src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.beans.*;
  21 import java.io.*;
  22 import java.util.*;
  23
  24 import java.awt.*;
  25 import java.awt.datatransfer.*;
  26 import java.awt.dnd.*;
  27 import java.awt.event.*;
  28 import java.awt.print.*;
  29 import javax.swing.*;
  30 import javax.swing.event.MenuEvent;
  31
  32 import jalview.analysis.*;
  33 import jalview.bin.Cache;
  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 import jalview.ws.jws1.Discoverer;
  41 import jalview.ws.jws2.Jws2Discoverer;
  42
  43 /**
  44  * DOCUMENT ME!
  45  *
  46  * @author $author$
  47  * @version $Revision$
  48  */
  49 public class AlignFrame extends GAlignFrame implements DropTargetListener,
  50         IProgressIndicator
  51 {
  52
  53   /** DOCUMENT ME!! */
  54   public static final int DEFAULT_WIDTH = 700;
  55
  56   /** DOCUMENT ME!! */
  57   public static final int DEFAULT_HEIGHT = 500;
  58
  59   public AlignmentPanel alignPanel;
  60
  61   AlignViewport viewport;
  62
  63   Vector alignPanels = new Vector();
  64
  65   /**
  66    * Last format used to load or save alignments in this window
  67    */
  68   String currentFileFormat = null;
  69
  70   /**
  71    * Current filename for this alignment
  72    */
  73   String fileName = null;
  74
  75   /**
  76    * Creates a new AlignFrame object with specific width and height.
  77    *
  78    * @param al
  79    * @param width
  80    * @param height
  81    */
  82   public AlignFrame(AlignmentI al, int width, int height)
  83   {
  84     this(al, null, width, height);
  85   }
  86
  87   /**
  88    * Creates a new AlignFrame object with specific width, height and
  89    * sequenceSetId
  90    *
  91    * @param al
  92    * @param width
  93    * @param height
  94    * @param sequenceSetId
  95    */
  96   public AlignFrame(AlignmentI al, int width, int height,
  97           String sequenceSetId)
  98   {
  99     this(al, null, width, height, sequenceSetId);
 100   }
 101
 102   /**
 103    * Creates a new AlignFrame object with specific width, height and
 104    * sequenceSetId
 105    *
 106    * @param al
 107    * @param width
 108    * @param height
 109    * @param sequenceSetId
 110    * @param viewId
 111    */
 112   public AlignFrame(AlignmentI al, int width, int height,
 113           String sequenceSetId, String viewId)
 114   {
 115     this(al, null, width, height, sequenceSetId, viewId);
 116   }
 117
 118   /**
 119    * new alignment window with hidden columns
 120    *
 121    * @param al
 122    *          AlignmentI
 123    * @param hiddenColumns
 124    *          ColumnSelection or null
 125    * @param width
 126    *          Width of alignment frame
 127    * @param height
 128    *          height of frame.
 129    */
 130   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 131           int width, int height)
 132   {
 133     this(al, hiddenColumns, width, height, null);
 134   }
 135
 136   /**
 137    * Create alignment frame for al with hiddenColumns, a specific width and
 138    * height, and specific sequenceId
 139    *
 140    * @param al
 141    * @param hiddenColumns
 142    * @param width
 143    * @param height
 144    * @param sequenceSetId
 145    *          (may be null)
 146    */
 147   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 148           int width, int height, String sequenceSetId)
 149   {
 150     this(al, hiddenColumns, width, height, sequenceSetId, null);
 151   }
 152
 153   /**
 154    * Create alignment frame for al with hiddenColumns, a specific width and
 155    * height, and specific sequenceId
 156    *
 157    * @param al
 158    * @param hiddenColumns
 159    * @param width
 160    * @param height
 161    * @param sequenceSetId
 162    *          (may be null)
 163    * @param viewId
 164    *          (may be null)
 165    */
 166   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 167           int width, int height, String sequenceSetId, String viewId)
 168   {
 169     setSize(width, height);
 170     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 171
 172     alignPanel = new AlignmentPanel(this, viewport);
 173
 174     if (al.getDataset() == null)
 175     {
 176       al.setDataset(null);
 177     }
 178
 179     addAlignmentPanel(alignPanel, true);
 180     init();
 181   }
 182
 183   /**
 184    * Make a new AlignFrame from exisiting alignmentPanels
 185    *
 186    * @param ap
 187    *          AlignmentPanel
 188    * @param av
 189    *          AlignViewport
 190    */
 191   public AlignFrame(AlignmentPanel ap)
 192   {
 193     viewport = ap.av;
 194     alignPanel = ap;
 195     addAlignmentPanel(ap, false);
 196     init();
 197   }
 198
 199   /**
 200    * initalise the alignframe from the underlying viewport data and the
 201    * configurations
 202    */
 203   void init()
 204   {
 205     if (viewport.conservation == null)
 206     {
 207       BLOSUM62Colour.setEnabled(false);
 208       conservationMenuItem.setEnabled(false);
 209       modifyConservation.setEnabled(false);
 210       // PIDColour.setEnabled(false);
 211       // abovePIDThreshold.setEnabled(false);
 212       // modifyPID.setEnabled(false);
 213     }
 214
 215     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 216             "No sort");
 217
 218     if (sortby.equals("Id"))
 219     {
 220       sortIDMenuItem_actionPerformed(null);
 221     }
 222     else if (sortby.equals("Pairwise Identity"))
 223     {
 224       sortPairwiseMenuItem_actionPerformed(null);
 225     }
 226
 227     if (Desktop.desktop != null)
 228     {
 229       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 230       addServiceListeners();
 231       setGUINucleotide(viewport.alignment.isNucleotide());
 232     }
 233
 234     setMenusFromViewport(viewport);
 235     buildSortByAnnotationScoresMenu();
 236     if (viewport.wrapAlignment)
 237     {
 238       wrapMenuItem_actionPerformed(null);
 239     }
 240
 241     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 242     {
 243       this.overviewMenuItem_actionPerformed(null);
 244     }
 245
 246     addKeyListener();
 247
 248   }
 249
 250   /**
 251    * Change the filename and format for the alignment, and enable the 'reload'
 252    * button functionality.
 253    *
 254    * @param file
 255    *          valid filename
 256    * @param format
 257    *          format of file
 258    */
 259   public void setFileName(String file, String format)
 260   {
 261     fileName = file;
 262     currentFileFormat = format;
 263     reload.setEnabled(true);
 264   }
 265
 266   void addKeyListener()
 267   {
 268     addKeyListener(new KeyAdapter()
 269     {
 270       public void keyPressed(KeyEvent evt)
 271       {
 272         if (viewport.cursorMode
 273                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 274                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 275                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 276                 && Character.isDigit(evt.getKeyChar()))
 277           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 278
 279         switch (evt.getKeyCode())
 280         {
 281
 282         case 27: // escape key
 283           deselectAllSequenceMenuItem_actionPerformed(null);
 284
 285           break;
 286
 287         case KeyEvent.VK_DOWN:
 288           if (evt.isAltDown() || !viewport.cursorMode)
 289             moveSelectedSequences(false);
 290           if (viewport.cursorMode)
 291             alignPanel.seqPanel.moveCursor(0, 1);
 292           break;
 293
 294         case KeyEvent.VK_UP:
 295           if (evt.isAltDown() || !viewport.cursorMode)
 296             moveSelectedSequences(true);
 297           if (viewport.cursorMode)
 298             alignPanel.seqPanel.moveCursor(0, -1);
 299
 300           break;
 301
 302         case KeyEvent.VK_LEFT:
 303           if (evt.isAltDown() || !viewport.cursorMode)
 304             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 305           else
 306             alignPanel.seqPanel.moveCursor(-1, 0);
 307
 308           break;
 309
 310         case KeyEvent.VK_RIGHT:
 311           if (evt.isAltDown() || !viewport.cursorMode)
 312             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 313           else
 314             alignPanel.seqPanel.moveCursor(1, 0);
 315           break;
 316
 317         case KeyEvent.VK_SPACE:
 318           if (viewport.cursorMode)
 319           {
 320             alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 321                     || evt.isShiftDown() || evt.isAltDown());
 322           }
 323           break;
 324
 325         case KeyEvent.VK_DELETE:
 326         case KeyEvent.VK_BACK_SPACE:
 327           if (!viewport.cursorMode)
 328           {
 329             cut_actionPerformed(null);
 330           }
 331           else
 332           {
 333             alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 334                     || evt.isShiftDown() || evt.isAltDown());
 335           }
 336
 337           break;
 338
 339         case KeyEvent.VK_S:
 340           if (viewport.cursorMode)
 341           {
 342             alignPanel.seqPanel.setCursorRow();
 343           }
 344           break;
 345         case KeyEvent.VK_C:
 346           if (viewport.cursorMode && !evt.isControlDown())
 347           {
 348             alignPanel.seqPanel.setCursorColumn();
 349           }
 350           break;
 351         case KeyEvent.VK_P:
 352           if (viewport.cursorMode)
 353           {
 354             alignPanel.seqPanel.setCursorPosition();
 355           }
 356           break;
 357
 358         case KeyEvent.VK_ENTER:
 359         case KeyEvent.VK_COMMA:
 360           if (viewport.cursorMode)
 361           {
 362             alignPanel.seqPanel.setCursorRowAndColumn();
 363           }
 364           break;
 365
 366         case KeyEvent.VK_Q:
 367           if (viewport.cursorMode)
 368           {
 369             alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 370           }
 371           break;
 372         case KeyEvent.VK_M:
 373           if (viewport.cursorMode)
 374           {
 375             alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 376           }
 377           break;
 378
 379         case KeyEvent.VK_F2:
 380           viewport.cursorMode = !viewport.cursorMode;
 381           statusBar.setText("Keyboard editing mode is "
 382                   + (viewport.cursorMode ? "on" : "off"));
 383           if (viewport.cursorMode)
 384           {
 385             alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 386             alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 387           }
 388           alignPanel.seqPanel.seqCanvas.repaint();
 389           break;
 390
 391         case KeyEvent.VK_F1:
 392           try
 393           {
 394             ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
 395             java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
 396                     "help/help");
 397             javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
 398
 399             javax.help.HelpBroker hb = hs.createHelpBroker();
 400             hb.setCurrentID("home");
 401             hb.setDisplayed(true);
 402           } catch (Exception ex)
 403           {
 404             ex.printStackTrace();
