src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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  */
  18 package jalview.gui;
  19
  20 import jalview.analysis.AAFrequency;
  21 import jalview.analysis.AlignmentSorter;
  22 import jalview.analysis.Conservation;
  23 import jalview.analysis.CrossRef;
  24 import jalview.analysis.NJTree;
  25 import jalview.analysis.ParseProperties;
  26 import jalview.analysis.SequenceIdMatcher;
  27 import jalview.api.AlignViewControllerI;
  28 import jalview.bin.Cache;
  29 import jalview.commands.CommandI;
  30 import jalview.commands.EditCommand;
  31 import jalview.commands.OrderCommand;
  32 import jalview.commands.RemoveGapColCommand;
  33 import jalview.commands.RemoveGapsCommand;
  34 import jalview.commands.SlideSequencesCommand;
  35 import jalview.commands.TrimRegionCommand;
  36 import jalview.datamodel.AlignedCodonFrame;
  37 import jalview.datamodel.Alignment;
  38 import jalview.datamodel.AlignmentAnnotation;
  39 import jalview.datamodel.AlignmentI;
  40 import jalview.datamodel.AlignmentOrder;
  41 import jalview.datamodel.AlignmentView;
  42 import jalview.datamodel.ColumnSelection;
  43 import jalview.datamodel.PDBEntry;
  44 import jalview.datamodel.SeqCigar;
  45 import jalview.datamodel.Sequence;
  46 import jalview.datamodel.SequenceGroup;
  47 import jalview.datamodel.SequenceI;
  48 import jalview.io.AlignmentProperties;
  49 import jalview.io.AnnotationFile;
  50 import jalview.io.FeaturesFile;
  51 import jalview.io.FileLoader;
  52 import jalview.io.FormatAdapter;
  53 import jalview.io.HTMLOutput;
  54 import jalview.io.IdentifyFile;
  55 import jalview.io.JalviewFileChooser;
  56 import jalview.io.JalviewFileView;
  57 import jalview.io.JnetAnnotationMaker;
  58 import jalview.io.NewickFile;
  59 import jalview.io.TCoffeeScoreFile;
  60 import jalview.jbgui.GAlignFrame;
  61 import jalview.schemes.Blosum62ColourScheme;
  62 import jalview.schemes.BuriedColourScheme;
  63 import jalview.schemes.ClustalxColourScheme;
  64 import jalview.schemes.ColourSchemeI;
  65 import jalview.schemes.ColourSchemeProperty;
  66 import jalview.schemes.HelixColourScheme;
  67 import jalview.schemes.HydrophobicColourScheme;
  68 import jalview.schemes.NucleotideColourScheme;
  69 import jalview.schemes.PIDColourScheme;
  70 import jalview.schemes.PurinePyrimidineColourScheme;
  71 import jalview.schemes.RNAHelicesColourChooser;
  72 import jalview.schemes.ResidueProperties;
  73 import jalview.schemes.StrandColourScheme;
  74 import jalview.schemes.TCoffeeColourScheme;
  75 import jalview.schemes.TaylorColourScheme;
  76 import jalview.schemes.TurnColourScheme;
  77 import jalview.schemes.UserColourScheme;
  78 import jalview.schemes.ZappoColourScheme;
  79 import jalview.util.MessageManager;
  80 import jalview.ws.jws1.Discoverer;
  81 import jalview.ws.jws2.Jws2Discoverer;
  82 import jalview.ws.jws2.jabaws2.Jws2Instance;
  83 import jalview.ws.seqfetcher.DbSourceProxy;
  84
  85 import java.awt.BorderLayout;
  86 import java.awt.Color;
  87 import java.awt.Component;
  88 import java.awt.GridLayout;
  89 import java.awt.Rectangle;
  90 import java.awt.Toolkit;
  91 import java.awt.datatransfer.Clipboard;
  92 import java.awt.datatransfer.DataFlavor;
  93 import java.awt.datatransfer.StringSelection;
  94 import java.awt.datatransfer.Transferable;
  95 import java.awt.dnd.DnDConstants;
  96 import java.awt.dnd.DropTargetDragEvent;
  97 import java.awt.dnd.DropTargetDropEvent;
  98 import java.awt.dnd.DropTargetEvent;
  99 import java.awt.dnd.DropTargetListener;
 100 import java.awt.event.ActionEvent;
 101 import java.awt.event.ActionListener;
 102 import java.awt.event.KeyAdapter;
 103 import java.awt.event.KeyEvent;
 104 import java.awt.event.MouseAdapter;
 105 import java.awt.event.MouseEvent;
 106 import java.awt.print.PageFormat;
 107 import java.awt.print.PrinterJob;
 108 import java.beans.PropertyChangeEvent;
 109 import java.io.File;
 110 import java.net.URL;
 111 import java.util.ArrayList;
 112 import java.util.Enumeration;
 113 import java.util.Hashtable;
 114 import java.util.List;
 115 import java.util.Vector;
 116
 117 import javax.swing.JButton;
 118 import javax.swing.JEditorPane;
 119 import javax.swing.JInternalFrame;
 120 import javax.swing.JLabel;
 121 import javax.swing.JLayeredPane;
 122 import javax.swing.JMenu;
 123 import javax.swing.JMenuItem;
 124 import javax.swing.JOptionPane;
 125 import javax.swing.JPanel;
 126 import javax.swing.JProgressBar;
 127 import javax.swing.JRadioButtonMenuItem;
 128 import javax.swing.JScrollPane;
 129 import javax.swing.SwingUtilities;
 130
 131 /**
 132  * DOCUMENT ME!
 133  *
 134  * @author $author$
 135  * @version $Revision$
 136  */
 137 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 138         IProgressIndicator
 139 {
 140
 141   /** DOCUMENT ME!! */
 142   public static final int DEFAULT_WIDTH = 700;
 143
 144   /** DOCUMENT ME!! */
 145   public static final int DEFAULT_HEIGHT = 500;
 146
 147   public AlignmentPanel alignPanel;
 148
 149   AlignViewport viewport;
 150
 151   public AlignViewControllerI avc;
 152
 153
 154   Vector alignPanels = new Vector();
 155
 156   /**
 157    * Last format used to load or save alignments in this window
 158    */
 159   String currentFileFormat = null;
 160
 161   /**
 162    * Current filename for this alignment
 163    */
 164   String fileName = null;
 165
 166   /**
 167    * Creates a new AlignFrame object with specific width and height.
 168    *
 169    * @param al
 170    * @param width
 171    * @param height
 172    */
 173   public AlignFrame(AlignmentI al, int width, int height)
 174   {
 175     this(al, null, width, height);
 176   }
 177
 178   /**
 179    * Creates a new AlignFrame object with specific width, height and
 180    * sequenceSetId
 181    *
 182    * @param al
 183    * @param width
 184    * @param height
 185    * @param sequenceSetId
 186    */
 187   public AlignFrame(AlignmentI al, int width, int height,
 188           String sequenceSetId)
 189   {
 190     this(al, null, width, height, sequenceSetId);
 191   }
 192
 193   /**
 194    * Creates a new AlignFrame object with specific width, height and
 195    * sequenceSetId
 196    *
 197    * @param al
 198    * @param width
 199    * @param height
 200    * @param sequenceSetId
 201    * @param viewId
 202    */
 203   public AlignFrame(AlignmentI al, int width, int height,
 204           String sequenceSetId, String viewId)
 205   {
 206     this(al, null, width, height, sequenceSetId, viewId);
 207   }
 208
 209   /**
 210    * new alignment window with hidden columns
 211    *
 212    * @param al
 213    *          AlignmentI
 214    * @param hiddenColumns
 215    *          ColumnSelection or null
 216    * @param width
 217    *          Width of alignment frame
 218    * @param height
 219    *          height of frame.
 220    */
 221   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 222           int width, int height)
 223   {
 224     this(al, hiddenColumns, width, height, null);
 225   }
 226
 227   /**
 228    * Create alignment frame for al with hiddenColumns, a specific width and
 229    * height, and specific sequenceId
 230    *
 231    * @param al
 232    * @param hiddenColumns
 233    * @param width
 234    * @param height
 235    * @param sequenceSetId
 236    *          (may be null)
 237    */
 238   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 239           int width, int height, String sequenceSetId)
 240   {
 241     this(al, hiddenColumns, width, height, sequenceSetId, null);
 242   }
 243
 244   /**
 245    * Create alignment frame for al with hiddenColumns, a specific width and
 246    * height, and specific sequenceId
 247    *
 248    * @param al
 249    * @param hiddenColumns
 250    * @param width
 251    * @param height
 252    * @param sequenceSetId
 253    *          (may be null)
 254    * @param viewId
 255    *          (may be null)
 256    */
 257   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 258           int width, int height, String sequenceSetId, String viewId)
 259   {
 260     setSize(width, height);
 261     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 262
 263     alignPanel = new AlignmentPanel(this, viewport);
 264
 265     if (al.getDataset() == null)
 266     {
 267       al.setDataset(null);
 268     }
 269
 270     addAlignmentPanel(alignPanel, true);
 271     init();
 272   }
 273
 274   /**
 275    * Make a new AlignFrame from exisiting alignmentPanels
 276    *
 277    * @param ap
 278    *          AlignmentPanel
 279    * @param av
 280    *          AlignViewport
 281    */
 282   public AlignFrame(AlignmentPanel ap)
 283   {
 284     viewport = ap.av;
 285     alignPanel = ap;
 286     addAlignmentPanel(ap, false);
 287     init();
 288   }
 289
 290   /**
 291    * initalise the alignframe from the underlying viewport data and the
 292    * configurations
 293    */
 294   void init()
 295   {
 296     avc = new jalview.controller.AlignViewController(viewport, alignPanel);
 297     if (viewport.getAlignmentConservationAnnotation() == null)
 298     {
 299       BLOSUM62Colour.setEnabled(false);
 300       conservationMenuItem.setEnabled(false);
 301       modifyConservation.setEnabled(false);
 302       // PIDColour.setEnabled(false);
 303       // abovePIDThreshold.setEnabled(false);
 304       // modifyPID.setEnabled(false);
 305     }
 306
 307     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 308             "No sort");
 309
 310     if (sortby.equals("Id"))
 311     {
 312       sortIDMenuItem_actionPerformed(null);
 313     }
 314     else if (sortby.equals("Pairwise Identity"))
 315     {
 316       sortPairwiseMenuItem_actionPerformed(null);
 317     }
 318
 319     if (Desktop.desktop != null)
 320     {
 321       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 322       addServiceListeners();
 323       setGUINucleotide(viewport.getAlignment().isNucleotide());
 324     }
 325
 326     setMenusFromViewport(viewport);
 327     buildSortByAnnotationScoresMenu();
 328     if (viewport.wrapAlignment)
 329     {
 330       wrapMenuItem_actionPerformed(null);
 331     }
 332
 333     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 334     {
 335       this.overviewMenuItem_actionPerformed(null);
 336     }
 337
 338     addKeyListener();
 339
 340   }
 341
 342   /**
 343    * Change the filename and format for the alignment, and enable the 'reload'
 344    * button functionality.
 345    *
 346    * @param file
 347    *          valid filename
 348    * @param format
 349    *          format of file
 350    */
 351   public void setFileName(String file, String format)
 352   {
 353     fileName = file;
 354     currentFileFormat = format;
 355     reload.setEnabled(true);
 356   }
 357
 358   void addKeyListener()
 359   {
 360     addKeyListener(new KeyAdapter()
 361     {
 362       @Override
 363       public void keyPressed(KeyEvent evt)
 364       {
 365         if (viewport.cursorMode
 366                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 367                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 368                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 369                 && Character.isDigit(evt.getKeyChar()))
 370           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 371
 372         switch (evt.getKeyCode())
 373         {
 374
 375         case 27: // escape key
 376           deselectAllSequenceMenuItem_actionPerformed(null);
 377
 378           break;
 379
 380         case KeyEvent.VK_DOWN:
 381           if (evt.isAltDown() || !viewport.cursorMode)
 382             moveSelectedSequences(false);
 383           if (viewport.cursorMode)
 384             alignPanel.seqPanel.moveCursor(0, 1);
 385           break;
 386
 387         case KeyEvent.VK_UP:
 388           if (evt.isAltDown() || !viewport.cursorMode)
 389             moveSelectedSequences(true);
 390           if (viewport.cursorMode)
 391             alignPanel.seqPanel.moveCursor(0, -1);
 392
 393           break;
 394
 395         case KeyEvent.VK_LEFT:
 396           if (evt.isAltDown() || !viewport.cursorMode)
 397             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 398           else
 399             alignPanel.seqPanel.moveCursor(-1, 0);
 400
 401           break;
 402
 403         case KeyEvent.VK_RIGHT:
 404           if (evt.isAltDown() || !viewport.cursorMode)
 405             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 406           else
 407             alignPanel.seqPanel.moveCursor(1, 0);
 408           break;
 409
 410         case KeyEvent.VK_SPACE:
 411           if (viewport.cursorMode)
 412           {
 413             alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 414                     || evt.isShiftDown() || evt.isAltDown());
 415           }
 416           break;
 417
 418         // case KeyEvent.VK_A:
 419         // if (viewport.cursorMode)
 420         // {
 421         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 422         // //System.out.println("A");
 423         // }
 424         // break;
 425         /*
 426          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 427          * System.out.println("closing bracket"); } break;
 428          */
 429         case KeyEvent.VK_DELETE:
 430         case KeyEvent.VK_BACK_SPACE:
 431           if (!viewport.cursorMode)
 432           {
 433             cut_actionPerformed(null);
 434           }
 435           else
 436           {
 437             alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 438                     || evt.isShiftDown() || evt.isAltDown());
 439           }
 440
 441           break;
 442
 443         case KeyEvent.VK_S:
 444           if (viewport.cursorMode)
 445           {
 446             alignPanel.seqPanel.setCursorRow();
 447           }
 448           break;
 449         case KeyEvent.VK_C:
 450           if (viewport.cursorMode && !evt.isControlDown())
 451           {
 452             alignPanel.seqPanel.setCursorColumn();
 453           }
 454           break;
 455         case KeyEvent.VK_P:
 456           if (viewport.cursorMode)
 457           {
 458             alignPanel.seqPanel.setCursorPosition();
 459           }
 460           break;
 461
 462         case KeyEvent.VK_ENTER:
 463         case KeyEvent.VK_COMMA:
 464           if (viewport.cursorMode)
 465           {
 466             alignPanel.seqPanel.setCursorRowAndColumn();
 467           }
 468           break;
 469
 470         case KeyEvent.VK_Q:
 471           if (viewport.cursorMode)
 472           {
 473             alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 474           }
 475           break;
 476         case KeyEvent.VK_M:
 477           if (viewport.cursorMode)
 478           {
 479             alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 480           }
 481           break;
 482
 483         case KeyEvent.VK_F2:
 484           viewport.cursorMode = !viewport.cursorMode;
 485           statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
 486           if (viewport.cursorMode)
 487           {
 488             alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 489             alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 490           }
 491           alignPanel.seqPanel.seqCanvas.repaint();
 492           break;
 493
 494         case KeyEvent.VK_F1:
 495           try
 496           {
 497             ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
 498             java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
 499                     "help/help");
 500             javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
 501
 502             javax.help.HelpBroker hb = hs.createHelpBroker();
 503             hb.setCurrentID("home");
 504             hb.setDisplayed(true);
 505           } catch (Exception ex)
 506           {
 507             ex.printStackTrace();
 508           }
 509           break;
 510         case KeyEvent.VK_H:
 511         {
 512           boolean toggleSeqs = !evt.isControlDown();
 513           boolean toggleCols = !evt.isShiftDown();
 514           toggleHiddenRegions(toggleSeqs, toggleCols);
 515           break;
 516         }
 517         case KeyEvent.VK_PAGE_UP:
 518           if (viewport.wrapAlignment)
 519           {
 520             alignPanel.scrollUp(true);
 521           }
 522           else
 523           {
 524             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 525                     - viewport.endSeq + viewport.startSeq);
 526           }
 527           break;
 528         case KeyEvent.VK_PAGE_DOWN:
 529           if (viewport.wrapAlignment)
 530           {
 531             alignPanel.scrollUp(false);
 532           }
 533           else
 534           {
 535             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 536                     + viewport.endSeq - viewport.startSeq);
 537           }
 538           break;
 539         }
 540       }
 541
 542       @Override
 543       public void keyReleased(KeyEvent evt)
 544       {
 545         switch (evt.getKeyCode())
 546         {
 547         case KeyEvent.VK_LEFT:
 548           if (evt.isAltDown() || !viewport.cursorMode)
 549             viewport.firePropertyChange("alignment", null, viewport
 550                     .getAlignment().getSequences());
 551           break;
 552
 553         case KeyEvent.VK_RIGHT:
 554           if (evt.isAltDown() || !viewport.cursorMode)
 555             viewport.firePropertyChange("alignment", null, viewport
 556                     .getAlignment().getSequences());
 557           break;
 558         }
 559       }
 560     });
 561   }
 562
 563   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 564   {
 565     ap.alignFrame = this;
 566     avc = new jalview.controller.AlignViewController(viewport, alignPanel);
 567
 568     alignPanels.addElement(ap);
 569
 570     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 571
 572     int aSize = alignPanels.size();
 573
 574     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 575
 576     if (aSize == 1 && ap.av.viewName == null)
 577     {
 578       this.getContentPane().add(ap, BorderLayout.CENTER);
 579     }
 580     else
 581     {
 582       if (aSize == 2)
 583       {
 584         setInitialTabVisible();
 585       }
 586
 587       expandViews.setEnabled(true);
 588       gatherViews.setEnabled(true);
 589       tabbedPane.addTab(ap.av.viewName, ap);
 590
 591       ap.setVisible(false);
 592     }
 593
 594     if (newPanel)
 595     {
 596       if (ap.av.isPadGaps())
 597       {
 598         ap.av.getAlignment().padGaps();
 599       }
 600       ap.av.updateConservation(ap);
 601       ap.av.updateConsensus(ap);
 602       ap.av.updateStrucConsensus(ap);
 603     }
 604   }
 605
 606   public void setInitialTabVisible()
 607   {
 608     expandViews.setEnabled(true);
 609     gatherViews.setEnabled(true);
 610     tabbedPane.setVisible(true);
 611     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
 612     tabbedPane.addTab(first.av.viewName, first);
 613     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 614   }
 615
 616   public AlignViewport getViewport()
 617   {
 618     return viewport;
 619   }
 620
 621   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 622   private void addServiceListeners()
 623   {
 624     final java.beans.PropertyChangeListener thisListener;
 625     Desktop.instance.addJalviewPropertyChangeListener("services",
 626             thisListener = new java.beans.PropertyChangeListener()
 627             {
 628               @Override
 629               public void propertyChange(PropertyChangeEvent evt)
 630               {
 631                 // // System.out.println("Discoverer property change.");
 632                 // if (evt.getPropertyName().equals("services"))
 633                 {
 634                   SwingUtilities.invokeLater(new Runnable()
 635                   {
 636
 637                     @Override
 638                     public void run()
 639                     {
 640                       System.err
 641                               .println("Rebuild WS Menu for service change");
 642                       BuildWebServiceMenu();
 643                     }
 644
 645                   });
 646                 }
 647               }
 648             });
 649     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 650     {
 651       @Override
 652       public void internalFrameClosed(
 653               javax.swing.event.InternalFrameEvent evt)
 654       {
 655         System.out.println("deregistering discoverer listener");
 656         Desktop.instance.removeJalviewPropertyChangeListener("services",
 657                 thisListener);
 658         closeMenuItem_actionPerformed(true);
 659       };
 660     });
 661     // Finally, build the menu once to get current service state
 662     new Thread(new Runnable()
 663     {
 664       @Override
 665       public void run()
 666       {
 667         BuildWebServiceMenu();
 668       }
 669     }).start();
 670   }
 671
 672   public void setGUINucleotide(boolean nucleotide)
 673   {
 674     showTranslation.setVisible(nucleotide);
 675     conservationMenuItem.setEnabled(!nucleotide);
 676     modifyConservation.setEnabled(!nucleotide);
 677     showGroupConservation.setEnabled(!nucleotide);
 678     rnahelicesColour.setEnabled(nucleotide);
 679     purinePyrimidineColour.setEnabled(nucleotide);
 680     // Remember AlignFrame always starts as protein
 681     // if (!nucleotide)
 682     // {
 683     // showTr
 684     // calculateMenu.remove(calculateMenu.getItemCount() - 2);
 685     // }
 686   }
 687
 688   /**
 689    * set up menus for the currently viewport. This may be called after any
 690    * operation that affects the data in the current view (selection changed,
 691    * etc) to update the menus to reflect the new state.
