654     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3655   }
3656
3657   /**
3658    * DOCUMENT ME!
3659    *
3660    * @param e
3661    *          DOCUMENT ME!
3662    */
3663   @Override
3664   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3665   {
3666     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3667   }
3668
3669   /**
3670    * DOCUMENT ME!
3671    *
3672    * @param e
3673    *          DOCUMENT ME!
3674    */
3675   @Override
3676   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3677   {
3678     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3679   }
3680
3681   /**
3682    * DOCUMENT ME!
3683    *
3684    * @param type
3685    *          DOCUMENT ME!
3686    * @param pwType
3687    *          DOCUMENT ME!
3688    * @param title
3689    *          DOCUMENT ME!
3690    */
3691   void NewTreePanel(String type, String pwType, String title)
3692   {
3693     TreePanel tp;
3694
3695     if (viewport.getSelectionGroup() != null
3696             && viewport.getSelectionGroup().getSize() > 0)
3697     {
3698       if (viewport.getSelectionGroup().getSize() < 3)
3699       {
3700         JOptionPane
3701                 .showMessageDialog(
3702                         Desktop.desktop,
3703                         MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
3704                         MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
3705         return;
3706       }
3707
3708       SequenceGroup sg = viewport.getSelectionGroup();
3709
3710       /* Decide if the selection is a column region */
3711       for (SequenceI _s : sg.getSequences())
3712       {
3713         if (_s.getLength() < sg.getEndRes())
3714         {
3715           JOptionPane
3716                   .showMessageDialog(
3717                           Desktop.desktop,
3718                           MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3719                           MessageManager.getString("label.sequences_selection_not_aligned"),
3720                           JOptionPane.WARNING_MESSAGE);
3721
3722           return;
3723         }
3724       }
3725
3726       title = title + " on region";
3727       tp = new TreePanel(alignPanel, type, pwType);
3728     }
3729     else
3730     {
3731       // are the visible sequences aligned?
3732       if (!viewport.getAlignment().isAligned(false))
3733       {
3734         JOptionPane
3735                 .showMessageDialog(
3736                         Desktop.desktop,
3737                         MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
3738                         MessageManager.getString("label.sequences_not_aligned"),
3739                         JOptionPane.WARNING_MESSAGE);
3740
3741         return;
3742       }
3743
3744       if (viewport.getAlignment().getHeight() < 2)
3745       {
3746         return;
3747       }
3748
3749       tp = new TreePanel(alignPanel, type, pwType);
3750     }
3751
3752     title += " from ";
3753
3754     if (viewport.viewName != null)
3755     {
3756       title += viewport.viewName + " of ";
3757     }
3758
3759     title += this.title;
3760
3761     Desktop.addInternalFrame(tp, title, 600, 500);
3762   }
3763
3764   /**
3765    * DOCUMENT ME!
3766    *
3767    * @param title
3768    *          DOCUMENT ME!
3769    * @param order
3770    *          DOCUMENT ME!
3771    */
3772   public void addSortByOrderMenuItem(String title,
3773           final AlignmentOrder order)
3774   {
3775     final JMenuItem item = new JMenuItem("by " + title);
3776     sort.add(item);
3777     item.addActionListener(new java.awt.event.ActionListener()
3778     {
3779       @Override
3780       public void actionPerformed(ActionEvent e)
3781       {
3782         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3783
3784         // TODO: JBPNote - have to map order entries to curent SequenceI
3785         // pointers
3786         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3787
3788         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3789                 .getAlignment()));
3790
3791         alignPanel.paintAlignment(true);
3792       }
3793     });
3794   }
3795
3796   /**
3797    * Add a new sort by annotation score menu item
3798    *
3799    * @param sort
3800    *          the menu to add the option to
3801    * @param scoreLabel
3802    *          the label used to retrieve scores for each sequence on the
3803    *          alignment
3804    */
3805   public void addSortByAnnotScoreMenuItem(JMenu sort,
3806           final String scoreLabel)
3807   {
3808     final JMenuItem item = new JMenuItem(scoreLabel);
3809     sort.add(item);
3810     item.addActionListener(new java.awt.event.ActionListener()
3811     {
3812       @Override
3813       public void actionPerformed(ActionEvent e)
3814       {
3815         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3816         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3817                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3818         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3819                 viewport.getAlignment()));
3820         alignPanel.paintAlignment(true);
3821       }
3822     });
3823   }
3824
3825   /**
3826    * last hash for alignment's annotation array - used to minimise cost of
3827    * rebuild.
3828    */
3829   protected int _annotationScoreVectorHash;
3830
3831   /**
3832    * search the alignment and rebuild the sort by annotation score submenu the
3833    * last alignment annotation vector hash is stored to minimize cost of
3834    * rebuilding in subsequence calls.
3835    *
3836    */
3837   @Override
3838   public void buildSortByAnnotationScoresMenu()
3839   {
3840     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3841     {
3842       return;
3843     }
3844
3845     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3846     {
3847       sortByAnnotScore.removeAll();
3848       // almost certainly a quicker way to do this - but we keep it simple
3849       Hashtable scoreSorts = new Hashtable();
3850       AlignmentAnnotation aann[];
3851       for (SequenceI sqa : viewport.getAlignment().getSequences())
3852       {
3853         aann = sqa.getAnnotation();
3854         for (int i = 0; aann != null && i < aann.length; i++)
3855         {
3856           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3857           {
3858             scoreSorts.put(aann[i].label, aann[i].label);
3859           }
3860         }
3861       }
3862       Enumeration labels = scoreSorts.keys();
3863       while (labels.hasMoreElements())
3864       {
3865         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3866                 (String) labels.nextElement());
3867       }
3868       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3869       scoreSorts.clear();
3870
3871       _annotationScoreVectorHash = viewport.getAlignment()
3872               .getAlignmentAnnotation().hashCode();
3873     }
3874   }
3875
3876   /**
3877    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3878    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3879    * call. Listeners are added to remove the menu item when the treePanel is
3880    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3881    * modified.
3882    *
3883    * @param treePanel
3884    *          Displayed tree window.
3885    * @param title
3886    *          SortBy menu item title.