 405           }
 406           break;
 407         case KeyEvent.VK_H:
 408         {
 409           boolean toggleSeqs = !evt.isControlDown();
 410           boolean toggleCols = !evt.isShiftDown();
 411           toggleHiddenRegions(toggleSeqs, toggleCols);
 412           break;
 413         }
 414         case KeyEvent.VK_PAGE_UP:
 415           if (viewport.wrapAlignment)
 416           {
 417             alignPanel.scrollUp(true);
 418           }
 419           else
 420           {
 421             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 422                     - viewport.endSeq + viewport.startSeq);
 423           }
 424           break;
 425         case KeyEvent.VK_PAGE_DOWN:
 426           if (viewport.wrapAlignment)
 427           {
 428             alignPanel.scrollUp(false);
 429           }
 430           else
 431           {
 432             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 433                     + viewport.endSeq - viewport.startSeq);
 434           }
 435           break;
 436         }
 437       }
 438
 439       public void keyReleased(KeyEvent evt)
 440       {
 441         switch (evt.getKeyCode())
 442         {
 443         case KeyEvent.VK_LEFT:
 444           if (evt.isAltDown() || !viewport.cursorMode)
 445             viewport.firePropertyChange("alignment", null, viewport
 446                     .getAlignment().getSequences());
 447           break;
 448
 449         case KeyEvent.VK_RIGHT:
 450           if (evt.isAltDown() || !viewport.cursorMode)
 451             viewport.firePropertyChange("alignment", null, viewport
 452                     .getAlignment().getSequences());
 453           break;
 454         }
 455       }
 456     });
 457   }
 458
 459   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 460   {
 461     ap.alignFrame = this;
 462
 463     alignPanels.addElement(ap);
 464
 465     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 466
 467     int aSize = alignPanels.size();
 468
 469     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 470
 471     if (aSize == 1 && ap.av.viewName == null)
 472     {
 473       this.getContentPane().add(ap, BorderLayout.CENTER);
 474     }
 475     else
 476     {
 477       if (aSize == 2)
 478       {
 479         setInitialTabVisible();
 480       }
 481
 482       expandViews.setEnabled(true);
 483       gatherViews.setEnabled(true);
 484       tabbedPane.addTab(ap.av.viewName, ap);
 485
 486       ap.setVisible(false);
 487     }
 488
 489     if (newPanel)
 490     {
 491       if (ap.av.padGaps)
 492       {
 493         ap.av.alignment.padGaps();
 494       }
 495       ap.av.updateConservation(ap);
 496       ap.av.updateConsensus(ap);
 497     }
 498   }
 499
 500   public void setInitialTabVisible()
 501   {
 502     expandViews.setEnabled(true);
 503     gatherViews.setEnabled(true);
 504     tabbedPane.setVisible(true);
 505     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
 506     tabbedPane.addTab(first.av.viewName, first);
 507     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 508   }
 509
 510   public AlignViewport getViewport()
 511   {
 512     return viewport;
 513   }
 514
 515   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 516   private void addServiceListeners()
 517   {
 518     final java.beans.PropertyChangeListener thisListener;
 519     Desktop.instance.addJalviewPropertyChangeListener("services",
 520             thisListener = new java.beans.PropertyChangeListener()
 521             {
 522               public void propertyChange(PropertyChangeEvent evt)
 523               {
 524                 // // System.out.println("Discoverer property change.");
 525                 // if (evt.getPropertyName().equals("services"))
 526                 {
 527                   SwingUtilities.invokeLater(new Runnable()
 528                   {
 529
 530                     public void run()
 531                     {
 532                       System.err
 533                               .println("Rebuild WS Menu for service change");
 534                       BuildWebServiceMenu();
 535                     }
 536
 537                   });
 538                 }
 539               }
 540             });
 541     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 542     {
 543       public void internalFrameClosed(
 544               javax.swing.event.InternalFrameEvent evt)
 545       {
 546         System.out.println("deregistering discoverer listener");
 547         Desktop.instance.removeJalviewPropertyChangeListener("services",
 548                 thisListener);
 549         closeMenuItem_actionPerformed(true);
 550       };
 551     });
 552     // Finally, build the menu once to get current service state
 553     javax.swing.SwingUtilities.invokeLater(new Runnable() {
 554     public void run() { BuildWebServiceMenu();}
 555     });
 556   }
 557
 558   public void setGUINucleotide(boolean nucleotide)
 559   {
 560     showTranslation.setVisible(nucleotide);
 561     conservationMenuItem.setEnabled(!nucleotide);
 562     modifyConservation.setEnabled(!nucleotide);
 563     showGroupConservation.setEnabled(!nucleotide);
 564     // Remember AlignFrame always starts as protein
 565     if (!nucleotide)
 566     {
 567       calculateMenu.remove(calculateMenu.getItemCount() - 2);
 568     }
 569   }
 570
 571   /**
 572    * set up menus for the currently viewport. This may be called after any
 573    * operation that affects the data in the current view (selection changed,
 574    * etc) to update the menus to reflect the new state.
 575    */
 576   public void setMenusForViewport()
 577   {
 578     setMenusFromViewport(viewport);
 579   }
 580
 581   /**
 582    * Need to call this method when tabs are selected for multiple views, or when
 583    * loading from Jalview2XML.java
 584    *
 585    * @param av
 586    *          AlignViewport
 587    */
 588   void setMenusFromViewport(AlignViewport av)
 589   {
 590     padGapsMenuitem.setSelected(av.padGaps);
 591     colourTextMenuItem.setSelected(av.showColourText);
 592     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 593     conservationMenuItem.setSelected(av.getConservationSelected());
 594     seqLimits.setSelected(av.getShowJVSuffix());
 595     idRightAlign.setSelected(av.rightAlignIds);
 596     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
 597     renderGapsMenuItem.setSelected(av.renderGaps);
 598     wrapMenuItem.setSelected(av.wrapAlignment);
 599     scaleAbove.setVisible(av.wrapAlignment);
 600     scaleLeft.setVisible(av.wrapAlignment);
 601     scaleRight.setVisible(av.wrapAlignment);
 602     annotationPanelMenuItem.setState(av.showAnnotation);
 603     viewBoxesMenuItem.setSelected(av.showBoxes);
 604     viewTextMenuItem.setSelected(av.showText);
 605     showNonconservedMenuItem.setSelected(av.showUnconserved);
 606     showGroupConsensus.setSelected(av.showGroupConsensus);
 607     showGroupConservation.setSelected(av.showGroupConservation);
 608     showConsensusHistogram.setSelected(av.showConsensusHistogram);
 609     showSequenceLogo.setSelected(av.showSequenceLogo);
 610     setColourSelected(ColourSchemeProperty.getColourName(av
 611             .getGlobalColourScheme()));
 612
 613     showSeqFeatures.setSelected(av.showSequenceFeatures);
 614     hiddenMarkers.setState(av.showHiddenMarkers);
 615     applyToAllGroups.setState(av.colourAppliesToAllGroups);
 616     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
 617     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
 618
 619     setShowProductsEnabled();
 620
 621     updateEditMenuBar();
 622   }
 623
 624   Hashtable progressBars, progressBarHandlers;
 625
 626   /*
 627    * (non-Javadoc)
 628    *
 629    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 630    */
 631   public void setProgressBar(String message, long id)
 632   {
 633     if (progressBars == null)
 634     {
 635       progressBars = new Hashtable();
 636       progressBarHandlers = new Hashtable();
 637     }
 638
 639     JPanel progressPanel;
 640     Long lId = new Long(id);
 641     GridLayout layout = (GridLayout) statusPanel.getLayout();
 642     if (progressBars.get(lId) != null)
 643     {
 644       progressPanel = (JPanel) progressBars.get(new Long(id));
 645       statusPanel.remove(progressPanel);
 646       progressBars.remove(lId);
 647       progressPanel = null;
 648       if (message != null)
 649       {
 650         statusBar.setText(message);
 651       }
 652       if (progressBarHandlers.contains(lId))
 653       {
 654         progressBarHandlers.remove(lId);
 655       }
 656       layout.setRows(layout.getRows() - 1);
 657     }
 658     else
 659     {
 660       progressPanel = new JPanel(new BorderLayout(10, 5));
 661
 662       JProgressBar progressBar = new JProgressBar();
 663       progressBar.setIndeterminate(true);
 664
 665       progressPanel.add(new JLabel(message), BorderLayout.WEST);
 666       progressPanel.add(progressBar, BorderLayout.CENTER);
 667
 668       layout.setRows(layout.getRows() + 1);
 669       statusPanel.add(progressPanel);
 670
 671       progressBars.put(lId, progressPanel);
 672     }
 673     // update GUI
 674     setMenusForViewport();
 675     validate();
 676   }
 677
 678   public void registerHandler(final long id,
 679           final IProgressIndicatorHandler handler)
 680   {
 681     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
 682     {
 683       throw new Error(
 684               "call setProgressBar before registering the progress bar's handler.");
 685     }
 686     progressBarHandlers.put(new Long(id), handler);
 687     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
 688     if (handler.canCancel())
 689     {
 690       JButton cancel = new JButton("Cancel");
 691       final IProgressIndicator us = this;
 692       cancel.addActionListener(new ActionListener()
 693       {
 694
 695         public void actionPerformed(ActionEvent e)
 696         {
 697           handler.cancelActivity(id);
 698           us.setProgressBar("Cancelled "
 699                   + ((JLabel) progressPanel.getComponent(0)).getText(), id);
 700         }
 701       });
 702       progressPanel.add(cancel, BorderLayout.EAST);
 703     }
 704   }
 705
 706   /**
 707    *
 708    * @return true if any progress bars are still active
 709    */
 710   public boolean operationInProgress()
 711   {
 712     if (progressBars != null && progressBars.size() > 0)
 713     {
 714       return true;
 715     }
 716     return false;
 717   }
 718
 719   /*
 720    * Added so Castor Mapping file can obtain Jalview Version
 721    */
 722   public String getVersion()
 723   {
 724     return jalview.bin.Cache.getProperty("VERSION");
 725   }
 726
 727   public FeatureRenderer getFeatureRenderer()
 728   {
 729     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
 730   }
 731
 732   public void fetchSequence_actionPerformed(ActionEvent e)
 733   {
 734     new SequenceFetcher(this);
 735   }
 736
 737   public void addFromFile_actionPerformed(ActionEvent e)
 738   {
 739     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 740   }
 741
 742   public void reload_actionPerformed(ActionEvent e)
 743   {
 744     if (fileName != null)
 745     {
 746       // TODO: work out how to recover feature settings for correct view(s) when
 747       // file is reloaded.