 692    */
 693   public void setMenusForViewport()
 694   {
 695     setMenusFromViewport(viewport);
 696   }
 697
 698   /**
 699    * Need to call this method when tabs are selected for multiple views, or when
 700    * loading from Jalview2XML.java
 701    *
 702    * @param av
 703    *          AlignViewport
 704    */
 705   void setMenusFromViewport(AlignViewport av)
 706   {
 707     padGapsMenuitem.setSelected(av.isPadGaps());
 708     colourTextMenuItem.setSelected(av.showColourText);
 709     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 710     conservationMenuItem.setSelected(av.getConservationSelected());
 711     seqLimits.setSelected(av.getShowJVSuffix());
 712     idRightAlign.setSelected(av.rightAlignIds);
 713     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
 714     renderGapsMenuItem.setSelected(av.renderGaps);
 715     wrapMenuItem.setSelected(av.wrapAlignment);
 716     scaleAbove.setVisible(av.wrapAlignment);
 717     scaleLeft.setVisible(av.wrapAlignment);
 718     scaleRight.setVisible(av.wrapAlignment);
 719     annotationPanelMenuItem.setState(av.showAnnotation);
 720     viewBoxesMenuItem.setSelected(av.showBoxes);
 721     viewTextMenuItem.setSelected(av.showText);
 722     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 723     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 724     showGroupConservation.setSelected(av.isShowGroupConservation());
 725     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 726     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 727     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 728
 729     setColourSelected(ColourSchemeProperty.getColourName(av
 730             .getGlobalColourScheme()));
 731
 732     showSeqFeatures.setSelected(av.showSequenceFeatures);
 733     hiddenMarkers.setState(av.showHiddenMarkers);
 734     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 735     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
 736     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
 737     autoCalculate.setSelected(av.autoCalculateConsensus);
 738     sortByTree.setSelected(av.sortByTree);
 739     listenToViewSelections.setSelected(av.followSelection);
 740     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 741     rnahelicesColour
 742             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 743     setShowProductsEnabled();
 744     updateEditMenuBar();
 745   }
 746
 747   // methods for implementing IProgressIndicator
 748   // need to refactor to a reusable stub class
 749   Hashtable progressBars, progressBarHandlers;
 750
 751   /*
 752    * (non-Javadoc)
 753    *
 754    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 755    */
 756   @Override
 757   public void setProgressBar(String message, long id)
 758   {
 759     if (progressBars == null)
 760     {
 761       progressBars = new Hashtable();
 762       progressBarHandlers = new Hashtable();
 763     }
 764
 765     JPanel progressPanel;
 766     Long lId = new Long(id);
 767     GridLayout layout = (GridLayout) statusPanel.getLayout();
 768     if (progressBars.get(lId) != null)
 769     {
 770       progressPanel = (JPanel) progressBars.get(new Long(id));
 771       statusPanel.remove(progressPanel);
 772       progressBars.remove(lId);
 773       progressPanel = null;
 774       if (message != null)
 775       {
 776         statusBar.setText(message);
 777       }
 778       if (progressBarHandlers.contains(lId))
 779       {
 780         progressBarHandlers.remove(lId);
 781       }
 782       layout.setRows(layout.getRows() - 1);
 783     }
 784     else
 785     {
 786       progressPanel = new JPanel(new BorderLayout(10, 5));
 787
 788       JProgressBar progressBar = new JProgressBar();
 789       progressBar.setIndeterminate(true);
 790
 791       progressPanel.add(new JLabel(message), BorderLayout.WEST);
 792       progressPanel.add(progressBar, BorderLayout.CENTER);
 793
 794       layout.setRows(layout.getRows() + 1);
 795       statusPanel.add(progressPanel);
 796
 797       progressBars.put(lId, progressPanel);
 798     }
 799     // update GUI
 800     // setMenusForViewport();
 801     validate();
 802   }
 803
 804   @Override
 805   public void registerHandler(final long id,
 806           final IProgressIndicatorHandler handler)
 807   {
 808     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
 809     {
 810       throw new Error(
 811               "call setProgressBar before registering the progress bar's handler.");
 812     }
 813     progressBarHandlers.put(new Long(id), handler);
 814     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
 815     if (handler.canCancel())
 816     {
 817       JButton cancel = new JButton(MessageManager.getString("action.cancel"));
 818       final IProgressIndicator us = this;
 819       cancel.addActionListener(new ActionListener()
 820       {
 821
 822         @Override
 823         public void actionPerformed(ActionEvent e)
 824         {
 825           handler.cancelActivity(id);
 826           us.setProgressBar(
 827                   "Cancelled "
 828                           + ((JLabel) progressPanel.getComponent(0))
 829                                   .getText(), id);
 830         }
 831       });
 832       progressPanel.add(cancel, BorderLayout.EAST);
 833     }
 834   }
 835
 836   /**
 837    *
 838    * @return true if any progress bars are still active
 839    */
 840   @Override
 841   public boolean operationInProgress()
 842   {
 843     if (progressBars != null && progressBars.size() > 0)
 844     {
 845       return true;
 846     }
 847     return false;
 848   }
 849
 850   /*
 851    * Added so Castor Mapping file can obtain Jalview Version
 852    */
 853   public String getVersion()
 854   {
 855     return jalview.bin.Cache.getProperty("VERSION");
 856   }
 857
 858   public FeatureRenderer getFeatureRenderer()
 859   {
 860     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
 861   }
 862
 863   @Override
 864   public void fetchSequence_actionPerformed(ActionEvent e)
 865   {
 866     new SequenceFetcher(this);
 867   }
 868
 869   @Override
 870   public void addFromFile_actionPerformed(ActionEvent e)
 871   {
 872     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 873   }
 874
 875   @Override
 876   public void reload_actionPerformed(ActionEvent e)
 877   {
 878     if (fileName != null)
 879     {
 880       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 881       // originating file's format
 882       // TODO: work out how to recover feature settings for correct view(s) when
 883       // file is reloaded.
 884       if (currentFileFormat.equals("Jalview"))
 885       {
 886         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 887         for (int i = 0; i < frames.length; i++)
 888         {
 889           if (frames[i] instanceof AlignFrame && frames[i] != this
 890                   && ((AlignFrame) frames[i]).fileName != null
 891                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 892           {
 893             try
 894             {
 895               frames[i].setSelected(true);
 896               Desktop.instance.closeAssociatedWindows();
 897             } catch (java.beans.PropertyVetoException ex)
 898             {
 899             }
 900           }
 901
 902         }
 903         Desktop.instance.closeAssociatedWindows();
 904
 905         FileLoader loader = new FileLoader();
 906         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 907         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
 908       }
 909       else
 910       {
 911         Rectangle bounds = this.getBounds();
 912
 913         FileLoader loader = new FileLoader();
 914         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 915         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
 916                 protocol, currentFileFormat);
 917
 918         newframe.setBounds(bounds);
 919         if (featureSettings != null && featureSettings.isShowing())
 920         {
 921           final Rectangle fspos = featureSettings.frame.getBounds();
 922           // TODO: need a 'show feature settings' function that takes bounds -
 923           // need to refactor Desktop.addFrame
 924           newframe.featureSettings_actionPerformed(null);
 925           final FeatureSettings nfs = newframe.featureSettings;
 926           SwingUtilities.invokeLater(new Runnable()
 927           {
 928             @Override
 929             public void run()
 930             {
 931               nfs.frame.setBounds(fspos);
 932             }
 933           });
 934           this.featureSettings.close();
 935           this.featureSettings = null;
 936         }
 937         this.closeMenuItem_actionPerformed(true);
 938       }
 939     }
 940   }
 941
 942   @Override
 943   public void addFromText_actionPerformed(ActionEvent e)
 944   {
 945     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
 946   }
 947
 948   @Override
 949   public void addFromURL_actionPerformed(ActionEvent e)
 950   {
 951     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
 952   }
 953
 954   @Override
 955   public void save_actionPerformed(ActionEvent e)
 956   {
 957     if (fileName == null
 958             || (currentFileFormat == null || !jalview.io.FormatAdapter
 959                     .isValidIOFormat(currentFileFormat, true))
 960             || fileName.startsWith("http"))
 961     {
 962       saveAs_actionPerformed(null);
 963     }
 964     else
 965     {
 966       saveAlignment(fileName, currentFileFormat);
 967     }
 968   }
 969
 970   /**
 971    * DOCUMENT ME!
 972    *
 973    * @param e
 974    *          DOCUMENT ME!
 975    */
 976   @Override
 977   public void saveAs_actionPerformed(ActionEvent e)
 978   {
 979     JalviewFileChooser chooser = new JalviewFileChooser(
 980             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 981             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
 982             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
 983             currentFileFormat, false);
 984
 985     chooser.setFileView(new JalviewFileView());
 986     chooser.setDialogTitle("Save Alignment to file");
 987     chooser.setToolTipText("Save");
 988
 989     int value = chooser.showSaveDialog(this);
 990
 991     if (value == JalviewFileChooser.APPROVE_OPTION)
 992     {
 993       currentFileFormat = chooser.getSelectedFormat();
 994       if (currentFileFormat == null)
 995       {
 996         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 997                 MessageManager.getString("label.select_file_format_before_saving"),
 998                 MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
 999         value = chooser.showSaveDialog(this);
1000         return;
1001       }
1002
1003       fileName = chooser.getSelectedFile().getPath();
1004
1005       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1006               currentFileFormat);
1007
1008       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1009       if (currentFileFormat.indexOf(" ") > -1)
1010       {
1011         currentFileFormat = currentFileFormat.substring(0,
1012                 currentFileFormat.indexOf(" "));
1013       }
1014       saveAlignment(fileName, currentFileFormat);
1015     }
1016   }
1017
1018   public boolean saveAlignment(String file, String format)
1019   {
1020     boolean success = true;
1021
1022     if (format.equalsIgnoreCase("Jalview"))
1023     {
1024       String shortName = title;
1025
1026       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1027       {
1028         shortName = shortName.substring(shortName
1029                 .lastIndexOf(java.io.File.separatorChar) + 1);
1030       }
1031
1032       success = new Jalview2XML().SaveAlignment(this, file, shortName);
1033
1034       statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
1035
1036
1037     }
1038     else
1039     {
1040       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1041       {
1042         warningMessage("Cannot save file " + fileName + " using format "
1043                 + format, "Alignment output format not supported");
1044         saveAs_actionPerformed(null);
1045         // JBPNote need to have a raise_gui flag here
1046         return false;
1047       }
1048
1049       String[] omitHidden = null;
1050
1051       if (viewport.hasHiddenColumns())
1052       {
1053         int reply = JOptionPane
1054                 .showInternalConfirmDialog(
1055                         Desktop.desktop,
1056                         MessageManager.getString("label.alignment_contains_hidden_columns"),
1057                         MessageManager.getString("action.save_omit_hidden_columns"),
1058                         JOptionPane.YES_NO_OPTION,
1059                         JOptionPane.QUESTION_MESSAGE);
1060
1061         if (reply == JOptionPane.YES_OPTION)
1062         {
1063           omitHidden = viewport.getViewAsString(false);
1064         }
1065       }
1066       FormatAdapter f = new FormatAdapter();
1067       String output = f.formatSequences(format,
1068               viewport.getAlignment(), // class cast exceptions will
1069               // occur in the distant future
1070               omitHidden, f.getCacheSuffixDefault(format),
1071               viewport.getColumnSelection());
1072
1073       if (output == null)
1074       {
1075         success = false;
1076       }
1077       else
1078       {
1079         try
1080         {
1081           java.io.PrintWriter out = new java.io.PrintWriter(
1082                   new java.io.FileWriter(file));
1083
1084           out.print(output);
1085           out.close();
1086           this.setTitle(file);
1087           statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
1088         } catch (Exception ex)
1089         {
1090           success = false;
1091           ex.printStackTrace();
1092         }
1093       }
1094     }
1095
1096     if (!success)
1097     {
1098       JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
1099               MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
1100     }
1101
1102     return success;
1103   }
1104
1105   private void warningMessage(String warning, String title)
1106   {
1107     if (new jalview.util.Platform().isHeadless())
1108     {
1109       System.err.println("Warning: " + title + "\nWarning: " + warning);
1110
1111     }
1112     else
1113     {
1114       JOptionPane.showInternalMessageDialog(this, warning, title,
1115               JOptionPane.WARNING_MESSAGE);
1116     }
1117     return;
1118   }
1119
1120   /**
1121    * DOCUMENT ME!
1122    *
1123    * @param e
1124    *          DOCUMENT ME!
1125    */
1126   @Override
1127   protected void outputText_actionPerformed(ActionEvent e)
1128   {
1129     String[] omitHidden = null;
1130
1131     if (viewport.hasHiddenColumns())
1132     {
1133       int reply = JOptionPane
1134               .showInternalConfirmDialog(
1135                       Desktop.desktop,
1136                       MessageManager.getString("label.alignment_contains_hidden_columns"),
1137                       MessageManager.getString("action.save_omit_hidden_columns"),
1138                       JOptionPane.YES_NO_OPTION,
1139                       JOptionPane.QUESTION_MESSAGE);
1140
1141       if (reply == JOptionPane.YES_OPTION)
1142       {
1143         omitHidden = viewport.getViewAsString(false);
1144       }
1145     }
1146
1147     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1148     cap.setForInput(null);
1149
1150     try
1151     {
1152       cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1153               viewport.getAlignment(), omitHidden,
1154               viewport.getColumnSelection()));
1155       Desktop.addInternalFrame(cap,
1156               "Alignment output - " + e.getActionCommand(), 600, 500);
1157     } catch (OutOfMemoryError oom)
1158     {
1159       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1160       cap.dispose();
1161     }
1162
1163   }
1164
1165   /**
1166    * DOCUMENT ME!
1167    *
1168    * @param e
1169    *          DOCUMENT ME!
1170    */
1171   @Override
1172   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1173   {
1174     new HTMLOutput(alignPanel,
1175             alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1176             alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1177   }
1178
1179   public void createImageMap(File file, String image)
1180   {
1181     alignPanel.makePNGImageMap(file, image);
1182   }
1183
1184   /**
1185    * DOCUMENT ME!
1186    *
1187    * @param e
1188    *          DOCUMENT ME!
1189    */
1190   @Override
1191   public void createPNG(File f)
1192   {
1193     alignPanel.makePNG(f);
1194   }
1195
1196   /**
1197    * DOCUMENT ME!
1198    *
1199    * @param e
1200    *          DOCUMENT ME!
1201    */
1202   @Override
1203   public void createEPS(File f)
1204   {
1205     alignPanel.makeEPS(f);
1206   }
1207
1208   @Override
1209   public void pageSetup_actionPerformed(ActionEvent e)
1210   {
1211     PrinterJob printJob = PrinterJob.getPrinterJob();
1212     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1213   }
1214
1215   /**
1216    * DOCUMENT ME!
1217    *
1218    * @param e
1219    *          DOCUMENT ME!
1220    */
1221   @Override
1222   public void printMenuItem_actionPerformed(ActionEvent e)
1223   {
1224     // Putting in a thread avoids Swing painting problems
1225     PrintThread thread = new PrintThread(alignPanel);
1226     thread.start();
1227   }
1228
1229   @Override
1230   public void exportFeatures_actionPerformed(ActionEvent e)
1231   {
1232     new AnnotationExporter().exportFeatures(alignPanel);
1233   }
1234
1235   @Override
1236   public void exportAnnotations_actionPerformed(ActionEvent e)
1237   {
1238     new AnnotationExporter().exportAnnotations(alignPanel,
1239             viewport.showAnnotation ? viewport.getAlignment()
1240                     .getAlignmentAnnotation() : null, viewport
1241                     .getAlignment().getGroups(), ((Alignment) viewport
1242                     .getAlignment()).alignmentProperties);
1243   }
1244
1245   @Override
1246   public void associatedData_actionPerformed(ActionEvent e)
1247   {
1248     // Pick the tree file
1249     JalviewFileChooser chooser = new JalviewFileChooser(
1250             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1251     chooser.setFileView(new JalviewFileView());
1252     chooser.setDialogTitle("Load Jalview Annotations or Features File");
1253     chooser.setToolTipText("Load Jalview Annotations / Features file");
1254
1255     int value = chooser.showOpenDialog(null);
1256
1257     if (value == JalviewFileChooser.APPROVE_OPTION)
1258     {
1259       String choice = chooser.getSelectedFile().getPath();
1260       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1261       loadJalviewDataFile(choice, null, null, null);
1262     }
1263
1264   }
1265
1266   /**
1267    * Close the current view or all views in the alignment frame. If the frame
1268    * only contains one view then the alignment will be removed from memory.