3887    */
3888   @Override
3889   public void buildTreeMenu()
3890   {
3891     sortByTreeMenu.removeAll();
3892
3893     Vector comps = (Vector) PaintRefresher.components.get(viewport
3894             .getSequenceSetId());
3895     Vector treePanels = new Vector();
3896     int i, iSize = comps.size();
3897     for (i = 0; i < iSize; i++)
3898     {
3899       if (comps.elementAt(i) instanceof TreePanel)
3900       {
3901         treePanels.add(comps.elementAt(i));
3902       }
3903     }
3904
3905     iSize = treePanels.size();
3906
3907     if (iSize < 1)
3908     {
3909       sortByTreeMenu.setVisible(false);
3910       return;
3911     }
3912
3913     sortByTreeMenu.setVisible(true);
3914
3915     for (i = 0; i < treePanels.size(); i++)
3916     {
3917       final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3918       final JMenuItem item = new JMenuItem(tp.getTitle());
3919       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3920       item.addActionListener(new java.awt.event.ActionListener()
3921       {
3922         @Override
3923         public void actionPerformed(ActionEvent e)
3924         {
3925           tp.sortByTree_actionPerformed(null);
3926           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3927
3928         }
3929       });
3930
3931       sortByTreeMenu.add(item);
3932     }
3933   }
3934
3935   public boolean sortBy(AlignmentOrder alorder, String undoname)
3936   {
3937     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3938     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3939     if (undoname != null)
3940     {
3941       addHistoryItem(new OrderCommand(undoname, oldOrder,
3942               viewport.getAlignment()));
3943     }
3944     alignPanel.paintAlignment(true);
3945     return true;
3946   }
3947
3948   /**
3949    * Work out whether the whole set of sequences or just the selected set will
3950    * be submitted for multiple alignment.
3951    *
3952    */
3953   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3954   {
3955     // Now, check we have enough sequences
3956     AlignmentView msa = null;
3957
3958     if ((viewport.getSelectionGroup() != null)
3959             && (viewport.getSelectionGroup().getSize() > 1))
3960     {
3961       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3962       // some common interface!
3963       /*
3964        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3965        * SequenceI[sz = seqs.getSize(false)];
3966        *
3967        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3968        * seqs.getSequenceAt(i); }
3969        */
3970       msa = viewport.getAlignmentView(true);
3971     }
3972     else
3973     {
3974       /*
3975        * Vector seqs = viewport.getAlignment().getSequences();
3976        *
3977        * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3978        *
3979        * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3980        * seqs.elementAt(i); } }
3981        */
3982       msa = viewport.getAlignmentView(false);
3983     }
3984     return msa;
3985   }
3986
3987   /**
3988    * Decides what is submitted to a secondary structure prediction service: the
3989    * first sequence in the alignment, or in the current selection, or, if the
3990    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3991    * region or the whole alignment. (where the first sequence in the set is the
3992    * one that the prediction will be for).
3993    */
3994   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3995   {
3996     AlignmentView seqs = null;
3997
3998     if ((viewport.getSelectionGroup() != null)
3999             && (viewport.getSelectionGroup().getSize() > 0))
4000     {
4001       seqs = viewport.getAlignmentView(true);
4002     }
4003     else
4004     {
4005       seqs = viewport.getAlignmentView(false);
4006     }
4007     // limit sequences - JBPNote in future - could spawn multiple prediction
4008     // jobs
4009     // TODO: viewport.getAlignment().isAligned is a global state - the local
4010     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4011     if (!viewport.getAlignment().isAligned(false))
4012     {
4013       seqs.setSequences(new SeqCigar[]
4014       { seqs.getSequences()[0] });
4015       // TODO: if seqs.getSequences().length>1 then should really have warned
4016       // user!
4017
4018     }
4019     return seqs;
4020   }
4021
4022   /**
4023    * DOCUMENT ME!
4024    *
4025    * @param e
4026    *          DOCUMENT ME!
4027    */
4028   @Override
4029   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4030   {
4031     // Pick the tree file
4032     JalviewFileChooser chooser = new JalviewFileChooser(
4033             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4034     chooser.setFileView(new JalviewFileView());
4035     chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file"));\r
4036     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));\r
4037
4038     int value = chooser.showOpenDialog(null);
4039
4040     if (value == JalviewFileChooser.APPROVE_OPTION)
4041     {
4042       String choice = chooser.getSelectedFile().getPath();
4043       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4044       jalview.io.NewickFile fin = null;
4045       try
4046       {
4047         fin = new jalview.io.NewickFile(choice, "File");
4048         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4049       } catch (Exception ex)
4050       {
4051         JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4052                 MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
4053         ex.printStackTrace();
4054       }
4055       if (fin != null && fin.hasWarningMessage())
4056       {
4057         JOptionPane.showMessageDialog(Desktop.desktop,
4058                 fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
4059                 JOptionPane.WARNING_MESSAGE);
4060       }
4061     }
4062   }
4063
4064   @Override
4065   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4066   {
4067     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4068   }
4069
4070   public TreePanel ShowNewickTree(NewickFile nf, String title)
4071   {
4072     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4073   }
4074
4075   public TreePanel ShowNewickTree(NewickFile nf, String title,
4076           AlignmentView input)
4077   {
4078     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4079   }
4080
4081   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4082           int h, int x, int y)
4083   {
4084     return ShowNewickTree(nf, title, null, w, h, x, y);
4085   }
4086
4087   /**
4088    * Add a treeviewer for the tree extracted from a newick file object to the
4089    * current alignment view
4090    *
4091    * @param nf
4092    *          the tree
4093    * @param title
4094    *          tree viewer title
4095    * @param input
4096    *          Associated alignment input data (or null)
4097    * @param w
4098    *          width
4099    * @param h
4100    *          height
4101    * @param x
4102    *          position
4103    * @param y
4104    *          position
4105    * @return TreePanel handle
4106    */
4107   public TreePanel ShowNewickTree(NewickFile nf, String title,
4108           AlignmentView input, int w, int h, int x, int y)
4109   {
4110     TreePanel tp = null;
4111
4112     try
4113     {
4114       nf.parse();
4115
4116       if (nf.getTree() != null)
4117       {
4118         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4119
4120         tp.setSize(w, h);
4121
4122         if (x > 0 && y > 0)
4123         {
4124           tp.setLocation(x, y);
4125         }
4126
4127         Desktop.addInternalFrame(tp, title, w, h);
4128       }
4129     } catch (Exception ex)
4130     {
4131       ex.printStackTrace();
4132     }
4133
4134     return tp;
4135   }
4136
4137   private boolean buildingMenu = false;
4138
4139   /**
4140    * Generates menu items and listener event actions for web service clients
4141    *
4142    */
4143   public void BuildWebServiceMenu()
4144   {
4145     while (buildingMenu)
4146     {
4147       try
4148       {
4149         System.err.println("Waiting for building menu to finish.");
4150         Thread.sleep(10);
4151       } catch (Exception e)
4152       {
4153       }
4154       ;
4155     }
4156     final AlignFrame me = this;
4157     buildingMenu = true;
4158     new Thread(new Runnable()
4159     {
4160       @Override
4161       public void run()
4162       {
4163         final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
4164         try
4165         {
4166           System.err.println("Building ws menu again "
4167                   + Thread.currentThread());
4168           // TODO: add support for context dependent disabling of services based
4169           // on
4170           // alignment and current selection
4171           // TODO: add additional serviceHandle parameter to specify abstract
4172           // handler
4173           // class independently of AbstractName
4174           // TODO: add in rediscovery GUI function to restart discoverer
4175           // TODO: group services by location as well as function and/or
4176           // introduce
4177           // object broker mechanism.