 748       if (currentFileFormat.equals("Jalview"))
 749       {
 750         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 751         for (int i = 0; i < frames.length; i++)
 752         {
 753           if (frames[i] instanceof AlignFrame && frames[i] != this
 754                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 755           {
 756             try
 757             {
 758               frames[i].setSelected(true);
 759               Desktop.instance.closeAssociatedWindows();
 760             } catch (java.beans.PropertyVetoException ex)
 761             {
 762             }
 763           }
 764
 765         }
 766         Desktop.instance.closeAssociatedWindows();
 767
 768         FileLoader loader = new FileLoader();
 769         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 770         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
 771       }
 772       else
 773       {
 774         Rectangle bounds = this.getBounds();
 775
 776         FileLoader loader = new FileLoader();
 777         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 778         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
 779                 protocol, currentFileFormat);
 780
 781         newframe.setBounds(bounds);
 782         if (featureSettings != null && featureSettings.isShowing())
 783         {
 784           final Rectangle fspos = featureSettings.frame.getBounds();
 785           // TODO: need a 'show feature settings' function that takes bounds -
 786           // need to refactor Desktop.addFrame
 787           newframe.featureSettings_actionPerformed(null);
 788           final FeatureSettings nfs = newframe.featureSettings;
 789           SwingUtilities.invokeLater(new Runnable()
 790           {
 791             public void run()
 792             {
 793               nfs.frame.setBounds(fspos);
 794             }
 795           });
 796           this.featureSettings.close();
 797           this.featureSettings = null;
 798         }
 799         this.closeMenuItem_actionPerformed(true);
 800       }
 801     }
 802   }
 803
 804   public void addFromText_actionPerformed(ActionEvent e)
 805   {
 806     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
 807   }
 808
 809   public void addFromURL_actionPerformed(ActionEvent e)
 810   {
 811     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
 812   }
 813
 814   public void save_actionPerformed(ActionEvent e)
 815   {
 816     if (fileName == null
 817             || (currentFileFormat == null || !jalview.io.FormatAdapter
 818                     .isValidIOFormat(currentFileFormat, true))
 819             || fileName.startsWith("http"))
 820     {
 821       saveAs_actionPerformed(null);
 822     }
 823     else
 824     {
 825       saveAlignment(fileName, currentFileFormat);
 826     }
 827   }
 828
 829   /**
 830    * DOCUMENT ME!
 831    *
 832    * @param e
 833    *          DOCUMENT ME!
 834    */
 835   public void saveAs_actionPerformed(ActionEvent e)
 836   {
 837     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
 838             .getProperty("LAST_DIRECTORY"),
 839             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
 840             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
 841             currentFileFormat, false);
 842
 843     chooser.setFileView(new JalviewFileView());
 844     chooser.setDialogTitle("Save Alignment to file");
 845     chooser.setToolTipText("Save");
 846
 847     int value = chooser.showSaveDialog(this);
 848
 849     if (value == JalviewFileChooser.APPROVE_OPTION)
 850     {
 851       currentFileFormat = chooser.getSelectedFormat();
 852       if (currentFileFormat == null)
 853       {
 854         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 855                 "You must select a file format before saving!",
 856                 "File format not specified", JOptionPane.WARNING_MESSAGE);
 857         value = chooser.showSaveDialog(this);
 858         return;
 859       }
 860
 861       fileName = chooser.getSelectedFile().getPath();
 862
 863       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
 864               currentFileFormat);
 865
 866       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
 867       if (currentFileFormat.indexOf(" ") > -1)
 868       {
 869         currentFileFormat = currentFileFormat.substring(0,
 870                 currentFileFormat.indexOf(" "));
 871       }
 872       saveAlignment(fileName, currentFileFormat);
 873     }
 874   }
 875
 876   public boolean saveAlignment(String file, String format)
 877   {
 878     boolean success = true;
 879
 880     if (format.equalsIgnoreCase("Jalview"))
 881     {
 882       String shortName = title;
 883
 884       if (shortName.indexOf(java.io.File.separatorChar) > -1)
 885       {
 886         shortName = shortName.substring(shortName
 887                 .lastIndexOf(java.io.File.separatorChar) + 1);
 888       }
 889
 890       success = new Jalview2XML().SaveAlignment(this, file, shortName);
 891
 892       statusBar.setText("Successfully saved to file: " + fileName + " in "
 893               + format + " format.");
 894
 895     }
 896     else
 897     {
 898       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
 899       {
 900         warningMessage("Cannot save file " + fileName + " using format "
 901                 + format, "Alignment output format not supported");
 902         saveAs_actionPerformed(null);
 903         // JBPNote need to have a raise_gui flag here
 904         return false;
 905       }
 906
 907       String[] omitHidden = null;
 908
 909       if (viewport.hasHiddenColumns)
 910       {
 911         int reply = JOptionPane
 912                 .showInternalConfirmDialog(
 913                         Desktop.desktop,
 914                         "The Alignment contains hidden columns."
 915                                 + "\nDo you want to save only the visible alignment?",
 916                         "Save / Omit Hidden Columns",
 917                         JOptionPane.YES_NO_OPTION,
 918                         JOptionPane.QUESTION_MESSAGE);
 919
 920         if (reply == JOptionPane.YES_OPTION)
 921         {
 922           omitHidden = viewport.getViewAsString(false);
 923         }
 924       }
 925       FormatAdapter f = new FormatAdapter();
 926       String output = f.formatSequences(format,
 927               (Alignment) viewport.alignment, // class cast exceptions will
 928               // occur in the distant future
 929               omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
 930
 931       if (output == null)
 932       {
 933         success = false;
 934       }
 935       else
 936       {
 937         try
 938         {
 939           java.io.PrintWriter out = new java.io.PrintWriter(
 940                   new java.io.FileWriter(file));
 941
 942           out.print(output);
 943           out.close();
 944           this.setTitle(file);
 945           statusBar.setText("Successfully saved to file: " + fileName
 946                   + " in " + format + " format.");
 947         } catch (Exception ex)
 948         {
 949           success = false;
 950           ex.printStackTrace();
 951         }
 952       }
 953     }
 954
 955     if (!success)
 956     {
 957       JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
 958               + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
 959     }
 960
 961     return success;
 962   }
 963
 964   private void warningMessage(String warning, String title)
 965   {
 966     if (new jalview.util.Platform().isHeadless())
 967     {
 968       System.err.println("Warning: " + title + "\nWarning: " + warning);
 969
 970     }
 971     else
 972     {
 973       JOptionPane.showInternalMessageDialog(this, warning, title,
 974               JOptionPane.WARNING_MESSAGE);
 975     }
 976     return;
 977   }
 978
 979   /**
 980    * DOCUMENT ME!
 981    *
 982    * @param e
 983    *          DOCUMENT ME!
 984    */
 985   protected void outputText_actionPerformed(ActionEvent e)
 986   {
 987     String[] omitHidden = null;
 988
 989     if (viewport.hasHiddenColumns)
 990     {
 991       int reply = JOptionPane
 992               .showInternalConfirmDialog(
 993                       Desktop.desktop,
 994                       "The Alignment contains hidden columns."
 995                               + "\nDo you want to output only the visible alignment?",
 996                       "Save / Omit Hidden Columns",
 997                       JOptionPane.YES_NO_OPTION,
 998                       JOptionPane.QUESTION_MESSAGE);
 999
1000       if (reply == JOptionPane.YES_OPTION)
1001       {
1002         omitHidden = viewport.getViewAsString(false);
1003       }
1004     }
1005
1006     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1007     cap.setForInput(null);
1008
1009     try {
1010       cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1011             viewport.alignment, omitHidden, viewport.colSel));
1012     Desktop.addInternalFrame(cap, "Alignment output - "
1013             + e.getActionCommand(), 600, 500);
1014     } catch (OutOfMemoryError oom)
1015     {
1016       new OOMWarning("Outputting alignment as "+e.getActionCommand(),oom);
1017       cap.dispose();
1018     }
1019
1020   }
1021
1022   /**
1023    * DOCUMENT ME!
1024    *
1025    * @param e
1026    *          DOCUMENT ME!
1027    */
1028   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1029   {
1030     new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1031             .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1032             .getFeatureRenderer());
1033   }
1034
1035   public void createImageMap(File file, String image)
1036   {
1037     alignPanel.makePNGImageMap(file, image);
1038   }
1039
1040   /**
1041    * DOCUMENT ME!
1042    *
1043    * @param e
1044    *          DOCUMENT ME!
1045    */
1046   public void createPNG(File f)
1047   {
1048     alignPanel.makePNG(f);
1049   }
1050
1051   /**
1052    * DOCUMENT ME!
1053    *
1054    * @param e
1055    *          DOCUMENT ME!
1056    */
1057   public void createEPS(File f)
1058   {
1059     alignPanel.makeEPS(f);
1060   }
1061
1062   public void pageSetup_actionPerformed(ActionEvent e)
1063   {
1064     PrinterJob printJob = PrinterJob.getPrinterJob();
1065     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1066   }
1067
1068   /**
1069    * DOCUMENT ME!