1269    *
1270    * @param closeAllTabs
1271    */
1272   @Override
1273   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1274   {
1275     if (alignPanels != null && alignPanels.size() < 2)
1276     {
1277       closeAllTabs = true;
1278     }
1279
1280     try
1281     {
1282       if (alignPanels != null)
1283       {
1284         if (closeAllTabs)
1285         {
1286           if (this.isClosed())
1287           {
1288             // really close all the windows - otherwise wait till
1289             // setClosed(true) is called
1290             for (int i = 0; i < alignPanels.size(); i++)
1291             {
1292               AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1293               ap.closePanel();
1294             }
1295           }
1296         }
1297         else
1298         {
1299           closeView(alignPanel);
1300         }
1301       }
1302
1303       if (closeAllTabs)
1304       {
1305         this.setClosed(true);
1306       }
1307     } catch (Exception ex)
1308     {
1309       ex.printStackTrace();
1310     }
1311   }
1312
1313   /**
1314    * close alignPanel2 and shuffle tabs appropriately.
1315    *
1316    * @param alignPanel2
1317    */
1318   public void closeView(AlignmentPanel alignPanel2)
1319   {
1320     int index = tabbedPane.getSelectedIndex();
1321     int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1322     alignPanels.removeElement(alignPanel2);
1323     // Unnecessary
1324     // if (viewport == alignPanel2.av)
1325     // {
1326     // viewport = null;
1327     // }
1328     alignPanel2.closePanel();
1329     alignPanel2 = null;
1330
1331     tabbedPane.removeTabAt(closedindex);
1332     tabbedPane.validate();
1333
1334     if (index > closedindex || index == tabbedPane.getTabCount())
1335     {
1336       // modify currently selected tab index if necessary.
1337       index--;
1338     }
1339
1340     this.tabSelectionChanged(index);
1341   }
1342
1343   /**
1344    * DOCUMENT ME!
1345    */
1346   void updateEditMenuBar()
1347   {
1348
1349     if (viewport.historyList.size() > 0)
1350     {
1351       undoMenuItem.setEnabled(true);
1352       CommandI command = (CommandI) viewport.historyList.peek();
1353       undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
1354     }
1355     else
1356     {
1357       undoMenuItem.setEnabled(false);
1358       undoMenuItem.setText(MessageManager.getString("action.undo"));
1359     }
1360
1361     if (viewport.redoList.size() > 0)
1362     {
1363       redoMenuItem.setEnabled(true);
1364
1365       CommandI command = (CommandI) viewport.redoList.peek();
1366       redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
1367     }
1368     else
1369     {
1370       redoMenuItem.setEnabled(false);
1371       redoMenuItem.setText(MessageManager.getString("action.redo"));
1372     }
1373   }
1374
1375   public void addHistoryItem(CommandI command)
1376   {
1377     if (command.getSize() > 0)
1378     {
1379       viewport.historyList.push(command);
1380       viewport.redoList.clear();
1381       updateEditMenuBar();
1382       viewport.updateHiddenColumns();
1383       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1384       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1385       // viewport.getColumnSelection()
1386       // .getHiddenColumns().size() > 0);
1387     }
1388   }
1389
1390   /**
1391    *
1392    * @return alignment objects for all views
1393    */
1394   AlignmentI[] getViewAlignments()
1395   {
1396     if (alignPanels != null)
1397     {
1398       Enumeration e = alignPanels.elements();
1399       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1400       for (int i = 0; e.hasMoreElements(); i++)
1401       {
1402         als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1403       }
1404       return als;
1405     }
1406     if (viewport != null)
1407     {
1408       return new AlignmentI[]
1409       { viewport.getAlignment() };
1410     }
1411     return null;
1412   }
1413
1414   /**
1415    * DOCUMENT ME!
1416    *
1417    * @param e
1418    *          DOCUMENT ME!
1419    */
1420   @Override
1421   protected void undoMenuItem_actionPerformed(ActionEvent e)
1422   {
1423     if (viewport.historyList.empty())
1424       return;
1425     CommandI command = (CommandI) viewport.historyList.pop();
1426     viewport.redoList.push(command);
1427     command.undoCommand(getViewAlignments());
1428
1429     AlignViewport originalSource = getOriginatingSource(command);
1430     updateEditMenuBar();
1431
1432     if (originalSource != null)
1433     {
1434       if (originalSource != viewport)
1435       {
1436         Cache.log
1437                 .warn("Implementation worry: mismatch of viewport origin for undo");
1438       }
1439       originalSource.updateHiddenColumns();
1440       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1441       // null
1442       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1443       // viewport.getColumnSelection()
1444       // .getHiddenColumns().size() > 0);
1445       originalSource.firePropertyChange("alignment", null, originalSource
1446               .getAlignment().getSequences());
1447     }
1448   }
1449
1450   /**
1451    * DOCUMENT ME!
1452    *
1453    * @param e
1454    *          DOCUMENT ME!
1455    */
1456   @Override
1457   protected void redoMenuItem_actionPerformed(ActionEvent e)
1458   {
1459     if (viewport.redoList.size() < 1)
1460     {
1461       return;
1462     }
1463
1464     CommandI command = (CommandI) viewport.redoList.pop();
1465     viewport.historyList.push(command);
1466     command.doCommand(getViewAlignments());
1467
1468     AlignViewport originalSource = getOriginatingSource(command);
1469     updateEditMenuBar();
1470
1471     if (originalSource != null)
1472     {
1473
1474       if (originalSource != viewport)
1475       {
1476         Cache.log
1477                 .warn("Implementation worry: mismatch of viewport origin for redo");
1478       }
1479       originalSource.updateHiddenColumns();
1480       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1481       // null
1482       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1483       // viewport.getColumnSelection()
1484       // .getHiddenColumns().size() > 0);
1485       originalSource.firePropertyChange("alignment", null, originalSource
1486               .getAlignment().getSequences());
1487     }
1488   }
1489
1490   AlignViewport getOriginatingSource(CommandI command)
1491   {
1492     AlignViewport originalSource = null;
1493     // For sequence removal and addition, we need to fire
1494     // the property change event FROM the viewport where the
1495     // original alignment was altered
1496     AlignmentI al = null;
1497     if (command instanceof EditCommand)
1498     {
1499       EditCommand editCommand = (EditCommand) command;
1500       al = editCommand.getAlignment();
1501       Vector comps = (Vector) PaintRefresher.components.get(viewport
1502               .getSequenceSetId());
1503
1504       for (int i = 0; i < comps.size(); i++)
1505       {
1506         if (comps.elementAt(i) instanceof AlignmentPanel)
1507         {
1508           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1509           {
1510             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1511             break;
1512           }
1513         }
1514       }
1515     }
1516
1517     if (originalSource == null)
1518     {
1519       // The original view is closed, we must validate
1520       // the current view against the closed view first
1521       if (al != null)
1522       {
1523         PaintRefresher.validateSequences(al, viewport.getAlignment());
1524       }
1525
1526       originalSource = viewport;
1527     }
1528
1529     return originalSource;
1530   }
1531
1532   /**
1533    * DOCUMENT ME!
1534    *
1535    * @param up
1536    *          DOCUMENT ME!
1537    */
1538   public void moveSelectedSequences(boolean up)
1539   {
1540     SequenceGroup sg = viewport.getSelectionGroup();
1541
1542     if (sg == null)
1543     {
1544       return;
1545     }
1546     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1547             viewport.getHiddenRepSequences(), up);
1548     alignPanel.paintAlignment(true);
1549   }
1550
1551   synchronized void slideSequences(boolean right, int size)
1552   {
1553     List<SequenceI> sg = new Vector();
1554     if (viewport.cursorMode)
1555     {
1556       sg.add(viewport.getAlignment().getSequenceAt(
1557               alignPanel.seqPanel.seqCanvas.cursorY));
1558     }
1559     else if (viewport.getSelectionGroup() != null
1560             && viewport.getSelectionGroup().getSize() != viewport
1561                     .getAlignment().getHeight())
1562     {
1563       sg = viewport.getSelectionGroup().getSequences(
1564               viewport.getHiddenRepSequences());
1565     }
1566
1567     if (sg.size() < 1)
1568     {
1569       return;
1570     }
1571
1572     Vector invertGroup = new Vector();
1573
1574     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1575     {
1576       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1577         invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1578     }
1579
1580     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1581
1582     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1583     for (int i = 0; i < invertGroup.size(); i++)
1584       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1585
1586     SlideSequencesCommand ssc;
1587     if (right)
1588       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1589               size, viewport.getGapCharacter());
1590     else
1591       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1592               size, viewport.getGapCharacter());
1593
1594     int groupAdjustment = 0;
1595     if (ssc.getGapsInsertedBegin() && right)
1596     {
1597       if (viewport.cursorMode)
1598         alignPanel.seqPanel.moveCursor(size, 0);
1599       else
1600         groupAdjustment = size;
1601     }
1602     else if (!ssc.getGapsInsertedBegin() && !right)
1603     {
1604       if (viewport.cursorMode)
1605         alignPanel.seqPanel.moveCursor(-size, 0);
1606       else
1607         groupAdjustment = -size;
1608     }
1609
1610     if (groupAdjustment != 0)
1611     {
1612       viewport.getSelectionGroup().setStartRes(
1613               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1614       viewport.getSelectionGroup().setEndRes(
1615               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1616     }
1617
1618     boolean appendHistoryItem = false;
1619     if (viewport.historyList != null && viewport.historyList.size() > 0
1620             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1621     {
1622       appendHistoryItem = ssc
1623               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1624                       .peek());
1625     }
1626
1627     if (!appendHistoryItem)
1628       addHistoryItem(ssc);
1629
1630     repaint();
1631   }
1632
1633   /**
1634    * DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   @Override
1640   protected void copy_actionPerformed(ActionEvent e)
1641   {
1642     System.gc();
1643     if (viewport.getSelectionGroup() == null)
1644     {
1645       return;
1646     }
1647     // TODO: preserve the ordering of displayed alignment annotation in any
1648     // internal paste (particularly sequence associated annotation)
1649     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1650     String[] omitHidden = null;
1651
1652     if (viewport.hasHiddenColumns())
1653     {
1654       omitHidden = viewport.getViewAsString(true);
1655     }
1656
1657     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1658             omitHidden);
1659
1660     StringSelection ss = new StringSelection(output);
1661
1662     try
1663     {
1664       jalview.gui.Desktop.internalCopy = true;
1665       // Its really worth setting the clipboard contents
1666       // to empty before setting the large StringSelection!!
1667       Toolkit.getDefaultToolkit().getSystemClipboard()
1668               .setContents(new StringSelection(""), null);
1669
1670       Toolkit.getDefaultToolkit().getSystemClipboard()
1671               .setContents(ss, Desktop.instance);
1672     } catch (OutOfMemoryError er)
1673     {
1674       new OOMWarning("copying region", er);
1675       return;
1676     }
1677
1678     Vector hiddenColumns = null;
1679     if (viewport.hasHiddenColumns())
1680     {
1681       hiddenColumns = new Vector();
1682       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1683               .getSelectionGroup().getEndRes();
1684       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1685               .size(); i++)
1686       {
1687         int[] region = (int[]) viewport.getColumnSelection()
1688                 .getHiddenColumns().elementAt(i);
1689         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1690         {
1691           hiddenColumns.addElement(new int[]
1692           { region[0] - hiddenOffset, region[1] - hiddenOffset });
1693         }
1694       }
1695     }
1696
1697     Desktop.jalviewClipboard = new Object[]
1698     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1699     statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
1700   }
1701
1702   /**
1703    * DOCUMENT ME!
1704    *
1705    * @param e
1706    *          DOCUMENT ME!
1707    */
1708   @Override
1709   protected void pasteNew_actionPerformed(ActionEvent e)
1710   {
1711     paste(true);
1712   }
1713
1714   /**
1715    * DOCUMENT ME!
1716    *
1717    * @param e
1718    *          DOCUMENT ME!
1719    */
1720   @Override
1721   protected void pasteThis_actionPerformed(ActionEvent e)
1722   {
1723     paste(false);
1724   }
1725
1726   /**
1727    * Paste contents of Jalview clipboard
1728    *
1729    * @param newAlignment
1730    *          true to paste to a new alignment, otherwise add to this.
1731    */
1732   void paste(boolean newAlignment)
1733   {
1734     boolean externalPaste = true;
1735     try
1736     {
1737       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1738       Transferable contents = c.getContents(this);
1739
1740       if (contents == null)
1741       {
1742         return;
1743       }
1744
1745       String str, format;
1746       try
1747       {
1748         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1749         if (str.length() < 1)
1750         {
1751           return;
1752         }
1753
1754         format = new IdentifyFile().Identify(str, "Paste");
1755
1756       } catch (OutOfMemoryError er)
1757       {
1758         new OOMWarning("Out of memory pasting sequences!!", er);
1759         return;
1760       }
1761
1762       SequenceI[] sequences;
1763       boolean annotationAdded = false;
1764       AlignmentI alignment = null;
1765
1766       if (Desktop.jalviewClipboard != null)
1767       {
1768         // The clipboard was filled from within Jalview, we must use the
1769         // sequences
1770         // And dataset from the copied alignment
1771         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1772         // be doubly sure that we create *new* sequence objects.
1773         sequences = new SequenceI[newseq.length];
1774         for (int i = 0; i < newseq.length; i++)
1775         {
1776           sequences[i] = new Sequence(newseq[i]);
1777         }
1778         alignment = new Alignment(sequences);
1779         externalPaste = false;
1780       }
1781       else
1782       {
1783         // parse the clipboard as an alignment.
1784         alignment = new FormatAdapter().readFile(str, "Paste", format);
1785         sequences = alignment.getSequencesArray();
1786       }
1787
1788       int alwidth = 0;
1789       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1790       int fgroup = -1;
1791
1792       if (newAlignment)
1793       {
1794
1795         if (Desktop.jalviewClipboard != null)
1796         {
1797           // dataset is inherited
1798           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1799         }
1800         else
1801         {
1802           // new dataset is constructed
1803           alignment.setDataset(null);
1804         }
1805         alwidth = alignment.getWidth() + 1;
1806       }
1807       else
1808       {
1809         AlignmentI pastedal = alignment; // preserve pasted alignment object
1810         // Add pasted sequences and dataset into existing alignment.
1811         alignment = viewport.getAlignment();
1812         alwidth = alignment.getWidth() + 1;
1813         // decide if we need to import sequences from an existing dataset
1814         boolean importDs = Desktop.jalviewClipboard != null
1815                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1816         // importDs==true instructs us to copy over new dataset sequences from
1817         // an existing alignment
1818         Vector newDs = (importDs) ? new Vector() : null; // used to create
1819         // minimum dataset set
1820
1821         for (int i = 0; i < sequences.length; i++)
1822         {
1823           if (importDs)
1824           {
1825             newDs.addElement(null);
1826           }
1827           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1828           // paste
1829           if (importDs && ds != null)
1830           {
1831             if (!newDs.contains(ds))
1832             {
1833               newDs.setElementAt(ds, i);
1834               ds = new Sequence(ds);
1835               // update with new dataset sequence
1836               sequences[i].setDatasetSequence(ds);
1837             }
1838             else
1839             {
1840               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1841             }
1842           }
1843           else
1844           {
1845             // copy and derive new dataset sequence
1846             sequences[i] = sequences[i].deriveSequence();
1847             alignment.getDataset().addSequence(
1848                     sequences[i].getDatasetSequence());
1849             // TODO: avoid creation of duplicate dataset sequences with a
1850             // 'contains' method using SequenceI.equals()/SequenceI.contains()
1851           }
1852           alignment.addSequence(sequences[i]); // merges dataset
1853         }
1854         if (newDs != null)
1855         {
1856           newDs.clear(); // tidy up
1857         }
1858         if (alignment.getAlignmentAnnotation() != null)
1859         {
1860           for (AlignmentAnnotation alan : alignment
1861                   .getAlignmentAnnotation())
1862           {
1863             if (alan.graphGroup > fgroup)
1864             {
1865               fgroup = alan.graphGroup;
1866             }
1867           }
1868         }
1869         if (pastedal.getAlignmentAnnotation() != null)
1870         {
1871           // Add any annotation attached to alignment.
1872           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1873           for (int i = 0; i < alann.length; i++)
1874           {
1875             annotationAdded = true;
1876             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1877             {
1878               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1879               if (newann.graphGroup > -1)
1880               {
1881                 if (newGraphGroups.size() <= newann.graphGroup
1882                         || newGraphGroups.get(newann.graphGroup) == null)
1883                 {
1884                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1885                   {
1886                     newGraphGroups.add(q, null);
1887                   }
1888                   newGraphGroups.set(newann.graphGroup, new Integer(
1889                           ++fgroup));
1890                 }
1891                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1892                         .intValue();
1893               }
1894
1895               newann.padAnnotation(alwidth);
1896               alignment.addAnnotation(newann);
1897             }
1898           }
1899         }
1900       }
1901       if (!newAlignment)
1902       {
1903         // /////
1904         // ADD HISTORY ITEM
1905         //
1906         addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1907                 sequences, 0, alignment.getWidth(), alignment));
1908       }
1909       // Add any annotations attached to sequences
1910       for (int i = 0; i < sequences.length; i++)
1911       {
1912         if (sequences[i].getAnnotation() != null)
1913         {
1914           AlignmentAnnotation newann;
1915           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1916           {
1917             annotationAdded = true;
1918             newann = sequences[i].getAnnotation()[a];
1919             newann.adjustForAlignment();
1920             newann.padAnnotation(alwidth);
1921             if (newann.graphGroup > -1)
1922             {
1923               if (newann.graphGroup > -1)
1924               {
1925                 if (newGraphGroups.size() <= newann.graphGroup
1926                         || newGraphGroups.get(newann.graphGroup) == null)
1927                 {
1928                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1929                   {
1930                     newGraphGroups.add(q, null);
1931                   }
1932                   newGraphGroups.set(newann.graphGroup, new Integer(
1933                           ++fgroup));
1934                 }
1935                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1936                         .intValue();
1937               }
1938             }
1939             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1940             // was
1941             // duplicated
1942             // earlier
1943             alignment
1944                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1945           }
1946         }
1947       }
1948       if (!newAlignment)
1949       {
1950
1951         // propagate alignment changed.
1952         viewport.setEndSeq(alignment.getHeight());
1953         if (annotationAdded)
1954         {
1955           // Duplicate sequence annotation in all views.