4178           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4179           final IProgressIndicator af = me;
4180           final JMenu msawsmenu = new JMenu("Alignment");
4181           final JMenu secstrmenu = new JMenu(
4182                   "Secondary Structure Prediction");
4183           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4184           final JMenu analymenu = new JMenu("Analysis");
4185           final JMenu dismenu = new JMenu("Protein Disorder");
4186           // JAL-940 - only show secondary structure prediction services from
4187           // the legacy server
4188           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4189               // &&
4190           Discoverer.services != null && (Discoverer.services.size() > 0))
4191           {
4192             // TODO: refactor to allow list of AbstractName/Handler bindings to
4193             // be
4194             // stored or retrieved from elsewhere
4195             // No MSAWS used any more:
4196             // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4197             Vector secstrpr = (Vector) Discoverer.services
4198                     .get("SecStrPred");
4199             if (secstrpr != null)
4200             {
4201               // Add any secondary structure prediction services
4202               for (int i = 0, j = secstrpr.size(); i < j; i++)
4203               {
4204                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4205                         .get(i);
4206                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4207                         .getServiceClient(sh);
4208                 int p=secstrmenu.getItemCount();
4209                 impl.attachWSMenuEntry(secstrmenu, me);
4210                 int q=secstrmenu.getItemCount();
4211                 for (int litm=p;litm<q; litm++)
4212                 {
4213                   legacyItems.add(secstrmenu.getItem(litm));
4214                 }
4215               }
4216             }
4217           }
4218
4219           // Add all submenus in the order they should appear on the web
4220           // services menu
4221           wsmenu.add(msawsmenu);
4222           wsmenu.add(secstrmenu);
4223           wsmenu.add(dismenu);
4224           wsmenu.add(analymenu);
4225           // No search services yet
4226           // wsmenu.add(seqsrchmenu);
4227
4228           javax.swing.SwingUtilities.invokeLater(new Runnable()
4229           {
4230             @Override
4231             public void run()
4232             {
4233               try
4234               {
4235                 webService.removeAll();
4236                 // first, add discovered services onto the webservices menu
4237                 if (wsmenu.size() > 0)
4238                 {
4239                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4240                   {
4241                     webService.add(wsmenu.get(i));
4242                   }
4243                 }
4244                 else
4245                 {
4246                   webService.add(me.webServiceNoServices);
4247                 }
4248                 // TODO: move into separate menu builder class.
4249                 boolean new_sspred=false;
4250                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4251                 {
4252                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4253                   if (jws2servs != null)
4254                   {
4255                     if (jws2servs.hasServices())
4256                     {
4257                       jws2servs.attachWSMenuEntry(webService, me);
4258                       for (Jws2Instance sv:jws2servs.getServices()) {
4259                         if (sv.description.toLowerCase().contains("jpred"))
4260                         {
4261                           for (JMenuItem jmi:legacyItems)
4262                           {
4263                             jmi.setVisible(false);
4264                           }
4265                         }
4266                       }
4267
4268                     }
4269                     if (jws2servs.isRunning())
4270                     {
4271                       JMenuItem tm = new JMenuItem(
4272                               "Still discovering JABA Services");
4273                       tm.setEnabled(false);
4274                       webService.add(tm);
4275                     }
4276                   }
4277                 }
4278                 build_urlServiceMenu(me.webService);
4279                 build_fetchdbmenu(webService);
4280                 for (JMenu item : wsmenu)
4281                 {
4282                   if (item.getItemCount() == 0)
4283                   {
4284                     item.setEnabled(false);
4285                   }
4286                   else
4287                   {
4288                     item.setEnabled(true);
4289                   }
4290                 }
4291               } catch (Exception e)
4292               {
4293                 Cache.log
4294                         .debug("Exception during web service menu building process.",
4295                                 e);
4296               }
4297               ;
4298             }
4299           });
4300         } catch (Exception e)
4301         {
4302         }
4303         ;
4304
4305         buildingMenu = false;
4306       }
4307     }).start();
4308
4309   }
4310
4311   /**
4312    * construct any groupURL type service menu entries.
4313    *
4314    * @param webService
4315    */
4316   private void build_urlServiceMenu(JMenu webService)
4317   {
4318     // TODO: remove this code when 2.7 is released
4319     // DEBUG - alignmentView
4320     /*
4321      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4322      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4323      *
4324      * @Override public void actionPerformed(ActionEvent e) {
4325      * jalview.datamodel.AlignmentView
4326      * .testSelectionViews(af.viewport.getAlignment(),
4327      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4328      *
4329      * }); webService.add(testAlView);
4330      */
4331     // TODO: refactor to RestClient discoverer and merge menu entries for
4332     // rest-style services with other types of analysis/calculation service
4333     // SHmmr test client - still being implemented.
4334     // DEBUG - alignmentView
4335
4336     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4337             .getRestClients())
4338     {
4339       client.attachWSMenuEntry(
4340               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4341               this);
4342     }
4343
4344     if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4345     {
4346       jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4347               webService, this);
4348     }
4349   }
4350
4351   /*
4352    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4353    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4354    * getProperty("LAST_DIRECTORY"));
4355    *
4356    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4357    * to Vamsas file"); chooser.setToolTipText("Export");
4358    *
4359    * int value = chooser.showSaveDialog(this);
4360    *
4361    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4362    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4363    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4364    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4365    */
4366   /**
4367    * prototype of an automatically enabled/disabled analysis function
4368    *
4369    */
4370   protected void setShowProductsEnabled()
4371   {
4372     SequenceI[] selection = viewport.getSequenceSelection();
4373     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4374             viewport.getAlignment().getDataset()))
4375     {
4376       showProducts.setEnabled(true);
4377
4378     }
4379     else
4380     {
4381       showProducts.setEnabled(false);
4382     }
4383   }
4384
4385   /**
4386    * search selection for sequence xRef products and build the show products
4387    * menu.