1070    *
1071    * @param e
1072    *          DOCUMENT ME!
1073    */
1074   public void printMenuItem_actionPerformed(ActionEvent e)
1075   {
1076     // Putting in a thread avoids Swing painting problems
1077     PrintThread thread = new PrintThread(alignPanel);
1078     thread.start();
1079   }
1080
1081   public void exportFeatures_actionPerformed(ActionEvent e)
1082   {
1083     new AnnotationExporter().exportFeatures(alignPanel);
1084   }
1085
1086   public void exportAnnotations_actionPerformed(ActionEvent e)
1087   {
1088     new AnnotationExporter().exportAnnotations(alignPanel,
1089             viewport.showAnnotation ? viewport.alignment
1090                     .getAlignmentAnnotation() : null, viewport.alignment
1091                     .getGroups(),
1092             ((Alignment) viewport.alignment).alignmentProperties);
1093   }
1094
1095   public void associatedData_actionPerformed(ActionEvent e)
1096   {
1097     // Pick the tree file
1098     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1099             .getProperty("LAST_DIRECTORY"));
1100     chooser.setFileView(new JalviewFileView());
1101     chooser.setDialogTitle("Load Jalview Annotations or Features File");
1102     chooser.setToolTipText("Load Jalview Annotations / Features file");
1103
1104     int value = chooser.showOpenDialog(null);
1105
1106     if (value == JalviewFileChooser.APPROVE_OPTION)
1107     {
1108       String choice = chooser.getSelectedFile().getPath();
1109       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1110       loadJalviewDataFile(choice);
1111     }
1112
1113   }
1114
1115   /**
1116    * Close the current view or all views in the alignment frame. If the frame
1117    * only contains one view then the alignment will be removed from memory.
1118    *
1119    * @param closeAllTabs
1120    */
1121   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1122   {
1123     if (alignPanels != null && alignPanels.size() < 2)
1124     {
1125       closeAllTabs = true;
1126     }
1127
1128     try
1129     {
1130       if (alignPanels != null)
1131       {
1132         if (closeAllTabs)
1133         {
1134           if (this.isClosed())
1135           {
1136             // really close all the windows - otherwise wait till
1137             // setClosed(true) is called
1138             for (int i = 0; i < alignPanels.size(); i++)
1139             {
1140               AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1141               ap.closePanel();
1142             }
1143           }
1144         }
1145         else
1146         {
1147           closeView(alignPanel);
1148         }
1149       }
1150
1151       if (closeAllTabs)
1152       {
1153         this.setClosed(true);
1154       }
1155     } catch (Exception ex)
1156     {
1157       ex.printStackTrace();
1158     }
1159   }
1160
1161   /**
1162    * close alignPanel2 and shuffle tabs appropriately.
1163    *
1164    * @param alignPanel2
1165    */
1166   public void closeView(AlignmentPanel alignPanel2)
1167   {
1168     int index = tabbedPane.getSelectedIndex();
1169     int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1170     alignPanels.removeElement(alignPanel2);
1171     // Unnecessary
1172     // if (viewport == alignPanel2.av)
1173     // {
1174     // viewport = null;
1175     // }
1176     alignPanel2.closePanel();
1177     alignPanel2 = null;
1178
1179     tabbedPane.removeTabAt(closedindex);
1180     tabbedPane.validate();
1181
1182     if (index > closedindex || index == tabbedPane.getTabCount())
1183     {
1184       // modify currently selected tab index if necessary.
1185       index--;
1186     }
1187
1188     this.tabSelectionChanged(index);
1189   }
1190
1191   /**
1192    * DOCUMENT ME!
1193    */
1194   void updateEditMenuBar()
1195   {
1196
1197     if (viewport.historyList.size() > 0)
1198     {
1199       undoMenuItem.setEnabled(true);
1200       CommandI command = (CommandI) viewport.historyList.peek();
1201       undoMenuItem.setText("Undo " + command.getDescription());
1202     }
1203     else
1204     {
1205       undoMenuItem.setEnabled(false);
1206       undoMenuItem.setText("Undo");
1207     }
1208
1209     if (viewport.redoList.size() > 0)
1210     {
1211       redoMenuItem.setEnabled(true);
1212
1213       CommandI command = (CommandI) viewport.redoList.peek();
1214       redoMenuItem.setText("Redo " + command.getDescription());
1215     }
1216     else
1217     {
1218       redoMenuItem.setEnabled(false);
1219       redoMenuItem.setText("Redo");
1220     }
1221   }
1222
1223   public void addHistoryItem(CommandI command)
1224   {
1225     if (command.getSize() > 0)
1226     {
1227       viewport.historyList.push(command);
1228       viewport.redoList.clear();
1229       updateEditMenuBar();
1230       viewport.hasHiddenColumns = (viewport.colSel != null
1231               && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1232               .getHiddenColumns().size() > 0);
1233     }
1234   }
1235
1236   /**
1237    *
1238    * @return alignment objects for all views
1239    */
1240   AlignmentI[] getViewAlignments()
1241   {
1242     if (alignPanels != null)
1243     {
1244       Enumeration e = alignPanels.elements();
1245       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1246       for (int i = 0; e.hasMoreElements(); i++)
1247       {
1248         als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1249       }
1250       return als;
1251     }
1252     if (viewport != null)
1253     {
1254       return new AlignmentI[]
1255       { viewport.alignment };
1256     }
1257     return null;
1258   }
1259
1260   /**
1261    * DOCUMENT ME!
1262    *
1263    * @param e
1264    *          DOCUMENT ME!
1265    */
1266   protected void undoMenuItem_actionPerformed(ActionEvent e)
1267   {
1268     if (viewport.historyList.empty())
1269       return;
1270     CommandI command = (CommandI) viewport.historyList.pop();
1271     viewport.redoList.push(command);
1272     command.undoCommand(getViewAlignments());
1273
1274     AlignViewport originalSource = getOriginatingSource(command);
1275     updateEditMenuBar();
1276
1277     if (originalSource != null)
1278     {
1279       originalSource.hasHiddenColumns = (viewport.colSel != null
1280               && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1281               .getHiddenColumns().size() > 0);
1282       originalSource.firePropertyChange("alignment", null,
1283               originalSource.alignment.getSequences());
1284     }
1285   }
1286
1287   /**
1288    * DOCUMENT ME!
1289    *
1290    * @param e
1291    *          DOCUMENT ME!
1292    */
1293   protected void redoMenuItem_actionPerformed(ActionEvent e)
1294   {
1295     if (viewport.redoList.size() < 1)
1296     {
1297       return;
1298     }
1299
1300     CommandI command = (CommandI) viewport.redoList.pop();
1301     viewport.historyList.push(command);
1302     command.doCommand(getViewAlignments());
1303
1304     AlignViewport originalSource = getOriginatingSource(command);
1305     updateEditMenuBar();
1306
1307     if (originalSource != null)
1308     {
1309       originalSource.hasHiddenColumns = (viewport.colSel != null
1310               && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1311               .getHiddenColumns().size() > 0);
1312       originalSource.firePropertyChange("alignment", null,
1313               originalSource.alignment.getSequences());
1314     }
1315   }
1316
1317   AlignViewport getOriginatingSource(CommandI command)
1318   {
1319     AlignViewport originalSource = null;
1320     // For sequence removal and addition, we need to fire
1321     // the property change event FROM the viewport where the
1322     // original alignment was altered
1323     AlignmentI al = null;
1324     if (command instanceof EditCommand)
1325     {
1326       EditCommand editCommand = (EditCommand) command;
1327       al = editCommand.getAlignment();
1328       Vector comps = (Vector) PaintRefresher.components.get(viewport
1329               .getSequenceSetId());
1330
1331       for (int i = 0; i < comps.size(); i++)
1332       {
1333         if (comps.elementAt(i) instanceof AlignmentPanel)
1334         {
1335           if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1336           {
1337             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1338             break;
1339           }
1340         }
1341       }
1342     }
1343
1344     if (originalSource == null)
1345     {
1346       // The original view is closed, we must validate
1347       // the current view against the closed view first
1348       if (al != null)
1349       {
1350         PaintRefresher.validateSequences(al, viewport.alignment);
1351       }
1352
1353       originalSource = viewport;
1354     }
1355
1356     return originalSource;
1357   }
1358
1359   /**
1360    * DOCUMENT ME!
1361    *
1362    * @param up
1363    *          DOCUMENT ME!