1956           AlignmentI[] alview = this.getViewAlignments();
1957           for (int i = 0; i < sequences.length; i++)
1958           {
1959             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1960             if (sann == null)
1961               continue;
1962             for (int avnum = 0; avnum < alview.length; avnum++)
1963             {
1964               if (alview[avnum] != alignment)
1965               {
1966                 // duplicate in a view other than the one with input focus
1967                 int avwidth = alview[avnum].getWidth() + 1;
1968                 // this relies on sann being preserved after we
1969                 // modify the sequence's annotation array for each duplication
1970                 for (int a = 0; a < sann.length; a++)
1971                 {
1972                   AlignmentAnnotation newann = new AlignmentAnnotation(
1973                           sann[a]);
1974                   sequences[i].addAlignmentAnnotation(newann);
1975                   newann.padAnnotation(avwidth);
1976                   alview[avnum].addAnnotation(newann); // annotation was
1977                   // duplicated earlier
1978                   // TODO JAL-1145 graphGroups are not updated for sequence
1979                   // annotation added to several views. This may cause
1980                   // strangeness
1981                   alview[avnum].setAnnotationIndex(newann, a);
1982                 }
1983               }
1984             }
1985           }
1986           buildSortByAnnotationScoresMenu();
1987         }
1988         viewport.firePropertyChange("alignment", null,
1989                 alignment.getSequences());
1990         if (alignPanels != null)
1991         {
1992           for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
1993           {
1994             ap.validateAnnotationDimensions(false);
1995           }
1996         }
1997         else
1998         {
1999           alignPanel.validateAnnotationDimensions(false);
2000         }
2001
2002       }
2003       else
2004       {
2005         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2006                 DEFAULT_HEIGHT);
2007         String newtitle = new String("Copied sequences");
2008
2009         if (Desktop.jalviewClipboard != null
2010                 && Desktop.jalviewClipboard[2] != null)
2011         {
2012           Vector hc = (Vector) Desktop.jalviewClipboard[2];
2013           for (int i = 0; i < hc.size(); i++)
2014           {
2015             int[] region = (int[]) hc.elementAt(i);
2016             af.viewport.hideColumns(region[0], region[1]);
2017           }
2018         }
2019
2020         // >>>This is a fix for the moment, until a better solution is
2021         // found!!<<<
2022         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2023                 .transferSettings(
2024                         alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2025
2026         // TODO: maintain provenance of an alignment, rather than just make the
2027         // title a concatenation of operations.
2028         if (!externalPaste)
2029         {
2030           if (title.startsWith("Copied sequences"))
2031           {
2032             newtitle = title;
2033           }
2034           else
2035           {
2036             newtitle = newtitle.concat("- from " + title);
2037           }
2038         }
2039         else
2040         {
2041           newtitle = new String("Pasted sequences");
2042         }
2043
2044         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2045                 DEFAULT_HEIGHT);
2046
2047       }
2048
2049     } catch (Exception ex)
2050     {
2051       ex.printStackTrace();
2052       System.out.println("Exception whilst pasting: " + ex);
2053       // could be anything being pasted in here
2054     }
2055
2056   }
2057
2058   /**
2059    * DOCUMENT ME!
2060    *
2061    * @param e
2062    *          DOCUMENT ME!
2063    */
2064   @Override
2065   protected void cut_actionPerformed(ActionEvent e)
2066   {
2067     copy_actionPerformed(null);
2068     delete_actionPerformed(null);
2069   }
2070
2071   /**
2072    * DOCUMENT ME!
2073    *
2074    * @param e
2075    *          DOCUMENT ME!
2076    */
2077   @Override
2078   protected void delete_actionPerformed(ActionEvent evt)
2079   {
2080
2081     SequenceGroup sg = viewport.getSelectionGroup();
2082     if (sg == null)
2083     {
2084       return;
2085     }
2086
2087     Vector seqs = new Vector();
2088     SequenceI seq;
2089     for (int i = 0; i < sg.getSize(); i++)
2090     {
2091       seq = sg.getSequenceAt(i);
2092       seqs.addElement(seq);
2093     }
2094
2095     // If the cut affects all sequences, remove highlighted columns
2096     if (sg.getSize() == viewport.getAlignment().getHeight())
2097     {
2098       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2099               sg.getEndRes() + 1);
2100     }
2101
2102     SequenceI[] cut = new SequenceI[seqs.size()];
2103     for (int i = 0; i < seqs.size(); i++)
2104     {
2105       cut[i] = (SequenceI) seqs.elementAt(i);
2106     }
2107
2108     /*
2109      * //ADD HISTORY ITEM
2110      */
2111     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2112             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2113             viewport.getAlignment()));
2114
2115     viewport.setSelectionGroup(null);
2116     viewport.sendSelection();
2117     viewport.getAlignment().deleteGroup(sg);
2118
2119     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2120             .getSequences());
2121     if (viewport.getAlignment().getHeight() < 1)
2122     {
2123       try
2124       {
2125         this.setClosed(true);
2126       } catch (Exception ex)
2127       {
2128       }
2129     }
2130   }
2131
2132   /**
2133    * DOCUMENT ME!
2134    *
2135    * @param e
2136    *          DOCUMENT ME!
2137    */
2138   @Override
2139   protected void deleteGroups_actionPerformed(ActionEvent e)
2140   {
2141     if (avc.deleteGroups()) {
2142       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2143       alignPanel.updateAnnotation();
2144       alignPanel.paintAlignment(true);
2145     }
2146   }
2147
2148   /**
2149    * DOCUMENT ME!
2150    *
2151    * @param e
2152    *          DOCUMENT ME!
2153    */
2154   @Override
2155   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2156   {
2157     SequenceGroup sg = new SequenceGroup();
2158
2159     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2160     {
2161       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2162     }
2163
2164     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2165     viewport.setSelectionGroup(sg);
2166     viewport.sendSelection();
2167     alignPanel.paintAlignment(true);
2168     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2169   }
2170
2171   /**
2172    * DOCUMENT ME!
2173    *
2174    * @param e
2175    *          DOCUMENT ME!
2176    */
2177   @Override
2178   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2179   {
2180     if (viewport.cursorMode)
2181     {
2182       alignPanel.seqPanel.keyboardNo1 = null;
2183       alignPanel.seqPanel.keyboardNo2 = null;
2184     }
2185     viewport.setSelectionGroup(null);
2186     viewport.getColumnSelection().clear();
2187     viewport.setSelectionGroup(null);
2188     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2189     alignPanel.idPanel.idCanvas.searchResults = null;
2190     alignPanel.paintAlignment(true);
2191     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2192     viewport.sendSelection();
2193   }
2194
2195   /**
2196    * DOCUMENT ME!
2197    *
2198    * @param e
2199    *          DOCUMENT ME!
2200    */
2201   @Override
2202   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2203   {
2204     SequenceGroup sg = viewport.getSelectionGroup();
2205
2206     if (sg == null)
2207     {
2208       selectAllSequenceMenuItem_actionPerformed(null);
2209
2210       return;
2211     }
2212
2213     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2214     {
2215       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2216     }
2217
2218     alignPanel.paintAlignment(true);
2219     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2220     viewport.sendSelection();
2221   }
2222
2223   @Override
2224   public void invertColSel_actionPerformed(ActionEvent e)
2225   {
2226     viewport.invertColumnSelection();
2227     alignPanel.paintAlignment(true);
2228     viewport.sendSelection();
2229   }
2230
2231   /**
2232    * DOCUMENT ME!
2233    *
2234    * @param e
2235    *          DOCUMENT ME!
2236    */
2237   @Override
2238   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2239   {
2240     trimAlignment(true);
2241   }
2242
2243   /**
2244    * DOCUMENT ME!
2245    *
2246    * @param e
2247    *          DOCUMENT ME!
2248    */
2249   @Override
2250   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2251   {
2252     trimAlignment(false);
2253   }
2254
2255   void trimAlignment(boolean trimLeft)
2256   {
2257     ColumnSelection colSel = viewport.getColumnSelection();
2258     int column;
2259
2260     if (colSel.size() > 0)
2261     {
2262       if (trimLeft)
2263       {
2264         column = colSel.getMin();
2265       }
2266       else
2267       {
2268         column = colSel.getMax();
2269       }
2270
2271       SequenceI[] seqs;
2272       if (viewport.getSelectionGroup() != null)
2273       {
2274         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2275                 viewport.getHiddenRepSequences());
2276       }
2277       else
2278       {
2279         seqs = viewport.getAlignment().getSequencesArray();
2280       }
2281
2282       TrimRegionCommand trimRegion;
2283       if (trimLeft)
2284       {
2285         trimRegion = new TrimRegionCommand("Remove Left",
2286                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2287                 viewport.getAlignment(), viewport.getColumnSelection(),
2288                 viewport.getSelectionGroup());
2289         viewport.setStartRes(0);
2290       }
2291       else
2292       {
2293         trimRegion = new TrimRegionCommand("Remove Right",
2294                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2295                 viewport.getAlignment(), viewport.getColumnSelection(),
2296                 viewport.getSelectionGroup());
2297       }
2298
2299       statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
2300
2301       addHistoryItem(trimRegion);
2302
2303       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2304       {
2305         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2306                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2307         {
2308           viewport.getAlignment().deleteGroup(sg);
2309         }
2310       }
2311
2312       viewport.firePropertyChange("alignment", null, viewport
2313               .getAlignment().getSequences());
2314     }
2315   }
2316
2317   /**
2318    * DOCUMENT ME!
2319    *
2320    * @param e
2321    *          DOCUMENT ME!
2322    */
2323   @Override
2324   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2325   {
2326     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2327
2328     SequenceI[] seqs;
2329     if (viewport.getSelectionGroup() != null)
2330     {
2331       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2332               viewport.getHiddenRepSequences());
2333       start = viewport.getSelectionGroup().getStartRes();
2334       end = viewport.getSelectionGroup().getEndRes();
2335     }
2336     else
2337     {
2338       seqs = viewport.getAlignment().getSequencesArray();
2339     }
2340
2341     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2342             "Remove Gapped Columns", seqs, start, end,
2343             viewport.getAlignment());
2344
2345     addHistoryItem(removeGapCols);
2346
2347     statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
2348
2349     // This is to maintain viewport position on first residue
2350     // of first sequence
2351     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2352     int startRes = seq.findPosition(viewport.startRes);
2353     // ShiftList shifts;
2354     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2355     // edit.alColumnChanges=shifts.getInverse();
2356     // if (viewport.hasHiddenColumns)
2357     // viewport.getColumnSelection().compensateForEdits(shifts);
2358     viewport.setStartRes(seq.findIndex(startRes) - 1);
2359     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2360             .getSequences());
2361
2362   }
2363
2364   /**
2365    * DOCUMENT ME!
2366    *
2367    * @param e
2368    *          DOCUMENT ME!
2369    */
2370   @Override
2371   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2372   {
2373     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2374
2375     SequenceI[] seqs;
2376     if (viewport.getSelectionGroup() != null)
2377     {
2378       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2379               viewport.getHiddenRepSequences());
2380       start = viewport.getSelectionGroup().getStartRes();
2381       end = viewport.getSelectionGroup().getEndRes();
2382     }
2383     else
2384     {
2385       seqs = viewport.getAlignment().getSequencesArray();
2386     }
2387
2388     // This is to maintain viewport position on first residue
2389     // of first sequence
2390     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2391     int startRes = seq.findPosition(viewport.startRes);
2392
2393     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2394             viewport.getAlignment()));
2395
2396     viewport.setStartRes(seq.findIndex(startRes) - 1);
2397
2398     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2399             .getSequences());
2400
2401   }
2402
2403   /**
2404    * DOCUMENT ME!
2405    *
2406    * @param e
2407    *          DOCUMENT ME!
2408    */
2409   @Override
2410   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2411   {
2412     viewport.setPadGaps(padGapsMenuitem.isSelected());
2413     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2414             .getSequences());
2415   }
2416
2417   // else
2418   {
2419     // if (justifySeqs>0)
2420     {
2421       // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2422     }
2423   }
2424
2425   // }
2426
2427   /**
2428    * DOCUMENT ME!
2429    *
2430    * @param e
2431    *          DOCUMENT ME!
2432    */
2433   @Override
2434   public void findMenuItem_actionPerformed(ActionEvent e)
2435   {
2436     new Finder();
2437   }
2438
2439   @Override
2440   public void newView_actionPerformed(ActionEvent e)
2441   {
2442     newView(true);
2443   }
2444
2445   /**
2446    *
2447    * @param copyAnnotation
2448    *          if true then duplicate all annnotation, groups and settings
2449    * @return new alignment panel, already displayed.
2450    */
2451   public AlignmentPanel newView(boolean copyAnnotation)
2452   {
2453     return newView(null, copyAnnotation);
2454   }
2455
2456   /**
2457    *
2458    * @param viewTitle
2459    *          title of newly created view
2460    * @return new alignment panel, already displayed.
2461    */
2462   public AlignmentPanel newView(String viewTitle)
2463   {
2464     return newView(viewTitle, true);
2465   }
2466
2467   /**
2468    *
2469    * @param viewTitle
2470    *          title of newly created view
2471    * @param copyAnnotation
2472    *          if true then duplicate all annnotation, groups and settings
2473    * @return new alignment panel, already displayed.
2474    */
2475   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2476   {
2477     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2478             true);
2479     if (!copyAnnotation)
2480     {
2481       // just remove all the current annotation except for the automatic stuff
2482       newap.av.getAlignment().deleteAllGroups();
2483       for (AlignmentAnnotation alan : newap.av.getAlignment()
2484               .getAlignmentAnnotation())
2485       {
2486         if (!alan.autoCalculated)
2487         {
2488           newap.av.getAlignment().deleteAnnotation(alan);
2489         }
2490         ;
2491       }
2492     }
2493
2494     newap.av.gatherViewsHere = false;
2495
2496     if (viewport.viewName == null)
2497     {
2498       viewport.viewName = "Original";
2499     }
2500
2501     newap.av.historyList = viewport.historyList;
2502     newap.av.redoList = viewport.redoList;
2503
2504     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2505     // make sure the new view has a unique name - this is essential for Jalview
2506     // 2 archives
2507     boolean addFirstIndex = false;
2508     if (viewTitle == null || viewTitle.trim().length() == 0)
2509     {
2510       viewTitle = "View";
2511       addFirstIndex = true;
2512     }
2513     else
2514     {
2515       index = 1;// we count from 1 if given a specific name
2516     }
2517     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2518     Vector comps = (Vector) PaintRefresher.components.get(viewport
2519             .getSequenceSetId());
2520     Vector existingNames = new Vector();
2521     for (int i = 0; i < comps.size(); i++)
2522     {
2523       if (comps.elementAt(i) instanceof AlignmentPanel)
2524       {
2525         AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2526         if (!existingNames.contains(ap.av.viewName))
2527         {
2528           existingNames.addElement(ap.av.viewName);
2529         }
2530       }
2531     }
2532
2533     while (existingNames.contains(newViewName))
2534     {
2535       newViewName = viewTitle + " " + (++index);
2536     }
2537
2538     newap.av.viewName = newViewName;
2539
2540     addAlignmentPanel(newap, true);
2541     newap.alignmentChanged();
2542
2543     if (alignPanels.size() == 2)
2544     {
2545       viewport.gatherViewsHere = true;
2546     }
2547     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2548     return newap;
2549   }
2550
2551   @Override
2552   public void expandViews_actionPerformed(ActionEvent e)
2553   {
2554     Desktop.instance.explodeViews(this);
2555   }
2556
2557   @Override
2558   public void gatherViews_actionPerformed(ActionEvent e)
2559   {
2560     Desktop.instance.gatherViews(this);
2561   }
2562
2563   /**
2564    * DOCUMENT ME!
2565    *
2566    * @param e
2567    *          DOCUMENT ME!
2568    */
2569   @Override
2570   public void font_actionPerformed(ActionEvent e)
2571   {
2572     new FontChooser(alignPanel);
2573   }
2574
2575   /**
2576    * DOCUMENT ME!
2577    *
2578    * @param e
2579    *          DOCUMENT ME!
2580    */
2581   @Override
2582   protected void seqLimit_actionPerformed(ActionEvent e)
2583   {
2584     viewport.setShowJVSuffix(seqLimits.isSelected());
2585
2586     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2587             .calculateIdWidth());
2588     alignPanel.paintAlignment(true);
2589   }
2590
2591   @Override
2592   public void idRightAlign_actionPerformed(ActionEvent e)
2593   {
2594     viewport.rightAlignIds = idRightAlign.isSelected();
2595     alignPanel.paintAlignment(true);
2596   }
2597
2598   @Override
2599   public void centreColumnLabels_actionPerformed(ActionEvent e)
2600   {
2601     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2602     alignPanel.paintAlignment(true);
2603   }
2604
2605   /*
2606    * (non-Javadoc)
2607    *
2608    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2609    */
2610   @Override
2611   protected void followHighlight_actionPerformed()
2612   {
2613     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2614     {
2615       alignPanel.scrollToPosition(
2616               alignPanel.seqPanel.seqCanvas.searchResults, false);
2617     }
2618   }
2619
2620   /**
2621    * DOCUMENT ME!
2622    *
2623    * @param e
2624    *          DOCUMENT ME!
2625    */
2626   @Override
2627   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2628   {
2629     viewport.setColourText(colourTextMenuItem.isSelected());
2630     alignPanel.paintAlignment(true);
2631   }
2632
2633   /**
2634    * DOCUMENT ME!
2635    *
2636    * @param e
2637    *          DOCUMENT ME!
2638    */
2639   @Override
2640   public void wrapMenuItem_actionPerformed(ActionEvent e)
2641   {
2642     scaleAbove.setVisible(wrapMenuItem.isSelected());
2643     scaleLeft.setVisible(wrapMenuItem.isSelected());
2644     scaleRight.setVisible(wrapMenuItem.isSelected());
2645     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2646     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2647   }
2648
2649   @Override
2650   public void showAllSeqs_actionPerformed(ActionEvent e)
2651   {
2652     viewport.showAllHiddenSeqs();
2653   }
2654
2655   @Override
2656   public void showAllColumns_actionPerformed(ActionEvent e)
2657   {
2658     viewport.showAllHiddenColumns();
2659     repaint();
2660   }
2661
2662   @Override
2663   public void hideSelSequences_actionPerformed(ActionEvent e)
2664   {
2665     viewport.hideAllSelectedSeqs();
2666     alignPanel.paintAlignment(true);
2667   }
2668
2669   /**
2670    * called by key handler and the hide all/show all menu items
2671    *
2672    * @param toggleSeqs
2673    * @param toggleCols
2674    */
2675   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2676   {
2677
2678     boolean hide = false;
2679     SequenceGroup sg = viewport.getSelectionGroup();
2680     if (!toggleSeqs && !toggleCols)
2681     {
2682       // Hide everything by the current selection - this is a hack - we do the
2683       // invert and then hide
2684       // first check that there will be visible columns after the invert.
2685       if ((viewport.getColumnSelection() != null
2686               && viewport.getColumnSelection().getSelected() != null && viewport
2687               .getColumnSelection().getSelected().size() > 0)
2688               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2689                       .getEndRes()))
2690       {
2691         // now invert the sequence set, if required - empty selection implies
2692         // that no hiding is required.
2693         if (sg != null)
2694         {
2695           invertSequenceMenuItem_actionPerformed(null);
2696           sg = viewport.getSelectionGroup();
2697           toggleSeqs = true;
2698
2699         }
2700         viewport.expandColSelection(sg, true);
2701         // finally invert the column selection and get the new sequence
2702         // selection.