4388    *
4389    * @param selection
4390    * @param dataset
4391    * @return true if showProducts menu should be enabled.
4392    */
4393   public boolean canShowProducts(SequenceI[] selection,
4394           boolean isRegionSelection, Alignment dataset)
4395   {
4396     boolean showp = false;
4397     try
4398     {
4399       showProducts.removeAll();
4400       final boolean dna = viewport.getAlignment().isNucleotide();
4401       final Alignment ds = dataset;
4402       String[] ptypes = (selection == null || selection.length == 0) ? null
4403               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4404       // Object[] prods =
4405       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4406       // selection, dataset, true);
4407       final SequenceI[] sel = selection;
4408       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4409       {
4410         showp = true;
4411         final boolean isRegSel = isRegionSelection;
4412         final AlignFrame af = this;
4413         final String source = ptypes[t];
4414         JMenuItem xtype = new JMenuItem(ptypes[t]);
4415         xtype.addActionListener(new ActionListener()
4416         {
4417
4418           @Override
4419           public void actionPerformed(ActionEvent e)
4420           {
4421             // TODO: new thread for this call with vis-delay
4422             af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4423                     isRegSel, dna, source);
4424           }
4425
4426         });
4427         showProducts.add(xtype);
4428       }
4429       showProducts.setVisible(showp);
4430       showProducts.setEnabled(showp);
4431     } catch (Exception e)
4432     {
4433       jalview.bin.Cache.log
4434               .warn("canTranslate threw an exception - please report to help@jalview.org",
4435                       e);
4436       return false;
4437     }
4438     return showp;
4439   }
4440
4441   protected void showProductsFor(SequenceI[] sel, Alignment ds,
4442           boolean isRegSel, boolean dna, String source)
4443   {
4444     final boolean fisRegSel = isRegSel;
4445     final boolean fdna = dna;
4446     final String fsrc = source;
4447     final AlignFrame ths = this;
4448     final SequenceI[] fsel = sel;
4449     Runnable foo = new Runnable()
4450     {
4451
4452       @Override
4453       public void run()
4454       {
4455         final long sttime = System.currentTimeMillis();
4456         ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4457         try
4458         {
4459           Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4460           // our local
4461           // dataset
4462           // reference
4463           Alignment prods = CrossRef
4464                   .findXrefSequences(fsel, fdna, fsrc, ds);
4465           if (prods != null)
4466           {
4467             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4468             for (int s = 0; s < sprods.length; s++)
4469             {
4470               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4471               if (ds.getSequences() == null
4472                       || !ds.getSequences().contains(
4473                               sprods[s].getDatasetSequence()))
4474                 ds.addSequence(sprods[s].getDatasetSequence());
4475               sprods[s].updatePDBIds();
4476             }
4477             Alignment al = new Alignment(sprods);
4478             AlignedCodonFrame[] cf = prods.getCodonFrames();
4479             al.setDataset(ds);
4480             for (int s = 0; cf != null && s < cf.length; s++)
4481             {
4482               al.addCodonFrame(cf[s]);
4483               cf[s] = null;
4484             }
4485             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4486                     DEFAULT_HEIGHT);
4487             String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4488                     + " for " + ((fisRegSel) ? "selected region of " : "")
4489                     + getTitle();
4490             Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4491                     DEFAULT_HEIGHT);
4492           }
4493           else
4494           {
4495             System.err.println("No Sequences generated for xRef type "
4496                     + fsrc);
4497           }
4498         } catch (Exception e)
4499         {
4500           jalview.bin.Cache.log.error(
4501                   "Exception when finding crossreferences", e);
4502         } catch (OutOfMemoryError e)
4503         {
4504           new OOMWarning("whilst fetching crossreferences", e);
4505         } catch (Error e)
4506         {
4507           jalview.bin.Cache.log.error("Error when finding crossreferences",
4508                   e);
4509         }
4510         ths.setProgressBar("Finished searching for sequences from " + fsrc,
4511                 sttime);
4512       }
4513
4514     };
4515     Thread frunner = new Thread(foo);
4516     frunner.start();
4517   }
4518
4519   public boolean canShowTranslationProducts(SequenceI[] selection,
4520           AlignmentI alignment)
4521   {
4522     // old way
4523     try
4524     {
4525       return (jalview.analysis.Dna.canTranslate(selection,
4526               viewport.getViewAsVisibleContigs(true)));
4527     } catch (Exception e)
4528     {
4529       jalview.bin.Cache.log
4530               .warn("canTranslate threw an exception - please report to help@jalview.org",
4531                       e);
4532       return false;
4533     }
4534   }
4535
4536   @Override
4537   public void showProducts_actionPerformed(ActionEvent e)
4538   {
4539     // /////////////////////////////
4540     // Collect Data to be translated/transferred
4541
4542     SequenceI[] selection = viewport.getSequenceSelection();
4543     AlignmentI al = null;
4544     try
4545     {
4546       al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4547               .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4548               viewport.getAlignment().getDataset());
4549     } catch (Exception ex)
4550     {
4551       al = null;
4552       jalview.bin.Cache.log.debug("Exception during translation.", ex);
4553     }
4554     if (al == null)
4555     {
4556       JOptionPane
4557               .showMessageDialog(
4558                       Desktop.desktop,
4559                       MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4560                       MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
4561     }
4562     else
4563     {
4564       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4565       Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
4566               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4567     }
4568   }
4569
4570   @Override
4571   public void showTranslation_actionPerformed(ActionEvent e)
4572   {
4573     // /////////////////////////////
4574     // Collect Data to be translated/transferred
4575
4576     SequenceI[] selection = viewport.getSequenceSelection();
4577     String[] seqstring = viewport.getViewAsString(true);
4578     AlignmentI al = null;
4579     try
4580     {
4581       al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4582               viewport.getViewAsVisibleContigs(true), viewport
4583                       .getGapCharacter(), viewport.getAlignment()
4584                       .getAlignmentAnnotation(), viewport.getAlignment()
4585                       .getWidth(), viewport.getAlignment().getDataset());
4586     } catch (Exception ex)
4587     {
4588       al = null;
4589       jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
4590       JOptionPane
4591       .showMessageDialog(
4592               Desktop.desktop,
4593               MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),
4594               MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);
4595       return;
4596     }
4597     if (al == null)
4598     {
4599       JOptionPane
4600               .showMessageDialog(
4601                       Desktop.desktop,
4602                       MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4603                       MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
4604     }
4605     else
4606     {
4607       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4608       Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),\r
4609               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4610     }
4611   }
4612
4613   /**
4614    * Try to load a features file onto the alignment.