1364    */
1365   public void moveSelectedSequences(boolean up)
1366   {
1367     SequenceGroup sg = viewport.getSelectionGroup();
1368
1369     if (sg == null)
1370     {
1371       return;
1372     }
1373
1374     if (up)
1375     {
1376       for (int i = 1; i < viewport.alignment.getHeight(); i++)
1377       {
1378         SequenceI seq = viewport.alignment.getSequenceAt(i);
1379
1380         if (!sg.getSequences(null).contains(seq))
1381         {
1382           continue;
1383         }
1384
1385         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1386
1387         if (sg.getSequences(null).contains(temp))
1388         {
1389           continue;
1390         }
1391
1392         viewport.alignment.getSequences().setElementAt(temp, i);
1393         viewport.alignment.getSequences().setElementAt(seq, i - 1);
1394       }
1395     }
1396     else
1397     {
1398       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1399       {
1400         SequenceI seq = viewport.alignment.getSequenceAt(i);
1401
1402         if (!sg.getSequences(null).contains(seq))
1403         {
1404           continue;
1405         }
1406
1407         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1408
1409         if (sg.getSequences(null).contains(temp))
1410         {
1411           continue;
1412         }
1413
1414         viewport.alignment.getSequences().setElementAt(temp, i);
1415         viewport.alignment.getSequences().setElementAt(seq, i + 1);
1416       }
1417     }
1418
1419     alignPanel.paintAlignment(true);
1420   }
1421
1422   synchronized void slideSequences(boolean right, int size)
1423   {
1424     Vector sg = new Vector();
1425     if (viewport.cursorMode)
1426     {
1427       sg.addElement(viewport.alignment
1428               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1429     }
1430     else if (viewport.getSelectionGroup() != null
1431             && viewport.getSelectionGroup().getSize() != viewport.alignment
1432                     .getHeight())
1433     {
1434       sg = viewport.getSelectionGroup().getSequences(
1435               viewport.hiddenRepSequences);
1436     }
1437
1438     if (sg.size() < 1)
1439     {
1440       return;
1441     }
1442
1443     Vector invertGroup = new Vector();
1444
1445     for (int i = 0; i < viewport.alignment.getHeight(); i++)
1446     {
1447       if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1448         invertGroup.add(viewport.alignment.getSequenceAt(i));
1449     }
1450
1451     SequenceI[] seqs1 = new SequenceI[sg.size()];
1452     for (int i = 0; i < sg.size(); i++)
1453       seqs1[i] = (SequenceI) sg.elementAt(i);
1454
1455     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1456     for (int i = 0; i < invertGroup.size(); i++)
1457       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1458
1459     SlideSequencesCommand ssc;
1460     if (right)
1461       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1462               size, viewport.getGapCharacter());
1463     else
1464       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1465               size, viewport.getGapCharacter());
1466
1467     int groupAdjustment = 0;
1468     if (ssc.getGapsInsertedBegin() && right)
1469     {
1470       if (viewport.cursorMode)
1471         alignPanel.seqPanel.moveCursor(size, 0);
1472       else
1473         groupAdjustment = size;
1474     }
1475     else if (!ssc.getGapsInsertedBegin() && !right)
1476     {
1477       if (viewport.cursorMode)
1478         alignPanel.seqPanel.moveCursor(-size, 0);
1479       else
1480         groupAdjustment = -size;
1481     }
1482
1483     if (groupAdjustment != 0)
1484     {
1485       viewport.getSelectionGroup().setStartRes(
1486               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1487       viewport.getSelectionGroup().setEndRes(
1488               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1489     }
1490
1491     boolean appendHistoryItem = false;
1492     if (viewport.historyList != null && viewport.historyList.size() > 0
1493             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1494     {
1495       appendHistoryItem = ssc
1496               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1497                       .peek());
1498     }
1499
1500     if (!appendHistoryItem)
1501       addHistoryItem(ssc);
1502
1503     repaint();
1504   }
1505
1506   /**
1507    * DOCUMENT ME!
1508    *
1509    * @param e
1510    *          DOCUMENT ME!
1511    */
1512   protected void copy_actionPerformed(ActionEvent e)
1513   {
1514     System.gc();
1515     if (viewport.getSelectionGroup() == null)
1516     {
1517       return;
1518     }
1519     // TODO: preserve the ordering of displayed alignment annotation in any
1520     // internal paste (particularly sequence associated annotation)
1521     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1522     String[] omitHidden = null;
1523
1524     if (viewport.hasHiddenColumns)
1525     {
1526       omitHidden = viewport.getViewAsString(true);
1527     }
1528
1529     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1530             omitHidden);
1531
1532     StringSelection ss = new StringSelection(output);
1533
1534     try
1535     {
1536       jalview.gui.Desktop.internalCopy = true;
1537       // Its really worth setting the clipboard contents
1538       // to empty before setting the large StringSelection!!
1539       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1540               new StringSelection(""), null);
1541
1542       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1543               Desktop.instance);
1544     } catch (OutOfMemoryError er)
1545     {
1546       new OOMWarning("copying region", er);
1547       return;
1548     }
1549
1550     Vector hiddenColumns = null;
1551     if (viewport.hasHiddenColumns)
1552     {
1553       hiddenColumns = new Vector();
1554       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1555               .getSelectionGroup().getEndRes();
1556       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1557               .size(); i++)
1558       {
1559         int[] region = (int[]) viewport.getColumnSelection()
1560                 .getHiddenColumns().elementAt(i);
1561         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1562         {
1563           hiddenColumns.addElement(new int[]
1564           { region[0] - hiddenOffset, region[1] - hiddenOffset });
1565         }
1566       }
1567     }
1568
1569     Desktop.jalviewClipboard = new Object[]
1570     { seqs, viewport.alignment.getDataset(), hiddenColumns };
1571     statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1572   }
1573
1574   /**
1575    * DOCUMENT ME!
1576    *
1577    * @param e
1578    *          DOCUMENT ME!
1579    */
1580   protected void pasteNew_actionPerformed(ActionEvent e)
1581   {
1582     paste(true);
1583   }
1584
1585   /**
1586    * DOCUMENT ME!
1587    *
1588    * @param e
1589    *          DOCUMENT ME!
1590    */
1591   protected void pasteThis_actionPerformed(ActionEvent e)
1592   {
1593     paste(false);
1594   }
1595
1596   /**
1597    * Paste contents of Jalview clipboard
1598    *
1599    * @param newAlignment
1600    *          true to paste to a new alignment, otherwise add to this.
1601    */
1602   void paste(boolean newAlignment)
1603   {
1604     boolean externalPaste = true;
1605     try
1606     {
1607       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1608       Transferable contents = c.getContents(this);
1609
1610       if (contents == null)
1611       {
1612         return;
1613       }
1614
1615       String str, format;
1616       try
1617       {
1618         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1619         if (str.length() < 1)
1620         {
1621           return;
1622         }
1623
1624         format = new IdentifyFile().Identify(str, "Paste");
1625
1626       } catch (OutOfMemoryError er)
1627       {
1628         new OOMWarning("Out of memory pasting sequences!!", er);
1629         return;
1630       }
1631
1632       SequenceI[] sequences;
1633       boolean annotationAdded = false;
1634       AlignmentI alignment = null;
1635
1636       if (Desktop.jalviewClipboard != null)
1637       {
1638         // The clipboard was filled from within Jalview, we must use the
1639         // sequences
1640         // And dataset from the copied alignment
1641         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1642         // be doubly sure that we create *new* sequence objects.
1643         sequences = new SequenceI[newseq.length];
1644         for (int i = 0; i < newseq.length; i++)
1645         {
1646           sequences[i] = new Sequence(newseq[i]);
1647         }
1648         alignment = new Alignment(sequences);
1649         externalPaste = false;
1650       }
1651       else
1652       {
1653         // parse the clipboard as an alignment.
1654         alignment = new FormatAdapter().readFile(str, "Paste", format);
1655         sequences = alignment.getSequencesArray();
1656       }
1657
1658       int alwidth = 0;
1659
1660       if (newAlignment)
1661       {
1662
1663         if (Desktop.jalviewClipboard != null)
1664         {
1665           // dataset is inherited
1666           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1667         }
1668         else
1669         {
1670           // new dataset is constructed
1671           alignment.setDataset(null);
1672         }
1673         alwidth = alignment.getWidth() + 1;
1674       }
1675       else
1676       {
1677         AlignmentI pastedal = alignment; // preserve pasted alignment object
1678         // Add pasted sequences and dataset into existing alignment.
1679         alignment = viewport.getAlignment();
1680         alwidth = alignment.getWidth() + 1;
1681         // decide if we need to import sequences from an existing dataset
1682         boolean importDs = Desktop.jalviewClipboard != null
1683                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1684         // importDs==true instructs us to copy over new dataset sequences from
1685         // an existing alignment
1686         Vector newDs = (importDs) ? new Vector() : null; // used to create
1687         // minimum dataset set
1688
1689         for (int i = 0; i < sequences.length; i++)
1690         {
1691           if (importDs)
1692           {
1693             newDs.addElement(null);
1694           }
1695           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1696           // paste
1697           if (importDs && ds != null)
1698           {
1699             if (!newDs.contains(ds))
1700             {
1701               newDs.setElementAt(ds, i);
1702               ds = new Sequence(ds);
1703               // update with new dataset sequence
1704               sequences[i].setDatasetSequence(ds);
1705             }
1706             else
1707             {
1708               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1709             }
1710           }
1711           else
1712           {
1713             // copy and derive new dataset sequence
1714             sequences[i] = sequences[i].deriveSequence();
1715             alignment.getDataset().addSequence(
1716                     sequences[i].getDatasetSequence());
1717             // TODO: avoid creation of duplicate dataset sequences with a
1718             // 'contains' method using SequenceI.equals()/SequenceI.contains()
1719           }
1720           alignment.addSequence(sequences[i]); // merges dataset
1721         }
1722         if (newDs != null)
1723         {
1724           newDs.clear(); // tidy up
1725         }
1726         if (pastedal.getAlignmentAnnotation() != null)
1727         {
1728           // Add any annotation attached to alignment.
1729           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1730           for (int i = 0; i < alann.length; i++)
1731           {
1732             annotationAdded = true;
1733             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1734             {
1735               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1736               newann.padAnnotation(alwidth);
1737               alignment.addAnnotation(newann);
1738             }
1739           }
1740         }
1741       }
1742       if (!newAlignment)
1743       {
1744         // /////
1745         // ADD HISTORY ITEM
1746         //
1747         addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1748                 sequences, 0, alignment.getWidth(), alignment));
1749       }
1750       // Add any annotations attached to sequences
1751       for (int i = 0; i < sequences.length; i++)
1752       {
1753         if (sequences[i].getAnnotation() != null)
1754         {
1755           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1756           {
1757             annotationAdded = true;
1758             sequences[i].getAnnotation()[a].adjustForAlignment();
1759             sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1760             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1761             // was
1762             // duplicated
1763             // earlier
1764             alignment
1765                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1766           }
1767         }
1768       }
1769       if (!newAlignment)
1770       {
1771
1772         // propagate alignment changed.
1773         viewport.setEndSeq(alignment.getHeight());
1774         if (annotationAdded)
1775         {
1776           // Duplicate sequence annotation in all views.
