src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.beans.*;
  22 import java.io.*;
  23 import java.util.*;
  24
  25 import java.awt.*;
  26 import java.awt.datatransfer.*;
  27 import java.awt.dnd.*;
  28 import java.awt.event.*;
  29 import java.awt.print.*;
  30 import javax.swing.*;
  31 import javax.swing.event.MenuEvent;
  32
  33 import jalview.analysis.*;
  34 import jalview.commands.*;
  35 import jalview.datamodel.*;
  36 import jalview.io.*;
  37 import jalview.jbgui.*;
  38 import jalview.schemes.*;
  39 import jalview.ws.*;
  40
  41 /**
  42  * DOCUMENT ME!
  43  *
  44  * @author $author$
  45  * @version $Revision$
  46  */
  47 public class AlignFrame extends GAlignFrame implements DropTargetListener,
  48         IProgressIndicator
  49 {
  50
  51   /** DOCUMENT ME!! */
  52   public static final int DEFAULT_WIDTH = 700;
  53
  54   /** DOCUMENT ME!! */
  55   public static final int DEFAULT_HEIGHT = 500;
  56
  57   public AlignmentPanel alignPanel;
  58
  59   AlignViewport viewport;
  60
  61   Vector alignPanels = new Vector();
  62
  63   /**
  64    * Last format used to load or save alignments in this window
  65    */
  66   String currentFileFormat = null;
  67
  68   /**
  69    * Current filename for this alignment
  70    */
  71   String fileName = null;
  72
  73   /**
  74    * Creates a new AlignFrame object with specific width and height.
  75    *
  76    * @param al
  77    * @param width
  78    * @param height
  79    */
  80   public AlignFrame(AlignmentI al, int width, int height)
  81   {
  82     this(al, null, width, height);
  83   }
  84
  85   /**
  86    * Creates a new AlignFrame object with specific width, height and
  87    * sequenceSetId
  88    *
  89    * @param al
  90    * @param width
  91    * @param height
  92    * @param sequenceSetId
  93    */
  94   public AlignFrame(AlignmentI al, int width, int height,
  95           String sequenceSetId)
  96   {
  97     this(al, null, width, height, sequenceSetId);
  98   }
  99
 100   /**
 101    * Creates a new AlignFrame object with specific width, height and
 102    * sequenceSetId
 103    *
 104    * @param al
 105    * @param width
 106    * @param height
 107    * @param sequenceSetId
 108    * @param viewId
 109    */
 110   public AlignFrame(AlignmentI al, int width, int height,
 111           String sequenceSetId, String viewId)
 112   {
 113     this(al, null, width, height, sequenceSetId, viewId);
 114   }
 115
 116   /**
 117    * new alignment window with hidden columns
 118    *
 119    * @param al
 120    *          AlignmentI
 121    * @param hiddenColumns
 122    *          ColumnSelection or null
 123    * @param width
 124    *          Width of alignment frame
 125    * @param height
 126    *          height of frame.
 127    */
 128   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 129           int width, int height)
 130   {
 131     this(al, hiddenColumns, width, height, null);
 132   }
 133
 134   /**
 135    * Create alignment frame for al with hiddenColumns, a specific width and
 136    * height, and specific sequenceId
 137    *
 138    * @param al
 139    * @param hiddenColumns
 140    * @param width
 141    * @param height
 142    * @param sequenceSetId
 143    *          (may be null)
 144    */
 145   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 146           int width, int height, String sequenceSetId)
 147   {
 148     this(al, hiddenColumns, width, height, sequenceSetId, null);
 149   }
 150
 151   /**
 152    * Create alignment frame for al with hiddenColumns, a specific width and
 153    * height, and specific sequenceId
 154    *
 155    * @param al
 156    * @param hiddenColumns
 157    * @param width
 158    * @param height
 159    * @param sequenceSetId
 160    *          (may be null)
 161    * @param viewId
 162    *          (may be null)
 163    */
 164   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 165           int width, int height, String sequenceSetId, String viewId)
 166   {
 167     setSize(width, height);
 168     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 169
 170     alignPanel = new AlignmentPanel(this, viewport);
 171
 172     if (al.getDataset() == null)
 173     {
 174       al.setDataset(null);
 175     }
 176
 177     addAlignmentPanel(alignPanel, true);
 178     init();
 179   }
 180
 181   /**
 182    * Make a new AlignFrame from exisiting alignmentPanels
 183    *
 184    * @param ap
 185    *          AlignmentPanel
 186    * @param av
 187    *          AlignViewport
 188    */
 189   public AlignFrame(AlignmentPanel ap)
 190   {
 191     viewport = ap.av;
 192     alignPanel = ap;
 193     addAlignmentPanel(ap, false);
 194     init();
 195   }
 196
 197   /**
 198    * initalise the alignframe from the underlying viewport data and the
 199    * configurations
 200    */
 201   void init()
 202   {
 203     if (viewport.conservation == null)
 204     {
 205       BLOSUM62Colour.setEnabled(false);
 206       conservationMenuItem.setEnabled(false);
 207       modifyConservation.setEnabled(false);
 208       // PIDColour.setEnabled(false);
 209       // abovePIDThreshold.setEnabled(false);
 210       // modifyPID.setEnabled(false);
 211     }
 212
 213     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 214             "No sort");
 215
 216     if (sortby.equals("Id"))
 217     {
 218       sortIDMenuItem_actionPerformed(null);
 219     }
 220     else if (sortby.equals("Pairwise Identity"))
 221     {
 222       sortPairwiseMenuItem_actionPerformed(null);
 223     }
 224
 225     if (Desktop.desktop != null)
 226     {
 227       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 228       addServiceListeners();
 229       setGUINucleotide(viewport.alignment.isNucleotide());
 230     }
 231
 232     setMenusFromViewport(viewport);
 233     buildSortByAnnotationScoresMenu();
 234     if (viewport.wrapAlignment)
 235     {
 236       wrapMenuItem_actionPerformed(null);
 237     }
 238
 239     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 240     {
 241       this.overviewMenuItem_actionPerformed(null);
 242     }
 243
 244     addKeyListener();
 245
 246   }
 247
 248   /**
 249    * Change the filename and format for the alignment, and enable the 'reload'
 250    * button functionality.
 251    *
 252    * @param file
 253    *          valid filename
 254    * @param format
 255    *          format of file
 256    */
 257   public void setFileName(String file, String format)
 258   {
 259     fileName = file;
 260     currentFileFormat = format;
 261     reload.setEnabled(true);
 262   }
 263
 264   void addKeyListener()
 265   {
 266     addKeyListener(new KeyAdapter()
 267     {
 268       public void keyPressed(KeyEvent evt)
 269       {
 270         if (viewport.cursorMode
 271                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 272                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 273                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 274                 && Character.isDigit(evt.getKeyChar()))
 275           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 276
 277         switch (evt.getKeyCode())
 278         {
 279
 280         case 27: // escape key
 281           deselectAllSequenceMenuItem_actionPerformed(null);
 282
 283           break;
 284
 285         case KeyEvent.VK_DOWN:
 286           if (evt.isAltDown() || !viewport.cursorMode)
 287             moveSelectedSequences(false);
 288           if (viewport.cursorMode)
 289             alignPanel.seqPanel.moveCursor(0, 1);
 290           break;
 291
 292         case KeyEvent.VK_UP:
 293           if (evt.isAltDown() || !viewport.cursorMode)
 294             moveSelectedSequences(true);
 295           if (viewport.cursorMode)
 296             alignPanel.seqPanel.moveCursor(0, -1);
 297
 298           break;
 299
 300         case KeyEvent.VK_LEFT:
 301           if (evt.isAltDown() || !viewport.cursorMode)
 302             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 303           else
 304             alignPanel.seqPanel.moveCursor(-1, 0);
 305
 306           break;
 307
 308         case KeyEvent.VK_RIGHT:
 309           if (evt.isAltDown() || !viewport.cursorMode)
 310             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 311           else
 312             alignPanel.seqPanel.moveCursor(1, 0);
 313           break;
 314
 315         case KeyEvent.VK_SPACE:
 316           if (viewport.cursorMode)
 317           {
 318             alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 319                     || evt.isShiftDown() || evt.isAltDown());
 320           }
 321           break;
 322
 323         case KeyEvent.VK_DELETE:
 324         case KeyEvent.VK_BACK_SPACE:
 325           if (!viewport.cursorMode)
 326           {
 327             cut_actionPerformed(null);
 328           }
 329           else
 330           {
 331             alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 332                     || evt.isShiftDown() || evt.isAltDown());
 333           }
 334
 335           break;
 336
 337         case KeyEvent.VK_S:
 338           if (viewport.cursorMode)
 339           {
 340             alignPanel.seqPanel.setCursorRow();
 341           }
 342           break;
 343         case KeyEvent.VK_C:
 344           if (viewport.cursorMode && !evt.isControlDown())
 345           {
 346             alignPanel.seqPanel.setCursorColumn();
 347           }
 348           break;
 349         case KeyEvent.VK_P:
 350           if (viewport.cursorMode)
 351           {
 352             alignPanel.seqPanel.setCursorPosition();
 353           }
 354           break;
 355
 356         case KeyEvent.VK_ENTER:
 357         case KeyEvent.VK_COMMA:
 358           if (viewport.cursorMode)
 359           {
 360             alignPanel.seqPanel.setCursorRowAndColumn();
 361           }
 362           break;
 363
 364         case KeyEvent.VK_Q:
 365           if (viewport.cursorMode)
 366           {
 367             alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 368           }
 369           break;
 370         case KeyEvent.VK_M:
 371           if (viewport.cursorMode)
 372           {
 373             alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 374           }
 375           break;
 376
 377         case KeyEvent.VK_F2:
 378           viewport.cursorMode = !viewport.cursorMode;
 379           statusBar.setText("Keyboard editing mode is "
 380                   + (viewport.cursorMode ? "on" : "off"));
 381           if (viewport.cursorMode)
 382           {
 383             alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 384             alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 385           }
 386           alignPanel.seqPanel.seqCanvas.repaint();
 387           break;
 388
 389         case KeyEvent.VK_F1:
 390           try
 391           {
 392             ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
 393             java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
 394                     "help/help");
 395             javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
 396
 397             javax.help.HelpBroker hb = hs.createHelpBroker();
 398             hb.setCurrentID("home");
 399             hb.setDisplayed(true);
 400           } catch (Exception ex)
 401           {
 402             ex.printStackTrace();
 403           }
 404           break;
 405         case KeyEvent.VK_H:
 406         {
 407           boolean toggleSeqs = !evt.isControlDown();
 408           boolean toggleCols = !evt.isShiftDown();
 409
 410           boolean hide = false;
 411           SequenceGroup sg = viewport.getSelectionGroup();
 412           // TODO: document ctrl-shift-h for show visible selected area and fix hack so columns for the current selected region get transferred.
 413           if (!toggleSeqs && !toggleCols)
 414           {
 415             // Hide everything by the current selection - this is a hack - we do the invert and then hide
 416             // first check that there will be visible columns after the invert.
 417             if ((viewport.colSel!=null && viewport.colSel.getSelected()!=null && viewport.colSel.getSelected().size()>0) || (sg!=null && sg.getSize()>0  && sg.getStartRes()<=sg.getEndRes()))
 418             {
 419             // now invert the sequence set, if required - empty selection implies that no hiding is required.
 420             if (sg!=null) {
 421               invertSequenceMenuItem_actionPerformed(null);
 422               sg = viewport.getSelectionGroup();
 423               toggleSeqs = true;
 424
 425             }
 426
 427             if (sg!=null && sg.getStartRes()>=0 && sg.getStartRes()<=sg.getEndRes()&& (viewport.colSel==null || viewport.colSel.getSelected()==null || viewport.colSel.getSelected().size()==0))
 428             {
 429               // synthesize a column selection if none exists. this happens if a single region has been selected rather than whole columns.
 430               if (viewport.colSel==null)
 431               {
 432                 viewport.colSel = new ColumnSelection();
 433               }
 434               for (int cspos = sg.getStartRes(); cspos<=sg.getEndRes(); cspos++) {
 435                 viewport.colSel.addElement(cspos);
 436               }
 437             }
 438             // finally invert the column selection and get the new sequence selection.
 439             invertColSel_actionPerformed(null);
 440             toggleCols = true;
 441             }
 442           }
 443
 444           if (toggleSeqs)
 445           {
 446             if (sg != null
 447                     && sg.getSize() != viewport.alignment.getHeight())
 448             {
 449               hideSelSequences_actionPerformed(null);
 450               hide = true;
 451             }
 452             else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
 453             {
 454               showAllSeqs_actionPerformed(null);
 455             }
 456           }
 457
 458           if (toggleCols)
 459           {
 460             if (viewport.colSel.getSelected().size() > 0)
 461             {
 462               hideSelColumns_actionPerformed(null);
 463               if (!toggleSeqs)
 464               {
 465                 viewport.selectionGroup = sg;
 466               }
 467             }
 468             else if (!hide)
 469             {
 470               showAllColumns_actionPerformed(null);
 471             }
 472           }
 473           break;
 474         }
 475         case KeyEvent.VK_PAGE_UP:
 476           if (viewport.wrapAlignment)
 477           {
 478             alignPanel.scrollUp(true);
 479           }
 480           else
 481           {
 482             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 483                     - viewport.endSeq + viewport.startSeq);
 484           }
 485           break;
 486         case KeyEvent.VK_PAGE_DOWN:
 487           if (viewport.wrapAlignment)
 488           {
 489             alignPanel.scrollUp(false);
 490           }
 491           else
 492           {
 493             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 494                     + viewport.endSeq - viewport.startSeq);
 495           }
 496           break;
 497         }
 498       }
 499
 500       public void keyReleased(KeyEvent evt)
 501       {
 502         switch (evt.getKeyCode())
 503         {
 504         case KeyEvent.VK_LEFT:
 505           if (evt.isAltDown() || !viewport.cursorMode)
 506             viewport.firePropertyChange("alignment", null, viewport
 507                     .getAlignment().getSequences());
 508           break;
 509
 510         case KeyEvent.VK_RIGHT:
 511           if (evt.isAltDown() || !viewport.cursorMode)
 512             viewport.firePropertyChange("alignment", null, viewport
 513                     .getAlignment().getSequences());
 514           break;
 515         }
 516       }
 517     });
 518   }
 519
 520   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 521   {
 522     ap.alignFrame = this;
 523
 524     alignPanels.addElement(ap);
 525
 526     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 527
 528     int aSize = alignPanels.size();
 529
 530     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 531
 532     if (aSize == 1 && ap.av.viewName == null)
 533     {
 534       this.getContentPane().add(ap, BorderLayout.CENTER);
 535     }
 536     else
 537     {
 538       if (aSize == 2)
 539       {
 540         setInitialTabVisible();
 541       }
 542
 543       expandViews.setEnabled(true);
 544       gatherViews.setEnabled(true);
 545       tabbedPane.addTab(ap.av.viewName, ap);
 546
 547       ap.setVisible(false);
 548     }
 549
 550     if (newPanel)
 551     {
 552       if (ap.av.padGaps)
 553       {
 554         ap.av.alignment.padGaps();
 555       }
 556       ap.av.updateConservation(ap);
 557       ap.av.updateConsensus(ap);
 558     }
 559   }
 560
 561   public void setInitialTabVisible()
 562   {
 563     expandViews.setEnabled(true);
 564     gatherViews.setEnabled(true);
 565     tabbedPane.setVisible(true);
 566     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
 567     tabbedPane.addTab(first.av.viewName, first);
 568     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 569   }
 570
 571   public AlignViewport getViewport()
 572   {
 573     return viewport;
 574   }
 575
 576   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 577   private void addServiceListeners()
 578   {
 579     final java.beans.PropertyChangeListener thisListener;
 580     // Do this once to get current state
 581     BuildWebServiceMenu();
 582     Desktop.discoverer
 583             .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
 584             {
 585               public void propertyChange(PropertyChangeEvent evt)
 586               {
 587                 // System.out.println("Discoverer property change.");
 588                 if (evt.getPropertyName().equals("services"))
 589                 {
 590                   // System.out.println("Rebuilding web service menu");
 591                   BuildWebServiceMenu();
 592                 }
 593               }
 594             });
 595
 596     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 597     {
 598       public void internalFrameClosed(
 599               javax.swing.event.InternalFrameEvent evt)
 600       {
 601         // System.out.println("deregistering discoverer listener");
 602         Desktop.discoverer.removePropertyChangeListener(thisListener);
 603         closeMenuItem_actionPerformed(true);
 604       };
 605     });
 606   }
 607
 608   public void setGUINucleotide(boolean nucleotide)
 609   {
 610     showTranslation.setVisible(nucleotide);
 611     conservationMenuItem.setEnabled(!nucleotide);
 612     modifyConservation.setEnabled(!nucleotide);
 613
 614     // Remember AlignFrame always starts as protein
 615     if (!nucleotide)
 616     {
 617       calculateMenu.remove(calculateMenu.getItemCount() - 2);
 618     }
 619   }
 620
 621   /**
 622    * set up menus for the currently viewport. This may be called after any
 623    * operation that affects the data in the current view (selection changed,
 624    * etc) to update the menus to reflect the new state.