4615    *
4616    * @param file
4617    *          contents or path to retrieve file
4618    * @param type
4619    *          access mode of file (see jalview.io.AlignFile)
4620    * @return true if features file was parsed corectly.
4621    */
4622   public boolean parseFeaturesFile(String file, String type)
4623   {
4624     boolean featuresFile = false;
4625     try
4626     {
4627       featuresFile = new FeaturesFile(file, type).parse(viewport
4628               .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4629               .getFeatureRenderer().featureColours, false,
4630               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4631     } catch (Exception ex)
4632     {
4633       ex.printStackTrace();
4634     }
4635
4636     if (featuresFile)
4637     {
4638       viewport.showSequenceFeatures = true;
4639       showSeqFeatures.setSelected(true);
4640       if (alignPanel.seqPanel.seqCanvas.fr != null)
4641       {
4642         // update the min/max ranges where necessary
4643         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4644       }
4645       if (featureSettings != null)
4646       {
4647         featureSettings.setTableData();
4648       }
4649       alignPanel.paintAlignment(true);
4650     }
4651
4652     return featuresFile;
4653   }
4654
4655   @Override
4656   public void dragEnter(DropTargetDragEvent evt)
4657   {
4658   }
4659
4660   @Override
4661   public void dragExit(DropTargetEvent evt)
4662   {
4663   }
4664
4665   @Override
4666   public void dragOver(DropTargetDragEvent evt)
4667   {
4668   }
4669
4670   @Override
4671   public void dropActionChanged(DropTargetDragEvent evt)
4672   {
4673   }
4674
4675   @Override
4676   public void drop(DropTargetDropEvent evt)
4677   {
4678     Transferable t = evt.getTransferable();
4679     java.util.List files = null;
4680
4681     try
4682     {
4683       DataFlavor uriListFlavor = new DataFlavor(
4684               "text/uri-list;class=java.lang.String");
4685       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4686       {
4687         // Works on Windows and MacOSX
4688         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4689         files = (java.util.List) t
4690                 .getTransferData(DataFlavor.javaFileListFlavor);
4691       }
4692       else if (t.isDataFlavorSupported(uriListFlavor))
4693       {
4694         // This is used by Unix drag system
4695         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4696         String data = (String) t.getTransferData(uriListFlavor);
4697         files = new java.util.ArrayList(1);
4698         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4699                 data, "\r\n"); st.hasMoreTokens();)
4700         {
4701           String s = st.nextToken();
4702           if (s.startsWith("#"))
4703           {
4704             // the line is a comment (as per the RFC 2483)
4705             continue;
4706           }
4707
4708           java.net.URI uri = new java.net.URI(s);
4709           // check to see if we can handle this kind of URI
4710           if (uri.getScheme().toLowerCase().startsWith("http"))
4711           {
4712             files.add(uri.toString());
4713           }
4714           else
4715           {
4716             // otherwise preserve old behaviour: catch all for file objects
4717             java.io.File file = new java.io.File(uri);
4718             files.add(file.toString());
4719           }
4720         }
4721       }
4722     } catch (Exception e)
4723     {
4724       e.printStackTrace();
4725     }
4726     if (files != null)
4727     {
4728       try
4729       {
4730         // check to see if any of these files have names matching sequences in
4731         // the alignment
4732         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4733                 .getAlignment().getSequencesArray());
4734         /**
4735          * Object[] { String,SequenceI}
4736          */
4737         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4738         ArrayList<String> filesnotmatched = new ArrayList<String>();
4739         for (int i = 0; i < files.size(); i++)
4740         {
4741           String file = files.get(i).toString();
4742           String pdbfn = "";
4743           String protocol = FormatAdapter.checkProtocol(file);
4744           if (protocol == jalview.io.FormatAdapter.FILE)
4745           {
4746             File fl = new File(file);
4747             pdbfn = fl.getName();
4748           }
4749           else if (protocol == jalview.io.FormatAdapter.URL)
4750           {
4751             URL url = new URL(file);
4752             pdbfn = url.getFile();
4753           }
4754           if (pdbfn.length() > 0)
4755           {
4756             // attempt to find a match in the alignment
4757             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4758             int l = 0, c = pdbfn.indexOf(".");
4759             while (mtch == null && c != -1)
4760             {
4761               do
4762               {
4763                 l = c;
4764               } while ((c = pdbfn.indexOf(".", l)) > l);
4765               if (l > -1)
4766               {
4767                 pdbfn = pdbfn.substring(0, l);
4768               }
4769               mtch = idm.findAllIdMatches(pdbfn);
4770             }
4771             if (mtch != null)
4772             {
4773               String type = null;
4774               try
4775               {
4776                 type = new IdentifyFile().Identify(file, protocol);
4777               } catch (Exception ex)
4778               {
4779                 type = null;
4780               }
4781               if (type != null)
4782               {
4783                 if (type.equalsIgnoreCase("PDB"))
4784                 {
4785                   filesmatched.add(new Object[]
4786                   { file, protocol, mtch });
4787                   continue;
4788                 }
4789               }
4790             }
4791             // File wasn't named like one of the sequences or wasn't a PDB file.
4792             filesnotmatched.add(file);
4793           }
4794         }
4795         int assocfiles = 0;
4796         if (filesmatched.size() > 0)
4797         {
4798           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4799                   || JOptionPane
4800                           .showConfirmDialog(
4801                                   this,
4802                                   MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",
4803                                                   new String[]{Integer.valueOf(filesmatched.size()).toString()}),
4804                                   MessageManager.getString("label.automatically_associate_pdb_files_by_name"),
4805                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4806
4807           {
4808             for (Object[] fm : filesmatched)
4809             {
4810               // try and associate
4811               // TODO: may want to set a standard ID naming formalism for
4812               // associating PDB files which have no IDs.