1777           AlignmentI[] alview = this.getViewAlignments();
1778           for (int i = 0; i < sequences.length; i++)
1779           {
1780             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1781             if (sann == null)
1782               continue;
1783             for (int avnum = 0; avnum < alview.length; avnum++)
1784             {
1785               if (alview[avnum] != alignment)
1786               {
1787                 // duplicate in a view other than the one with input focus
1788                 int avwidth = alview[avnum].getWidth() + 1;
1789                 // this relies on sann being preserved after we
1790                 // modify the sequence's annotation array for each duplication
1791                 for (int a = 0; a < sann.length; a++)
1792                 {
1793                   AlignmentAnnotation newann = new AlignmentAnnotation(
1794                           sann[a]);
1795                   sequences[i].addAlignmentAnnotation(newann);
1796                   newann.padAnnotation(avwidth);
1797                   alview[avnum].addAnnotation(newann); // annotation was
1798                   // duplicated earlier
1799                   alview[avnum].setAnnotationIndex(newann, a);
1800                 }
1801               }
1802             }
1803           }
1804           buildSortByAnnotationScoresMenu();
1805         }
1806         viewport.firePropertyChange("alignment", null, alignment
1807                 .getSequences());
1808
1809       }
1810       else
1811       {
1812         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1813                 DEFAULT_HEIGHT);
1814         String newtitle = new String("Copied sequences");
1815
1816         if (Desktop.jalviewClipboard != null
1817                 && Desktop.jalviewClipboard[2] != null)
1818         {
1819           Vector hc = (Vector) Desktop.jalviewClipboard[2];
1820           for (int i = 0; i < hc.size(); i++)
1821           {
1822             int[] region = (int[]) hc.elementAt(i);
1823             af.viewport.hideColumns(region[0], region[1]);
1824           }
1825         }
1826
1827         // >>>This is a fix for the moment, until a better solution is
1828         // found!!<<<
1829         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1830                 .transferSettings(
1831                         alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1832
1833         // TODO: maintain provenance of an alignment, rather than just make the
1834         // title a concatenation of operations.
1835         if (!externalPaste)
1836         {
1837           if (title.startsWith("Copied sequences"))
1838           {
1839             newtitle = title;
1840           }
1841           else
1842           {
1843             newtitle = newtitle.concat("- from " + title);
1844           }
1845         }
1846         else
1847         {
1848           newtitle = new String("Pasted sequences");
1849         }
1850
1851         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1852                 DEFAULT_HEIGHT);
1853
1854       }
1855
1856     } catch (Exception ex)
1857     {
1858       ex.printStackTrace();
1859       System.out.println("Exception whilst pasting: " + ex);
1860       // could be anything being pasted in here
1861     }
1862
1863   }
1864
1865   /**
1866    * DOCUMENT ME!
1867    *
1868    * @param e
1869    *          DOCUMENT ME!
1870    */
1871   protected void cut_actionPerformed(ActionEvent e)
1872   {
1873     copy_actionPerformed(null);
1874     delete_actionPerformed(null);
1875   }
1876
1877   /**
1878    * DOCUMENT ME!
1879    *
1880    * @param e
1881    *          DOCUMENT ME!
1882    */
1883   protected void delete_actionPerformed(ActionEvent evt)
1884   {
1885
1886     SequenceGroup sg = viewport.getSelectionGroup();
1887     if (sg == null)
1888     {
1889       return;
1890     }
1891
1892     Vector seqs = new Vector();
1893     SequenceI seq;
1894     for (int i = 0; i < sg.getSize(); i++)
1895     {
1896       seq = sg.getSequenceAt(i);
1897       seqs.addElement(seq);
1898     }
1899
1900     // If the cut affects all sequences, remove highlighted columns
1901     if (sg.getSize() == viewport.alignment.getHeight())
1902     {
1903       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1904               sg.getEndRes() + 1);
1905     }
1906
1907     SequenceI[] cut = new SequenceI[seqs.size()];
1908     for (int i = 0; i < seqs.size(); i++)
1909     {
1910       cut[i] = (SequenceI) seqs.elementAt(i);
1911     }
1912
1913     /*
1914      * //ADD HISTORY ITEM
1915      */
1916     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1917             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1918             viewport.alignment));
1919
1920     viewport.setSelectionGroup(null);
1921     viewport.sendSelection();
1922     viewport.alignment.deleteGroup(sg);
1923
1924     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1925             .getSequences());
1926     if (viewport.getAlignment().getHeight() < 1)
1927     {
1928       try
1929       {
1930         this.setClosed(true);
1931       } catch (Exception ex)
1932       {
1933       }
1934     }
1935   }
1936
1937   /**
1938    * DOCUMENT ME!
1939    *
1940    * @param e
1941    *          DOCUMENT ME!
1942    */
1943   protected void deleteGroups_actionPerformed(ActionEvent e)
1944   {
1945     viewport.alignment.deleteAllGroups();
1946     viewport.sequenceColours = null;
1947     viewport.setSelectionGroup(null);
1948     PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1949     alignPanel.updateAnnotation();
1950     alignPanel.paintAlignment(true);
1951   }
1952
1953   /**
1954    * DOCUMENT ME!
1955    *
1956    * @param e
1957    *          DOCUMENT ME!
1958    */
1959   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1960   {
1961     SequenceGroup sg = new SequenceGroup();
1962
1963     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1964     {
1965       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1966     }
1967
1968     sg.setEndRes(viewport.alignment.getWidth() - 1);
1969     viewport.setSelectionGroup(sg);
1970     viewport.sendSelection();
1971     alignPanel.paintAlignment(true);
1972     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1973   }
1974
1975   /**
1976    * DOCUMENT ME!
1977    *
1978    * @param e
1979    *          DOCUMENT ME!
1980    */
1981   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1982   {
1983     if (viewport.cursorMode)
1984     {
1985       alignPanel.seqPanel.keyboardNo1 = null;
1986       alignPanel.seqPanel.keyboardNo2 = null;
1987     }
1988     viewport.setSelectionGroup(null);
1989     viewport.getColumnSelection().clear();
1990     viewport.setSelectionGroup(null);
1991     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1992     alignPanel.idPanel.idCanvas.searchResults = null;
1993     alignPanel.paintAlignment(true);
1994     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1995   }
1996
1997   /**
1998    * DOCUMENT ME!
1999    *
2000    * @param e
2001    *          DOCUMENT ME!
2002    */
2003   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2004   {
2005     SequenceGroup sg = viewport.getSelectionGroup();
2006
2007     if (sg == null)
2008     {
2009       selectAllSequenceMenuItem_actionPerformed(null);
2010
2011       return;
2012     }
2013
2014     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2015     {
2016       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2017     }
2018
2019     alignPanel.paintAlignment(true);
2020     viewport.sendSelection();
2021     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2022   }
2023
2024   public void invertColSel_actionPerformed(ActionEvent e)
2025   {
2026     viewport.invertColumnSelection();
2027     alignPanel.paintAlignment(true);
2028   }
2029
2030   /**
2031    * DOCUMENT ME!
2032    *
2033    * @param e
2034    *          DOCUMENT ME!
2035    */
2036   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2037   {
2038     trimAlignment(true);
2039   }
2040
2041   /**
2042    * DOCUMENT ME!
2043    *
2044    * @param e
2045    *          DOCUMENT ME!
2046    */
2047   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2048   {
2049     trimAlignment(false);
2050   }
2051
2052   void trimAlignment(boolean trimLeft)
2053   {
2054     ColumnSelection colSel = viewport.getColumnSelection();
2055     int column;
2056
2057     if (colSel.size() > 0)
2058     {
2059       if (trimLeft)
2060       {
2061         column = colSel.getMin();
2062       }
2063       else
2064       {
2065         column = colSel.getMax();
2066       }
2067
2068       SequenceI[] seqs;
2069       if (viewport.getSelectionGroup() != null)
2070       {
2071         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2072                 viewport.hiddenRepSequences);
2073       }
2074       else
2075       {
2076         seqs = viewport.alignment.getSequencesArray();
2077       }
2078
2079       TrimRegionCommand trimRegion;
2080       if (trimLeft)
2081       {
2082         trimRegion = new TrimRegionCommand("Remove Left",
2083                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2084                 viewport.alignment, viewport.colSel,
2085                 viewport.selectionGroup);
2086         viewport.setStartRes(0);
2087       }
2088       else
2089       {
2090         trimRegion = new TrimRegionCommand("Remove Right",
2091                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2092                 viewport.alignment, viewport.colSel,
2093                 viewport.selectionGroup);
2094       }
2095
2096       statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2097
2098       addHistoryItem(trimRegion);
2099
2100       Vector groups = viewport.alignment.getGroups();
2101
2102       for (int i = 0; i < groups.size(); i++)
2103       {
2104         SequenceGroup sg = (SequenceGroup) groups.get(i);
2105
2106         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2107                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2108         {
2109           viewport.alignment.deleteGroup(sg);
2110         }
2111       }
2112
2113       viewport.firePropertyChange("alignment", null, viewport
2114               .getAlignment().getSequences());
2115     }
2116   }
2117
2118   /**
2119    * DOCUMENT ME!
2120    *
2121    * @param e
2122    *          DOCUMENT ME!
2123    */
2124   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2125   {
2126     int start = 0, end = viewport.alignment.getWidth() - 1;
2127
2128     SequenceI[] seqs;
2129     if (viewport.getSelectionGroup() != null)
2130     {
2131       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2132               viewport.hiddenRepSequences);
2133       start = viewport.getSelectionGroup().getStartRes();
2134       end = viewport.getSelectionGroup().getEndRes();
2135     }
2136     else
2137     {
2138       seqs = viewport.alignment.getSequencesArray();
2139     }
2140
2141     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2142             "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2143
2144     addHistoryItem(removeGapCols);
2145
2146     statusBar.setText("Removed " + removeGapCols.getSize()
2147             + " empty columns.");
2148
2149     // This is to maintain viewport position on first residue
2150     // of first sequence
2151     SequenceI seq = viewport.alignment.getSequenceAt(0);
2152     int startRes = seq.findPosition(viewport.startRes);
2153     // ShiftList shifts;
2154     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2155     // edit.alColumnChanges=shifts.getInverse();
2156     // if (viewport.hasHiddenColumns)
2157     // viewport.getColumnSelection().compensateForEdits(shifts);
2158     viewport.setStartRes(seq.findIndex(startRes) - 1);
2159     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2160             .getSequences());
2161
2162   }
2163
2164   /**
2165    * DOCUMENT ME!