 625    */
 626   public void setMenusForViewport()
 627   {
 628     setMenusFromViewport(viewport);
 629   }
 630
 631   /**
 632    * Need to call this method when tabs are selected for multiple views, or when
 633    * loading from Jalview2XML.java
 634    *
 635    * @param av
 636    *          AlignViewport
 637    */
 638   void setMenusFromViewport(AlignViewport av)
 639   {
 640     padGapsMenuitem.setSelected(av.padGaps);
 641     colourTextMenuItem.setSelected(av.showColourText);
 642     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 643     conservationMenuItem.setSelected(av.getConservationSelected());
 644     seqLimits.setSelected(av.getShowJVSuffix());
 645     idRightAlign.setSelected(av.rightAlignIds);
 646     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
 647     renderGapsMenuItem.setSelected(av.renderGaps);
 648     wrapMenuItem.setSelected(av.wrapAlignment);
 649     scaleAbove.setVisible(av.wrapAlignment);
 650     scaleLeft.setVisible(av.wrapAlignment);
 651     scaleRight.setVisible(av.wrapAlignment);
 652     annotationPanelMenuItem.setState(av.showAnnotation);
 653     viewBoxesMenuItem.setSelected(av.showBoxes);
 654     viewTextMenuItem.setSelected(av.showText);
 655     showUnconservedMenuItem.setSelected(av.showUnconserved);
 656     showGroupConsensus.setSelected(av.showGroupConsensus);
 657     showGroupConservation.setSelected(av.showGroupConservation);
 658     setColourSelected(ColourSchemeProperty.getColourName(av
 659             .getGlobalColourScheme()));
 660
 661     showSeqFeatures.setSelected(av.showSequenceFeatures);
 662     hiddenMarkers.setState(av.showHiddenMarkers);
 663     applyToAllGroups.setState(av.colourAppliesToAllGroups);
 664     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
 665     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
 666
 667     setShowProductsEnabled();
 668
 669     updateEditMenuBar();
 670   }
 671
 672   Hashtable progressBars, progressBarHandlers;
 673
 674   /*
 675    * (non-Javadoc)
 676    *
 677    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 678    */
 679   public void setProgressBar(String message, long id)
 680   {
 681     if (progressBars == null)
 682     {
 683       progressBars = new Hashtable();
 684       progressBarHandlers = new Hashtable();
 685     }
 686
 687     JPanel progressPanel;
 688     Long lId=new Long(id);
 689     GridLayout layout = (GridLayout) statusPanel.getLayout();
 690     if (progressBars.get(lId) != null)
 691     {
 692       progressPanel = (JPanel) progressBars.get(new Long(id));
 693       statusPanel.remove(progressPanel);
 694       progressBars.remove(lId);
 695       progressPanel = null;
 696       if (message != null)
 697       {
 698         statusBar.setText(message);
 699       }
 700       if (progressBarHandlers.contains(lId))
 701       {
 702         progressBarHandlers.remove(lId);
 703       }
 704       layout.setRows(layout.getRows() - 1);
 705     }
 706     else
 707     {
 708       progressPanel = new JPanel(new BorderLayout(10, 5));
 709
 710       JProgressBar progressBar = new JProgressBar();
 711       progressBar.setIndeterminate(true);
 712
 713       progressPanel.add(new JLabel(message), BorderLayout.WEST);
 714       progressPanel.add(progressBar, BorderLayout.CENTER);
 715
 716       layout.setRows(layout.getRows() + 1);
 717       statusPanel.add(progressPanel);
 718
 719       progressBars.put(lId, progressPanel);
 720     }
 721     // update GUI
 722     setMenusForViewport();
 723     validate();
 724   }
 725
 726   public void registerHandler(final long id,
 727           final IProgressIndicatorHandler handler)
 728   {
 729     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
 730     {
 731       throw new Error(
 732               "call setProgressBar before registering the progress bar's handler.");
 733     }
 734     progressBarHandlers.put(new Long(id), handler);
 735     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
 736     if (handler.canCancel())
 737     {
 738       JButton cancel = new JButton("Cancel");
 739       final IProgressIndicator us = this;
 740       cancel.addActionListener(new ActionListener()
 741       {
 742
 743         public void actionPerformed(ActionEvent e)
 744         {
 745           handler.cancelActivity(id);
 746           us.setProgressBar("Cancelled "
 747                   + ((JLabel) progressPanel.getComponent(0)).getText(), id);
 748         }
 749       });
 750       progressPanel.add(cancel, BorderLayout.EAST);
 751     }
 752   }
 753
 754   /**
 755    *
 756    * @return true if any progress bars are still active
 757    */
 758   public boolean operationInProgress()
 759   {
 760     if (progressBars != null && progressBars.size() > 0)
 761     {
 762       return true;
 763     }
 764     return false;
 765   }
 766
 767   /*
 768    * Added so Castor Mapping file can obtain Jalview Version
 769    */
 770   public String getVersion()
 771   {
 772     return jalview.bin.Cache.getProperty("VERSION");
 773   }
 774
 775   public FeatureRenderer getFeatureRenderer()
 776   {
 777     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
 778   }
 779
 780   public void fetchSequence_actionPerformed(ActionEvent e)
 781   {
 782     new SequenceFetcher(this);
 783   }
 784
 785   public void addFromFile_actionPerformed(ActionEvent e)
 786   {
 787     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 788   }
 789
 790   public void reload_actionPerformed(ActionEvent e)
 791   {
 792     if (fileName != null)
 793     {
 794       if (currentFileFormat.equals("Jalview"))
 795       {
 796         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 797         for (int i = 0; i < frames.length; i++)
 798         {
 799           if (frames[i] instanceof AlignFrame && frames[i] != this
 800                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 801           {
 802             try
 803             {
 804               frames[i].setSelected(true);
 805               Desktop.instance.closeAssociatedWindows();
 806             } catch (java.beans.PropertyVetoException ex)
 807             {
 808             }
 809           }
 810
 811         }
 812         Desktop.instance.closeAssociatedWindows();
 813
 814         FileLoader loader = new FileLoader();
 815         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 816         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
 817       }
 818       else
 819       {
 820         Rectangle bounds = this.getBounds();
 821
 822         FileLoader loader = new FileLoader();
 823         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 824         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
 825                 protocol, currentFileFormat);
 826
 827         newframe.setBounds(bounds);
 828
 829         this.closeMenuItem_actionPerformed(true);
 830       }
 831     }
 832   }
 833
 834   public void addFromText_actionPerformed(ActionEvent e)
 835   {
 836     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
 837   }
 838
 839   public void addFromURL_actionPerformed(ActionEvent e)
 840   {
 841     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
 842   }
 843
 844   public void save_actionPerformed(ActionEvent e)
 845   {
 846     if (fileName == null
 847             || (currentFileFormat == null || !jalview.io.FormatAdapter
 848                     .isValidIOFormat(currentFileFormat, true))
 849             || fileName.startsWith("http"))
 850     {
 851       saveAs_actionPerformed(null);
 852     }
 853     else
 854     {
 855       saveAlignment(fileName, currentFileFormat);
 856     }
 857   }
 858
 859   /**
 860    * DOCUMENT ME!
 861    *
 862    * @param e
 863    *          DOCUMENT ME!
 864    */
 865   public void saveAs_actionPerformed(ActionEvent e)
 866   {
 867     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 868             .getProperty("LAST_DIRECTORY"),
 869             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
 870             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
 871             currentFileFormat, false);
 872
 873     chooser.setFileView(new JalviewFileView());
 874     chooser.setDialogTitle("Save Alignment to file");
 875     chooser.setToolTipText("Save");
 876
 877     int value = chooser.showSaveDialog(this);
 878
 879     if (value == JalviewFileChooser.APPROVE_OPTION)
 880     {
 881       currentFileFormat = chooser.getSelectedFormat();
 882       if (currentFileFormat == null)
 883       {
 884         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 885                 "You must select a file format before saving!",
 886                 "File format not specified", JOptionPane.WARNING_MESSAGE);
 887         value = chooser.showSaveDialog(this);
 888         return;
 889       }
 890
 891       fileName = chooser.getSelectedFile().getPath();
 892
 893       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
 894               currentFileFormat);
 895
 896       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
 897       if (currentFileFormat.indexOf(" ") > -1)
 898       {
 899         currentFileFormat = currentFileFormat.substring(0,
 900                 currentFileFormat.indexOf(" "));
 901       }
 902       saveAlignment(fileName, currentFileFormat);
 903     }
 904   }
 905
 906   public boolean saveAlignment(String file, String format)
 907   {
 908     boolean success = true;
 909
 910     if (format.equalsIgnoreCase("Jalview"))
 911     {
 912       String shortName = title;
 913
 914       if (shortName.indexOf(java.io.File.separatorChar) > -1)
 915       {
 916         shortName = shortName.substring(shortName
 917                 .lastIndexOf(java.io.File.separatorChar) + 1);
 918       }
 919
 920       success = new Jalview2XML().SaveAlignment(this, file, shortName);
 921
 922       statusBar.setText("Successfully saved to file: " + fileName + " in "
 923               + format + " format.");
 924
 925     }
 926     else
 927     {
 928       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
 929       {
 930         warningMessage("Cannot save file " + fileName + " using format "
 931                 + format, "Alignment output format not supported");
 932         saveAs_actionPerformed(null);
 933         // JBPNote need to have a raise_gui flag here
 934         return false;
 935       }
 936
 937       String[] omitHidden = null;
 938
 939       if (viewport.hasHiddenColumns)
 940       {
 941         int reply = JOptionPane
 942                 .showInternalConfirmDialog(
 943                         Desktop.desktop,
 944                         "The Alignment contains hidden columns."
 945                                 + "\nDo you want to save only the visible alignment?",
 946                         "Save / Omit Hidden Columns",
 947                         JOptionPane.YES_NO_OPTION,
 948                         JOptionPane.QUESTION_MESSAGE);
 949
 950         if (reply == JOptionPane.YES_OPTION)
 951         {
 952           omitHidden = viewport.getViewAsString(false);
 953         }
 954       }
 955       FormatAdapter f = new FormatAdapter();
 956       String output = f.formatSequences(format,
 957               (Alignment) viewport.alignment, // class cast exceptions will
 958               // occur in the distant future
 959               omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
 960
 961       if (output == null)
 962       {
 963         success = false;
 964       }
 965       else
 966       {
 967         try
 968         {
 969           java.io.PrintWriter out = new java.io.PrintWriter(
 970                   new java.io.FileWriter(file));
 971
 972           out.print(output);
 973           out.close();
 974           this.setTitle(file);
 975           statusBar.setText("Successfully saved to file: " + fileName
 976                   + " in " + format + " format.");
 977         } catch (Exception ex)
 978         {
 979           success = false;
 980           ex.printStackTrace();
 981         }
 982       }
 983     }
 984
 985     if (!success)
 986     {
 987       JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
 988               + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
 989     }
 990
 991     return success;
 992   }
 993
 994   private void warningMessage(String warning, String title)
 995   {
 996     if (new jalview.util.Platform().isHeadless())
 997     {
 998       System.err.println("Warning: " + title + "\nWarning: " + warning);
 999
1000     }
1001     else
1002     {
1003       JOptionPane.showInternalMessageDialog(this, warning, title,
1004               JOptionPane.WARNING_MESSAGE);
1005     }
1006     return;
1007   }
1008
1009   /**
1010    * DOCUMENT ME!
1011    *
1012    * @param e
1013    *          DOCUMENT ME!
1014    */
1015   protected void outputText_actionPerformed(ActionEvent e)
1016   {
1017     String[] omitHidden = null;
1018
1019     if (viewport.hasHiddenColumns)
1020     {
1021       int reply = JOptionPane
1022               .showInternalConfirmDialog(
1023                       Desktop.desktop,
1024                       "The Alignment contains hidden columns."
1025                               + "\nDo you want to output only the visible alignment?",
1026                       "Save / Omit Hidden Columns",
1027                       JOptionPane.YES_NO_OPTION,
1028                       JOptionPane.QUESTION_MESSAGE);
1029
1030       if (reply == JOptionPane.YES_OPTION)
1031       {
1032         omitHidden = viewport.getViewAsString(false);
1033       }
1034     }
1035
1036     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1037     cap.setForInput(null);
1038     Desktop.addInternalFrame(cap, "Alignment output - "
1039             + e.getActionCommand(), 600, 500);
1040
1041     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1042             viewport.alignment, omitHidden, viewport.colSel));
1043   }
1044
1045   /**
1046    * DOCUMENT ME!
1047    *
1048    * @param e
1049    *          DOCUMENT ME!
1050    */
1051   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1052   {
1053     new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1054             .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1055             .getFeatureRenderer());
1056   }
1057
1058   public void createImageMap(File file, String image)
1059   {
1060     alignPanel.makePNGImageMap(file, image);
1061   }
1062
1063   /**
1064    * DOCUMENT ME!
1065    *
1066    * @param e
1067    *          DOCUMENT ME!
1068    */
1069   public void createPNG(File f)
1070   {
1071     alignPanel.makePNG(f);
1072   }
1073
1074   /**
1075    * DOCUMENT ME!
1076    *
1077    * @param e
1078    *          DOCUMENT ME!
1079    */
1080   public void createEPS(File f)
1081   {
1082     alignPanel.makeEPS(f);
1083   }
1084
1085   public void pageSetup_actionPerformed(ActionEvent e)
1086   {
1087     PrinterJob printJob = PrinterJob.getPrinterJob();
1088     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1089   }
1090
1091   /**
1092    * DOCUMENT ME!
1093    *
1094    * @param e
1095    *          DOCUMENT ME!
1096    */
1097   public void printMenuItem_actionPerformed(ActionEvent e)
1098   {
1099     // Putting in a thread avoids Swing painting problems
1100     PrintThread thread = new PrintThread(alignPanel);
1101     thread.start();
1102   }
1103
1104   public void exportFeatures_actionPerformed(ActionEvent e)
1105   {
1106     new AnnotationExporter().exportFeatures(alignPanel);
1107   }
1108
1109   public void exportAnnotations_actionPerformed(ActionEvent e)
1110   {
1111     new AnnotationExporter().exportAnnotations(alignPanel,
1112             viewport.showAnnotation ? viewport.alignment
1113                     .getAlignmentAnnotation() : null, viewport.alignment
1114                     .getGroups(),
1115             ((Alignment) viewport.alignment).alignmentProperties);
1116   }
1117
1118   public void associatedData_actionPerformed(ActionEvent e)
1119   {
1120     // Pick the tree file
1121     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1122             .getProperty("LAST_DIRECTORY"));
1123     chooser.setFileView(new JalviewFileView());
1124     chooser.setDialogTitle("Load Jalview Annotations or Features File");
1125     chooser.setToolTipText("Load Jalview Annotations / Features file");
1126
1127     int value = chooser.showOpenDialog(null);
1128
1129     if (value == JalviewFileChooser.APPROVE_OPTION)
1130     {
1131       String choice = chooser.getSelectedFile().getPath();
1132       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1133       loadJalviewDataFile(choice);
1134     }
1135
1136   }
1137
1138   /**
1139    * Close the current view or all views in the alignment frame. If the frame
1140    * only contains one view then the alignment will be removed from memory.