4813               for (SequenceI toassoc : (SequenceI[]) fm[2])
4814               {
4815                 PDBEntry pe = new AssociatePdbFileWithSeq()
4816                         .associatePdbWithSeq((String) fm[0],
4817                                 (String) fm[1], toassoc, false);
4818                 if (pe != null)
4819                 {
4820                   System.err.println("Associated file : "
4821                           + ((String) fm[0]) + " with "
4822                           + toassoc.getDisplayId(true));
4823                   assocfiles++;
4824                 }
4825               }
4826               alignPanel.paintAlignment(true);
4827             }
4828           }
4829         }
4830         if (filesnotmatched.size() > 0)
4831         {
4832           if (assocfiles > 0
4833                   && (Cache.getDefault(
4834                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4835                           .showConfirmDialog(
4836                                   this,
4837                                   MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
4838                                   MessageManager.getString("label.ignore_unmatched_dropped_files"),
4839                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4840           {
4841             return;
4842           }
4843           for (String fn : filesnotmatched)
4844           {
4845             loadJalviewDataFile(fn, null, null, null);
4846           }
4847
4848         }
4849       } catch (Exception ex)
4850       {
4851         ex.printStackTrace();
4852       }
4853     }
4854   }
4855
4856   /**
4857    * Attempt to load a "dropped" file or URL string: First by testing whether
4858    * it's and Annotation file, then a JNet file, and finally a features file. If
4859    * all are false then the user may have dropped an alignment file onto this
4860    * AlignFrame.
4861    *
4862    * @param file
4863    *          either a filename or a URL string.
4864    */
4865   public void loadJalviewDataFile(String file, String protocol,
4866           String format, SequenceI assocSeq)
4867   {
4868     try
4869     {
4870       if (protocol == null)
4871       {
4872         protocol = jalview.io.FormatAdapter.checkProtocol(file);
4873       }
4874       // if the file isn't identified, or not positively identified as some
4875       // other filetype (PFAM is default unidentified alignment file type) then
4876       // try to parse as annotation.
4877       boolean isAnnotation = (format == null || format
4878               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4879               .readAnnotationFile(viewport.getAlignment(), file, protocol)
4880               : false;
4881
4882       if (!isAnnotation)
4883       {
4884         // first see if its a T-COFFEE score file
4885         TCoffeeScoreFile tcf = null;
4886         try
4887         {
4888           tcf = new TCoffeeScoreFile(file, protocol);
4889           if (tcf.isValid())
4890           {
4891             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4892             {
4893               tcoffeeColour.setEnabled(true);
4894               tcoffeeColour.setSelected(true);
4895               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4896               isAnnotation = true;
4897               statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4898             }
4899             else
4900             {
4901               // some problem - if no warning its probable that the ID matching
4902               // process didn't work
4903               JOptionPane
4904                       .showMessageDialog(
4905                               Desktop.desktop,
4906                               tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
4907                                       : tcf.getWarningMessage(),
4908                               MessageManager.getString("label.problem_reading_tcoffee_score_file"),
4909                               JOptionPane.WARNING_MESSAGE);
4910             }
4911           }
4912           else
4913           {
4914             tcf = null;
4915           }
4916         } catch (Exception x)
4917         {
4918           Cache.log
4919                   .debug("Exception when processing data source as T-COFFEE score file",
4920                           x);
4921           tcf = null;
4922         }
4923         if (tcf == null)
4924         {
4925           // try to see if its a JNet 'concise' style annotation file *before*
4926           // we
4927           // try to parse it as a features file
4928           if (format == null)
4929           {
4930             format = new IdentifyFile().Identify(file, protocol);
4931           }
4932           if (format.equalsIgnoreCase("JnetFile"))
4933           {
4934             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
4935                     file, protocol);
4936             new JnetAnnotationMaker().add_annotation(predictions,
4937                     viewport.getAlignment(), 0, false);
4938             isAnnotation = true;
4939           }
4940           else
4941           {
4942             /*
4943              * if (format.equalsIgnoreCase("PDB")) {
4944              *
4945              * String pdbfn = ""; // try to match up filename with sequence id
4946              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
4947              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
4948              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4949              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
4950              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4951              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
4952              * // attempt to find a match in the alignment SequenceI mtch =
4953              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4954              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
4955              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
4956              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
4957              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4958              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
4959              * { System.err.println("Associated file : " + file + " with " +
4960              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4961              * TODO: maybe need to load as normal otherwise return; } }
4962              */
4963             // try to parse it as a features file
4964             boolean isGroupsFile = parseFeaturesFile(file, protocol);
4965             // if it wasn't a features file then we just treat it as a general
4966             // alignment file to load into the current view.
4967             if (!isGroupsFile)
4968             {
4969               new FileLoader().LoadFile(viewport, file, protocol, format);
4970             }
4971             else
4972             {
4973               alignPanel.paintAlignment(true);
4974             }
4975           }
4976         }
4977       }
4978       if (isAnnotation)
4979       {
4980
4981         alignPanel.adjustAnnotationHeight();
4982         viewport.updateSequenceIdColours();
4983         buildSortByAnnotationScoresMenu();
4984         alignPanel.paintAlignment(true);
4985       }
4986     } catch (Exception ex)
4987     {
4988       ex.printStackTrace();
4989     } catch (OutOfMemoryError oom)
4990     {
4991       try
4992       {
4993         System.gc();
4994       } catch (Exception x)
4995       {
4996       }
4997       ;
4998       new OOMWarning(
4999               "loading data "
5000                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5001                               : "using " + protocol + " from " + file)
5002                               : ".")
5003                       + (format != null ? "(parsing as '" + format
5004                               + "' file)" : ""), oom, Desktop.desktop);
5005     }
5006   }
5007
5008   @Override
5009   public void tabSelectionChanged(int index)
5010   {
5011     if (index > -1)
5012     {
5013       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5014       viewport = alignPanel.av;
5015       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5016       setMenusFromViewport(viewport);
5017     }
5018   }
5019
5020   @Override
5021   public void tabbedPane_mousePressed(MouseEvent e)
5022   {
5023     if (SwingUtilities.isRightMouseButton(e))
5024     {
5025       String reply = JOptionPane.showInternalInputDialog(this,
5026               MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),
5027               JOptionPane.QUESTION_MESSAGE);
5028
5029       if (reply != null)
5030       {
5031         viewport.viewName = reply;
5032         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5033       }
5034     }
5035   }
5036
5037   public AlignViewport getCurrentView()
5038   {
5039     return viewport;
5040   }
5041
5042   /**
5043    * Open the dialog for regex description parsing.