2166    *
2167    * @param e
2168    *          DOCUMENT ME!
2169    */
2170   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2171   {
2172     int start = 0, end = viewport.alignment.getWidth() - 1;
2173
2174     SequenceI[] seqs;
2175     if (viewport.getSelectionGroup() != null)
2176     {
2177       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2178               viewport.hiddenRepSequences);
2179       start = viewport.getSelectionGroup().getStartRes();
2180       end = viewport.getSelectionGroup().getEndRes();
2181     }
2182     else
2183     {
2184       seqs = viewport.alignment.getSequencesArray();
2185     }
2186
2187     // This is to maintain viewport position on first residue
2188     // of first sequence
2189     SequenceI seq = viewport.alignment.getSequenceAt(0);
2190     int startRes = seq.findPosition(viewport.startRes);
2191
2192     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2193             viewport.alignment));
2194
2195     viewport.setStartRes(seq.findIndex(startRes) - 1);
2196
2197     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2198             .getSequences());
2199
2200   }
2201
2202   /**
2203    * DOCUMENT ME!
2204    *
2205    * @param e
2206    *          DOCUMENT ME!
2207    */
2208   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2209   {
2210     viewport.padGaps = padGapsMenuitem.isSelected();
2211     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2212             .getSequences());
2213   }
2214
2215   // else
2216   {
2217     // if (justifySeqs>0)
2218     {
2219       // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2220     }
2221   }
2222
2223   // }
2224
2225   /**
2226    * DOCUMENT ME!
2227    *
2228    * @param e
2229    *          DOCUMENT ME!
2230    */
2231   public void findMenuItem_actionPerformed(ActionEvent e)
2232   {
2233     new Finder();
2234   }
2235
2236   public void newView_actionPerformed(ActionEvent e)
2237   {
2238     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2239             true);
2240
2241     newap.av.gatherViewsHere = false;
2242
2243     if (viewport.viewName == null)
2244     {
2245       viewport.viewName = "Original";
2246     }
2247
2248     newap.av.historyList = viewport.historyList;
2249     newap.av.redoList = viewport.redoList;
2250
2251     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2252     String newViewName = "View " + index;
2253
2254     Vector comps = (Vector) PaintRefresher.components.get(viewport
2255             .getSequenceSetId());
2256     Vector existingNames = new Vector();
2257     for (int i = 0; i < comps.size(); i++)
2258     {
2259       if (comps.elementAt(i) instanceof AlignmentPanel)
2260       {
2261         AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2262         if (!existingNames.contains(ap.av.viewName))
2263         {
2264           existingNames.addElement(ap.av.viewName);
2265         }
2266       }
2267     }
2268
2269     while (existingNames.contains(newViewName))
2270     {
2271       newViewName = "View " + (++index);
2272     }
2273
2274     newap.av.viewName = newViewName;
2275
2276     addAlignmentPanel(newap, true);
2277
2278     if (alignPanels.size() == 2)
2279     {
2280       viewport.gatherViewsHere = true;
2281     }
2282     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2283   }
2284
2285   public void expandViews_actionPerformed(ActionEvent e)
2286   {
2287     Desktop.instance.explodeViews(this);
2288   }
2289
2290   public void gatherViews_actionPerformed(ActionEvent e)
2291   {
2292     Desktop.instance.gatherViews(this);
2293   }
2294
2295   /**
2296    * DOCUMENT ME!
2297    *
2298    * @param e
2299    *          DOCUMENT ME!
2300    */
2301   public void font_actionPerformed(ActionEvent e)
2302   {
2303     new FontChooser(alignPanel);
2304   }
2305
2306   /**
2307    * DOCUMENT ME!
2308    *
2309    * @param e
2310    *          DOCUMENT ME!
2311    */
2312   protected void seqLimit_actionPerformed(ActionEvent e)
2313   {
2314     viewport.setShowJVSuffix(seqLimits.isSelected());
2315
2316     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2317             .calculateIdWidth());
2318     alignPanel.paintAlignment(true);
2319   }
2320
2321   public void idRightAlign_actionPerformed(ActionEvent e)
2322   {
2323     viewport.rightAlignIds = idRightAlign.isSelected();
2324     alignPanel.paintAlignment(true);
2325   }
2326
2327   public void centreColumnLabels_actionPerformed(ActionEvent e)
2328   {
2329     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2330     alignPanel.paintAlignment(true);
2331   }
2332
2333   /*
2334    * (non-Javadoc)
2335    *
2336    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2337    */
2338   protected void followHighlight_actionPerformed()
2339   {
2340     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2341     {
2342       alignPanel.scrollToPosition(
2343               alignPanel.seqPanel.seqCanvas.searchResults, false);
2344     }
2345   }
2346
2347   /**
2348    * DOCUMENT ME!
2349    *
2350    * @param e
2351    *          DOCUMENT ME!
2352    */
2353   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2354   {
2355     viewport.setColourText(colourTextMenuItem.isSelected());
2356     alignPanel.paintAlignment(true);
2357   }
2358
2359   /**
2360    * DOCUMENT ME!
2361    *
2362    * @param e
2363    *          DOCUMENT ME!
2364    */
2365   public void wrapMenuItem_actionPerformed(ActionEvent e)
2366   {
2367     scaleAbove.setVisible(wrapMenuItem.isSelected());
2368     scaleLeft.setVisible(wrapMenuItem.isSelected());
2369     scaleRight.setVisible(wrapMenuItem.isSelected());
2370     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2371     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2372   }
2373
2374   public void showAllSeqs_actionPerformed(ActionEvent e)
2375   {
2376     viewport.showAllHiddenSeqs();
2377   }
2378
2379   public void showAllColumns_actionPerformed(ActionEvent e)
2380   {
2381     viewport.showAllHiddenColumns();
2382     repaint();
2383   }
2384
2385   public void hideSelSequences_actionPerformed(ActionEvent e)
2386   {
2387     viewport.hideAllSelectedSeqs();
2388     alignPanel.paintAlignment(true);
2389   }
2390
2391   /**
2392    * called by key handler and the hide all/show all menu items
2393    *
2394    * @param toggleSeqs
2395    * @param toggleCols
2396    */
2397   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2398   {
2399
2400     boolean hide = false;
2401     SequenceGroup sg = viewport.getSelectionGroup();
2402     if (!toggleSeqs && !toggleCols)
2403     {
2404       // Hide everything by the current selection - this is a hack - we do the
2405       // invert and then hide
2406       // first check that there will be visible columns after the invert.
2407       if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2408               .getSelected().size() > 0)
2409               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2410                       .getEndRes()))
2411       {
2412         // now invert the sequence set, if required - empty selection implies
2413         // that no hiding is required.
2414         if (sg != null)
2415         {
2416           invertSequenceMenuItem_actionPerformed(null);
2417           sg = viewport.getSelectionGroup();
2418           toggleSeqs = true;
2419
2420         }
2421         viewport.expandColSelection(sg, true);
2422         // finally invert the column selection and get the new sequence
2423         // selection.
2424         invertColSel_actionPerformed(null);
2425         toggleCols = true;
2426       }
2427     }
2428
2429     if (toggleSeqs)
2430     {
2431       if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2432       {
2433         hideSelSequences_actionPerformed(null);
2434         hide = true;
2435       }
2436       else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2437       {
2438         showAllSeqs_actionPerformed(null);
2439       }
2440     }
2441
2442     if (toggleCols)
2443     {
2444       if (viewport.colSel.getSelected().size() > 0)
2445       {
2446         hideSelColumns_actionPerformed(null);
2447         if (!toggleSeqs)
2448         {
2449           viewport.selectionGroup = sg;
2450         }
2451       }
2452       else if (!hide)
2453       {
2454         showAllColumns_actionPerformed(null);
2455       }
2456     }
2457   }
2458
2459   /*
2460    * (non-Javadoc)
2461    *
2462    * @see
2463    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2464    * event.ActionEvent)
2465    */
2466   public void hideAllButSelection_actionPerformed(ActionEvent e)
2467   {
2468     toggleHiddenRegions(false, false);
2469   }
2470
2471   /*
2472    * (non-Javadoc)
2473    *
2474    * @see
2475    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2476    * .ActionEvent)
2477    */
2478   public void hideAllSelection_actionPerformed(ActionEvent e)
2479   {
2480     SequenceGroup sg = viewport.getSelectionGroup();
2481     viewport.expandColSelection(sg, false);
2482     viewport.hideAllSelectedSeqs();
2483     viewport.hideSelectedColumns();
2484     alignPanel.paintAlignment(true);
2485   }
2486
2487   /*
2488    * (non-Javadoc)
2489    *
2490    * @see
2491    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2492    * ActionEvent)
2493    */
2494   public void showAllhidden_actionPerformed(ActionEvent e)
2495   {
2496     viewport.showAllHiddenColumns();
2497     viewport.showAllHiddenSeqs();
2498     alignPanel.paintAlignment(true);
2499   }
2500
2501   public void hideSelColumns_actionPerformed(ActionEvent e)
2502   {
2503     viewport.hideSelectedColumns();
2504     alignPanel.paintAlignment(true);
2505   }
2506
2507   public void hiddenMarkers_actionPerformed(ActionEvent e)
2508   {
2509     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2510     repaint();
2511   }
2512
2513   /**
2514    * DOCUMENT ME!
2515    *
2516    * @param e
2517    *          DOCUMENT ME!
2518    */
2519   protected void scaleAbove_actionPerformed(ActionEvent e)
2520   {
2521     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2522     alignPanel.paintAlignment(true);
2523   }
2524
2525   /**
2526    * DOCUMENT ME!