1141    *
1142    * @param closeAllTabs
1143    */
1144   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1145   {
1146     if (alignPanels != null && alignPanels.size() < 2)
1147     {
1148       closeAllTabs = true;
1149     }
1150
1151     try
1152     {
1153       if (alignPanels != null)
1154       {
1155         if (closeAllTabs)
1156         {
1157           if (this.isClosed())
1158           {
1159             // really close all the windows - otherwise wait till
1160             // setClosed(true) is called
1161             for (int i = 0; i < alignPanels.size(); i++)
1162             {
1163               AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1164               ap.closePanel();
1165             }
1166           }
1167         }
1168         else
1169         {
1170           closeView(alignPanel);
1171         }
1172       }
1173
1174       if (closeAllTabs)
1175       {
1176         this.setClosed(true);
1177       }
1178     } catch (Exception ex)
1179     {
1180       ex.printStackTrace();
1181     }
1182   }
1183
1184   /**
1185    * close alignPanel2 and shuffle tabs appropriately.
1186    *
1187    * @param alignPanel2
1188    */
1189   public void closeView(AlignmentPanel alignPanel2)
1190   {
1191     int index = tabbedPane.getSelectedIndex();
1192     int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1193     alignPanels.removeElement(alignPanel2);
1194     // Unnecessary
1195     // if (viewport == alignPanel2.av)
1196     // {
1197     // viewport = null;
1198     // }
1199     alignPanel2.closePanel();
1200     alignPanel2 = null;
1201
1202     tabbedPane.removeTabAt(closedindex);
1203     tabbedPane.validate();
1204
1205     if (index > closedindex || index == tabbedPane.getTabCount())
1206     {
1207       // modify currently selected tab index if necessary.
1208       index--;
1209     }
1210
1211     this.tabSelectionChanged(index);
1212   }
1213
1214   /**
1215    * DOCUMENT ME!
1216    */
1217   void updateEditMenuBar()
1218   {
1219
1220     if (viewport.historyList.size() > 0)
1221     {
1222       undoMenuItem.setEnabled(true);
1223       CommandI command = (CommandI) viewport.historyList.peek();
1224       undoMenuItem.setText("Undo " + command.getDescription());
1225     }
1226     else
1227     {
1228       undoMenuItem.setEnabled(false);
1229       undoMenuItem.setText("Undo");
1230     }
1231
1232     if (viewport.redoList.size() > 0)
1233     {
1234       redoMenuItem.setEnabled(true);
1235
1236       CommandI command = (CommandI) viewport.redoList.peek();
1237       redoMenuItem.setText("Redo " + command.getDescription());
1238     }
1239     else
1240     {
1241       redoMenuItem.setEnabled(false);
1242       redoMenuItem.setText("Redo");
1243     }
1244   }
1245
1246   public void addHistoryItem(CommandI command)
1247   {
1248     if (command.getSize() > 0)
1249     {
1250       viewport.historyList.push(command);
1251       viewport.redoList.clear();
1252       updateEditMenuBar();
1253       viewport.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
1254     }
1255   }
1256
1257   /**
1258    *
1259    * @return alignment objects for all views
1260    */
1261   AlignmentI[] getViewAlignments()
1262   {
1263     if (alignPanels != null)
1264     {
1265       Enumeration e = alignPanels.elements();
1266       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1267       for (int i = 0; e.hasMoreElements(); i++)
1268       {
1269         als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1270       }
1271       return als;
1272     }
1273     if (viewport != null)
1274     {
1275       return new AlignmentI[]
1276       { viewport.alignment };
1277     }
1278     return null;
1279   }
1280
1281   /**
1282    * DOCUMENT ME!
1283    *
1284    * @param e
1285    *          DOCUMENT ME!
1286    */
1287   protected void undoMenuItem_actionPerformed(ActionEvent e)
1288   {
1289     if (viewport.historyList.empty())
1290       return;
1291     CommandI command = (CommandI) viewport.historyList.pop();
1292     viewport.redoList.push(command);
1293     command.undoCommand(getViewAlignments());
1294
1295     AlignViewport originalSource = getOriginatingSource(command);
1296     updateEditMenuBar();
1297
1298     if (originalSource != null)
1299     {
1300       originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
1301       originalSource.firePropertyChange("alignment", null,
1302               originalSource.alignment.getSequences());
1303     }
1304   }
1305
1306   /**
1307    * DOCUMENT ME!
1308    *
1309    * @param e
1310    *          DOCUMENT ME!
1311    */
1312   protected void redoMenuItem_actionPerformed(ActionEvent e)
1313   {
1314     if (viewport.redoList.size() < 1)
1315     {
1316       return;
1317     }
1318
1319     CommandI command = (CommandI) viewport.redoList.pop();
1320     viewport.historyList.push(command);
1321     command.doCommand(getViewAlignments());
1322
1323     AlignViewport originalSource = getOriginatingSource(command);
1324     updateEditMenuBar();
1325
1326     if (originalSource != null)
1327     {
1328       originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
1329       originalSource.firePropertyChange("alignment", null,
1330               originalSource.alignment.getSequences());
1331     }
1332   }
1333
1334   AlignViewport getOriginatingSource(CommandI command)
1335   {
1336     AlignViewport originalSource = null;
1337     // For sequence removal and addition, we need to fire
1338     // the property change event FROM the viewport where the
1339     // original alignment was altered
1340     AlignmentI al = null;
1341     if (command instanceof EditCommand)
1342     {
1343       EditCommand editCommand = (EditCommand) command;
1344       al = editCommand.getAlignment();
1345       Vector comps = (Vector) PaintRefresher.components.get(viewport
1346               .getSequenceSetId());
1347
1348       for (int i = 0; i < comps.size(); i++)
1349       {
1350         if (comps.elementAt(i) instanceof AlignmentPanel)
1351         {
1352           if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1353           {
1354             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1355             break;
1356           }
1357         }
1358       }
1359     }
1360
1361     if (originalSource == null)
1362     {
1363       // The original view is closed, we must validate
1364       // the current view against the closed view first
1365       if (al != null)
1366       {
1367         PaintRefresher.validateSequences(al, viewport.alignment);
1368       }
1369
1370       originalSource = viewport;
1371     }
1372
1373     return originalSource;
1374   }
1375
1376   /**
1377    * DOCUMENT ME!
1378    *
1379    * @param up
1380    *          DOCUMENT ME!
1381    */
1382   public void moveSelectedSequences(boolean up)
1383   {
1384     SequenceGroup sg = viewport.getSelectionGroup();
1385
1386     if (sg == null)
1387     {
1388       return;
1389     }
1390
1391     if (up)
1392     {
1393       for (int i = 1; i < viewport.alignment.getHeight(); i++)
1394       {
1395         SequenceI seq = viewport.alignment.getSequenceAt(i);
1396
1397         if (!sg.getSequences(null).contains(seq))
1398         {
1399           continue;
1400         }
1401
1402         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1403
1404         if (sg.getSequences(null).contains(temp))
1405         {
1406           continue;
1407         }
1408
1409         viewport.alignment.getSequences().setElementAt(temp, i);
1410         viewport.alignment.getSequences().setElementAt(seq, i - 1);
1411       }
1412     }
1413     else
1414     {
1415       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1416       {
1417         SequenceI seq = viewport.alignment.getSequenceAt(i);
1418
1419         if (!sg.getSequences(null).contains(seq))
1420         {
1421           continue;
1422         }
1423
1424         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1425
1426         if (sg.getSequences(null).contains(temp))
1427         {
1428           continue;
1429         }
1430
1431         viewport.alignment.getSequences().setElementAt(temp, i);
1432         viewport.alignment.getSequences().setElementAt(seq, i + 1);
1433       }
1434     }
1435
1436     alignPanel.paintAlignment(true);
1437   }
1438
1439   synchronized void slideSequences(boolean right, int size)
1440   {
1441     Vector sg = new Vector();
1442     if (viewport.cursorMode)
1443     {
1444       sg.addElement(viewport.alignment
1445               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1446     }
1447     else if (viewport.getSelectionGroup() != null
1448             && viewport.getSelectionGroup().getSize() != viewport.alignment
1449                     .getHeight())
1450     {
1451       sg = viewport.getSelectionGroup().getSequences(
1452               viewport.hiddenRepSequences);
1453     }
1454
1455     if (sg.size() < 1)
1456     {
1457       return;
1458     }
1459
1460     Vector invertGroup = new Vector();
1461
1462     for (int i = 0; i < viewport.alignment.getHeight(); i++)
1463     {
1464       if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1465         invertGroup.add(viewport.alignment.getSequenceAt(i));
1466     }
1467
1468     SequenceI[] seqs1 = new SequenceI[sg.size()];
1469     for (int i = 0; i < sg.size(); i++)
1470       seqs1[i] = (SequenceI) sg.elementAt(i);
1471
1472     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1473     for (int i = 0; i < invertGroup.size(); i++)
1474       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1475
1476     SlideSequencesCommand ssc;
1477     if (right)
1478       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1479               size, viewport.getGapCharacter());
1480     else
1481       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1482               size, viewport.getGapCharacter());
1483
1484     int groupAdjustment = 0;
1485     if (ssc.getGapsInsertedBegin() && right)
1486     {
1487       if (viewport.cursorMode)
1488         alignPanel.seqPanel.moveCursor(size, 0);
1489       else
1490         groupAdjustment = size;
1491     }
1492     else if (!ssc.getGapsInsertedBegin() && !right)
1493     {
1494       if (viewport.cursorMode)
1495         alignPanel.seqPanel.moveCursor(-size, 0);
1496       else
1497         groupAdjustment = -size;
1498     }
1499
1500     if (groupAdjustment != 0)
1501     {
1502       viewport.getSelectionGroup().setStartRes(
1503               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1504       viewport.getSelectionGroup().setEndRes(
1505               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1506     }
1507
1508     boolean appendHistoryItem = false;
1509     if (viewport.historyList != null && viewport.historyList.size() > 0
1510             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1511     {
1512       appendHistoryItem = ssc
1513               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1514                       .peek());
1515     }
1516
1517     if (!appendHistoryItem)
1518       addHistoryItem(ssc);
1519
1520     repaint();
1521   }
1522
1523   /**
1524    * DOCUMENT ME!
1525    *
1526    * @param e
1527    *          DOCUMENT ME!
1528    */
1529   protected void copy_actionPerformed(ActionEvent e)
1530   {
1531     System.gc();
1532     if (viewport.getSelectionGroup() == null)
1533     {
1534       return;
1535     }
1536     // TODO: preserve the ordering of displayed alignment annotation in any
1537     // internal paste (particularly sequence associated annotation)
1538     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1539     String[] omitHidden = null;
1540
1541     if (viewport.hasHiddenColumns)
1542     {
1543       omitHidden = viewport.getViewAsString(true);
1544     }
1545
1546     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1547             omitHidden);
1548
1549     StringSelection ss = new StringSelection(output);
1550
1551     try
1552     {
1553       jalview.gui.Desktop.internalCopy = true;
1554       // Its really worth setting the clipboard contents
1555       // to empty before setting the large StringSelection!!
1556       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1557               new StringSelection(""), null);
1558
1559       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1560               Desktop.instance);
1561     } catch (OutOfMemoryError er)
1562     {
1563       new OOMWarning("copying region", er);
1564       return;
1565     }
1566
1567     Vector hiddenColumns = null;
1568     if (viewport.hasHiddenColumns)
1569     {
1570       hiddenColumns = new Vector();
1571       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1572       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1573               .size(); i++)
1574       {
1575         int[] region = (int[]) viewport.getColumnSelection()
1576                 .getHiddenColumns().elementAt(i);
1577
1578         hiddenColumns.addElement(new int[]
1579         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1580       }
1581     }
1582
1583     Desktop.jalviewClipboard = new Object[]
1584     { seqs, viewport.alignment.getDataset(), hiddenColumns };
1585     statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1586   }
1587
1588   /**
1589    * DOCUMENT ME!
1590    *
1591    * @param e
1592    *          DOCUMENT ME!
1593    */
1594   protected void pasteNew_actionPerformed(ActionEvent e)
1595   {
1596     paste(true);
1597   }
1598
1599   /**
1600    * DOCUMENT ME!
1601    *
1602    * @param e
1603    *          DOCUMENT ME!
1604    */
1605   protected void pasteThis_actionPerformed(ActionEvent e)
1606   {
1607     paste(false);
1608   }
1609
1610   /**
1611    * Paste contents of Jalview clipboard
1612    *
1613    * @param newAlignment
1614    *          true to paste to a new alignment, otherwise add to this.
1615    */
1616   void paste(boolean newAlignment)
1617   {
1618     boolean externalPaste = true;
1619     try
1620     {
1621       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1622       Transferable contents = c.getContents(this);
1623
1624       if (contents == null)
1625       {
1626         return;
1627       }
1628
1629       String str, format;
1630       try
1631       {
1632         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1633         if (str.length() < 1)
1634         {
1635           return;
1636         }
1637
1638         format = new IdentifyFile().Identify(str, "Paste");
1639
1640       } catch (OutOfMemoryError er)
1641       {
1642         new OOMWarning("Out of memory pasting sequences!!", er);
1643         return;
1644       }
1645
1646       SequenceI[] sequences;
1647       boolean annotationAdded = false;
1648       AlignmentI alignment = null;
1649
1650       if (Desktop.jalviewClipboard != null)
1651       {
1652         // The clipboard was filled from within Jalview, we must use the
1653         // sequences
1654         // And dataset from the copied alignment
1655         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1656         // be doubly sure that we create *new* sequence objects.
1657         sequences = new SequenceI[newseq.length];
1658         for (int i = 0; i < newseq.length; i++)
1659         {
1660           sequences[i] = new Sequence(newseq[i]);
1661         }
1662         alignment = new Alignment(sequences);
1663         externalPaste = false;
1664       }
1665       else
1666       {
1667         // parse the clipboard as an alignment.
1668         alignment = new FormatAdapter().readFile(str, "Paste", format);
1669         sequences = alignment.getSequencesArray();
1670       }
1671
1672       int alwidth = 0;
1673
1674       if (newAlignment)
1675       {
1676
1677         if (Desktop.jalviewClipboard != null)
1678         {
1679           // dataset is inherited
1680           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1681         }
1682         else
1683         {
1684           // new dataset is constructed
1685           alignment.setDataset(null);
1686         }
1687         alwidth = alignment.getWidth() + 1;
1688       }
1689       else
1690       {
1691         AlignmentI pastedal = alignment; // preserve pasted alignment object
1692         // Add pasted sequences and dataset into existing alignment.