2703         invertColSel_actionPerformed(null);
2704         toggleCols = true;
2705       }
2706     }
2707
2708     if (toggleSeqs)
2709     {
2710       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2711       {
2712         hideSelSequences_actionPerformed(null);
2713         hide = true;
2714       }
2715       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2716               .size() > 0))
2717       {
2718         showAllSeqs_actionPerformed(null);
2719       }
2720     }
2721
2722     if (toggleCols)
2723     {
2724       if (viewport.getColumnSelection().getSelected().size() > 0)
2725       {
2726         hideSelColumns_actionPerformed(null);
2727         if (!toggleSeqs)
2728         {
2729           viewport.setSelectionGroup(sg);
2730         }
2731       }
2732       else if (!hide)
2733       {
2734         showAllColumns_actionPerformed(null);
2735       }
2736     }
2737   }
2738
2739   /*
2740    * (non-Javadoc)
2741    *
2742    * @see
2743    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2744    * event.ActionEvent)
2745    */
2746   @Override
2747   public void hideAllButSelection_actionPerformed(ActionEvent e)
2748   {
2749     toggleHiddenRegions(false, false);
2750   }
2751
2752   /*
2753    * (non-Javadoc)
2754    *
2755    * @see
2756    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2757    * .ActionEvent)
2758    */
2759   @Override
2760   public void hideAllSelection_actionPerformed(ActionEvent e)
2761   {
2762     SequenceGroup sg = viewport.getSelectionGroup();
2763     viewport.expandColSelection(sg, false);
2764     viewport.hideAllSelectedSeqs();
2765     viewport.hideSelectedColumns();
2766     alignPanel.paintAlignment(true);
2767   }
2768
2769   /*
2770    * (non-Javadoc)
2771    *
2772    * @see
2773    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2774    * ActionEvent)
2775    */
2776   @Override
2777   public void showAllhidden_actionPerformed(ActionEvent e)
2778   {
2779     viewport.showAllHiddenColumns();
2780     viewport.showAllHiddenSeqs();
2781     alignPanel.paintAlignment(true);
2782   }
2783
2784   @Override
2785   public void hideSelColumns_actionPerformed(ActionEvent e)
2786   {
2787     viewport.hideSelectedColumns();
2788     alignPanel.paintAlignment(true);
2789   }
2790
2791   @Override
2792   public void hiddenMarkers_actionPerformed(ActionEvent e)
2793   {
2794     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2795     repaint();
2796   }
2797
2798   /**
2799    * DOCUMENT ME!
2800    *
2801    * @param e
2802    *          DOCUMENT ME!
2803    */
2804   @Override
2805   protected void scaleAbove_actionPerformed(ActionEvent e)
2806   {
2807     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2808     alignPanel.paintAlignment(true);
2809   }
2810
2811   /**
2812    * DOCUMENT ME!
2813    *
2814    * @param e
2815    *          DOCUMENT ME!
2816    */
2817   @Override
2818   protected void scaleLeft_actionPerformed(ActionEvent e)
2819   {
2820     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2821     alignPanel.paintAlignment(true);
2822   }
2823
2824   /**
2825    * DOCUMENT ME!
2826    *
2827    * @param e
2828    *          DOCUMENT ME!
2829    */
2830   @Override
2831   protected void scaleRight_actionPerformed(ActionEvent e)
2832   {
2833     viewport.setScaleRightWrapped(scaleRight.isSelected());
2834     alignPanel.paintAlignment(true);
2835   }
2836
2837   /**
2838    * DOCUMENT ME!
2839    *
2840    * @param e
2841    *          DOCUMENT ME!
2842    */
2843   @Override
2844   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2845   {
2846     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2847     alignPanel.paintAlignment(true);
2848   }
2849
2850   /**
2851    * DOCUMENT ME!
2852    *
2853    * @param e
2854    *          DOCUMENT ME!
2855    */
2856   @Override
2857   public void viewTextMenuItem_actionPerformed(ActionEvent e)
2858   {
2859     viewport.setShowText(viewTextMenuItem.isSelected());
2860     alignPanel.paintAlignment(true);
2861   }
2862
2863   /**
2864    * DOCUMENT ME!
2865    *
2866    * @param e
2867    *          DOCUMENT ME!
2868    */
2869   @Override
2870   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2871   {
2872     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2873     alignPanel.paintAlignment(true);
2874   }
2875
2876   public FeatureSettings featureSettings;
2877
2878   @Override
2879   public void featureSettings_actionPerformed(ActionEvent e)
2880   {
2881     if (featureSettings != null)
2882     {
2883       featureSettings.close();
2884       featureSettings = null;
2885     }
2886     if (!showSeqFeatures.isSelected())
2887     {
2888       // make sure features are actually displayed
2889       showSeqFeatures.setSelected(true);
2890       showSeqFeatures_actionPerformed(null);
2891     }
2892     featureSettings = new FeatureSettings(this);
2893   }
2894
2895   /**
2896    * Set or clear 'Show Sequence Features'
2897    *
2898    * @param evt
2899    *          DOCUMENT ME!
2900    */
2901   @Override
2902   public void showSeqFeatures_actionPerformed(ActionEvent evt)
2903   {
2904     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2905     alignPanel.paintAlignment(true);
2906     if (alignPanel.getOverviewPanel() != null)
2907     {
2908       alignPanel.getOverviewPanel().updateOverviewImage();
2909     }
2910   }
2911
2912   /**
2913    * Set or clear 'Show Sequence Features'
2914    *
2915    * @param evt
2916    *          DOCUMENT ME!
2917    */
2918   @Override
2919   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2920   {
2921     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2922             .isSelected());
2923     if (viewport.getShowSequenceFeaturesHeight())
2924     {
2925       // ensure we're actually displaying features
2926       viewport.setShowSequenceFeatures(true);
2927       showSeqFeatures.setSelected(true);
2928     }
2929     alignPanel.paintAlignment(true);
2930     if (alignPanel.getOverviewPanel() != null)
2931     {
2932       alignPanel.getOverviewPanel().updateOverviewImage();
2933     }
2934   }
2935
2936   /**
2937    * DOCUMENT ME!
2938    *
2939    * @param e
2940    *          DOCUMENT ME!
2941    */
2942   @Override
2943   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2944   {
2945     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2946     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2947   }
2948
2949   @Override
2950   public void alignmentProperties()
2951   {
2952     JEditorPane editPane = new JEditorPane("text/html", "");
2953     editPane.setEditable(false);
2954     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2955             .formatAsHtml();
2956     editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
2957     JInternalFrame frame = new JInternalFrame();
2958     frame.getContentPane().add(new JScrollPane(editPane));
2959
2960     Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2961             + getTitle(), 500, 400);
2962   }
2963
2964   /**
2965    * DOCUMENT ME!
2966    *
2967    * @param e
2968    *          DOCUMENT ME!
2969    */
2970   @Override
2971   public void overviewMenuItem_actionPerformed(ActionEvent e)
2972   {
2973     if (alignPanel.overviewPanel != null)
2974     {
2975       return;
2976     }
2977
2978     JInternalFrame frame = new JInternalFrame();
2979     OverviewPanel overview = new OverviewPanel(alignPanel);
2980     frame.setContentPane(overview);
2981     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2982             frame.getWidth(), frame.getHeight());
2983     frame.pack();
2984     frame.setLayer(JLayeredPane.PALETTE_LAYER);
2985     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2986     {
2987       @Override
2988       public void internalFrameClosed(
2989               javax.swing.event.InternalFrameEvent evt)
2990       {
2991         alignPanel.setOverviewPanel(null);
2992       };
2993     });
2994
2995     alignPanel.setOverviewPanel(overview);
2996   }
2997
2998   @Override
2999   public void textColour_actionPerformed(ActionEvent e)
3000   {
3001     new TextColourChooser().chooseColour(alignPanel, null);
3002   }
3003
3004   /**
3005    * DOCUMENT ME!
3006    *
3007    * @param e
3008    *          DOCUMENT ME!
3009    */
3010   @Override
3011   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3012   {
3013     changeColour(null);
3014   }
3015
3016   /**
3017    * DOCUMENT ME!
3018    *
3019    * @param e
3020    *          DOCUMENT ME!
3021    */
3022   @Override
3023   public void clustalColour_actionPerformed(ActionEvent e)
3024   {
3025     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3026             viewport.getHiddenRepSequences()));
3027   }
3028
3029   /**
3030    * DOCUMENT ME!
3031    *
3032    * @param e
3033    *          DOCUMENT ME!
3034    */
3035   @Override
3036   public void zappoColour_actionPerformed(ActionEvent e)
3037   {
3038     changeColour(new ZappoColourScheme());
3039   }
3040
3041   /**
3042    * DOCUMENT ME!
3043    *
3044    * @param e
3045    *          DOCUMENT ME!
3046    */
3047   @Override
3048   public void taylorColour_actionPerformed(ActionEvent e)
3049   {
3050     changeColour(new TaylorColourScheme());
3051   }
3052
3053   /**
3054    * DOCUMENT ME!
3055    *
3056    * @param e
3057    *          DOCUMENT ME!
3058    */
3059   @Override
3060   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3061   {
3062     changeColour(new HydrophobicColourScheme());
3063   }
3064
3065   /**
3066    * DOCUMENT ME!
3067    *
3068    * @param e
3069    *          DOCUMENT ME!
3070    */
3071   @Override
3072   public void helixColour_actionPerformed(ActionEvent e)
3073   {
3074     changeColour(new HelixColourScheme());
3075   }
3076
3077   /**
3078    * DOCUMENT ME!
3079    *
3080    * @param e
3081    *          DOCUMENT ME!
3082    */
3083   @Override
3084   public void strandColour_actionPerformed(ActionEvent e)
3085   {
3086     changeColour(new StrandColourScheme());
3087   }
3088
3089   /**
3090    * DOCUMENT ME!
3091    *
3092    * @param e
3093    *          DOCUMENT ME!
3094    */
3095   @Override
3096   public void turnColour_actionPerformed(ActionEvent e)
3097   {
3098     changeColour(new TurnColourScheme());
3099   }
3100
3101   /**
3102    * DOCUMENT ME!
3103    *
3104    * @param e
3105    *          DOCUMENT ME!
3106    */
3107   @Override
3108   public void buriedColour_actionPerformed(ActionEvent e)
3109   {
3110     changeColour(new BuriedColourScheme());
3111   }
3112
3113   /**
3114    * DOCUMENT ME!
3115    *
3116    * @param e
3117    *          DOCUMENT ME!
3118    */
3119   @Override
3120   public void nucleotideColour_actionPerformed(ActionEvent e)
3121   {
3122     changeColour(new NucleotideColourScheme());
3123   }
3124
3125   @Override
3126   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3127   {
3128     changeColour(new PurinePyrimidineColourScheme());
3129   }
3130
3131   /*
3132    * public void covariationColour_actionPerformed(ActionEvent e) {
3133    * changeColour(new
3134    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3135    * ()[0])); }
3136    */
3137   @Override
3138   public void annotationColour_actionPerformed(ActionEvent e)
3139   {
3140     new AnnotationColourChooser(viewport, alignPanel);
3141   }
3142
3143   @Override
3144   public void rnahelicesColour_actionPerformed(ActionEvent e)
3145   {
3146     new RNAHelicesColourChooser(viewport, alignPanel);
3147   }
3148
3149   /**
3150    * DOCUMENT ME!
3151    *
3152    * @param e
3153    *          DOCUMENT ME!
3154    */
3155   @Override
3156   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3157   {
3158     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3159   }
3160
3161   /**
3162    * DOCUMENT ME!
3163    *
3164    * @param cs
3165    *          DOCUMENT ME!
3166    */
3167   public void changeColour(ColourSchemeI cs)
3168   {
3169     // TODO: compare with applet and pull up to model method
3170     int threshold = 0;
3171
3172     if (cs != null)
3173     {
3174       if (viewport.getAbovePIDThreshold())
3175       {
3176         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3177                 "Background");
3178
3179         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3180
3181         viewport.setGlobalColourScheme(cs);
3182       }
3183       else
3184       {
3185         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3186       }
3187
3188       if (viewport.getConservationSelected())
3189       {
3190
3191         Alignment al = (Alignment) viewport.getAlignment();
3192         Conservation c = new Conservation("All",
3193                 ResidueProperties.propHash, 3, al.getSequences(), 0,
3194                 al.getWidth() - 1);
3195
3196         c.calculate();
3197         c.verdict(false, viewport.getConsPercGaps());
3198
3199         cs.setConservation(c);
3200
3201         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3202                 cs, "Background"));
3203       }
3204       else
3205       {
3206         cs.setConservation(null);
3207       }
3208
3209       cs.setConsensus(viewport.getSequenceConsensusHash());
3210     }
3211
3212     viewport.setGlobalColourScheme(cs);
3213
3214     if (viewport.getColourAppliesToAllGroups())
3215     {
3216
3217       for (SequenceGroup sg : viewport.getAlignment().getGroups())
3218       {
3219         if (cs == null)
3220         {
3221           sg.cs = null;
3222           continue;
3223         }
3224
3225         if (cs instanceof ClustalxColourScheme)
3226         {
3227           sg.cs = new ClustalxColourScheme(sg,
3228                   viewport.getHiddenRepSequences());
3229         }
3230         else if (cs instanceof UserColourScheme)
3231         {
3232           sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3233         }
3234         else
3235         {
3236           try
3237           {
3238             sg.cs = cs.getClass().newInstance();
3239           } catch (Exception ex)
3240           {
3241           }
3242         }
3243
3244         if (viewport.getAbovePIDThreshold()
3245                 || cs instanceof PIDColourScheme
3246                 || cs instanceof Blosum62ColourScheme)
3247         {
3248           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3249
3250           sg.cs.setConsensus(AAFrequency.calculate(
3251                   sg.getSequences(viewport.getHiddenRepSequences()),
3252                   sg.getStartRes(), sg.getEndRes() + 1));
3253         }
3254         else
3255         {
3256           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3257         }
3258
3259         if (viewport.getConservationSelected())
3260         {
3261           Conservation c = new Conservation("Group",
3262                   ResidueProperties.propHash, 3, sg.getSequences(viewport
3263                           .getHiddenRepSequences()), sg.getStartRes(),
3264                   sg.getEndRes() + 1);
3265           c.calculate();
3266           c.verdict(false, viewport.getConsPercGaps());
3267           sg.cs.setConservation(c);
3268         }
3269         else
3270         {
3271           sg.cs.setConservation(null);
3272         }
3273       }
3274     }
3275
3276     if (alignPanel.getOverviewPanel() != null)
3277     {
3278       alignPanel.getOverviewPanel().updateOverviewImage();
3279     }
3280
3281     alignPanel.paintAlignment(true);
3282   }
3283
3284   /**
3285    * DOCUMENT ME!
3286    *
3287    * @param e
3288    *          DOCUMENT ME!
3289    */
3290   @Override
3291   protected void modifyPID_actionPerformed(ActionEvent e)
3292   {
3293     if (viewport.getAbovePIDThreshold()
3294             && viewport.getGlobalColourScheme() != null)
3295     {
3296       SliderPanel.setPIDSliderSource(alignPanel,
3297               viewport.getGlobalColourScheme(), "Background");
3298       SliderPanel.showPIDSlider();
3299     }
3300   }
3301
3302   /**
3303    * DOCUMENT ME!
3304    *
3305    * @param e
3306    *          DOCUMENT ME!
3307    */
3308   @Override
3309   protected void modifyConservation_actionPerformed(ActionEvent e)
3310   {
3311     if (viewport.getConservationSelected()
3312             && viewport.getGlobalColourScheme() != null)
3313     {
3314       SliderPanel.setConservationSlider(alignPanel,
3315               viewport.getGlobalColourScheme(), "Background");
3316       SliderPanel.showConservationSlider();
3317     }
3318   }
3319
3320   /**
3321    * DOCUMENT ME!
3322    *
3323    * @param e
3324    *          DOCUMENT ME!
3325    */
3326   @Override
3327   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3328   {
3329     viewport.setConservationSelected(conservationMenuItem.isSelected());
3330
3331     viewport.setAbovePIDThreshold(false);
3332     abovePIDThreshold.setSelected(false);
3333
3334     changeColour(viewport.getGlobalColourScheme());
3335
3336     modifyConservation_actionPerformed(null);
3337   }
3338
3339   /**
3340    * DOCUMENT ME!
3341    *
3342    * @param e
3343    *          DOCUMENT ME!
3344    */
3345   @Override
3346   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3347   {
3348     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3349
3350     conservationMenuItem.setSelected(false);
3351     viewport.setConservationSelected(false);
3352
3353     changeColour(viewport.getGlobalColourScheme());
3354
3355     modifyPID_actionPerformed(null);
3356   }
3357
3358   /**
3359    * DOCUMENT ME!
3360    *
3361    * @param e
3362    *          DOCUMENT ME!
3363    */
3364   @Override
3365   public void userDefinedColour_actionPerformed(ActionEvent e)
3366   {
3367     if (e.getActionCommand().equals("User Defined..."))
3368     {
3369       new UserDefinedColours(alignPanel, null);
3370     }
3371     else
3372     {
3373       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3374               .getUserColourSchemes().get(e.getActionCommand());
3375
3376       changeColour(udc);
3377     }
3378   }
3379
3380   public void updateUserColourMenu()
3381   {
3382
3383     Component[] menuItems = colourMenu.getMenuComponents();
3384     int i, iSize = menuItems.length;
3385     for (i = 0; i < iSize; i++)
3386     {
3387       if (menuItems[i].getName() != null
3388               && menuItems[i].getName().equals("USER_DEFINED"))
3389       {
3390         colourMenu.remove(menuItems[i]);
3391         iSize--;
3392       }
3393     }
3394     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3395     {
3396       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3397               .getUserColourSchemes().keys();
3398
3399       while (userColours.hasMoreElements())
3400       {
3401         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3402                 userColours.nextElement().toString());
3403         radioItem.setName("USER_DEFINED");
3404         radioItem.addMouseListener(new MouseAdapter()
3405         {
3406           @Override
3407           public void mousePressed(MouseEvent evt)
3408           {
3409             if (evt.isControlDown()
3410                     || SwingUtilities.isRightMouseButton(evt))
3411             {
3412               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3413
3414               int option = JOptionPane.showInternalConfirmDialog(
3415                       jalview.gui.Desktop.desktop,
3416                       MessageManager.getString("label.remove_from_default_list"),
3417                       MessageManager.getString("label.remove_user_defined_colour"),
3418                       JOptionPane.YES_NO_OPTION);
3419               if (option == JOptionPane.YES_OPTION)
3420               {
3421                 jalview.gui.UserDefinedColours
3422                         .removeColourFromDefaults(radioItem.getText());
3423                 colourMenu.remove(radioItem);
3424               }
3425               else
3426               {
3427                 radioItem.addActionListener(new ActionListener()
3428                 {
3429                   @Override
3430                   public void actionPerformed(ActionEvent evt)
3431                   {
3432                     userDefinedColour_actionPerformed(evt);
3433                   }
3434                 });
3435               }
3436             }
3437           }
3438         });
3439         radioItem.addActionListener(new ActionListener()
3440         {
3441           @Override
3442           public void actionPerformed(ActionEvent evt)
3443           {
3444             userDefinedColour_actionPerformed(evt);
3445           }
3446         });
3447
3448         colourMenu.insert(radioItem, 15);
3449         colours.add(radioItem);
3450       }
3451     }
3452   }
3453
3454   /**
3455    * DOCUMENT ME!