5044    */
5045   @Override
5046   protected void extractScores_actionPerformed(ActionEvent e)
5047   {
5048     ParseProperties pp = new jalview.analysis.ParseProperties(
5049             viewport.getAlignment());
5050     // TODO: verify regex and introduce GUI dialog for version 2.5
5051     // if (pp.getScoresFromDescription("col", "score column ",
5052     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5053     // true)>0)
5054     if (pp.getScoresFromDescription("description column",
5055             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5056     {
5057       buildSortByAnnotationScoresMenu();
5058     }
5059   }
5060
5061   /*
5062    * (non-Javadoc)
5063    *
5064    * @see
5065    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5066    * )
5067    */
5068   @Override
5069   protected void showDbRefs_actionPerformed(ActionEvent e)
5070   {
5071     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5072   }
5073
5074   /*
5075    * (non-Javadoc)
5076    *
5077    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5078    * ActionEvent)
5079    */
5080   @Override
5081   protected void showNpFeats_actionPerformed(ActionEvent e)
5082   {
5083     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5084   }
5085
5086   /**
5087    * find the viewport amongst the tabs in this alignment frame and close that
5088    * tab
5089    *
5090    * @param av
5091    */
5092   public boolean closeView(AlignViewport av)
5093   {
5094     if (viewport == av)
5095     {
5096       this.closeMenuItem_actionPerformed(false);
5097       return true;
5098     }
5099     Component[] comp = tabbedPane.getComponents();
5100     for (int i = 0; comp != null && i < comp.length; i++)
5101     {
5102       if (comp[i] instanceof AlignmentPanel)
5103       {
5104         if (((AlignmentPanel) comp[i]).av == av)
5105         {
5106           // close the view.
5107           closeView((AlignmentPanel) comp[i]);
5108           return true;
5109         }
5110       }
5111     }
5112     return false;
5113   }
5114
5115   protected void build_fetchdbmenu(JMenu webService)
5116   {
5117     // Temporary hack - DBRef Fetcher always top level ws entry.
5118     // TODO We probably want to store a sequence database checklist in
5119     // preferences and have checkboxes.. rather than individual sources selected
5120     // here
5121     final JMenu rfetch = new JMenu(MessageManager.getString("action.fetch_db_references"));\r
5122     rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));\r
5123     webService.add(rfetch);
5124
5125     JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases"));\r
5126     fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot"));\r
5127     fetchr.addActionListener(new ActionListener()
5128     {
5129
5130       @Override
5131       public void actionPerformed(ActionEvent e)
5132       {
5133         new Thread(new Runnable()
5134         {
5135
5136           @Override
5137           public void run()
5138           {
5139             new jalview.ws.DBRefFetcher(alignPanel.av
5140                     .getSequenceSelection(), alignPanel.alignFrame)
5141                     .fetchDBRefs(false);
5142           }
5143         }).start();
5144
5145       }
5146
5147     });
5148     rfetch.add(fetchr);
5149     final AlignFrame me = this;
5150     new Thread(new Runnable()
5151     {
5152       @Override
5153       public void run()
5154       {
5155         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5156                 .getSequenceFetcherSingleton(me);
5157         javax.swing.SwingUtilities.invokeLater(new Runnable()
5158         {
5159           @Override
5160           public void run()
5161           {
5162             String[] dbclasses = sf.getOrderedSupportedSources();
5163             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5164             // jalview.util.QuickSort.sort(otherdb, otherdb);
5165             List<DbSourceProxy> otherdb;
5166             JMenu dfetch = new JMenu();
5167             JMenu ifetch = new JMenu();
5168             JMenuItem fetchr = null;
5169             int comp = 0, icomp = 0, mcomp = 15;
5170             String mname = null;
5171             int dbi = 0;
5172             for (String dbclass : dbclasses)
5173             {
5174               otherdb = sf.getSourceProxy(dbclass);
5175               // add a single entry for this class, or submenu allowing 'fetch
5176               // all' or pick one
5177               if (otherdb == null || otherdb.size() < 1)
5178               {
5179                 continue;
5180               }
5181               // List<DbSourceProxy> dbs=otherdb;
5182               // otherdb=new ArrayList<DbSourceProxy>();
5183               // for (DbSourceProxy db:dbs)
5184               // {
5185               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5186               // }
5187               if (mname == null)
5188               {
5189                 mname = "From " + dbclass;
5190               }
5191               if (otherdb.size() == 1)
5192               {
5193                 final DbSourceProxy[] dassource = otherdb
5194                         .toArray(new DbSourceProxy[0]);
5195                 DbSourceProxy src = otherdb.get(0);
5196                 fetchr = new JMenuItem(src.getDbSource());
5197                 fetchr.addActionListener(new ActionListener()
5198                 {
5199
5200                   @Override
5201                   public void actionPerformed(ActionEvent e)
5202                   {
5203                     new Thread(new Runnable()
5204                     {
5205
5206                       @Override
5207                       public void run()
5208                       {
5209                         new jalview.ws.DBRefFetcher(alignPanel.av
5210                                 .getSequenceSelection(),
5211                                 alignPanel.alignFrame, dassource)
5212                                 .fetchDBRefs(false);
5213                       }
5214                     }).start();
5215                   }
5216
5217                 });
5218                 fetchr.setToolTipText("<html>"
5219                         + JvSwingUtils.wrapTooltip("Retrieve from "
5220                                 + src.getDbName()) + "<html>");
5221                 dfetch.add(fetchr);
5222                 comp++;
5223               }
5224               else
5225               {
5226                 final DbSourceProxy[] dassource = otherdb
5227                         .toArray(new DbSourceProxy[0]);
5228                 // fetch all entry
5229                 DbSourceProxy src = otherdb.get(0);
5230                 fetchr = new JMenuItem(MessageManager.formatMessage("label.fetch_all_param", new String[]{src.getDbSource()}));\r
5231                 fetchr.addActionListener(new ActionListener()
5232                 {
5233                   @Override
5234                   public void actionPerformed(ActionEvent e)
5235                   {
5236                     new Thread(new Runnable()
5237                     {
5238
5239                       @Override
5240                       public void run()
5241                       {
5242                         new jalview.ws.DBRefFetcher(alignPanel.av
5243                                 .getSequenceSelection(),
5244                                 alignPanel.alignFrame, dassource)
5245                                 .fetchDBRefs(false);
5246                       }
5247                     }).start();
5248                   }
5249                 });
5250
5251                 fetchr.setToolTipText("<html>"
5252                         + JvSwingUtils.wrapTooltip("Retrieve from all "
5253                                 + otherdb.size() + " sources in "
5254                                 + src.getDbSource() + "<br>First is :"
5255                                 + src.getDbName()) + "<html>");
5256                 dfetch.add(fetchr);
5257                 comp++;
5258                 // and then build the rest of the individual menus
5259                 ifetch = new JMenu("Sources from " + src.getDbSource());
5260                 icomp = 0;
5261                 String imname = null;