1693         alignment = viewport.getAlignment();
1694         alwidth = alignment.getWidth() + 1;
1695         // decide if we need to import sequences from an existing dataset
1696         boolean importDs = Desktop.jalviewClipboard != null
1697                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1698         // importDs==true instructs us to copy over new dataset sequences from
1699         // an existing alignment
1700         Vector newDs = (importDs) ? new Vector() : null; // used to create
1701         // minimum dataset set
1702
1703         for (int i = 0; i < sequences.length; i++)
1704         {
1705           if (importDs)
1706           {
1707             newDs.addElement(null);
1708           }
1709           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1710           // paste
1711           if (importDs && ds != null)
1712           {
1713             if (!newDs.contains(ds))
1714             {
1715               newDs.setElementAt(ds, i);
1716               ds = new Sequence(ds);
1717               // update with new dataset sequence
1718               sequences[i].setDatasetSequence(ds);
1719             }
1720             else
1721             {
1722               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1723             }
1724           }
1725           else
1726           {
1727             // copy and derive new dataset sequence
1728             sequences[i] = sequences[i].deriveSequence();
1729             alignment.getDataset().addSequence(
1730                     sequences[i].getDatasetSequence());
1731             // TODO: avoid creation of duplicate dataset sequences with a
1732             // 'contains' method using SequenceI.equals()/SequenceI.contains()
1733           }
1734           alignment.addSequence(sequences[i]); // merges dataset
1735         }
1736         if (newDs != null)
1737         {
1738           newDs.clear(); // tidy up
1739         }
1740         if (pastedal.getAlignmentAnnotation() != null)
1741         {
1742           // Add any annotation attached to alignment.
1743           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1744           for (int i = 0; i < alann.length; i++)
1745           {
1746             annotationAdded = true;
1747             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1748             {
1749               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1750               newann.padAnnotation(alwidth);
1751               alignment.addAnnotation(newann);
1752             }
1753           }
1754         }
1755       }
1756       if (!newAlignment)
1757       {
1758         // /////
1759         // ADD HISTORY ITEM
1760         //
1761         addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1762                 sequences, 0, alignment.getWidth(), alignment));
1763       }
1764       // Add any annotations attached to sequences
1765       for (int i = 0; i < sequences.length; i++)
1766       {
1767         if (sequences[i].getAnnotation() != null)
1768         {
1769           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1770           {
1771             annotationAdded = true;
1772             sequences[i].getAnnotation()[a].adjustForAlignment();
1773             sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1774             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1775             // was
1776             // duplicated
1777             // earlier
1778             alignment
1779                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1780           }
1781         }
1782       }
1783       if (!newAlignment)
1784       {
1785
1786         // propagate alignment changed.
1787         viewport.setEndSeq(alignment.getHeight());
1788         if (annotationAdded)
1789         {
1790           // Duplicate sequence annotation in all views.
1791           AlignmentI[] alview = this.getViewAlignments();
1792           for (int i = 0; i < sequences.length; i++)
1793           {
1794             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1795             if (sann == null)
1796               continue;
1797             for (int avnum = 0; avnum < alview.length; avnum++)
1798             {
1799               if (alview[avnum] != alignment)
1800               {
1801                 // duplicate in a view other than the one with input focus
1802                 int avwidth = alview[avnum].getWidth() + 1;
1803                 // this relies on sann being preserved after we
1804                 // modify the sequence's annotation array for each duplication
1805                 for (int a = 0; a < sann.length; a++)
1806                 {
1807                   AlignmentAnnotation newann = new AlignmentAnnotation(
1808                           sann[a]);
1809                   sequences[i].addAlignmentAnnotation(newann);
1810                   newann.padAnnotation(avwidth);
1811                   alview[avnum].addAnnotation(newann); // annotation was
1812                   // duplicated earlier
1813                   alview[avnum].setAnnotationIndex(newann, a);
1814                 }
1815               }
1816             }
1817           }
1818           buildSortByAnnotationScoresMenu();
1819         }
1820         viewport.firePropertyChange("alignment", null, alignment
1821                 .getSequences());
1822
1823       }
1824       else
1825       {
1826         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1827                 DEFAULT_HEIGHT);
1828         String newtitle = new String("Copied sequences");
1829
1830         if (Desktop.jalviewClipboard != null
1831                 && Desktop.jalviewClipboard[2] != null)
1832         {
1833           Vector hc = (Vector) Desktop.jalviewClipboard[2];
1834           for (int i = 0; i < hc.size(); i++)
1835           {
1836             int[] region = (int[]) hc.elementAt(i);
1837             af.viewport.hideColumns(region[0], region[1]);
1838           }
1839         }
1840
1841         // >>>This is a fix for the moment, until a better solution is
1842         // found!!<<<
1843         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1844                 .transferSettings(
1845                         alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1846
1847         // TODO: maintain provenance of an alignment, rather than just make the
1848         // title a concatenation of operations.
1849         if (!externalPaste)
1850         {
1851           if (title.startsWith("Copied sequences"))
1852           {
1853             newtitle = title;
1854           }
1855           else
1856           {
1857             newtitle = newtitle.concat("- from " + title);
1858           }
1859         }
1860         else
1861         {
1862           newtitle = new String("Pasted sequences");
1863         }
1864
1865         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1866                 DEFAULT_HEIGHT);
1867
1868       }
1869
1870     } catch (Exception ex)
1871     {
1872       ex.printStackTrace();
1873       System.out.println("Exception whilst pasting: " + ex);
1874       // could be anything being pasted in here
1875     }
1876
1877   }
1878
1879   /**
1880    * DOCUMENT ME!
1881    *
1882    * @param e
1883    *          DOCUMENT ME!
1884    */
1885   protected void cut_actionPerformed(ActionEvent e)
1886   {
1887     copy_actionPerformed(null);
1888     delete_actionPerformed(null);
1889   }
1890
1891   /**
1892    * DOCUMENT ME!
1893    *
1894    * @param e
1895    *          DOCUMENT ME!
1896    */
1897   protected void delete_actionPerformed(ActionEvent evt)
1898   {
1899
1900     SequenceGroup sg = viewport.getSelectionGroup();
1901     if (sg == null)
1902     {
1903       return;
1904     }
1905
1906     Vector seqs = new Vector();
1907     SequenceI seq;
1908     for (int i = 0; i < sg.getSize(); i++)
1909     {
1910       seq = sg.getSequenceAt(i);
1911       seqs.addElement(seq);
1912     }
1913
1914     // If the cut affects all sequences, remove highlighted columns
1915     if (sg.getSize() == viewport.alignment.getHeight())
1916     {
1917       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1918               sg.getEndRes() + 1);
1919     }
1920
1921     SequenceI[] cut = new SequenceI[seqs.size()];
1922     for (int i = 0; i < seqs.size(); i++)
1923     {
1924       cut[i] = (SequenceI) seqs.elementAt(i);
1925     }
1926
1927     /*
1928      * //ADD HISTORY ITEM
1929      */
1930     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1931             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1932             viewport.alignment));
1933
1934     viewport.setSelectionGroup(null);
1935     viewport.sendSelection();
1936     viewport.alignment.deleteGroup(sg);
1937
1938     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1939             .getSequences());
1940     if (viewport.getAlignment().getHeight() < 1)
1941     {
1942       try
1943       {
1944         this.setClosed(true);
1945       } catch (Exception ex)
1946       {
1947       }
1948     }
1949   }
1950
1951   /**
1952    * DOCUMENT ME!
1953    *
1954    * @param e
1955    *          DOCUMENT ME!
1956    */
1957   protected void deleteGroups_actionPerformed(ActionEvent e)
1958   {
1959     viewport.alignment.deleteAllGroups();
1960     viewport.sequenceColours = null;
1961     viewport.setSelectionGroup(null);
1962     PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1963     alignPanel.updateAnnotation();
1964     alignPanel.paintAlignment(true);
1965   }
1966
1967   /**
1968    * DOCUMENT ME!
1969    *
1970    * @param e
1971    *          DOCUMENT ME!
1972    */
1973   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1974   {
1975     SequenceGroup sg = new SequenceGroup();
1976
1977     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1978     {
1979       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1980     }
1981
1982     sg.setEndRes(viewport.alignment.getWidth() - 1);
1983     viewport.setSelectionGroup(sg);
1984     viewport.sendSelection();
1985     alignPanel.paintAlignment(true);
1986     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1987   }
1988
1989   /**
1990    * DOCUMENT ME!
1991    *
1992    * @param e
1993    *          DOCUMENT ME!
1994    */
1995   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1996   {
1997     if (viewport.cursorMode)
1998     {
1999       alignPanel.seqPanel.keyboardNo1 = null;
2000       alignPanel.seqPanel.keyboardNo2 = null;
2001     }
2002     viewport.setSelectionGroup(null);
2003     viewport.getColumnSelection().clear();
2004     viewport.setSelectionGroup(null);
2005     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2006     alignPanel.idPanel.idCanvas.searchResults = null;
2007     alignPanel.paintAlignment(true);
2008     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2009   }
2010
2011   /**
2012    * DOCUMENT ME!
2013    *
2014    * @param e
2015    *          DOCUMENT ME!
2016    */
2017   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2018   {
2019     SequenceGroup sg = viewport.getSelectionGroup();
2020
2021     if (sg == null)
2022     {
2023       selectAllSequenceMenuItem_actionPerformed(null);
2024
2025       return;
2026     }
2027
2028     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2029     {
2030       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2031     }
2032
2033     alignPanel.paintAlignment(true);
2034     viewport.sendSelection();
2035     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2036   }
2037
2038   public void invertColSel_actionPerformed(ActionEvent e)
2039   {
2040     viewport.invertColumnSelection();
2041     alignPanel.paintAlignment(true);
2042   }
2043
2044   /**
2045    * DOCUMENT ME!
2046    *
2047    * @param e
2048    *          DOCUMENT ME!
2049    */
2050   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2051   {
2052     trimAlignment(true);
2053   }
2054
2055   /**
2056    * DOCUMENT ME!
2057    *
2058    * @param e
2059    *          DOCUMENT ME!
2060    */
2061   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2062   {
2063     trimAlignment(false);
2064   }
2065
2066   void trimAlignment(boolean trimLeft)
2067   {
2068     ColumnSelection colSel = viewport.getColumnSelection();
2069     int column;
2070
2071     if (colSel.size() > 0)
2072     {
2073       if (trimLeft)
2074       {
2075         column = colSel.getMin();
2076       }
2077       else
2078       {
2079         column = colSel.getMax();
2080       }
2081
2082       SequenceI[] seqs;
2083       if (viewport.getSelectionGroup() != null)
2084       {
2085         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2086                 viewport.hiddenRepSequences);
2087       }
2088       else
2089       {
2090         seqs = viewport.alignment.getSequencesArray();
2091       }
2092
2093       TrimRegionCommand trimRegion;
2094       if (trimLeft)
2095       {
2096         trimRegion = new TrimRegionCommand("Remove Left",
2097                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2098                 viewport.alignment, viewport.colSel,
2099                 viewport.selectionGroup);
2100         viewport.setStartRes(0);
2101       }
2102       else
2103       {
2104         trimRegion = new TrimRegionCommand("Remove Right",
2105                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2106                 viewport.alignment, viewport.colSel,
2107                 viewport.selectionGroup);
2108       }
2109
2110       statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2111
2112       addHistoryItem(trimRegion);
2113
2114       Vector groups = viewport.alignment.getGroups();
2115
2116       for (int i = 0; i < groups.size(); i++)
2117       {
2118         SequenceGroup sg = (SequenceGroup) groups.get(i);
2119
2120         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2121                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2122         {
2123           viewport.alignment.deleteGroup(sg);
2124         }
2125       }
2126
2127       viewport.firePropertyChange("alignment", null, viewport
2128               .getAlignment().getSequences());
2129     }
2130   }
2131
2132   /**
2133    * DOCUMENT ME!
2134    *
2135    * @param e
2136    *          DOCUMENT ME!
2137    */
2138   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2139   {
2140     int start = 0, end = viewport.alignment.getWidth() - 1;
2141
2142     SequenceI[] seqs;
2143     if (viewport.getSelectionGroup() != null)
2144     {
2145       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2146               viewport.hiddenRepSequences);
2147       start = viewport.getSelectionGroup().getStartRes();
2148       end = viewport.getSelectionGroup().getEndRes();
2149     }
2150     else
2151     {
2152       seqs = viewport.alignment.getSequencesArray();
2153     }
2154
2155     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2156             "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2157
2158     addHistoryItem(removeGapCols);
2159
2160     statusBar.setText("Removed " + removeGapCols.getSize()
2161             + " empty columns.");
2162
2163     // This is to maintain viewport position on first residue
2164     // of first sequence
2165     SequenceI seq = viewport.alignment.getSequenceAt(0);
2166     int startRes = seq.findPosition(viewport.startRes);
2167     // ShiftList shifts;
2168     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2169     // edit.alColumnChanges=shifts.getInverse();
2170     // if (viewport.hasHiddenColumns)
2171     // viewport.getColumnSelection().compensateForEdits(shifts);
2172     viewport.setStartRes(seq.findIndex(startRes) - 1);
2173     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2174             .getSequences());
2175
2176   }
2177
2178   /**
2179    * DOCUMENT ME!
2180    *
2181    * @param e
2182    *          DOCUMENT ME!
2183    */
2184   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2185   {
2186     int start = 0, end = viewport.alignment.getWidth() - 1;
2187
2188     SequenceI[] seqs;
2189     if (viewport.getSelectionGroup() != null)
2190     {
2191       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2192               viewport.hiddenRepSequences);
2193       start = viewport.getSelectionGroup().getStartRes();
2194       end = viewport.getSelectionGroup().getEndRes();
2195     }
2196     else
2197     {
2198       seqs = viewport.alignment.getSequencesArray();
2199     }
2200
2201     // This is to maintain viewport position on first residue
2202     // of first sequence
2203     SequenceI seq = viewport.alignment.getSequenceAt(0);
2204     int startRes = seq.findPosition(viewport.startRes);
2205
2206     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2207             viewport.alignment));
2208
2209     viewport.setStartRes(seq.findIndex(startRes) - 1);
2210
2211     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2212             .getSequences());
2213
2214   }
2215
2216   /**
2217    * DOCUMENT ME!
2218    *
2219    * @param e
2220    *          DOCUMENT ME!
2221    */
2222   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2223   {
2224     viewport.padGaps = padGapsMenuitem.isSelected();
2225     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2226             .getSequences());
2227   }
2228
2229   // else
2230   {
2231     // if (justifySeqs>0)
2232     {
2233       // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2234     }
2235   }
2236
2237   // }
2238
2239   /**
2240    * DOCUMENT ME!
2241    *
2242    * @param e
2243    *          DOCUMENT ME!
2244    */
2245   public void findMenuItem_actionPerformed(ActionEvent e)
2246   {
2247     new Finder();
2248   }
2249
2250   public void newView_actionPerformed(ActionEvent e)
2251   {
2252     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2253             true);
2254
2255     newap.av.gatherViewsHere = false;
2256
2257     if (viewport.viewName == null)
2258     {
2259       viewport.viewName = "Original";
2260     }
2261
2262     newap.av.historyList = viewport.historyList;
2263     newap.av.redoList = viewport.redoList;
2264
2265     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2266     String newViewName = "View " + index;
2267
2268     Vector comps = (Vector) PaintRefresher.components.get(viewport
2269             .getSequenceSetId());
2270     Vector existingNames = new Vector();
2271     for (int i = 0; i < comps.size(); i++)
2272     {
2273       if (comps.elementAt(i) instanceof AlignmentPanel)
2274       {
2275         AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2276         if (!existingNames.contains(ap.av.viewName))
2277         {
2278           existingNames.addElement(ap.av.viewName);
2279         }
2280       }
2281     }
2282
2283     while (existingNames.contains(newViewName))
2284     {
2285       newViewName = "View " + (++index);
2286     }
2287
2288     newap.av.viewName = newViewName;
2289
2290     addAlignmentPanel(newap, true);
2291
2292     if (alignPanels.size() == 2)
2293     {
2294       viewport.gatherViewsHere = true;
2295     }
2296     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2297   }
2298
2299   public void expandViews_actionPerformed(ActionEvent e)
2300   {
2301     Desktop.instance.explodeViews(this);
2302   }
2303
2304   public void gatherViews_actionPerformed(ActionEvent e)
2305   {
2306     Desktop.instance.gatherViews(this);
2307   }
2308
2309   /**
2310    * DOCUMENT ME!