3456    *
3457    * @param e
3458    *          DOCUMENT ME!
3459    */
3460   @Override
3461   public void PIDColour_actionPerformed(ActionEvent e)
3462   {
3463     changeColour(new PIDColourScheme());
3464   }
3465
3466   /**
3467    * DOCUMENT ME!
3468    *
3469    * @param e
3470    *          DOCUMENT ME!
3471    */
3472   @Override
3473   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3474   {
3475     changeColour(new Blosum62ColourScheme());
3476   }
3477
3478   /**
3479    * DOCUMENT ME!
3480    *
3481    * @param e
3482    *          DOCUMENT ME!
3483    */
3484   @Override
3485   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3486   {
3487     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3488     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3489             .getAlignment().getSequenceAt(0), null);
3490     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3491             viewport.getAlignment()));
3492     alignPanel.paintAlignment(true);
3493   }
3494
3495   /**
3496    * DOCUMENT ME!
3497    *
3498    * @param e
3499    *          DOCUMENT ME!
3500    */
3501   @Override
3502   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3503   {
3504     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3505     AlignmentSorter.sortByID(viewport.getAlignment());
3506     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3507             viewport.getAlignment()));
3508     alignPanel.paintAlignment(true);
3509   }
3510
3511   /**
3512    * DOCUMENT ME!
3513    *
3514    * @param e
3515    *          DOCUMENT ME!
3516    */
3517   @Override
3518   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3519   {
3520     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3521     AlignmentSorter.sortByLength(viewport.getAlignment());
3522     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3523             viewport.getAlignment()));
3524     alignPanel.paintAlignment(true);
3525   }
3526
3527   /**
3528    * DOCUMENT ME!
3529    *
3530    * @param e
3531    *          DOCUMENT ME!
3532    */
3533   @Override
3534   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3535   {
3536     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3537     AlignmentSorter.sortByGroup(viewport.getAlignment());
3538     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3539             viewport.getAlignment()));
3540
3541     alignPanel.paintAlignment(true);
3542   }
3543
3544   /**
3545    * DOCUMENT ME!
3546    *
3547    * @param e
3548    *          DOCUMENT ME!
3549    */
3550   @Override
3551   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3552   {
3553     new RedundancyPanel(alignPanel, this);
3554   }
3555
3556   /**
3557    * DOCUMENT ME!
3558    *
3559    * @param e
3560    *          DOCUMENT ME!
3561    */
3562   @Override
3563   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3564   {
3565     if ((viewport.getSelectionGroup() == null)
3566             || (viewport.getSelectionGroup().getSize() < 2))
3567     {
3568       JOptionPane.showInternalMessageDialog(this,
3569               MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
3570               JOptionPane.WARNING_MESSAGE);
3571     }
3572     else
3573     {
3574       JInternalFrame frame = new JInternalFrame();
3575       frame.setContentPane(new PairwiseAlignPanel(viewport));
3576       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3577     }
3578   }
3579
3580   /**
3581    * DOCUMENT ME!
3582    *
3583    * @param e
3584    *          DOCUMENT ME!
3585    */
3586   @Override
3587   public void PCAMenuItem_actionPerformed(ActionEvent e)
3588   {
3589     if (((viewport.getSelectionGroup() != null)
3590             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3591             .getSelectionGroup().getSize() > 0))
3592             || (viewport.getAlignment().getHeight() < 4))
3593     {
3594       JOptionPane.showInternalMessageDialog(this,
3595               MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3596               MessageManager.getString("label.sequence_selection_insufficient"),
3597               JOptionPane.WARNING_MESSAGE);
3598
3599       return;
3600     }
3601
3602     new PCAPanel(alignPanel);
3603   }
3604
3605   @Override
3606   public void autoCalculate_actionPerformed(ActionEvent e)
3607   {
3608     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3609     if (viewport.autoCalculateConsensus)
3610     {
3611       viewport.firePropertyChange("alignment", null, viewport
3612               .getAlignment().getSequences());
3613     }
3614   }
3615
3616   @Override
3617   public void sortByTreeOption_actionPerformed(ActionEvent e)
3618   {
3619     viewport.sortByTree = sortByTree.isSelected();
3620   }
3621
3622   @Override
3623   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3624   {
3625     viewport.followSelection = listenToViewSelections.isSelected();
3626   }
3627
3628   /**
3629    * DOCUMENT ME!
3630    *
3631    * @param e
3632    *          DOCUMENT ME!
3633    */
3634   @Override
3635   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3636   {
3637     NewTreePanel("AV", "PID", "Average distance tree using PID");
3638   }
3639
3640   /**
3641    * DOCUMENT ME!
3642    *
3643    * @param e
3644    *          DOCUMENT ME!
3645    */
3646   @Override
3647   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3648   {
3649     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3650   }
3651
3652   /**
3653    * DOCUMENT ME!
3654    *
3655    * @param e
3656    *          DOCUMENT ME!
3657    */
3658   @Override
3659   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3660   {
3661     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3662   }
3663
3664   /**
3665    * DOCUMENT ME!
3666    *
3667    * @param e
3668    *          DOCUMENT ME!
3669    */
3670   @Override
3671   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3672   {
3673     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3674   }
3675
3676   /**
3677    * DOCUMENT ME!
3678    *
3679    * @param type
3680    *          DOCUMENT ME!
3681    * @param pwType
3682    *          DOCUMENT ME!
3683    * @param title
3684    *          DOCUMENT ME!
3685    */
3686   void NewTreePanel(String type, String pwType, String title)
3687   {
3688     TreePanel tp;
3689
3690     if (viewport.getSelectionGroup() != null
3691             && viewport.getSelectionGroup().getSize() > 0)
3692     {
3693       if (viewport.getSelectionGroup().getSize() < 3)
3694       {
3695         JOptionPane
3696                 .showMessageDialog(
3697                         Desktop.desktop,
3698                         MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
3699                         MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
3700         return;
3701       }
3702
3703       SequenceGroup sg = viewport.getSelectionGroup();
3704
3705       /* Decide if the selection is a column region */
3706       for (SequenceI _s : sg.getSequences())
3707       {
3708         if (_s.getLength() < sg.getEndRes())
3709         {
3710           JOptionPane
3711                   .showMessageDialog(
3712                           Desktop.desktop,
3713                           MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3714                           MessageManager.getString("label.sequences_selection_not_aligned"),
3715                           JOptionPane.WARNING_MESSAGE);
3716
3717           return;
3718         }
3719       }
3720
3721       title = title + " on region";
3722       tp = new TreePanel(alignPanel, type, pwType);
3723     }
3724     else
3725     {
3726       // are the visible sequences aligned?
3727       if (!viewport.getAlignment().isAligned(false))
3728       {
3729         JOptionPane
3730                 .showMessageDialog(
3731                         Desktop.desktop,
3732                         MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
3733                         MessageManager.getString("label.sequences_not_aligned"),
3734                         JOptionPane.WARNING_MESSAGE);
3735
3736         return;
3737       }
3738
3739       if (viewport.getAlignment().getHeight() < 2)
3740       {
3741         return;
3742       }
3743
3744       tp = new TreePanel(alignPanel, type, pwType);
3745     }
3746
3747     title += " from ";
3748
3749     if (viewport.viewName != null)
3750     {
3751       title += viewport.viewName + " of ";
3752     }
3753
3754     title += this.title;
3755
3756     Desktop.addInternalFrame(tp, title, 600, 500);
3757   }
3758
3759   /**
3760    * DOCUMENT ME!
3761    *
3762    * @param title
3763    *          DOCUMENT ME!
3764    * @param order
3765    *          DOCUMENT ME!
3766    */
3767   public void addSortByOrderMenuItem(String title,
3768           final AlignmentOrder order)
3769   {
3770     final JMenuItem item = new JMenuItem("by " + title);
3771     sort.add(item);
3772     item.addActionListener(new java.awt.event.ActionListener()
3773     {
3774       @Override
3775       public void actionPerformed(ActionEvent e)
3776       {
3777         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3778
3779         // TODO: JBPNote - have to map order entries to curent SequenceI
3780         // pointers
3781         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3782
3783         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3784                 .getAlignment()));
3785
3786         alignPanel.paintAlignment(true);
3787       }
3788     });
3789   }
3790
3791   /**
3792    * Add a new sort by annotation score menu item
3793    *
3794    * @param sort
3795    *          the menu to add the option to
3796    * @param scoreLabel
3797    *          the label used to retrieve scores for each sequence on the
3798    *          alignment
3799    */
3800   public void addSortByAnnotScoreMenuItem(JMenu sort,
3801           final String scoreLabel)
3802   {
3803     final JMenuItem item = new JMenuItem(scoreLabel);
3804     sort.add(item);
3805     item.addActionListener(new java.awt.event.ActionListener()
3806     {
3807       @Override
3808       public void actionPerformed(ActionEvent e)
3809       {
3810         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3811         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3812                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3813         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3814                 viewport.getAlignment()));
3815         alignPanel.paintAlignment(true);
3816       }
3817     });
3818   }
3819
3820   /**
3821    * last hash for alignment's annotation array - used to minimise cost of
3822    * rebuild.
3823    */
3824   protected int _annotationScoreVectorHash;
3825
3826   /**
3827    * search the alignment and rebuild the sort by annotation score submenu the
3828    * last alignment annotation vector hash is stored to minimize cost of
3829    * rebuilding in subsequence calls.
3830    *
3831    */
3832   @Override
3833   public void buildSortByAnnotationScoresMenu()
3834   {
3835     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3836     {
3837       return;
3838     }
3839
3840     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3841     {
3842       sortByAnnotScore.removeAll();
3843       // almost certainly a quicker way to do this - but we keep it simple
3844       Hashtable scoreSorts = new Hashtable();
3845       AlignmentAnnotation aann[];
3846       for (SequenceI sqa : viewport.getAlignment().getSequences())
3847       {
3848         aann = sqa.getAnnotation();
3849         for (int i = 0; aann != null && i < aann.length; i++)
3850         {
3851           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3852           {
3853             scoreSorts.put(aann[i].label, aann[i].label);
3854           }
3855         }
3856       }
3857       Enumeration labels = scoreSorts.keys();
3858       while (labels.hasMoreElements())
3859       {
3860         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3861                 (String) labels.nextElement());
3862       }
3863       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3864       scoreSorts.clear();
3865
3866       _annotationScoreVectorHash = viewport.getAlignment()
3867               .getAlignmentAnnotation().hashCode();
3868     }
3869   }
3870
3871   /**
3872    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3873    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3874    * call. Listeners are added to remove the menu item when the treePanel is
3875    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3876    * modified.
3877    *
3878    * @param treePanel
3879    *          Displayed tree window.
3880    * @param title
3881    *          SortBy menu item title.
3882    */
3883   @Override
3884   public void buildTreeMenu()
3885   {
3886     sortByTreeMenu.removeAll();
3887
3888     Vector comps = (Vector) PaintRefresher.components.get(viewport
3889             .getSequenceSetId());
3890     Vector treePanels = new Vector();
3891     int i, iSize = comps.size();
3892     for (i = 0; i < iSize; i++)
3893     {
3894       if (comps.elementAt(i) instanceof TreePanel)
3895       {
3896         treePanels.add(comps.elementAt(i));
3897       }
3898     }
3899
3900     iSize = treePanels.size();
3901
3902     if (iSize < 1)
3903     {
3904       sortByTreeMenu.setVisible(false);
3905       return;
3906     }
3907
3908     sortByTreeMenu.setVisible(true);
3909
3910     for (i = 0; i < treePanels.size(); i++)
3911     {
3912       final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3913       final JMenuItem item = new JMenuItem(tp.getTitle());
3914       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3915       item.addActionListener(new java.awt.event.ActionListener()
3916       {
3917         @Override
3918         public void actionPerformed(ActionEvent e)
3919         {
3920           tp.sortByTree_actionPerformed(null);
3921           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3922
3923         }
3924       });
3925
3926       sortByTreeMenu.add(item);
3927     }
3928   }
3929
3930   public boolean sortBy(AlignmentOrder alorder, String undoname)
3931   {
3932     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3933     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3934     if (undoname != null)
3935     {
3936       addHistoryItem(new OrderCommand(undoname, oldOrder,
3937               viewport.getAlignment()));
3938     }
3939     alignPanel.paintAlignment(true);
3940     return true;
3941   }
3942
3943   /**
3944    * Work out whether the whole set of sequences or just the selected set will
3945    * be submitted for multiple alignment.
3946    *
3947    */
3948   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3949   {
3950     // Now, check we have enough sequences
3951     AlignmentView msa = null;
3952
3953     if ((viewport.getSelectionGroup() != null)
3954             && (viewport.getSelectionGroup().getSize() > 1))
3955     {
3956       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3957       // some common interface!
3958       /*
3959        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3960        * SequenceI[sz = seqs.getSize(false)];
3961        *
3962        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3963        * seqs.getSequenceAt(i); }
3964        */
3965       msa = viewport.getAlignmentView(true);
3966     }
3967     else
3968     {
3969       /*
3970        * Vector seqs = viewport.getAlignment().getSequences();
3971        *
3972        * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3973        *
3974        * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3975        * seqs.elementAt(i); } }
3976        */
3977       msa = viewport.getAlignmentView(false);
3978     }
3979     return msa;
3980   }
3981
3982   /**
3983    * Decides what is submitted to a secondary structure prediction service: the
3984    * first sequence in the alignment, or in the current selection, or, if the
3985    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3986    * region or the whole alignment. (where the first sequence in the set is the
3987    * one that the prediction will be for).
3988    */
3989   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3990   {
3991     AlignmentView seqs = null;
3992
3993     if ((viewport.getSelectionGroup() != null)
3994             && (viewport.getSelectionGroup().getSize() > 0))
3995     {
3996       seqs = viewport.getAlignmentView(true);
3997     }
3998     else
3999     {
4000       seqs = viewport.getAlignmentView(false);
4001     }
4002     // limit sequences - JBPNote in future - could spawn multiple prediction
4003     // jobs
4004     // TODO: viewport.getAlignment().isAligned is a global state - the local
4005     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4006     if (!viewport.getAlignment().isAligned(false))
4007     {
4008       seqs.setSequences(new SeqCigar[]
4009       { seqs.getSequences()[0] });
4010       // TODO: if seqs.getSequences().length>1 then should really have warned
4011       // user!
4012
4013     }
4014     return seqs;
4015   }
4016
4017   /**
4018    * DOCUMENT ME!
4019    *
4020    * @param e
4021    *          DOCUMENT ME!
4022    */
4023   @Override
4024   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4025   {
4026     // Pick the tree file
4027     JalviewFileChooser chooser = new JalviewFileChooser(
4028             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4029     chooser.setFileView(new JalviewFileView());
4030     chooser.setDialogTitle("Select a newick-like tree file");
4031     chooser.setToolTipText("Load a tree file");
4032
4033     int value = chooser.showOpenDialog(null);
4034
4035     if (value == JalviewFileChooser.APPROVE_OPTION)
4036     {
4037       String choice = chooser.getSelectedFile().getPath();
4038       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4039       jalview.io.NewickFile fin = null;
4040       try
4041       {
4042         fin = new jalview.io.NewickFile(choice, "File");
4043         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4044       } catch (Exception ex)
4045       {
4046         JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4047                 MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
4048         ex.printStackTrace();
4049       }
4050       if (fin != null && fin.hasWarningMessage())
4051       {
4052         JOptionPane.showMessageDialog(Desktop.desktop,
4053                 fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
4054                 JOptionPane.WARNING_MESSAGE);
4055       }
4056     }
4057   }
4058
4059   @Override
4060   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4061   {
4062     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4063   }
4064
4065   public TreePanel ShowNewickTree(NewickFile nf, String title)
4066   {
4067     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4068   }
4069
4070   public TreePanel ShowNewickTree(NewickFile nf, String title,
4071           AlignmentView input)
4072   {
4073     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4074   }
4075
4076   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4077           int h, int x, int y)
4078   {
4079     return ShowNewickTree(nf, title, null, w, h, x, y);
4080   }
4081
4082   /**
4083    * Add a treeviewer for the tree extracted from a newick file object to the
4084    * current alignment view
4085    *
4086    * @param nf
4087    *          the tree
4088    * @param title
4089    *          tree viewer title
4090    * @param input
4091    *          Associated alignment input data (or null)
4092    * @param w
4093    *          width
4094    * @param h
4095    *          height
4096    * @param x
4097    *          position
4098    * @param y
4099    *          position
4100    * @return TreePanel handle
4101    */
4102   public TreePanel ShowNewickTree(NewickFile nf, String title,
4103           AlignmentView input, int w, int h, int x, int y)
4104   {
4105     TreePanel tp = null;
4106
4107     try
4108     {
4109       nf.parse();
4110
4111       if (nf.getTree() != null)
4112       {
4113         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4114
4115         tp.setSize(w, h);
4116
4117         if (x > 0 && y > 0)
4118         {
4119           tp.setLocation(x, y);
4120         }
4121
4122         Desktop.addInternalFrame(tp, title, w, h);
4123       }
4124     } catch (Exception ex)
4125     {
4126       ex.printStackTrace();
4127     }
4128
4129     return tp;
4130   }
4131
4132   private boolean buildingMenu = false;
4133
4134   /**
4135    * Generates menu items and listener event actions for web service clients
4136    *
4137    */
4138   public void BuildWebServiceMenu()
4139   {
4140     while (buildingMenu)
4141     {
4142       try
4143       {
4144         System.err.println("Waiting for building menu to finish.");
4145         Thread.sleep(10);
4146       } catch (Exception e)
4147       {
4148       }
4149       ;
4150     }
4151     final AlignFrame me = this;
4152     buildingMenu = true;
4153     new Thread(new Runnable()
4154     {
4155       @Override
4156       public void run()
4157       {
4158         final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
4159         try
4160         {
4161           System.err.println("Building ws menu again "
4162                   + Thread.currentThread());
4163           // TODO: add support for context dependent disabling of services based
4164           // on
4165           // alignment and current selection
4166           // TODO: add additional serviceHandle parameter to specify abstract
4167           // handler
4168           // class independently of AbstractName
4169           // TODO: add in rediscovery GUI function to restart discoverer
4170           // TODO: group services by location as well as function and/or
4171           // introduce
4172           // object broker mechanism.