5262                 int i = 0;
5263                 for (DbSourceProxy sproxy : otherdb)
5264                 {
5265                   String dbname = sproxy.getDbName();
5266                   String sname = dbname.length() > 5 ? dbname.substring(0,
5267                           5) + "..." : dbname;
5268                   String msname = dbname.length() > 10 ? dbname.substring(
5269                           0, 10) + "..." : dbname;
5270                   if (imname == null)
5271                   {
5272                     imname = "from '" + sname + "'";
5273                   }
5274                   fetchr = new JMenuItem(msname);
5275                   final DbSourceProxy[] dassrc =
5276                   { sproxy };
5277                   fetchr.addActionListener(new ActionListener()
5278                   {
5279
5280                     @Override
5281                     public void actionPerformed(ActionEvent e)
5282                     {
5283                       new Thread(new Runnable()
5284                       {
5285
5286                         @Override
5287                         public void run()
5288                         {
5289                           new jalview.ws.DBRefFetcher(alignPanel.av
5290                                   .getSequenceSelection(),
5291                                   alignPanel.alignFrame, dassrc)
5292                                   .fetchDBRefs(false);
5293                         }
5294                       }).start();
5295                     }
5296
5297                   });
5298                   fetchr.setToolTipText("<html>"
5299                           + JvSwingUtils.wrapTooltip("Retrieve from "
5300                                   + dbname) + "</html>");
5301                   ifetch.add(fetchr);
5302                   ++i;
5303                   if (++icomp >= mcomp || i == (otherdb.size()))
5304                   {
5305                     ifetch.setText(MessageManager.formatMessage("label.source_to_target",imname,sname));
5306                     dfetch.add(ifetch);
5307                     ifetch = new JMenu();
5308                     imname = null;
5309                     icomp = 0;
5310                     comp++;
5311                   }
5312                 }
5313               }
5314               ++dbi;
5315               if (comp >= mcomp || dbi >= (dbclasses.length))
5316               {
5317                 dfetch.setText(MessageManager.formatMessage("label.source_to_target",mname,dbclass));
5318                 rfetch.add(dfetch);
5319                 dfetch = new JMenu();
5320                 mname = null;
5321                 comp = 0;
5322               }
5323             }
5324           }
5325         });
5326       }
5327     }).start();
5328
5329   }
5330
5331   /**
5332    * Left justify the whole alignment.
5333    */
5334   @Override
5335   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5336   {
5337     AlignmentI al = viewport.getAlignment();
5338     al.justify(false);
5339     viewport.firePropertyChange("alignment", null, al);
5340   }
5341
5342   /**
5343    * Right justify the whole alignment.
5344    */
5345   @Override
5346   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5347   {
5348     AlignmentI al = viewport.getAlignment();
5349     al.justify(true);
5350     viewport.firePropertyChange("alignment", null, al);
5351   }
5352
5353   public void setShowSeqFeatures(boolean b)
5354   {
5355     showSeqFeatures.setSelected(true);
5356     viewport.setShowSequenceFeatures(true);
5357   }
5358
5359   /*
5360    * (non-Javadoc)
5361    *
5362    * @see
5363    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5364    * awt.event.ActionEvent)
5365    */
5366   @Override
5367   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5368   {
5369     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5370     alignPanel.paintAlignment(true);
5371   }
5372
5373   /*
5374    * (non-Javadoc)
5375    *
5376    * @see
5377    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5378    * .ActionEvent)
5379    */
5380   @Override
5381   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5382   {
5383     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5384     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5385
5386   }
5387
5388   /*
5389    * (non-Javadoc)
5390    *
5391    * @see
5392    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5393    * .event.ActionEvent)
5394    */
5395   @Override
5396   protected void showGroupConservation_actionPerformed(ActionEvent e)
5397   {
5398     viewport.setShowGroupConservation(showGroupConservation.getState());
5399     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5400   }
5401
5402   /*
5403    * (non-Javadoc)
5404    *
5405    * @see
5406    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5407    * .event.ActionEvent)
5408    */
5409   @Override
5410   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5411   {
5412     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5413     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5414   }
5415
5416   /*
5417    * (non-Javadoc)
5418    *
5419    * @see
5420    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5421    * .event.ActionEvent)
5422    */
5423   @Override
5424   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5425   {
5426     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5427     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5428   }
5429
5430   @Override
5431   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5432   {
5433     showSequenceLogo.setState(true);
5434     viewport.setShowSequenceLogo(true);
5435     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5436     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5437   }
5438
5439   @Override
5440   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5441   {
5442     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5443   }
5444
5445   /*
5446    * (non-Javadoc)
5447    *
5448    * @see
5449    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5450    * .event.ActionEvent)
5451    */
5452   @Override
5453   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5454   {
5455     if (avc.makeGroupsFromSelection()) {
5456       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5457       alignPanel.updateAnnotation();
5458       alignPanel.paintAlignment(true);
5459     }
5460   }
5461
5462   @Override
5463   protected void createGroup_actionPerformed(ActionEvent e)
5464   {
5465     if (avc.createGroup())
5466     {
5467       alignPanel.alignmentChanged();
5468     }
5469   }
5470
5471   @Override
5472   protected void unGroup_actionPerformed(ActionEvent e)
5473   {
5474     if (avc.unGroup())
5475     {
5476       alignPanel.alignmentChanged();
5477     }
5478   }
5479
5480   /**
5481    * make the given alignmentPanel the currently selected tab
5482    *
5483    * @param alignmentPanel
5484    */
5485   public void setDisplayedView(AlignmentPanel alignmentPanel)
5486   {
5487     if (!viewport.getSequenceSetId().equals(
5488             alignmentPanel.av.getSequenceSetId()))
5489     {
5490       throw new Error(
5491               "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5492     }
5493     if (tabbedPane != null
5494             & alignPanels.indexOf(alignmentPanel) != tabbedPane
5495                     .getSelectedIndex())
5496     {
5497       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5498     }
5499   }
5500 }
5501
5502 class PrintThread extends Thread
5503 {
5504   AlignmentPanel ap;
5505
5506   public PrintThread(AlignmentPanel ap)
5507   {
5508     this.ap = ap;
5509   }
5510
5511   static PageFormat pf;
5512
5513   @Override
5514   public void run()
5515   {
5516     PrinterJob printJob = PrinterJob.getPrinterJob();
5517
5518     if (pf != null)
5519     {
5520       printJob.setPrintable(ap, pf);
5521     }
5522     else
5523     {
5524       printJob.setPrintable(ap);
5525     }
5526
5527     if (printJob.printDialog())
5528     {
5529       try
5530       {
5531         printJob.print();
5532       } catch (Exception PrintException)
5533       {
5534         PrintException.printStackTrace();
5535       }
5536     }
5537   }
5538 }