2311    *
2312    * @param e
2313    *          DOCUMENT ME!
2314    */
2315   public void font_actionPerformed(ActionEvent e)
2316   {
2317     new FontChooser(alignPanel);
2318   }
2319
2320   /**
2321    * DOCUMENT ME!
2322    *
2323    * @param e
2324    *          DOCUMENT ME!
2325    */
2326   protected void seqLimit_actionPerformed(ActionEvent e)
2327   {
2328     viewport.setShowJVSuffix(seqLimits.isSelected());
2329
2330     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2331             .calculateIdWidth());
2332     alignPanel.paintAlignment(true);
2333   }
2334
2335   public void idRightAlign_actionPerformed(ActionEvent e)
2336   {
2337     viewport.rightAlignIds = idRightAlign.isSelected();
2338     alignPanel.paintAlignment(true);
2339   }
2340
2341   public void centreColumnLabels_actionPerformed(ActionEvent e)
2342   {
2343     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2344     alignPanel.paintAlignment(true);
2345   }
2346
2347   /*
2348    * (non-Javadoc)
2349    *
2350    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2351    */
2352   protected void followHighlight_actionPerformed()
2353   {
2354     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2355     {
2356       alignPanel.scrollToPosition(
2357               alignPanel.seqPanel.seqCanvas.searchResults, false);
2358     }
2359   }
2360
2361   /**
2362    * DOCUMENT ME!
2363    *
2364    * @param e
2365    *          DOCUMENT ME!
2366    */
2367   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2368   {
2369     viewport.setColourText(colourTextMenuItem.isSelected());
2370     alignPanel.paintAlignment(true);
2371   }
2372
2373   /**
2374    * DOCUMENT ME!
2375    *
2376    * @param e
2377    *          DOCUMENT ME!
2378    */
2379   public void wrapMenuItem_actionPerformed(ActionEvent e)
2380   {
2381     scaleAbove.setVisible(wrapMenuItem.isSelected());
2382     scaleLeft.setVisible(wrapMenuItem.isSelected());
2383     scaleRight.setVisible(wrapMenuItem.isSelected());
2384     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2385     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2386   }
2387
2388   public void showAllSeqs_actionPerformed(ActionEvent e)
2389   {
2390     viewport.showAllHiddenSeqs();
2391   }
2392
2393   public void showAllColumns_actionPerformed(ActionEvent e)
2394   {
2395     viewport.showAllHiddenColumns();
2396     repaint();
2397   }
2398
2399   public void hideSelSequences_actionPerformed(ActionEvent e)
2400   {
2401     viewport.hideAllSelectedSeqs();
2402     alignPanel.paintAlignment(true);
2403   }
2404
2405   public void hideSelColumns_actionPerformed(ActionEvent e)
2406   {
2407     viewport.hideSelectedColumns();
2408     alignPanel.paintAlignment(true);
2409   }
2410
2411   public void hiddenMarkers_actionPerformed(ActionEvent e)
2412   {
2413     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2414     repaint();
2415   }
2416
2417   /**
2418    * DOCUMENT ME!
2419    *
2420    * @param e
2421    *          DOCUMENT ME!
2422    */
2423   protected void scaleAbove_actionPerformed(ActionEvent e)
2424   {
2425     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2426     alignPanel.paintAlignment(true);
2427   }
2428
2429   /**
2430    * DOCUMENT ME!
2431    *
2432    * @param e
2433    *          DOCUMENT ME!
2434    */
2435   protected void scaleLeft_actionPerformed(ActionEvent e)
2436   {
2437     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2438     alignPanel.paintAlignment(true);
2439   }
2440
2441   /**
2442    * DOCUMENT ME!
2443    *
2444    * @param e
2445    *          DOCUMENT ME!
2446    */
2447   protected void scaleRight_actionPerformed(ActionEvent e)
2448   {
2449     viewport.setScaleRightWrapped(scaleRight.isSelected());
2450     alignPanel.paintAlignment(true);
2451   }
2452
2453   /**
2454    * DOCUMENT ME!
2455    *
2456    * @param e
2457    *          DOCUMENT ME!
2458    */
2459   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2460   {
2461     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2462     alignPanel.paintAlignment(true);
2463   }
2464
2465   /**
2466    * DOCUMENT ME!
2467    *
2468    * @param e
2469    *          DOCUMENT ME!
2470    */
2471   public void viewTextMenuItem_actionPerformed(ActionEvent e)
2472   {
2473     viewport.setShowText(viewTextMenuItem.isSelected());
2474     alignPanel.paintAlignment(true);
2475   }
2476
2477   /**
2478    * DOCUMENT ME!
2479    *
2480    * @param e
2481    *          DOCUMENT ME!
2482    */
2483   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2484   {
2485     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2486     alignPanel.paintAlignment(true);
2487   }
2488
2489   public FeatureSettings featureSettings;
2490
2491   public void featureSettings_actionPerformed(ActionEvent e)
2492   {
2493     if (featureSettings != null)
2494     {
2495       featureSettings.close();
2496       featureSettings = null;
2497     }
2498     if (!showSeqFeatures.isSelected())
2499     {
2500       // make sure features are actually displayed
2501       showSeqFeatures.setSelected(true);
2502       showSeqFeatures_actionPerformed(null);
2503     }
2504     featureSettings = new FeatureSettings(this);
2505   }
2506
2507   /**
2508    * Set or clear 'Show Sequence Features'
2509    *
2510    * @param evt
2511    *          DOCUMENT ME!
2512    */
2513   public void showSeqFeatures_actionPerformed(ActionEvent evt)
2514   {
2515     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2516     alignPanel.paintAlignment(true);
2517     if (alignPanel.getOverviewPanel() != null)
2518     {
2519       alignPanel.getOverviewPanel().updateOverviewImage();
2520     }
2521   }
2522
2523   /**
2524    * Set or clear 'Show Sequence Features'
2525    *
2526    * @param evt
2527    *          DOCUMENT ME!
2528    */
2529   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2530   {
2531     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2532             .isSelected());
2533     if (viewport.getShowSequenceFeaturesHeight())
2534     {
2535       // ensure we're actually displaying features
2536       viewport.setShowSequenceFeatures(true);
2537       showSeqFeatures.setSelected(true);
2538     }
2539     alignPanel.paintAlignment(true);
2540     if (alignPanel.getOverviewPanel() != null)
2541     {
2542       alignPanel.getOverviewPanel().updateOverviewImage();
2543     }
2544   }
2545
2546   /**
2547    * DOCUMENT ME!
2548    *
2549    * @param e
2550    *          DOCUMENT ME!
2551    */
2552   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2553   {
2554     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2555     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2556   }
2557
2558   public void alignmentProperties()
2559   {
2560     JEditorPane editPane = new JEditorPane("text/html", "");
2561     editPane.setEditable(false);
2562     StringBuffer contents = new StringBuffer("<html>");
2563
2564     float avg = 0;
2565     int min = Integer.MAX_VALUE, max = 0;
2566     for (int i = 0; i < viewport.alignment.getHeight(); i++)
2567     {
2568       int size = viewport.alignment.getSequenceAt(i).getEnd()
2569               - viewport.alignment.getSequenceAt(i).getStart();
2570       avg += size;
2571       if (size > max)
2572         max = size;
2573       if (size < min)
2574         min = size;
2575     }
2576     avg = avg / (float) viewport.alignment.getHeight();
2577
2578     contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2579     contents.append("<br>Minimum Sequence Length: " + min);
2580     contents.append("<br>Maximum Sequence Length: " + max);
2581     contents.append("<br>Average Length: " + (int) avg);
2582
2583     if (((Alignment) viewport.alignment).getProperties() != null)
2584     {
2585       Hashtable props = ((Alignment) viewport.alignment).getProperties();
2586       Enumeration en = props.keys();
2587       contents.append("<br><br><table border=\"1\">");
2588       while (en.hasMoreElements())
2589       {
2590         String key = en.nextElement().toString();
2591         StringBuffer val = new StringBuffer();
2592         String vals = props.get(key).toString();
2593         int pos = 0, npos;
2594         do
2595         {
2596           npos = vals.indexOf("\n", pos);
2597           if (npos == -1)
2598           {
2599             val.append(vals.substring(pos));
2600           }
2601           else
2602           {
2603             val.append(vals.substring(pos, npos));
2604             val.append("<br>");
2605           }
2606           pos = npos + 1;
2607         } while (npos != -1);
2608         contents
2609                 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2610       }
2611       contents.append("</table>");
2612     }
2613     editPane.setText(contents.toString() + "</html>");
2614     JInternalFrame frame = new JInternalFrame();
2615     frame.getContentPane().add(new JScrollPane(editPane));
2616
2617     Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2618             + getTitle(), 500, 400);
2619   }
2620
2621   /**
2622    * DOCUMENT ME!
2623    *
2624    * @param e
2625    *          DOCUMENT ME!
2626    */
2627   public void overviewMenuItem_actionPerformed(ActionEvent e)
2628   {
2629     if (alignPanel.overviewPanel != null)
2630     {
2631       return;
2632     }
2633
2634     JInternalFrame frame = new JInternalFrame();
2635     OverviewPanel overview = new OverviewPanel(alignPanel);
2636     frame.setContentPane(overview);
2637     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2638             .getWidth(), frame.getHeight());
2639     frame.pack();
2640     frame.setLayer(JLayeredPane.PALETTE_LAYER);
2641     frame
2642             .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2643             {
2644               public void internalFrameClosed(
2645                       javax.swing.event.InternalFrameEvent evt)
2646               {
2647                 alignPanel.setOverviewPanel(null);
2648               };
2649             });
2650
2651     alignPanel.setOverviewPanel(overview);
2652   }
2653
2654   public void textColour_actionPerformed(ActionEvent e)
2655   {
2656     new TextColourChooser().chooseColour(alignPanel, null);
2657   }
2658
2659   /**
2660    * DOCUMENT ME!
2661    *
2662    * @param e
2663    *          DOCUMENT ME!
2664    */
2665   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2666   {
2667     changeColour(null);
2668   }
2669
2670   /**
2671    * DOCUMENT ME!
2672    *
2673    * @param e
2674    *          DOCUMENT ME!
2675    */
2676   public void clustalColour_actionPerformed(ActionEvent e)
2677   {
2678     changeColour(new ClustalxColourScheme(
2679             viewport.alignment.getSequences(), viewport.alignment
2680                     .getWidth()));
2681   }
2682
2683   /**
2684    * DOCUMENT ME!
2685    *
2686    * @param e
2687    *          DOCUMENT ME!
2688    */
2689   public void zappoColour_actionPerformed(ActionEvent e)
2690   {
2691     changeColour(new ZappoColourScheme());
2692   }
2693
2694   /**
2695    * DOCUMENT ME!
2696    *
2697    * @param e
2698    *          DOCUMENT ME!
2699    */
2700   public void taylorColour_actionPerformed(ActionEvent e)
2701   {
2702     changeColour(new TaylorColourScheme());
2703   }
2704
2705   /**
2706    * DOCUMENT ME!
2707    *
2708    * @param e
2709    *          DOCUMENT ME!
2710    */
2711   public void hydrophobicityColour_actionPerformed(ActionEvent e)
2712   {
2713     changeColour(new HydrophobicColourScheme());
2714   }
2715
2716   /**
2717    * DOCUMENT ME!
2718    *
2719    * @param e
2720    *          DOCUMENT ME!
2721    */
2722   public void helixColour_actionPerformed(ActionEvent e)
2723   {
2724     changeColour(new HelixColourScheme());
2725   }
2726
2727   /**
2728    * DOCUMENT ME!
2729    *
2730    * @param e
2731    *          DOCUMENT ME!
2732    */
2733   public void strandColour_actionPerformed(ActionEvent e)
2734   {
2735     changeColour(new StrandColourScheme());
2736   }
2737
2738   /**
2739    * DOCUMENT ME!
2740    *
2741    * @param e
2742    *          DOCUMENT ME!
2743    */
2744   public void turnColour_actionPerformed(ActionEvent e)
2745   {
2746     changeColour(new TurnColourScheme());
2747   }
2748
2749   /**
2750    * DOCUMENT ME!
2751    *
2752    * @param e
2753    *          DOCUMENT ME!
2754    */
2755   public void buriedColour_actionPerformed(ActionEvent e)
2756   {
2757     changeColour(new BuriedColourScheme());
2758   }
2759
2760   /**
2761    * DOCUMENT ME!
2762    *
2763    * @param e
2764    *          DOCUMENT ME!
2765    */
2766   public void nucleotideColour_actionPerformed(ActionEvent e)
2767   {
2768     changeColour(new NucleotideColourScheme());
2769   }
2770
2771   public void annotationColour_actionPerformed(ActionEvent e)
2772   {
2773     new AnnotationColourChooser(viewport, alignPanel);
2774   }
2775
2776   /**
2777    * DOCUMENT ME!
2778    *
2779    * @param e
2780    *          DOCUMENT ME!
2781    */
2782   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2783   {
2784     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2785   }
2786
2787   /**
2788    * DOCUMENT ME!
2789    *
2790    * @param cs
2791    *          DOCUMENT ME!
2792    */
2793   public void changeColour(ColourSchemeI cs)
2794   {
2795     int threshold = 0;
2796
2797     if (cs != null)
2798     {
2799       if (viewport.getAbovePIDThreshold())
2800       {
2801         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2802                 "Background");
2803
2804         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2805
2806         viewport.setGlobalColourScheme(cs);
2807       }
2808       else
2809       {
2810         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2811       }
2812
2813       if (viewport.getConservationSelected())
2814       {
2815
2816         Alignment al = (Alignment) viewport.alignment;
2817         Conservation c = new Conservation("All",
2818                 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2819                         .getWidth() - 1);
2820
2821         c.calculate();
2822         c.verdict(false, viewport.ConsPercGaps);
2823
2824         cs.setConservation(c);
2825
2826         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2827                 cs, "Background"));
2828       }
2829       else
2830       {
2831         cs.setConservation(null);
2832       }
2833
2834       cs.setConsensus(viewport.hconsensus);
2835     }
2836
2837     viewport.setGlobalColourScheme(cs);
2838
2839     if (viewport.getColourAppliesToAllGroups())
2840     {
2841       Vector groups = viewport.alignment.getGroups();
2842
2843       for (int i = 0; i < groups.size(); i++)
2844       {
2845         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2846
2847         if (cs == null)
2848         {
2849           sg.cs = null;
2850           continue;
2851         }
2852
2853         if (cs instanceof ClustalxColourScheme)
2854         {
2855           sg.cs = new ClustalxColourScheme(sg
2856                   .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2857         }
2858         else if (cs instanceof UserColourScheme)
2859         {
2860           sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2861         }
2862         else
2863         {
2864           try
2865           {
2866             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2867           } catch (Exception ex)
2868           {
2869           }
2870         }
2871
2872         if (viewport.getAbovePIDThreshold()
2873                 || cs instanceof PIDColourScheme
2874                 || cs instanceof Blosum62ColourScheme)
2875         {
2876           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2877
2878           sg.cs.setConsensus(AAFrequency.calculate(sg
2879                   .getSequences(viewport.hiddenRepSequences), sg
2880                   .getStartRes(), sg.getEndRes() + 1));
2881         }
2882         else
2883         {
2884           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2885         }
2886
2887         if (viewport.getConservationSelected())
2888         {
2889           Conservation c = new Conservation("Group",
2890                   ResidueProperties.propHash, 3, sg
2891                           .getSequences(viewport.hiddenRepSequences), sg
2892                           .getStartRes(), sg.getEndRes() + 1);
2893           c.calculate();
2894           c.verdict(false, viewport.ConsPercGaps);
2895           sg.cs.setConservation(c);
2896         }
2897         else
2898         {
2899           sg.cs.setConservation(null);
2900         }
2901       }
2902     }
2903
2904     if (alignPanel.getOverviewPanel() != null)
2905     {
2906       alignPanel.getOverviewPanel().updateOverviewImage();
2907     }
2908
2909     alignPanel.paintAlignment(true);
2910   }
2911
2912   /**
2913    * DOCUMENT ME!