4173           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4174           final IProgressIndicator af = me;
4175           final JMenu msawsmenu = new JMenu("Alignment");
4176           final JMenu secstrmenu = new JMenu(
4177                   "Secondary Structure Prediction");
4178           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4179           final JMenu analymenu = new JMenu("Analysis");
4180           final JMenu dismenu = new JMenu("Protein Disorder");
4181           // JAL-940 - only show secondary structure prediction services from
4182           // the legacy server
4183           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4184               // &&
4185           Discoverer.services != null && (Discoverer.services.size() > 0))
4186           {
4187             // TODO: refactor to allow list of AbstractName/Handler bindings to
4188             // be
4189             // stored or retrieved from elsewhere
4190             // No MSAWS used any more:
4191             // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4192             Vector secstrpr = (Vector) Discoverer.services
4193                     .get("SecStrPred");
4194             if (secstrpr != null)
4195             {
4196               // Add any secondary structure prediction services
4197               for (int i = 0, j = secstrpr.size(); i < j; i++)
4198               {
4199                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4200                         .get(i);
4201                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4202                         .getServiceClient(sh);
4203                 int p=secstrmenu.getItemCount();
4204                 impl.attachWSMenuEntry(secstrmenu, me);
4205                 int q=secstrmenu.getItemCount();
4206                 for (int litm=p;litm<q; litm++)
4207                 {
4208                   legacyItems.add(secstrmenu.getItem(litm));
4209                 }
4210               }
4211             }
4212           }
4213
4214           // Add all submenus in the order they should appear on the web
4215           // services menu
4216           wsmenu.add(msawsmenu);
4217           wsmenu.add(secstrmenu);
4218           wsmenu.add(dismenu);
4219           wsmenu.add(analymenu);
4220           // No search services yet
4221           // wsmenu.add(seqsrchmenu);
4222
4223           javax.swing.SwingUtilities.invokeLater(new Runnable()
4224           {
4225             @Override
4226             public void run()
4227             {
4228               try
4229               {
4230                 webService.removeAll();
4231                 // first, add discovered services onto the webservices menu
4232                 if (wsmenu.size() > 0)
4233                 {
4234                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4235                   {
4236                     webService.add(wsmenu.get(i));
4237                   }
4238                 }
4239                 else
4240                 {
4241                   webService.add(me.webServiceNoServices);
4242                 }
4243                 // TODO: move into separate menu builder class.
4244                 boolean new_sspred=false;
4245                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4246                 {
4247                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4248                   if (jws2servs != null)
4249                   {
4250                     if (jws2servs.hasServices())
4251                     {
4252                       jws2servs.attachWSMenuEntry(webService, me);
4253                       for (Jws2Instance sv:jws2servs.getServices()) {
4254                         if (sv.description.toLowerCase().contains("jpred"))
4255                         {
4256                           for (JMenuItem jmi:legacyItems)
4257                           {
4258                             jmi.setVisible(false);
4259                           }
4260                         }
4261                       }
4262
4263                     }
4264                     if (jws2servs.isRunning())
4265                     {
4266                       JMenuItem tm = new JMenuItem(
4267                               "Still discovering JABA Services");
4268                       tm.setEnabled(false);
4269                       webService.add(tm);
4270                     }
4271                   }
4272                 }
4273                 build_urlServiceMenu(me.webService);
4274                 build_fetchdbmenu(webService);
4275                 for (JMenu item : wsmenu)
4276                 {
4277                   if (item.getItemCount() == 0)
4278                   {
4279                     item.setEnabled(false);
4280                   }
4281                   else
4282                   {
4283                     item.setEnabled(true);
4284                   }
4285                 }
4286               } catch (Exception e)
4287               {
4288                 Cache.log
4289                         .debug("Exception during web service menu building process.",
4290                                 e);
4291               }
4292               ;
4293             }
4294           });
4295         } catch (Exception e)
4296         {
4297         }
4298         ;
4299
4300         buildingMenu = false;
4301       }
4302     }).start();
4303
4304   }
4305
4306   /**
4307    * construct any groupURL type service menu entries.
4308    *
4309    * @param webService
4310    */
4311   private void build_urlServiceMenu(JMenu webService)
4312   {
4313     // TODO: remove this code when 2.7 is released
4314     // DEBUG - alignmentView
4315     /*
4316      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4317      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4318      *
4319      * @Override public void actionPerformed(ActionEvent e) {
4320      * jalview.datamodel.AlignmentView
4321      * .testSelectionViews(af.viewport.getAlignment(),
4322      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4323      *
4324      * }); webService.add(testAlView);
4325      */
4326     // TODO: refactor to RestClient discoverer and merge menu entries for
4327     // rest-style services with other types of analysis/calculation service
4328     // SHmmr test client - still being implemented.
4329     // DEBUG - alignmentView
4330
4331     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4332             .getRestClients())
4333     {
4334       client.attachWSMenuEntry(
4335               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4336               this);
4337     }
4338
4339     if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4340     {
4341       jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4342               webService, this);
4343     }
4344   }
4345
4346   /*
4347    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4348    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4349    * getProperty("LAST_DIRECTORY"));
4350    *
4351    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4352    * to Vamsas file"); chooser.setToolTipText("Export");
4353    *
4354    * int value = chooser.showSaveDialog(this);
4355    *
4356    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4357    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4358    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4359    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4360    */
4361   /**
4362    * prototype of an automatically enabled/disabled analysis function
4363    *
4364    */
4365   protected void setShowProductsEnabled()
4366   {
4367     SequenceI[] selection = viewport.getSequenceSelection();
4368     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4369             viewport.getAlignment().getDataset()))
4370     {
4371       showProducts.setEnabled(true);
4372
4373     }
4374     else
4375     {
4376       showProducts.setEnabled(false);
4377     }
4378   }
4379
4380   /**
4381    * search selection for sequence xRef products and build the show products
4382    * menu.
4383    *
4384    * @param selection
4385    * @param dataset
4386    * @return true if showProducts menu should be enabled.
4387    */
4388   public boolean canShowProducts(SequenceI[] selection,
4389           boolean isRegionSelection, Alignment dataset)
4390   {
4391     boolean showp = false;
4392     try
4393     {
4394       showProducts.removeAll();
4395       final boolean dna = viewport.getAlignment().isNucleotide();
4396       final Alignment ds = dataset;
4397       String[] ptypes = (selection == null || selection.length == 0) ? null
4398               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4399       // Object[] prods =
4400       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4401       // selection, dataset, true);
4402       final SequenceI[] sel = selection;
4403       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4404       {
4405         showp = true;
4406         final boolean isRegSel = isRegionSelection;
4407         final AlignFrame af = this;
4408         final String source = ptypes[t];
4409         JMenuItem xtype = new JMenuItem(ptypes[t]);
4410         xtype.addActionListener(new ActionListener()
4411         {
4412
4413           @Override
4414           public void actionPerformed(ActionEvent e)
4415           {
4416             // TODO: new thread for this call with vis-delay
4417             af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4418                     isRegSel, dna, source);
4419           }
4420
4421         });
4422         showProducts.add(xtype);
4423       }
4424       showProducts.setVisible(showp);
4425       showProducts.setEnabled(showp);
4426     } catch (Exception e)
4427     {
4428       jalview.bin.Cache.log
4429               .warn("canTranslate threw an exception - please report to help@jalview.org",
4430                       e);
4431       return false;
4432     }
4433     return showp;
4434   }
4435
4436   protected void showProductsFor(SequenceI[] sel, Alignment ds,
4437           boolean isRegSel, boolean dna, String source)
4438   {
4439     final boolean fisRegSel = isRegSel;
4440     final boolean fdna = dna;
4441     final String fsrc = source;
4442     final AlignFrame ths = this;
4443     final SequenceI[] fsel = sel;
4444     Runnable foo = new Runnable()
4445     {
4446
4447       @Override
4448       public void run()
4449       {
4450         final long sttime = System.currentTimeMillis();
4451         ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4452         try
4453         {
4454           Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4455           // our local
4456           // dataset
4457           // reference
4458           Alignment prods = CrossRef
4459                   .findXrefSequences(fsel, fdna, fsrc, ds);
4460           if (prods != null)
4461           {
4462             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4463             for (int s = 0; s < sprods.length; s++)
4464             {
4465               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4466               if (ds.getSequences() == null
4467                       || !ds.getSequences().contains(
4468                               sprods[s].getDatasetSequence()))
4469                 ds.addSequence(sprods[s].getDatasetSequence());
4470               sprods[s].updatePDBIds();
4471             }
4472             Alignment al = new Alignment(sprods);
4473             AlignedCodonFrame[] cf = prods.getCodonFrames();
4474             al.setDataset(ds);
4475             for (int s = 0; cf != null && s < cf.length; s++)
4476             {
4477               al.addCodonFrame(cf[s]);
4478               cf[s] = null;
4479             }
4480             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4481                     DEFAULT_HEIGHT);
4482             String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4483                     + " for " + ((fisRegSel) ? "selected region of " : "")
4484                     + getTitle();
4485             Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4486                     DEFAULT_HEIGHT);
4487           }
4488           else
4489           {
4490             System.err.println("No Sequences generated for xRef type "
4491                     + fsrc);
4492           }
4493         } catch (Exception e)
4494         {
4495           jalview.bin.Cache.log.error(
4496                   "Exception when finding crossreferences", e);
4497         } catch (OutOfMemoryError e)
4498         {
4499           new OOMWarning("whilst fetching crossreferences", e);
4500         } catch (Error e)
4501         {
4502           jalview.bin.Cache.log.error("Error when finding crossreferences",
4503                   e);
4504         }
4505         ths.setProgressBar("Finished searching for sequences from " + fsrc,
4506                 sttime);
4507       }
4508
4509     };
4510     Thread frunner = new Thread(foo);
4511     frunner.start();
4512   }
4513
4514   public boolean canShowTranslationProducts(SequenceI[] selection,
4515           AlignmentI alignment)
4516   {
4517     // old way
4518     try
4519     {
4520       return (jalview.analysis.Dna.canTranslate(selection,
4521               viewport.getViewAsVisibleContigs(true)));
4522     } catch (Exception e)
4523     {
4524       jalview.bin.Cache.log
4525               .warn("canTranslate threw an exception - please report to help@jalview.org",
4526                       e);
4527       return false;
4528     }
4529   }
4530
4531   @Override
4532   public void showProducts_actionPerformed(ActionEvent e)
4533   {
4534     // /////////////////////////////
4535     // Collect Data to be translated/transferred
4536
4537     SequenceI[] selection = viewport.getSequenceSelection();
4538     AlignmentI al = null;
4539     try
4540     {
4541       al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4542               .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4543               viewport.getAlignment().getDataset());
4544     } catch (Exception ex)
4545     {
4546       al = null;
4547       jalview.bin.Cache.log.debug("Exception during translation.", ex);
4548     }
4549     if (al == null)
4550     {
4551       JOptionPane
4552               .showMessageDialog(
4553                       Desktop.desktop,
4554                       MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4555                       MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
4556     }
4557     else
4558     {
4559       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4560       Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4561               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4562     }
4563   }
4564
4565   @Override
4566   public void showTranslation_actionPerformed(ActionEvent e)
4567   {
4568     // /////////////////////////////
4569     // Collect Data to be translated/transferred
4570
4571     SequenceI[] selection = viewport.getSequenceSelection();
4572     String[] seqstring = viewport.getViewAsString(true);
4573     AlignmentI al = null;
4574     try
4575     {
4576       al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4577               viewport.getViewAsVisibleContigs(true), viewport
4578                       .getGapCharacter(), viewport.getAlignment()
4579                       .getAlignmentAnnotation(), viewport.getAlignment()
4580                       .getWidth(), viewport.getAlignment().getDataset());
4581     } catch (Exception ex)
4582     {
4583       al = null;
4584       jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
4585       JOptionPane
4586       .showMessageDialog(
4587               Desktop.desktop,
4588               MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),
4589               MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);
4590       return;
4591     }
4592     if (al == null)
4593     {
4594       JOptionPane
4595               .showMessageDialog(
4596                       Desktop.desktop,
4597                       MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4598                       MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
4599     }
4600     else
4601     {
4602       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4603       Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4604               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4605     }
4606   }
4607
4608   /**
4609    * Try to load a features file onto the alignment.
4610    *
4611    * @param file
4612    *          contents or path to retrieve file
4613    * @param type
4614    *          access mode of file (see jalview.io.AlignFile)
4615    * @return true if features file was parsed corectly.
4616    */
4617   public boolean parseFeaturesFile(String file, String type)
4618   {
4619     boolean featuresFile = false;
4620     try
4621     {
4622       featuresFile = new FeaturesFile(file, type).parse(viewport
4623               .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4624               .getFeatureRenderer().featureColours, false,
4625               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4626     } catch (Exception ex)
4627     {
4628       ex.printStackTrace();
4629     }
4630
4631     if (featuresFile)
4632     {
4633       viewport.showSequenceFeatures = true;
4634       showSeqFeatures.setSelected(true);
4635       if (alignPanel.seqPanel.seqCanvas.fr != null)
4636       {
4637         // update the min/max ranges where necessary
4638         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4639       }
4640       if (featureSettings != null)
4641       {
4642         featureSettings.setTableData();
4643       }
4644       alignPanel.paintAlignment(true);
4645     }
4646
4647     return featuresFile;
4648   }
4649
4650   @Override
4651   public void dragEnter(DropTargetDragEvent evt)
4652   {
4653   }
4654
4655   @Override
4656   public void dragExit(DropTargetEvent evt)
4657   {
4658   }
4659
4660   @Override
4661   public void dragOver(DropTargetDragEvent evt)
4662   {
4663   }
4664
4665   @Override
4666   public void dropActionChanged(DropTargetDragEvent evt)
4667   {
4668   }
4669
4670   @Override
4671   public void drop(DropTargetDropEvent evt)
4672   {
4673     Transferable t = evt.getTransferable();
4674     java.util.List files = null;
4675
4676     try
4677     {
4678       DataFlavor uriListFlavor = new DataFlavor(
4679               "text/uri-list;class=java.lang.String");
4680       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4681       {
4682         // Works on Windows and MacOSX
4683         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4684         files = (java.util.List) t
4685                 .getTransferData(DataFlavor.javaFileListFlavor);
4686       }
4687       else if (t.isDataFlavorSupported(uriListFlavor))
4688       {
4689         // This is used by Unix drag system
4690         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4691         String data = (String) t.getTransferData(uriListFlavor);
4692         files = new java.util.ArrayList(1);
4693         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4694                 data, "\r\n"); st.hasMoreTokens();)
4695         {
4696           String s = st.nextToken();
4697           if (s.startsWith("#"))
4698           {
4699             // the line is a comment (as per the RFC 2483)
4700             continue;
4701           }
4702
4703           java.net.URI uri = new java.net.URI(s);
4704           // check to see if we can handle this kind of URI
4705           if (uri.getScheme().toLowerCase().startsWith("http"))
4706           {
4707             files.add(uri.toString());
4708           }
4709           else
4710           {
4711             // otherwise preserve old behaviour: catch all for file objects
4712             java.io.File file = new java.io.File(uri);
4713             files.add(file.toString());
4714           }
4715         }
4716       }
4717     } catch (Exception e)
4718     {
4719       e.printStackTrace();
4720     }
4721     if (files != null)
4722     {
4723       try
4724       {
4725         // check to see if any of these files have names matching sequences in
4726         // the alignment
4727         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4728                 .getAlignment().getSequencesArray());
4729         /**
4730          * Object[] { String,SequenceI}
4731          */
4732         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4733         ArrayList<String> filesnotmatched = new ArrayList<String>();
4734         for (int i = 0; i < files.size(); i++)
4735         {
4736           String file = files.get(i).toString();
4737           String pdbfn = "";
4738           String protocol = FormatAdapter.checkProtocol(file);
4739           if (protocol == jalview.io.FormatAdapter.FILE)
4740           {
4741             File fl = new File(file);
4742             pdbfn = fl.getName();
4743           }
4744           else if (protocol == jalview.io.FormatAdapter.URL)
4745           {
4746             URL url = new URL(file);
4747             pdbfn = url.getFile();
4748           }
4749           if (pdbfn.length() > 0)
4750           {
4751             // attempt to find a match in the alignment
4752             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4753             int l = 0, c = pdbfn.indexOf(".");
4754             while (mtch == null && c != -1)
4755             {
4756               do
4757               {
4758                 l = c;
4759               } while ((c = pdbfn.indexOf(".", l)) > l);
4760               if (l > -1)
4761               {
4762                 pdbfn = pdbfn.substring(0, l);
4763               }
4764               mtch = idm.findAllIdMatches(pdbfn);
4765             }
4766             if (mtch != null)
4767             {
4768               String type = null;
4769               try
4770               {
4771                 type = new IdentifyFile().Identify(file, protocol);
4772               } catch (Exception ex)
4773               {
4774                 type = null;
4775               }
4776               if (type != null)
4777               {
4778                 if (type.equalsIgnoreCase("PDB"))
4779                 {
4780                   filesmatched.add(new Object[]
4781                   { file, protocol, mtch });
4782                   continue;
4783                 }
4784               }
4785             }
4786             // File wasn't named like one of the sequences or wasn't a PDB file.
4787             filesnotmatched.add(file);
4788           }
4789         }
4790         int assocfiles = 0;
4791         if (filesmatched.size() > 0)
4792         {
4793           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4794                   || JOptionPane
4795                           .showConfirmDialog(
4796                                   this,
4797                                   MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",
4798                                                   new String[]{Integer.valueOf(filesmatched.size()).toString()}),
4799                                   MessageManager.getString("label.automatically_associate_pdb_files_by_name"),
4800                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4801
4802           {
4803             for (Object[] fm : filesmatched)
4804             {
4805               // try and associate
4806               // TODO: may want to set a standard ID naming formalism for
4807               // associating PDB files which have no IDs.
4808               for (SequenceI toassoc : (SequenceI[]) fm[2])
4809               {
4810                 PDBEntry pe = new AssociatePdbFileWithSeq()
4811                         .associatePdbWithSeq((String) fm[0],
4812                                 (String) fm[1], toassoc, false);
4813                 if (pe != null)
4814                 {
4815                   System.err.println("Associated file : "
4816                           + ((String) fm[0]) + " with "
4817                           + toassoc.getDisplayId(true));
4818                   assocfiles++;
4819                 }
4820               }
4821               alignPanel.paintAlignment(true);
4822             }
4823           }
4824         }
4825         if (filesnotmatched.size() > 0)
4826         {
4827           if (assocfiles > 0
4828                   && (Cache.getDefault(
4829                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4830                           .showConfirmDialog(
4831                                   this,
4832                                   MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
4833                                   MessageManager.getString("label.ignore_unmatched_dropped_files"),
4834                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4835           {
4836             return;
4837           }
4838           for (String fn : filesnotmatched)
4839           {
4840             loadJalviewDataFile(fn, null, null, null);
4841           }
4842
4843         }
4844       } catch (Exception ex)
4845       {
4846         ex.printStackTrace();
4847       }
4848     }
4849   }
4850
4851   /**
4852    * Attempt to load a "dropped" file or URL string: First by testing whether
4853    * it's and Annotation file, then a JNet file, and finally a features file. If
4854    * all are false then the user may have dropped an alignment file onto this
4855    * AlignFrame.