2914    *
2915    * @param e
2916    *          DOCUMENT ME!
2917    */
2918   protected void modifyPID_actionPerformed(ActionEvent e)
2919   {
2920     if (viewport.getAbovePIDThreshold()
2921             && viewport.globalColourScheme != null)
2922     {
2923       SliderPanel.setPIDSliderSource(alignPanel, viewport
2924               .getGlobalColourScheme(), "Background");
2925       SliderPanel.showPIDSlider();
2926     }
2927   }
2928
2929   /**
2930    * DOCUMENT ME!
2931    *
2932    * @param e
2933    *          DOCUMENT ME!
2934    */
2935   protected void modifyConservation_actionPerformed(ActionEvent e)
2936   {
2937     if (viewport.getConservationSelected()
2938             && viewport.globalColourScheme != null)
2939     {
2940       SliderPanel.setConservationSlider(alignPanel,
2941               viewport.globalColourScheme, "Background");
2942       SliderPanel.showConservationSlider();
2943     }
2944   }
2945
2946   /**
2947    * DOCUMENT ME!
2948    *
2949    * @param e
2950    *          DOCUMENT ME!
2951    */
2952   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2953   {
2954     viewport.setConservationSelected(conservationMenuItem.isSelected());
2955
2956     viewport.setAbovePIDThreshold(false);
2957     abovePIDThreshold.setSelected(false);
2958
2959     changeColour(viewport.getGlobalColourScheme());
2960
2961     modifyConservation_actionPerformed(null);
2962   }
2963
2964   /**
2965    * DOCUMENT ME!
2966    *
2967    * @param e
2968    *          DOCUMENT ME!
2969    */
2970   public void abovePIDThreshold_actionPerformed(ActionEvent e)
2971   {
2972     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2973
2974     conservationMenuItem.setSelected(false);
2975     viewport.setConservationSelected(false);
2976
2977     changeColour(viewport.getGlobalColourScheme());
2978
2979     modifyPID_actionPerformed(null);
2980   }
2981
2982   /**
2983    * DOCUMENT ME!
2984    *
2985    * @param e
2986    *          DOCUMENT ME!
2987    */
2988   public void userDefinedColour_actionPerformed(ActionEvent e)
2989   {
2990     if (e.getActionCommand().equals("User Defined..."))
2991     {
2992       new UserDefinedColours(alignPanel, null);
2993     }
2994     else
2995     {
2996       UserColourScheme udc = (UserColourScheme) UserDefinedColours
2997               .getUserColourSchemes().get(e.getActionCommand());
2998
2999       changeColour(udc);
3000     }
3001   }
3002
3003   public void updateUserColourMenu()
3004   {
3005
3006     Component[] menuItems = colourMenu.getMenuComponents();
3007     int i, iSize = menuItems.length;
3008     for (i = 0; i < iSize; i++)
3009     {
3010       if (menuItems[i].getName() != null
3011               && menuItems[i].getName().equals("USER_DEFINED"))
3012       {
3013         colourMenu.remove(menuItems[i]);
3014         iSize--;
3015       }
3016     }
3017     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3018     {
3019       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3020               .getUserColourSchemes().keys();
3021
3022       while (userColours.hasMoreElements())
3023       {
3024         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3025                 userColours.nextElement().toString());
3026         radioItem.setName("USER_DEFINED");
3027         radioItem.addMouseListener(new MouseAdapter()
3028         {
3029           public void mousePressed(MouseEvent evt)
3030           {
3031             if (evt.isControlDown()
3032                     || SwingUtilities.isRightMouseButton(evt))
3033             {
3034               radioItem
3035                       .removeActionListener(radioItem.getActionListeners()[0]);
3036
3037               int option = JOptionPane.showInternalConfirmDialog(
3038                       jalview.gui.Desktop.desktop,
3039                       "Remove from default list?",
3040                       "Remove user defined colour",
3041                       JOptionPane.YES_NO_OPTION);
3042               if (option == JOptionPane.YES_OPTION)
3043               {
3044                 jalview.gui.UserDefinedColours
3045                         .removeColourFromDefaults(radioItem.getText());
3046                 colourMenu.remove(radioItem);
3047               }
3048               else
3049               {
3050                 radioItem.addActionListener(new ActionListener()
3051                 {
3052                   public void actionPerformed(ActionEvent evt)
3053                   {
3054                     userDefinedColour_actionPerformed(evt);
3055                   }
3056                 });
3057               }
3058             }
3059           }
3060         });
3061         radioItem.addActionListener(new ActionListener()
3062         {
3063           public void actionPerformed(ActionEvent evt)
3064           {
3065             userDefinedColour_actionPerformed(evt);
3066           }
3067         });
3068
3069         colourMenu.insert(radioItem, 15);
3070         colours.add(radioItem);
3071       }
3072     }
3073   }
3074
3075   /**
3076    * DOCUMENT ME!
3077    *
3078    * @param e
3079    *          DOCUMENT ME!
3080    */
3081   public void PIDColour_actionPerformed(ActionEvent e)
3082   {
3083     changeColour(new PIDColourScheme());
3084   }
3085
3086   /**
3087    * DOCUMENT ME!
3088    *
3089    * @param e
3090    *          DOCUMENT ME!
3091    */
3092   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3093   {
3094     changeColour(new Blosum62ColourScheme());
3095   }
3096
3097   /**
3098    * DOCUMENT ME!
3099    *
3100    * @param e
3101    *          DOCUMENT ME!
3102    */
3103   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3104   {
3105     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3106     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3107             .getAlignment().getSequenceAt(0), null);
3108     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3109             viewport.alignment));
3110     alignPanel.paintAlignment(true);
3111   }
3112
3113   /**
3114    * DOCUMENT ME!
3115    *
3116    * @param e
3117    *          DOCUMENT ME!
3118    */
3119   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3120   {
3121     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3122     AlignmentSorter.sortByID(viewport.getAlignment());
3123     addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3124     alignPanel.paintAlignment(true);
3125   }
3126
3127   /**
3128    * DOCUMENT ME!
3129    *
3130    * @param e
3131    *          DOCUMENT ME!
3132    */
3133   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3134   {
3135     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3136     AlignmentSorter.sortByLength(viewport.getAlignment());
3137     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3138             viewport.alignment));
3139     alignPanel.paintAlignment(true);
3140   }
3141
3142   /**
3143    * DOCUMENT ME!
3144    *
3145    * @param e
3146    *          DOCUMENT ME!
3147    */
3148   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3149   {
3150     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3151     AlignmentSorter.sortByGroup(viewport.getAlignment());
3152     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3153             viewport.alignment));
3154
3155     alignPanel.paintAlignment(true);
3156   }
3157
3158   /**
3159    * DOCUMENT ME!
3160    *
3161    * @param e
3162    *          DOCUMENT ME!
3163    */
3164   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3165   {
3166     new RedundancyPanel(alignPanel, this);
3167   }
3168
3169   /**
3170    * DOCUMENT ME!
3171    *
3172    * @param e
3173    *          DOCUMENT ME!
3174    */
3175   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3176   {
3177     if ((viewport.getSelectionGroup() == null)
3178             || (viewport.getSelectionGroup().getSize() < 2))
3179     {
3180       JOptionPane.showInternalMessageDialog(this,
3181               "You must select at least 2 sequences.", "Invalid Selection",
3182               JOptionPane.WARNING_MESSAGE);
3183     }
3184     else
3185     {
3186       JInternalFrame frame = new JInternalFrame();
3187       frame.setContentPane(new PairwiseAlignPanel(viewport));
3188       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3189     }
3190   }
3191
3192   /**
3193    * DOCUMENT ME!
3194    *
3195    * @param e
3196    *          DOCUMENT ME!
3197    */
3198   public void PCAMenuItem_actionPerformed(ActionEvent e)
3199   {
3200     if (((viewport.getSelectionGroup() != null)
3201             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3202             .getSelectionGroup().getSize() > 0))
3203             || (viewport.getAlignment().getHeight() < 4))
3204     {
3205       JOptionPane.showInternalMessageDialog(this,
3206               "Principal component analysis must take\n"
3207                       + "at least 4 input sequences.",
3208               "Sequence selection insufficient",
3209               JOptionPane.WARNING_MESSAGE);
3210
3211       return;
3212     }
3213
3214     new PCAPanel(alignPanel);
3215   }
3216
3217   public void autoCalculate_actionPerformed(ActionEvent e)
3218   {
3219     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3220     if (viewport.autoCalculateConsensus)
3221     {
3222       viewport.firePropertyChange("alignment", null, viewport
3223               .getAlignment().getSequences());
3224     }
3225   }
3226
3227   /**
3228    * DOCUMENT ME!
3229    *
3230    * @param e
3231    *          DOCUMENT ME!
3232    */
3233   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3234   {
3235     NewTreePanel("AV", "PID", "Average distance tree using PID");
3236   }
3237
3238   /**
3239    * DOCUMENT ME!
3240    *
3241    * @param e
3242    *          DOCUMENT ME!
3243    */
3244   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3245   {
3246     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3247   }
3248
3249   /**
3250    * DOCUMENT ME!
3251    *
3252    * @param e
3253    *          DOCUMENT ME!
3254    */
3255   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3256   {
3257     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3258   }
3259
3260   /**
3261    * DOCUMENT ME!
3262    *
3263    * @param e
3264    *          DOCUMENT ME!
3265    */
3266   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3267   {
3268     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3269   }
3270
3271   /**
3272    * DOCUMENT ME!
3273    *
3274    * @param type
3275    *          DOCUMENT ME!
3276    * @param pwType
3277    *          DOCUMENT ME!
3278    * @param title
3279    *          DOCUMENT ME!
3280    */
3281   void NewTreePanel(String type, String pwType, String title)
3282   {
3283     TreePanel tp;
3284
3285     if (viewport.getSelectionGroup() != null)
3286     {
3287       if (viewport.getSelectionGroup().getSize() < 3)
3288       {
3289         JOptionPane
3290                 .showMessageDialog(
3291                         Desktop.desktop,
3292                         "You need to have more than two sequences selected to build a tree!",
3293                         "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3294         return;
3295       }
3296
3297       int s = 0;
3298       SequenceGroup sg = viewport.getSelectionGroup();
3299
3300       /* Decide if the selection is a column region */
3301       while (s < sg.getSize())
3302       {
3303         if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3304                 .getEndRes())
3305         {
3306           JOptionPane
3307                   .showMessageDialog(
3308                           Desktop.desktop,
3309                           "The selected region to create a tree may\nonly contain residues or gaps.\n"
3310                                   + "Try using the Pad function in the edit menu,\n"
3311                                   + "or one of the multiple sequence alignment web services.",
3312                           "Sequences in selection are not aligned",
3313                           JOptionPane.WARNING_MESSAGE);
3314
3315           return;
3316         }
3317       }
3318
3319       title = title + " on region";
3320       tp = new TreePanel(alignPanel, type, pwType);
3321     }
3322     else
3323     {
3324       // are the sequences aligned?
3325       if (!viewport.alignment.isAligned())
3326       {
3327         JOptionPane
3328                 .showMessageDialog(
3329                         Desktop.desktop,
3330                         "The sequences must be aligned before creating a tree.\n"
3331                                 + "Try using the Pad function in the edit menu,\n"
3332                                 + "or one of the multiple sequence alignment web services.",
3333                         "Sequences not aligned",
3334                         JOptionPane.WARNING_MESSAGE);
3335
3336         return;
3337       }
3338
3339       if (viewport.alignment.getHeight() < 2)
3340       {
3341         return;
3342       }
3343
3344       tp = new TreePanel(alignPanel, type, pwType);
3345     }
3346
3347     title += " from ";
3348
3349     if (viewport.viewName != null)
3350     {
3351       title += viewport.viewName + " of ";
3352     }
3353
3354     title += this.title;
3355
3356     Desktop.addInternalFrame(tp, title, 600, 500);
3357   }
3358
3359   /**
3360    * DOCUMENT ME!
3361    *
3362    * @param title
3363    *          DOCUMENT ME!
3364    * @param order
3365    *          DOCUMENT ME!
3366    */
3367   public void addSortByOrderMenuItem(String title,
3368           final AlignmentOrder order)
3369   {
3370     final JMenuItem item = new JMenuItem("by " + title);
3371     sort.add(item);
3372     item.addActionListener(new java.awt.event.ActionListener()
3373     {
3374       public void actionPerformed(ActionEvent e)
3375       {
3376         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3377
3378         // TODO: JBPNote - have to map order entries to curent SequenceI
3379         // pointers
3380         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3381
3382         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3383                 viewport.alignment));
3384
3385         alignPanel.paintAlignment(true);
3386       }
3387     });
3388   }
3389
3390   /**
3391    * Add a new sort by annotation score menu item
3392    *
3393    * @param sort
3394    *          the menu to add the option to
3395    * @param scoreLabel
3396    *          the label used to retrieve scores for each sequence on the
3397    *          alignment
3398    */
3399   public void addSortByAnnotScoreMenuItem(JMenu sort,
3400           final String scoreLabel)
3401   {
3402     final JMenuItem item = new JMenuItem(scoreLabel);
3403     sort.add(item);
3404     item.addActionListener(new java.awt.event.ActionListener()
3405     {
3406       public void actionPerformed(ActionEvent e)
3407       {
3408         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3409         AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3410                 .getAlignment());// ,viewport.getSelectionGroup());
3411         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3412                 viewport.alignment));
3413         alignPanel.paintAlignment(true);
3414       }
3415     });
3416   }
3417
3418   /**
3419    * last hash for alignment's annotation array - used to minimise cost of
3420    * rebuild.
3421    */
3422   protected int _annotationScoreVectorHash;
3423
3424   /**
3425    * search the alignment and rebuild the sort by annotation score submenu the
3426    * last alignment annotation vector hash is stored to minimize cost of
3427    * rebuilding in subsequence calls.
3428    *
3429    */
3430   public void buildSortByAnnotationScoresMenu()
3431   {
3432     if (viewport.alignment.getAlignmentAnnotation() == null)
3433     {
3434       return;
3435     }
3436
3437     if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3438     {
3439       sortByAnnotScore.removeAll();
3440       // almost certainly a quicker way to do this - but we keep it simple
3441       Hashtable scoreSorts = new Hashtable();
3442       AlignmentAnnotation aann[];
3443       Enumeration sq = viewport.alignment.getSequences().elements();
3444       while (sq.hasMoreElements())
3445       {
3446         aann = ((SequenceI) sq.nextElement()).getAnnotation();
3447         for (int i = 0; aann != null && i < aann.length; i++)
3448         {
3449           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3450           {
3451             scoreSorts.put(aann[i].label, aann[i].label);
3452           }
3453         }
3454       }
3455       Enumeration labels = scoreSorts.keys();
3456       while (labels.hasMoreElements())
3457       {
3458         addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3459                 .nextElement());
3460       }
3461       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3462       scoreSorts.clear();
3463
3464       _annotationScoreVectorHash = viewport.alignment
3465               .getAlignmentAnnotation().hashCode();
3466     }
3467   }
3468
3469   /**
3470    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3471    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3472    * call. Listeners are added to remove the menu item when the treePanel is
3473    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3474    * modified.
3475    *
3476    * @param treePanel
3477    *          Displayed tree window.
3478    * @param title
3479    *          SortBy menu item title.
3480    */
3481   public void buildTreeMenu()
3482   {
3483     sortByTreeMenu.removeAll();
3484
3485     Vector comps = (Vector) PaintRefresher.components.get(viewport
3486             .getSequenceSetId());
3487     Vector treePanels = new Vector();
3488     int i, iSize = comps.size();
3489     for (i = 0; i < iSize; i++)
3490     {
3491       if (comps.elementAt(i) instanceof TreePanel)
3492       {
3493         treePanels.add(comps.elementAt(i));
3494       }
3495     }
3496
3497     iSize = treePanels.size();
3498
3499     if (iSize < 1)
3500     {
3501       sortByTreeMenu.setVisible(false);
3502       return;
3503     }
3504
3505     sortByTreeMenu.setVisible(true);
3506
3507     for (i = 0; i < treePanels.size(); i++)
3508     {
3509       TreePanel tp = (TreePanel) treePanels.elementAt(i);
3510       final JMenuItem item = new JMenuItem(tp.getTitle());
3511       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3512       item.addActionListener(new java.awt.event.ActionListener()
3513       {
3514         public void actionPerformed(ActionEvent e)
3515         {
3516           SequenceI[] oldOrder = viewport.getAlignment()
3517                   .getSequencesArray();
3518           AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3519
3520           addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3521                   viewport.alignment));
3522
3523           alignPanel.paintAlignment(true);
3524         }
3525       });
3526
3527       sortByTreeMenu.add(item);
3528     }
3529   }
3530
3531   /**
3532    * Work out whether the whole set of sequences or just the selected set will
3533    * be submitted for multiple alignment.
3534    *
3535    */
3536   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3537   {
3538     // Now, check we have enough sequences
3539     AlignmentView msa = null;
3540
3541     if ((viewport.getSelectionGroup() != null)
3542             && (viewport.getSelectionGroup().getSize() > 1))
3543     {
3544       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3545       // some common interface!
3546       /*
3547        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3548        * SequenceI[sz = seqs.getSize(false)];
3549        *
3550        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3551        * seqs.getSequenceAt(i); }
3552        */
3553       msa = viewport.getAlignmentView(true);
3554     }
3555     else
3556     {
3557       /*
3558        * Vector seqs = viewport.getAlignment().getSequences();
3559        *
3560        * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3561        *
3562        * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3563        * seqs.elementAt(i); } }
3564        */
3565       msa = viewport.getAlignmentView(false);
3566     }
3567     return msa;
3568   }
3569
3570   /**
3571    * Decides what is submitted to a secondary structure prediction service: the
3572    * first sequence in the alignment, or in the current selection, or, if the
3573    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3574    * region or the whole alignment. (where the first sequence in the set is the
3575    * one that the prediction will be for).
3576    */
3577   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3578   {
3579     AlignmentView seqs = null;
3580
3581     if ((viewport.getSelectionGroup() != null)
3582             && (viewport.getSelectionGroup().getSize() > 0))
3583     {
3584       seqs = viewport.getAlignmentView(true);
3585     }
3586     else
3587     {
3588       seqs = viewport.getAlignmentView(false);
3589     }
3590     // limit sequences - JBPNote in future - could spawn multiple prediction
3591     // jobs
3592     // TODO: viewport.alignment.isAligned is a global state - the local
3593     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3594     if (!viewport.alignment.isAligned())
3595     {
3596       seqs.setSequences(new SeqCigar[]
3597       { seqs.getSequences()[0] });
3598       // TODO: if seqs.getSequences().length>1 then should really have warned user!
3599
3600     }
3601     return seqs;
3602   }
3603
3604   /**
3605    * DOCUMENT ME!
3606    *
3607    * @param e
3608    *          DOCUMENT ME!
3609    */
3610   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3611   {
3612     // Pick the tree file
3613     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3614             .getProperty("LAST_DIRECTORY"));
3615     chooser.setFileView(new JalviewFileView());
3616     chooser.setDialogTitle("Select a newick-like tree file");
3617     chooser.setToolTipText("Load a tree file");
3618
3619     int value = chooser.showOpenDialog(null);
3620
3621     if (value == JalviewFileChooser.APPROVE_OPTION)
3622     {
3623       String choice = chooser.getSelectedFile().getPath();
3624       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3625       jalview.io.NewickFile fin = null;
3626       try
3627       {
3628         fin = new jalview.io.NewickFile(choice, "File");
3629         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3630       } catch (Exception ex)
3631       {
3632         JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3633                 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3634         ex.printStackTrace();
3635       }
3636       if (fin != null && fin.hasWarningMessage())
3637       {
3638         JOptionPane.showMessageDialog(Desktop.desktop, fin
3639                 .getWarningMessage(), "Possible problem with tree file",
3640                 JOptionPane.WARNING_MESSAGE);
3641       }
3642     }
3643   }
3644
3645   public TreePanel ShowNewickTree(NewickFile nf, String title)
3646   {
3647     return ShowNewickTree(nf, title, 600, 500, 4, 5);
3648   }
3649
3650   public TreePanel ShowNewickTree(NewickFile nf, String title,
3651           AlignmentView input)
3652   {
3653     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3654   }
3655
3656   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3657           int h, int x, int y)
3658   {
3659     return ShowNewickTree(nf, title, null, w, h, x, y);
3660   }
3661
3662   /**
3663    * Add a treeviewer for the tree extracted from a newick file object to the
3664    * current alignment view
3665    *
3666    * @param nf
3667    *          the tree
3668    * @param title
3669    *          tree viewer title
3670    * @param input
3671    *          Associated alignment input data (or null)
3672    * @param w
3673    *          width
3674    * @param h
3675    *          height
3676    * @param x
3677    *          position
3678    * @param y
3679    *          position
3680    * @return TreePanel handle
3681    */
3682   public TreePanel ShowNewickTree(NewickFile nf, String title,
3683           AlignmentView input, int w, int h, int x, int y)
3684   {
3685     TreePanel tp = null;
3686
3687     try
3688     {
3689       nf.parse();
3690
3691       if (nf.getTree() != null)
3692       {
3693         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3694
3695         tp.setSize(w, h);
3696
3697         if (x > 0 && y > 0)
3698         {
3699           tp.setLocation(x, y);
3700         }
3701
3702         Desktop.addInternalFrame(tp, title, w, h);
3703       }
3704     } catch (Exception ex)
3705     {
3706       ex.printStackTrace();
3707     }
3708
3709     return tp;
3710   }
3711
3712   /**
3713    * Generates menu items and listener event actions for web service clients
3714    *
3715    */
3716   public void BuildWebServiceMenu()
3717   {
3718     // TODO: add support for context dependent disabling of services based on
3719     // alignment and current selection
3720     // TODO: add additional serviceHandle parameter to specify abstract handler
3721     // class independently of AbstractName
3722     // TODO: add in rediscovery GUI function to restart discoverer
3723     // TODO: group services by location as well as function and/or introduce
3724     // object broker mechanism.
3725     if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
3726     {
3727       // TODO: refactor to allow list of AbstractName/Handler bindings to be
3728       // stored or retrieved from elsewhere
3729       Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3730       Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3731       Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3732       // TODO: move GUI generation code onto service implementation - so a
3733       // client instance attaches itself to the GUI with method call like
3734       // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3735       // alignframe)
3736       Vector wsmenu = new Vector();
3737       final IProgressIndicator af = this;
3738       if (msaws != null)
3739       {
3740         // Add any Multiple Sequence Alignment Services
3741         final JMenu msawsmenu = new JMenu("Alignment");
3742         for (int i = 0, j = msaws.size(); i < j; i++)
3743         {
3744           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3745                   .get(i);
3746           jalview.ws.WSClient impl = jalview.ws.Discoverer
3747                   .getServiceClient(sh);
3748           impl.attachWSMenuEntry(msawsmenu, this);
3749
3750         }
3751         wsmenu.add(msawsmenu);
3752       }
3753       if (secstrpr != null)
3754       {
3755         // Add any secondary structure prediction services
3756         final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3757         for (int i = 0, j = secstrpr.size(); i < j; i++)
3758         {
3759           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3760                   .get(i);
3761           jalview.ws.WSClient impl = jalview.ws.Discoverer
3762                   .getServiceClient(sh);
3763           impl.attachWSMenuEntry(secstrmenu, this);
3764         }
3765         wsmenu.add(secstrmenu);
3766       }
3767       if (seqsrch != null)
3768       {
3769         // Add any sequence search services
3770         final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3771         for (int i = 0, j = seqsrch.size(); i < j; i++)
3772         {
3773           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3774                   .elementAt(i);
3775           jalview.ws.WSClient impl = jalview.ws.Discoverer
3776                   .getServiceClient(sh);
3777           impl.attachWSMenuEntry(seqsrchmenu, this);
3778         }
3779         // finally, add the whole shebang onto the webservices menu
3780         wsmenu.add(seqsrchmenu);
3781       }
3782       resetWebServiceMenu();
3783       for (int i = 0, j = wsmenu.size(); i < j; i++)
3784       {
3785         webService.add((JMenu) wsmenu.get(i));
3786       }
3787     }
3788     else
3789     {
3790       resetWebServiceMenu();
3791       this.webService.add(this.webServiceNoServices);
3792     }
3793   }
3794
3795   /**
3796    * empty the web service menu and add any ad-hoc functions not dynamically
3797    * discovered.
3798    *
3799    */
3800   private void resetWebServiceMenu()
3801   {
3802     webService.removeAll();
3803     build_fetchdbmenu(webService);
3804   }
3805
3806   /*
3807    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3808    * chooser = new JalviewFileChooser(jalview.bin.Cache.
3809    * getProperty("LAST_DIRECTORY"));
3810    *
3811    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3812    * to Vamsas file"); chooser.setToolTipText("Export");
3813    *
3814    * int value = chooser.showSaveDialog(this);
3815    *
3816    * if (value == JalviewFileChooser.APPROVE_OPTION) {
3817    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3818    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3819    * chooser.getSelectedFile().getAbsolutePath(), this); } }
3820    */
3821   /**
3822    * prototype of an automatically enabled/disabled analysis function
3823    *
3824    */
3825   protected void setShowProductsEnabled()
3826   {
3827     SequenceI[] selection = viewport.getSequenceSelection();
3828     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3829             viewport.getAlignment().getDataset()))
3830     {
3831       showProducts.setEnabled(true);
3832
3833     }
3834     else
3835     {
3836       showProducts.setEnabled(false);
3837     }
3838   }
3839
3840   /**
3841    * search selection for sequence xRef products and build the show products
3842    * menu.
3843    *
3844    * @param selection
3845    * @param dataset
3846    * @return true if showProducts menu should be enabled.
3847    */
3848   public boolean canShowProducts(SequenceI[] selection,
3849           boolean isRegionSelection, Alignment dataset)
3850   {
3851     boolean showp = false;
3852     try
3853     {
3854       showProducts.removeAll();
3855       final boolean dna = viewport.getAlignment().isNucleotide();
3856       final Alignment ds = dataset;
3857       String[] ptypes = (selection == null || selection.length == 0) ? null
3858               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
3859       // Object[] prods =
3860       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
3861       // selection, dataset, true);
3862       final SequenceI[] sel = selection;
3863       for (int t = 0; ptypes != null && t < ptypes.length; t++)
3864       {
3865         showp = true;
3866         final boolean isRegSel = isRegionSelection;
3867         final AlignFrame af = this;
3868         final String source = ptypes[t];
3869         JMenuItem xtype = new JMenuItem(ptypes[t]);
3870         xtype.addActionListener(new ActionListener()
3871         {
3872
3873           public void actionPerformed(ActionEvent e)
3874           {
3875             // TODO: new thread for this call with vis-delay
3876             af.showProductsFor(af.viewport.getSequenceSelection(), ds,
3877                     isRegSel, dna, source);
3878           }
3879
3880         });
3881         showProducts.add(xtype);
3882       }
3883       showProducts.setVisible(showp);
3884       showProducts.setEnabled(showp);
3885     } catch (Exception e)
3886     {
3887       jalview.bin.Cache.log
3888               .warn(
3889                       "canTranslate threw an exception - please report to help@jalview.org",
3890                       e);
3891       return false;
3892     }
3893     return showp;
3894   }
3895
3896   protected void showProductsFor(SequenceI[] sel, Alignment ds,
3897           boolean isRegSel, boolean dna, String source)
3898   {
3899     final boolean fisRegSel = isRegSel;
3900     final boolean fdna = dna;
3901     final String fsrc = source;
3902     final AlignFrame ths = this;
3903     final SequenceI[] fsel = sel;
3904     Runnable foo = new Runnable()
3905     {
3906
3907       public void run()
3908       {
3909         final long sttime = System.currentTimeMillis();
3910         ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
3911         try
3912         {
3913           Alignment ds = ths.getViewport().alignment.getDataset(); // update
3914           // our local
3915           // dataset
3916           // reference
3917           Alignment prods = CrossRef
3918                   .findXrefSequences(fsel, fdna, fsrc, ds);
3919           if (prods != null)
3920           {
3921             SequenceI[] sprods = new SequenceI[prods.getHeight()];
3922             for (int s = 0; s < sprods.length; s++)
3923             {
3924               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
3925               if (ds.getSequences() == null
3926                       || !ds.getSequences().contains(
3927                               sprods[s].getDatasetSequence()))
3928                 ds.addSequence(sprods[s].getDatasetSequence());
3929               sprods[s].updatePDBIds();
3930             }
3931             Alignment al = new Alignment(sprods);
3932             AlignedCodonFrame[] cf = prods.getCodonFrames();
3933             al.setDataset(ds);
3934             for (int s = 0; cf != null && s < cf.length; s++)
3935             {
3936               al.addCodonFrame(cf[s]);
3937               cf[s] = null;
3938             }
3939             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
3940                     DEFAULT_HEIGHT);
3941             String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
3942                     + " for " + ((fisRegSel) ? "selected region of " : "")
3943                     + getTitle();
3944             Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
3945                     DEFAULT_HEIGHT);
3946           }
3947           else
3948           {
3949             System.err.println("No Sequences generated for xRef type "
3950                     + fsrc);
3951           }
3952         } catch (Exception e)
3953         {
3954           jalview.bin.Cache.log.error(
3955                   "Exception when finding crossreferences", e);
3956         } catch (OutOfMemoryError e)
3957         {
3958           new OOMWarning("whilst fetching crossreferences", e);
3959         } catch (Error e)
3960         {
3961           jalview.bin.Cache.log.error("Error when finding crossreferences",
3962                   e);
3963         }
3964         ths.setProgressBar("Finished searching for sequences from " + fsrc,
3965                 sttime);
3966       }
3967
3968     };
3969     Thread frunner = new Thread(foo);
3970     frunner.start();
3971   }
3972
3973   public boolean canShowTranslationProducts(SequenceI[] selection,
3974           AlignmentI alignment)
3975   {
3976     // old way
3977     try
3978     {
3979       return (jalview.analysis.Dna.canTranslate(selection, viewport
3980               .getViewAsVisibleContigs(true)));
3981     } catch (Exception e)
3982     {
3983       jalview.bin.Cache.log
3984               .warn(
3985                       "canTranslate threw an exception - please report to help@jalview.org",
3986                       e);
3987       return false;
3988     }
3989   }
3990
3991   public void showProducts_actionPerformed(ActionEvent e)
3992   {
3993     // /////////////////////////////
3994     // Collect Data to be translated/transferred
3995
3996     SequenceI[] selection = viewport.getSequenceSelection();
3997     AlignmentI al = null;
3998     try
3999     {
4000       al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4001               .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4002               viewport.getAlignment().getDataset());
4003     } catch (Exception ex)
4004     {
4005       al = null;
4006       jalview.bin.Cache.log.debug("Exception during translation.", ex);
4007     }
4008     if (al == null)
4009     {
4010       JOptionPane
4011               .showMessageDialog(
4012                       Desktop.desktop,
4013                       "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4014                       "Translation Failed", JOptionPane.WARNING_MESSAGE);
4015     }
4016     else
4017     {
4018       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4019       Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4020               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4021     }
4022   }
4023
4024   public void showTranslation_actionPerformed(ActionEvent e)
4025   {
4026     // /////////////////////////////
4027     // Collect Data to be translated/transferred
4028
4029     SequenceI[] selection = viewport.getSequenceSelection();
4030     String[] seqstring = viewport.getViewAsString(true);
4031     AlignmentI al = null;
4032     try
4033     {
4034       al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4035               viewport.getViewAsVisibleContigs(true), viewport
4036                       .getGapCharacter(), viewport.alignment
4037                       .getAlignmentAnnotation(), viewport.alignment
4038                       .getWidth(), viewport.getAlignment().getDataset());
4039     } catch (Exception ex)
4040     {
4041       al = null;
4042       jalview.bin.Cache.log.debug("Exception during translation.", ex);
4043     }
4044     if (al == null)
4045     {
4046       JOptionPane
4047               .showMessageDialog(
4048                       Desktop.desktop,
4049                       "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4050                       "Translation Failed", JOptionPane.WARNING_MESSAGE);
4051     }
4052     else
4053     {
4054       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4055       Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4056               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4057     }
4058   }
4059
4060   /**
4061    * Try to load a features file onto the alignment.