4856    *
4857    * @param file
4858    *          either a filename or a URL string.
4859    */
4860   public void loadJalviewDataFile(String file, String protocol,
4861           String format, SequenceI assocSeq)
4862   {
4863     try
4864     {
4865       if (protocol == null)
4866       {
4867         protocol = jalview.io.FormatAdapter.checkProtocol(file);
4868       }
4869       // if the file isn't identified, or not positively identified as some
4870       // other filetype (PFAM is default unidentified alignment file type) then
4871       // try to parse as annotation.
4872       boolean isAnnotation = (format == null || format
4873               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4874               .readAnnotationFile(viewport.getAlignment(), file, protocol)
4875               : false;
4876
4877       if (!isAnnotation)
4878       {
4879         // first see if its a T-COFFEE score file
4880         TCoffeeScoreFile tcf = null;
4881         try
4882         {
4883           tcf = new TCoffeeScoreFile(file, protocol);
4884           if (tcf.isValid())
4885           {
4886             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4887             {
4888               tcoffeeColour.setEnabled(true);
4889               tcoffeeColour.setSelected(true);
4890               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4891               isAnnotation = true;
4892               statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4893             }
4894             else
4895             {
4896               // some problem - if no warning its probable that the ID matching
4897               // process didn't work
4898               JOptionPane
4899                       .showMessageDialog(
4900                               Desktop.desktop,
4901                               tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
4902                                       : tcf.getWarningMessage(),
4903                               MessageManager.getString("label.problem_reading_tcoffee_score_file"),
4904                               JOptionPane.WARNING_MESSAGE);
4905             }
4906           }
4907           else
4908           {
4909             tcf = null;
4910           }
4911         } catch (Exception x)
4912         {
4913           Cache.log
4914                   .debug("Exception when processing data source as T-COFFEE score file",
4915                           x);
4916           tcf = null;
4917         }
4918         if (tcf == null)
4919         {
4920           // try to see if its a JNet 'concise' style annotation file *before*
4921           // we
4922           // try to parse it as a features file
4923           if (format == null)
4924           {
4925             format = new IdentifyFile().Identify(file, protocol);
4926           }
4927           if (format.equalsIgnoreCase("JnetFile"))
4928           {
4929             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
4930                     file, protocol);
4931             new JnetAnnotationMaker().add_annotation(predictions,
4932                     viewport.getAlignment(), 0, false);
4933             isAnnotation = true;
4934           }
4935           else
4936           {
4937             /*
4938              * if (format.equalsIgnoreCase("PDB")) {
4939              *
4940              * String pdbfn = ""; // try to match up filename with sequence id
4941              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
4942              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
4943              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4944              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
4945              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4946              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
4947              * // attempt to find a match in the alignment SequenceI mtch =
4948              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4949              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
4950              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
4951              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
4952              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4953              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
4954              * { System.err.println("Associated file : " + file + " with " +
4955              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4956              * TODO: maybe need to load as normal otherwise return; } }
4957              */
4958             // try to parse it as a features file
4959             boolean isGroupsFile = parseFeaturesFile(file, protocol);
4960             // if it wasn't a features file then we just treat it as a general
4961             // alignment file to load into the current view.
4962             if (!isGroupsFile)
4963             {
4964               new FileLoader().LoadFile(viewport, file, protocol, format);
4965             }
4966             else
4967             {
4968               alignPanel.paintAlignment(true);
4969             }
4970           }
4971         }
4972       }
4973       if (isAnnotation)
4974       {
4975
4976         alignPanel.adjustAnnotationHeight();
4977         viewport.updateSequenceIdColours();
4978         buildSortByAnnotationScoresMenu();
4979         alignPanel.paintAlignment(true);
4980       }
4981     } catch (Exception ex)
4982     {
4983       ex.printStackTrace();
4984     } catch (OutOfMemoryError oom)
4985     {
4986       try
4987       {
4988         System.gc();
4989       } catch (Exception x)
4990       {
4991       }
4992       ;
4993       new OOMWarning(
4994               "loading data "
4995                       + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
4996                               : "using " + protocol + " from " + file)
4997                               : ".")
4998                       + (format != null ? "(parsing as '" + format
4999                               + "' file)" : ""), oom, Desktop.desktop);
5000     }
5001   }
5002
5003   @Override
5004   public void tabSelectionChanged(int index)
5005   {
5006     if (index > -1)
5007     {
5008       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5009       viewport = alignPanel.av;
5010       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5011       setMenusFromViewport(viewport);
5012     }
5013   }
5014
5015   @Override
5016   public void tabbedPane_mousePressed(MouseEvent e)
5017   {
5018     if (SwingUtilities.isRightMouseButton(e))
5019     {
5020       String reply = JOptionPane.showInternalInputDialog(this,
5021               MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),
5022               JOptionPane.QUESTION_MESSAGE);
5023
5024       if (reply != null)
5025       {
5026         viewport.viewName = reply;
5027         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5028       }
5029     }
5030   }
5031
5032   public AlignViewport getCurrentView()
5033   {
5034     return viewport;
5035   }
5036
5037   /**
5038    * Open the dialog for regex description parsing.
5039    */
5040   @Override
5041   protected void extractScores_actionPerformed(ActionEvent e)
5042   {
5043     ParseProperties pp = new jalview.analysis.ParseProperties(
5044             viewport.getAlignment());
5045     // TODO: verify regex and introduce GUI dialog for version 2.5
5046     // if (pp.getScoresFromDescription("col", "score column ",
5047     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5048     // true)>0)
5049     if (pp.getScoresFromDescription("description column",
5050             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5051     {
5052       buildSortByAnnotationScoresMenu();
5053     }
5054   }
5055
5056   /*
5057    * (non-Javadoc)
5058    *
5059    * @see
5060    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5061    * )
5062    */
5063   @Override
5064   protected void showDbRefs_actionPerformed(ActionEvent e)
5065   {
5066     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5067   }
5068
5069   /*
5070    * (non-Javadoc)
5071    *
5072    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5073    * ActionEvent)
5074    */
5075   @Override
5076   protected void showNpFeats_actionPerformed(ActionEvent e)
5077   {
5078     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5079   }
5080
5081   /**
5082    * find the viewport amongst the tabs in this alignment frame and close that
5083    * tab
5084    *
5085    * @param av
5086    */
5087   public boolean closeView(AlignViewport av)
5088   {
5089     if (viewport == av)
5090     {
5091       this.closeMenuItem_actionPerformed(false);
5092       return true;
5093     }
5094     Component[] comp = tabbedPane.getComponents();
5095     for (int i = 0; comp != null && i < comp.length; i++)
5096     {
5097       if (comp[i] instanceof AlignmentPanel)
5098       {
5099         if (((AlignmentPanel) comp[i]).av == av)
5100         {
5101           // close the view.
5102           closeView((AlignmentPanel) comp[i]);
5103           return true;
5104         }
5105       }
5106     }
5107     return false;
5108   }
5109
5110   protected void build_fetchdbmenu(JMenu webService)
5111   {
5112     // Temporary hack - DBRef Fetcher always top level ws entry.
5113     // TODO We probably want to store a sequence database checklist in
5114     // preferences and have checkboxes.. rather than individual sources selected
5115     // here
5116     final JMenu rfetch = new JMenu("Fetch DB References");
5117     rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
5118     webService.add(rfetch);
5119
5120     JMenuItem fetchr = new JMenuItem("Standard Databases");
5121     fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
5122     fetchr.addActionListener(new ActionListener()
5123     {
5124
5125       @Override
5126       public void actionPerformed(ActionEvent e)
5127       {
5128         new Thread(new Runnable()
5129         {
5130
5131           @Override
5132           public void run()
5133           {
5134             new jalview.ws.DBRefFetcher(alignPanel.av
5135                     .getSequenceSelection(), alignPanel.alignFrame)
5136                     .fetchDBRefs(false);
5137           }
5138         }).start();
5139
5140       }
5141
5142     });
5143     rfetch.add(fetchr);
5144     final AlignFrame me = this;
5145     new Thread(new Runnable()
5146     {
5147       @Override
5148       public void run()
5149       {
5150         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5151                 .getSequenceFetcherSingleton(me);
5152         javax.swing.SwingUtilities.invokeLater(new Runnable()
5153         {
5154           @Override
5155           public void run()
5156           {
5157             String[] dbclasses = sf.getOrderedSupportedSources();
5158             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5159             // jalview.util.QuickSort.sort(otherdb, otherdb);
5160             List<DbSourceProxy> otherdb;
5161             JMenu dfetch = new JMenu();
5162             JMenu ifetch = new JMenu();
5163             JMenuItem fetchr = null;
5164             int comp = 0, icomp = 0, mcomp = 15;
5165             String mname = null;
5166             int dbi = 0;
5167             for (String dbclass : dbclasses)
5168             {
5169               otherdb = sf.getSourceProxy(dbclass);
5170               // add a single entry for this class, or submenu allowing 'fetch
5171               // all' or pick one
5172               if (otherdb == null || otherdb.size() < 1)
5173               {
5174                 continue;
5175               }
5176               // List<DbSourceProxy> dbs=otherdb;
5177               // otherdb=new ArrayList<DbSourceProxy>();
5178               // for (DbSourceProxy db:dbs)
5179               // {
5180               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5181               // }
5182               if (mname == null)
5183               {
5184                 mname = "From " + dbclass;
5185               }
5186               if (otherdb.size() == 1)
5187               {
5188                 final DbSourceProxy[] dassource = otherdb
5189                         .toArray(new DbSourceProxy[0]);
5190                 DbSourceProxy src = otherdb.get(0);
5191                 fetchr = new JMenuItem(src.getDbSource());
5192                 fetchr.addActionListener(new ActionListener()
5193                 {
5194
5195                   @Override
5196                   public void actionPerformed(ActionEvent e)
5197                   {
5198                     new Thread(new Runnable()
5199                     {
5200
5201                       @Override
5202                       public void run()
5203                       {
5204                         new jalview.ws.DBRefFetcher(alignPanel.av
5205                                 .getSequenceSelection(),
5206                                 alignPanel.alignFrame, dassource)
5207                                 .fetchDBRefs(false);
5208                       }
5209                     }).start();
5210                   }
5211
5212                 });
5213                 fetchr.setToolTipText("<html>"
5214                         + JvSwingUtils.wrapTooltip("Retrieve from "
5215                                 + src.getDbName()) + "<html>");
5216                 dfetch.add(fetchr);
5217                 comp++;
5218               }
5219               else
5220               {
5221                 final DbSourceProxy[] dassource = otherdb
5222                         .toArray(new DbSourceProxy[0]);
5223                 // fetch all entry
5224                 DbSourceProxy src = otherdb.get(0);
5225                 fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
5226                         + "'");
5227                 fetchr.addActionListener(new ActionListener()
5228                 {
5229                   @Override
5230                   public void actionPerformed(ActionEvent e)
5231                   {
5232                     new Thread(new Runnable()
5233                     {
5234
5235                       @Override
5236                       public void run()
5237                       {
5238                         new jalview.ws.DBRefFetcher(alignPanel.av
5239                                 .getSequenceSelection(),
5240                                 alignPanel.alignFrame, dassource)
5241                                 .fetchDBRefs(false);
5242                       }
5243                     }).start();
5244                   }
5245                 });
5246
5247                 fetchr.setToolTipText("<html>"
5248                         + JvSwingUtils.wrapTooltip("Retrieve from all "
5249                                 + otherdb.size() + " sources in "
5250                                 + src.getDbSource() + "<br>First is :"
5251                                 + src.getDbName()) + "<html>");
5252                 dfetch.add(fetchr);
5253                 comp++;
5254                 // and then build the rest of the individual menus
5255                 ifetch = new JMenu("Sources from " + src.getDbSource());
5256                 icomp = 0;
5257                 String imname = null;
5258                 int i = 0;
5259                 for (DbSourceProxy sproxy : otherdb)
5260                 {
5261                   String dbname = sproxy.getDbName();
5262                   String sname = dbname.length() > 5 ? dbname.substring(0,
5263                           5) + "..." : dbname;
5264                   String msname = dbname.length() > 10 ? dbname.substring(
5265                           0, 10) + "..." : dbname;
5266                   if (imname == null)
5267                   {
5268                     imname = "from '" + sname + "'";
5269                   }
5270                   fetchr = new JMenuItem(msname);
5271                   final DbSourceProxy[] dassrc =
5272                   { sproxy };
5273                   fetchr.addActionListener(new ActionListener()
5274                   {
5275
5276                     @Override
5277                     public void actionPerformed(ActionEvent e)
5278                     {
5279                       new Thread(new Runnable()
5280                       {
5281
5282                         @Override
5283                         public void run()
5284                         {
5285                           new jalview.ws.DBRefFetcher(alignPanel.av
5286                                   .getSequenceSelection(),
5287                                   alignPanel.alignFrame, dassrc)
5288                                   .fetchDBRefs(false);
5289                         }
5290                       }).start();
5291                     }
5292
5293                   });
5294                   fetchr.setToolTipText("<html>"
5295                           + JvSwingUtils.wrapTooltip("Retrieve from "
5296                                   + dbname) + "</html>");
5297                   ifetch.add(fetchr);
5298                   ++i;
5299                   if (++icomp >= mcomp || i == (otherdb.size()))
5300                   {
5301                     ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
5302                     dfetch.add(ifetch);
5303                     ifetch = new JMenu();
5304                     imname = null;
5305                     icomp = 0;
5306                     comp++;
5307                   }
5308                 }
5309               }
5310               ++dbi;
5311               if (comp >= mcomp || dbi >= (dbclasses.length))
5312               {
5313                 dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
5314                 rfetch.add(dfetch);
5315                 dfetch = new JMenu();
5316                 mname = null;
5317                 comp = 0;
5318               }
5319             }
5320           }
5321         });
5322       }
5323     }).start();
5324
5325   }
5326
5327   /**
5328    * Left justify the whole alignment.
5329    */
5330   @Override
5331   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5332   {
5333     AlignmentI al = viewport.getAlignment();
5334     al.justify(false);
5335     viewport.firePropertyChange("alignment", null, al);
5336   }
5337
5338   /**
5339    * Right justify the whole alignment.
5340    */
5341   @Override
5342   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5343   {
5344     AlignmentI al = viewport.getAlignment();
5345     al.justify(true);
5346     viewport.firePropertyChange("alignment", null, al);
5347   }
5348
5349   public void setShowSeqFeatures(boolean b)
5350   {
5351     showSeqFeatures.setSelected(true);
5352     viewport.setShowSequenceFeatures(true);
5353   }
5354
5355   /*
5356    * (non-Javadoc)
5357    *
5358    * @see
5359    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5360    * awt.event.ActionEvent)
5361    */
5362   @Override
5363   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5364   {
5365     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5366     alignPanel.paintAlignment(true);
5367   }
5368
5369   /*
5370    * (non-Javadoc)
5371    *
5372    * @see
5373    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5374    * .ActionEvent)
5375    */
5376   @Override
5377   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5378   {
5379     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5380     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5381
5382   }
5383
5384   /*
5385    * (non-Javadoc)
5386    *
5387    * @see
5388    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5389    * .event.ActionEvent)
5390    */
5391   @Override
5392   protected void showGroupConservation_actionPerformed(ActionEvent e)
5393   {
5394     viewport.setShowGroupConservation(showGroupConservation.getState());
5395     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5396   }
5397
5398   /*
5399    * (non-Javadoc)
5400    *
5401    * @see
5402    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5403    * .event.ActionEvent)
5404    */
5405   @Override
5406   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5407   {
5408     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5409     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5410   }
5411
5412   /*
5413    * (non-Javadoc)
5414    *
5415    * @see
5416    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5417    * .event.ActionEvent)
5418    */
5419   @Override
5420   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5421   {
5422     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5423     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5424   }
5425
5426   @Override
5427   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5428   {
5429     showSequenceLogo.setState(true);
5430     viewport.setShowSequenceLogo(true);
5431     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5432     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5433   }
5434
5435   @Override
5436   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5437   {
5438     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5439   }
5440
5441   /*
5442    * (non-Javadoc)
5443    *
5444    * @see
5445    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5446    * .event.ActionEvent)
5447    */
5448   @Override
5449   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5450   {
5451     if (avc.makeGroupsFromSelection()) {
5452       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5453       alignPanel.updateAnnotation();
5454       alignPanel.paintAlignment(true);
5455     }
5456   }
5457
5458   @Override
5459   protected void createGroup_actionPerformed(ActionEvent e)
5460   {
5461     if (avc.createGroup())
5462     {
5463       alignPanel.alignmentChanged();
5464     }
5465   }
5466
5467   @Override
5468   protected void unGroup_actionPerformed(ActionEvent e)
5469   {
5470     if (avc.unGroup())
5471     {
5472       alignPanel.alignmentChanged();
5473     }
5474   }
5475
5476   /**
5477    * make the given alignmentPanel the currently selected tab
5478    *
5479    * @param alignmentPanel
5480    */
5481   public void setDisplayedView(AlignmentPanel alignmentPanel)
5482   {
5483     if (!viewport.getSequenceSetId().equals(
5484             alignmentPanel.av.getSequenceSetId()))
5485     {
5486       throw new Error(
5487               "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5488     }
5489     if (tabbedPane != null
5490             & alignPanels.indexOf(alignmentPanel) != tabbedPane
5491                     .getSelectedIndex())
5492     {
5493       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5494     }
5495   }
5496 }
5497
5498 class PrintThread extends Thread
5499 {
5500   AlignmentPanel ap;
5501
5502   public PrintThread(AlignmentPanel ap)
5503   {
5504     this.ap = ap;
5505   }
5506
5507   static PageFormat pf;
5508
5509   @Override
5510   public void run()
5511   {
5512     PrinterJob printJob = PrinterJob.getPrinterJob();
5513
5514     if (pf != null)
5515     {
5516       printJob.setPrintable(ap, pf);
5517     }
5518     else
5519     {
5520       printJob.setPrintable(ap);
5521     }
5522
5523     if (printJob.printDialog())
5524     {
5525       try
5526       {
5527         printJob.print();
5528       } catch (Exception PrintException)
5529       {
5530         PrintException.printStackTrace();
5531       }
5532     }
5533   }
5534 }