4062    *
4063    * @param file
4064    *          contents or path to retrieve file
4065    * @param type
4066    *          access mode of file (see jalview.io.AlignFile)
4067    * @return true if features file was parsed corectly.
4068    */
4069   public boolean parseFeaturesFile(String file, String type)
4070   {
4071     boolean featuresFile = false;
4072     try
4073     {
4074       featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4075               .getDataset(), alignPanel.seqPanel.seqCanvas
4076               .getFeatureRenderer().featureColours, false);
4077     } catch (Exception ex)
4078     {
4079       ex.printStackTrace();
4080     }
4081
4082     if (featuresFile)
4083     {
4084       viewport.showSequenceFeatures = true;
4085       showSeqFeatures.setSelected(true);
4086       if (alignPanel.seqPanel.seqCanvas.fr != null)
4087       {
4088         // update the min/max ranges where necessary
4089         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4090       }
4091       alignPanel.paintAlignment(true);
4092     }
4093
4094     return featuresFile;
4095   }
4096
4097   public void dragEnter(DropTargetDragEvent evt)
4098   {
4099   }
4100
4101   public void dragExit(DropTargetEvent evt)
4102   {
4103   }
4104
4105   public void dragOver(DropTargetDragEvent evt)
4106   {
4107   }
4108
4109   public void dropActionChanged(DropTargetDragEvent evt)
4110   {
4111   }
4112
4113   public void drop(DropTargetDropEvent evt)
4114   {
4115     Transferable t = evt.getTransferable();
4116     java.util.List files = null;
4117
4118     try
4119     {
4120       DataFlavor uriListFlavor = new DataFlavor(
4121               "text/uri-list;class=java.lang.String");
4122       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4123       {
4124         // Works on Windows and MacOSX
4125         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4126         files = (java.util.List) t
4127                 .getTransferData(DataFlavor.javaFileListFlavor);
4128       }
4129       else if (t.isDataFlavorSupported(uriListFlavor))
4130       {
4131         // This is used by Unix drag system
4132         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4133         String data = (String) t.getTransferData(uriListFlavor);
4134         files = new java.util.ArrayList(1);
4135         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4136                 data, "\r\n"); st.hasMoreTokens();)
4137         {
4138           String s = st.nextToken();
4139           if (s.startsWith("#"))
4140           {
4141             // the line is a comment (as per the RFC 2483)
4142             continue;
4143           }
4144
4145           java.net.URI uri = new java.net.URI(s);
4146           // check to see if we can handle this kind of URI
4147           if (uri.getScheme().toLowerCase().startsWith("http"))
4148           {
4149             files.add(uri.toString());
4150           }
4151           else
4152           {
4153             // otherwise preserve old behaviour: catch all for file objects
4154             java.io.File file = new java.io.File(uri);
4155             files.add(file.toString());
4156           }
4157         }
4158       }
4159     } catch (Exception e)
4160     {
4161       e.printStackTrace();
4162     }
4163     if (files != null)
4164     {
4165       try
4166       {
4167
4168         for (int i = 0; i < files.size(); i++)
4169         {
4170           loadJalviewDataFile(files.get(i).toString());
4171         }
4172       } catch (Exception ex)
4173       {
4174         ex.printStackTrace();
4175       }
4176     }
4177   }
4178
4179   /**
4180    * Attempt to load a "dropped" file or URL string: First by testing whether
4181    * it's and Annotation file, then a JNet file, and finally a features file. If
4182    * all are false then the user may have dropped an alignment file onto this
4183    * AlignFrame.
4184    *
4185    * @param file
4186    *          either a filename or a URL string.
4187    */
4188   public void loadJalviewDataFile(String file)
4189   {
4190     try
4191     {
4192       String protocol = jalview.io.FormatAdapter.FILE;
4193       String f = file.toLowerCase();
4194       if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4195               || f.indexOf("file:") == 0)
4196       {
4197         protocol = jalview.io.FormatAdapter.URL;
4198       }
4199
4200       boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4201               viewport.alignment, file, protocol);
4202
4203       if (!isAnnotation)
4204       {
4205         // try to see if its a JNet 'concise' style annotation file *before* we
4206         // try to parse it as a features file
4207         String format = new IdentifyFile().Identify(file, protocol);
4208         if (format.equalsIgnoreCase("JnetFile"))
4209         {
4210           jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4211                   protocol);
4212           new JnetAnnotationMaker().add_annotation(predictions, viewport
4213                   .getAlignment(), 0, false);
4214           isAnnotation = true;
4215         }
4216         else
4217         {
4218           // try to parse it as a features file
4219           boolean isGroupsFile = parseFeaturesFile(file, protocol);
4220           // if it wasn't a features file then we just treat it as a general
4221           // alignment file to load into the current view.
4222           if (!isGroupsFile)
4223           {
4224             new FileLoader().LoadFile(viewport, file, protocol, format);
4225           }
4226           else
4227           {
4228             alignPanel.paintAlignment(true);
4229           }
4230         }
4231       }
4232       if (isAnnotation)
4233       {
4234
4235         alignPanel.adjustAnnotationHeight();
4236         viewport.updateSequenceIdColours();
4237         buildSortByAnnotationScoresMenu();
4238         alignPanel.paintAlignment(true);
4239       }
4240     } catch (Exception ex)
4241     {
4242       ex.printStackTrace();
4243     }
4244   }
4245
4246   public void tabSelectionChanged(int index)
4247   {
4248     if (index > -1)
4249     {
4250       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4251       viewport = alignPanel.av;
4252       setMenusFromViewport(viewport);
4253     }
4254   }
4255
4256   public void tabbedPane_mousePressed(MouseEvent e)
4257   {
4258     if (SwingUtilities.isRightMouseButton(e))
4259     {
4260       String reply = JOptionPane.showInternalInputDialog(this,
4261               "Enter View Name", "Edit View Name",
4262               JOptionPane.QUESTION_MESSAGE);
4263
4264       if (reply != null)
4265       {
4266         viewport.viewName = reply;
4267         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4268       }
4269     }
4270   }
4271
4272   public AlignViewport getCurrentView()
4273   {
4274     return viewport;
4275   }
4276
4277   /**
4278    * Open the dialog for regex description parsing.
4279    */
4280   protected void extractScores_actionPerformed(ActionEvent e)
4281   {
4282     ParseProperties pp = new jalview.analysis.ParseProperties(
4283             viewport.alignment);
4284     // TODO: verify regex and introduce GUI dialog for version 2.5
4285     // if (pp.getScoresFromDescription("col", "score column ",
4286     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4287     // true)>0)
4288     if (pp.getScoresFromDescription("description column",
4289             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4290     {
4291       buildSortByAnnotationScoresMenu();
4292     }
4293   }
4294
4295   /*
4296    * (non-Javadoc)
4297    *
4298    * @see
4299    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4300    * )
4301    */
4302   protected void showDbRefs_actionPerformed(ActionEvent e)
4303   {
4304     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4305   }
4306
4307   /*
4308    * (non-Javadoc)
4309    *
4310    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4311    * ActionEvent)
4312    */
4313   protected void showNpFeats_actionPerformed(ActionEvent e)
4314   {
4315     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4316   }
4317
4318   /**
4319    * find the viewport amongst the tabs in this alignment frame and close that
4320    * tab
4321    *
4322    * @param av
4323    */
4324   public boolean closeView(AlignViewport av)
4325   {
4326     if (viewport == av)
4327     {
4328       this.closeMenuItem_actionPerformed(false);
4329       return true;
4330     }
4331     Component[] comp = tabbedPane.getComponents();
4332     for (int i = 0; comp != null && i < comp.length; i++)
4333     {
4334       if (comp[i] instanceof AlignmentPanel)
4335       {
4336         if (((AlignmentPanel) comp[i]).av == av)
4337         {
4338           // close the view.
4339           closeView((AlignmentPanel) comp[i]);
4340           return true;
4341         }
4342       }
4343     }
4344     return false;
4345   }
4346
4347   protected void build_fetchdbmenu(JMenu webService)
4348   {
4349     // Temporary hack - DBRef Fetcher always top level ws entry.
4350     // TODO We probably want to store a sequence database checklist in
4351     // preferences and have checkboxes.. rather than individual sources selected
4352     // here
4353     JMenu rfetch = new JMenu("Fetch DB References");
4354     rfetch
4355             .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4356     webService.add(rfetch);
4357
4358     JMenuItem fetchr = new JMenuItem("Standard Databases");
4359     fetchr
4360             .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4361     fetchr.addActionListener(new ActionListener()
4362     {
4363
4364       public void actionPerformed(ActionEvent e)
4365       {
4366         new Thread(new Runnable()
4367         {
4368
4369           public void run()
4370           {
4371             new jalview.ws.DBRefFetcher(alignPanel.av
4372                     .getSequenceSelection(), alignPanel.alignFrame)
4373                     .fetchDBRefs(false);
4374           }
4375         }).start();
4376
4377       }
4378
4379     });
4380     rfetch.add(fetchr);
4381     JMenu dfetch = new JMenu();
4382     rfetch.add(dfetch);
4383     jalview.ws.SequenceFetcher sf = SequenceFetcher
4384             .getSequenceFetcherSingleton(this);
4385     String[] otherdb = sf.getOrderedSupportedSources();
4386     // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4387     // jalview.util.QuickSort.sort(otherdb, otherdb);
4388     int comp = 0, mcomp = 15;
4389     String mname = null;
4390     if (otherdb != null && otherdb.length > 0)
4391     {
4392       for (int i = 0; i < otherdb.length; i++)
4393       {
4394         String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4395         if (mname == null)
4396         {
4397           mname = "from '" + dbname + "'";
4398         }
4399         fetchr = new JMenuItem(otherdb[i]);
4400         final String[] dassource = new String[]
4401         { otherdb[i] };
4402         fetchr.addActionListener(new ActionListener()
4403         {
4404
4405           public void actionPerformed(ActionEvent e)
4406           {
4407             new Thread(new Runnable()
4408             {
4409
4410               public void run()
4411               {
4412                 new jalview.ws.DBRefFetcher(alignPanel.av
4413                         .getSequenceSelection(), alignPanel.alignFrame,
4414                         dassource).fetchDBRefs(false);
4415               }
4416             }).start();
4417           }
4418
4419         });
4420         fetchr.setToolTipText("Retrieve from " + dbname);
4421         dfetch.add(fetchr);
4422         if (comp++ == mcomp || i == (otherdb.length - 1))
4423         {
4424           dfetch.setText(mname + " to '" + dbname + "'");
4425           rfetch.add(dfetch);
4426           dfetch = new JMenu();
4427           mname = null;
4428           comp = 0;
4429         }
4430       }
4431     }
4432   }
4433
4434   /**
4435    * Left justify the whole alignment.
4436    */
4437   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4438   {
4439     AlignmentI al = viewport.getAlignment();
4440     al.justify(false);
4441     viewport.firePropertyChange("alignment", null, al);
4442   }
4443
4444   /**
4445    * Right justify the whole alignment.
4446    */
4447   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4448   {
4449     AlignmentI al = viewport.getAlignment();
4450     al.justify(true);
4451     viewport.firePropertyChange("alignment", null, al);
4452   }
4453
4454   public void setShowSeqFeatures(boolean b)
4455   {
4456     showSeqFeatures.setSelected(true);
4457     viewport.setShowSequenceFeatures(true);
4458   }
4459
4460   /*
4461    * (non-Javadoc)
4462    *
4463    * @see
4464    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4465    * awt.event.ActionEvent)
4466    */
4467   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4468   {
4469     viewport.setShowUnconserved(showUnconservedMenuItem.getState());
4470     alignPanel.paintAlignment(true);
4471   }
4472
4473   /*
4474    * (non-Javadoc)
4475    *
4476    * @see
4477    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4478    * .ActionEvent)
4479    */
4480   protected void showGroupConsensus_actionPerformed(ActionEvent e)
4481   {
4482     viewport.setShowGroupConsensus(showGroupConsensus.getState());
4483     alignPanel.updateAnnotation();
4484
4485   }
4486
4487   /*
4488    * (non-Javadoc)
4489    *
4490    * @see
4491    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4492    * .event.ActionEvent)
4493    */
4494   protected void showGroupConservation_actionPerformed(ActionEvent e)
4495   {
4496     viewport.setShowGroupConservation(showGroupConservation.getState());
4497     alignPanel.updateAnnotation();
4498   }
4499
4500   /*
4501    * (non-Javadoc)
4502    *
4503    * @see
4504    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4505    * .event.ActionEvent)
4506    */
4507   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4508   {
4509     if (viewport.getSelectionGroup() != null)
4510     {
4511       SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4512               viewport.getSequenceSelection(), viewport.getAlignmentView(
4513                       true).getSequenceStrings(viewport.getGapCharacter()),
4514               viewport.alignment.getGroups());
4515       viewport.alignment.deleteAllGroups();
4516       viewport.sequenceColours = null;
4517       viewport.setSelectionGroup(null);
4518       // set view properties for each group
4519       for (int g = 0; g < gps.length; g++)
4520       {
4521         gps[g].setShowunconserved(viewport.getShowUnconserved());
4522         gps[g].setIncludeAllConsSymbols(viewport.isIncludeAllConsensusSymbols());
4523         viewport.alignment.addGroup(gps[g]);
4524         Color col = new Color((int) (Math.random() * 255), (int) (Math
4525                 .random() * 255), (int) (Math.random() * 255));
4526         col = col.brighter();
4527         for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4528                 .hasMoreElements(); viewport.setSequenceColour(
4529                 (SequenceI) sq.nextElement(), col))
4530           ;
4531       }
4532       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4533       alignPanel.updateAnnotation();
4534       alignPanel.paintAlignment(true);
4535     }
4536   }
4537 }
4538
4539 class PrintThread extends Thread
4540 {
4541   AlignmentPanel ap;
4542
4543   public PrintThread(AlignmentPanel ap)
4544   {
4545     this.ap = ap;
4546   }
4547
4548   static PageFormat pf;
4549
4550   public void run()
4551   {
4552     PrinterJob printJob = PrinterJob.getPrinterJob();
4553
4554     if (pf != null)
4555     {
4556       printJob.setPrintable(ap, pf);
4557     }
4558     else
4559     {
4560       printJob.setPrintable(ap);
4561     }
4562
4563     if (printJob.printDialog())
4564     {
4565       try
4566       {
4567         printJob.print();
4568       } catch (Exception PrintException)
4569       {
4570         PrintException.printStackTrace();
4571       }
4572     }
4573   }
4574 }