2527    *
2528    * @param e
2529    *          DOCUMENT ME!
2530    */
2531   protected void scaleLeft_actionPerformed(ActionEvent e)
2532   {
2533     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2534     alignPanel.paintAlignment(true);
2535   }
2536
2537   /**
2538    * DOCUMENT ME!
2539    *
2540    * @param e
2541    *          DOCUMENT ME!
2542    */
2543   protected void scaleRight_actionPerformed(ActionEvent e)
2544   {
2545     viewport.setScaleRightWrapped(scaleRight.isSelected());
2546     alignPanel.paintAlignment(true);
2547   }
2548
2549   /**
2550    * DOCUMENT ME!
2551    *
2552    * @param e
2553    *          DOCUMENT ME!
2554    */
2555   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2556   {
2557     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2558     alignPanel.paintAlignment(true);
2559   }
2560
2561   /**
2562    * DOCUMENT ME!
2563    *
2564    * @param e
2565    *          DOCUMENT ME!
2566    */
2567   public void viewTextMenuItem_actionPerformed(ActionEvent e)
2568   {
2569     viewport.setShowText(viewTextMenuItem.isSelected());
2570     alignPanel.paintAlignment(true);
2571   }
2572
2573   /**
2574    * DOCUMENT ME!
2575    *
2576    * @param e
2577    *          DOCUMENT ME!
2578    */
2579   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2580   {
2581     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2582     alignPanel.paintAlignment(true);
2583   }
2584
2585   public FeatureSettings featureSettings;
2586
2587   public void featureSettings_actionPerformed(ActionEvent e)
2588   {
2589     if (featureSettings != null)
2590     {
2591       featureSettings.close();
2592       featureSettings = null;
2593     }
2594     if (!showSeqFeatures.isSelected())
2595     {
2596       // make sure features are actually displayed
2597       showSeqFeatures.setSelected(true);
2598       showSeqFeatures_actionPerformed(null);
2599     }
2600     featureSettings = new FeatureSettings(this);
2601   }
2602
2603   /**
2604    * Set or clear 'Show Sequence Features'
2605    *
2606    * @param evt
2607    *          DOCUMENT ME!
2608    */
2609   public void showSeqFeatures_actionPerformed(ActionEvent evt)
2610   {
2611     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2612     alignPanel.paintAlignment(true);
2613     if (alignPanel.getOverviewPanel() != null)
2614     {
2615       alignPanel.getOverviewPanel().updateOverviewImage();
2616     }
2617   }
2618
2619   /**
2620    * Set or clear 'Show Sequence Features'
2621    *
2622    * @param evt
2623    *          DOCUMENT ME!
2624    */
2625   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2626   {
2627     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2628             .isSelected());
2629     if (viewport.getShowSequenceFeaturesHeight())
2630     {
2631       // ensure we're actually displaying features
2632       viewport.setShowSequenceFeatures(true);
2633       showSeqFeatures.setSelected(true);
2634     }
2635     alignPanel.paintAlignment(true);
2636     if (alignPanel.getOverviewPanel() != null)
2637     {
2638       alignPanel.getOverviewPanel().updateOverviewImage();
2639     }
2640   }
2641
2642   /**
2643    * DOCUMENT ME!
2644    *
2645    * @param e
2646    *          DOCUMENT ME!
2647    */
2648   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2649   {
2650     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2651     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2652   }
2653
2654   public void alignmentProperties()
2655   {
2656     JEditorPane editPane = new JEditorPane("text/html", "");
2657     editPane.setEditable(false);
2658     StringBuffer contents = new StringBuffer("<html>");
2659
2660     float avg = 0;
2661     int min = Integer.MAX_VALUE, max = 0;
2662     for (int i = 0; i < viewport.alignment.getHeight(); i++)
2663     {
2664       int size = viewport.alignment.getSequenceAt(i).getEnd()
2665               - viewport.alignment.getSequenceAt(i).getStart();
2666       avg += size;
2667       if (size > max)
2668         max = size;
2669       if (size < min)
2670         min = size;
2671     }
2672     avg = avg / (float) viewport.alignment.getHeight();
2673
2674     contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2675     contents.append("<br>Minimum Sequence Length: " + min);
2676     contents.append("<br>Maximum Sequence Length: " + max);
2677     contents.append("<br>Average Length: " + (int) avg);
2678
2679     if (((Alignment) viewport.alignment).getProperties() != null)
2680     {
2681       Hashtable props = ((Alignment) viewport.alignment).getProperties();
2682       Enumeration en = props.keys();
2683       contents.append("<br><br><table border=\"1\">");
2684       while (en.hasMoreElements())
2685       {
2686         String key = en.nextElement().toString();
2687         StringBuffer val = new StringBuffer();
2688         String vals = props.get(key).toString();
2689         int pos = 0, npos;
2690         do
2691         {
2692           npos = vals.indexOf("\n", pos);
2693           if (npos == -1)
2694           {
2695             val.append(vals.substring(pos));
2696           }
2697           else
2698           {
2699             val.append(vals.substring(pos, npos));
2700             val.append("<br>");
2701           }
2702           pos = npos + 1;
2703         } while (npos != -1);
2704         contents
2705                 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2706       }
2707       contents.append("</table>");
2708     }
2709     editPane.setText(contents.toString() + "</html>");
2710     JInternalFrame frame = new JInternalFrame();
2711     frame.getContentPane().add(new JScrollPane(editPane));
2712
2713     Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2714             + getTitle(), 500, 400);
2715   }
2716
2717   /**
2718    * DOCUMENT ME!
2719    *
2720    * @param e
2721    *          DOCUMENT ME!
2722    */
2723   public void overviewMenuItem_actionPerformed(ActionEvent e)
2724   {
2725     if (alignPanel.overviewPanel != null)
2726     {
2727       return;
2728     }
2729
2730     JInternalFrame frame = new JInternalFrame();
2731     OverviewPanel overview = new OverviewPanel(alignPanel);
2732     frame.setContentPane(overview);
2733     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2734             .getWidth(), frame.getHeight());
2735     frame.pack();
2736     frame.setLayer(JLayeredPane.PALETTE_LAYER);
2737     frame
2738             .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2739             {
2740               public void internalFrameClosed(
2741                       javax.swing.event.InternalFrameEvent evt)
2742               {
2743                 alignPanel.setOverviewPanel(null);
2744               };
2745             });
2746
2747     alignPanel.setOverviewPanel(overview);
2748   }
2749
2750   public void textColour_actionPerformed(ActionEvent e)
2751   {
2752     new TextColourChooser().chooseColour(alignPanel, null);
2753   }
2754
2755   /**
2756    * DOCUMENT ME!
2757    *
2758    * @param e
2759    *          DOCUMENT ME!
2760    */
2761   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2762   {
2763     changeColour(null);
2764   }
2765
2766   /**
2767    * DOCUMENT ME!
2768    *
2769    * @param e
2770    *          DOCUMENT ME!
2771    */
2772   public void clustalColour_actionPerformed(ActionEvent e)
2773   {
2774     changeColour(new ClustalxColourScheme(
2775             viewport.alignment.getSequences(), viewport.alignment
2776                     .getWidth()));
2777   }
2778
2779   /**
2780    * DOCUMENT ME!
2781    *
2782    * @param e
2783    *          DOCUMENT ME!
2784    */
2785   public void zappoColour_actionPerformed(ActionEvent e)
2786   {
2787     changeColour(new ZappoColourScheme());
2788   }
2789
2790   /**
2791    * DOCUMENT ME!
2792    *
2793    * @param e
2794    *          DOCUMENT ME!
2795    */
2796   public void taylorColour_actionPerformed(ActionEvent e)
2797   {
2798     changeColour(new TaylorColourScheme());
2799   }
2800
2801   /**
2802    * DOCUMENT ME!
2803    *
2804    * @param e
2805    *          DOCUMENT ME!
2806    */
2807   public void hydrophobicityColour_actionPerformed(ActionEvent e)
2808   {
2809     changeColour(new HydrophobicColourScheme());
2810   }
2811
2812   /**
2813    * DOCUMENT ME!
2814    *
2815    * @param e
2816    *          DOCUMENT ME!
2817    */
2818   public void helixColour_actionPerformed(ActionEvent e)
2819   {
2820     changeColour(new HelixColourScheme());
2821   }
2822
2823   /**
2824    * DOCUMENT ME!
2825    *
2826    * @param e
2827    *          DOCUMENT ME!
2828    */
2829   public void strandColour_actionPerformed(ActionEvent e)
2830   {
2831     changeColour(new StrandColourScheme());
2832   }
2833
2834   /**
2835    * DOCUMENT ME!
2836    *
2837    * @param e
2838    *          DOCUMENT ME!
2839    */
2840   public void turnColour_actionPerformed(ActionEvent e)
2841   {
2842     changeColour(new TurnColourScheme());
2843   }
2844
2845   /**
2846    * DOCUMENT ME!
2847    *
2848    * @param e
2849    *          DOCUMENT ME!
2850    */
2851   public void buriedColour_actionPerformed(ActionEvent e)
2852   {
2853     changeColour(new BuriedColourScheme());
2854   }
2855
2856   /**
2857    * DOCUMENT ME!
2858    *
2859    * @param e
2860    *          DOCUMENT ME!
2861    */
2862   public void nucleotideColour_actionPerformed(ActionEvent e)
2863   {
2864     changeColour(new NucleotideColourScheme());
2865   }
2866
2867   public void annotationColour_actionPerformed(ActionEvent e)
2868   {
2869     new AnnotationColourChooser(viewport, alignPanel);
2870   }
2871
2872   /**
2873    * DOCUMENT ME!
2874    *
2875    * @param e
2876    *          DOCUMENT ME!
2877    */
2878   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2879   {
2880     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2881   }
2882
2883   /**
2884    * DOCUMENT ME!
2885    *
2886    * @param cs
2887    *          DOCUMENT ME!
2888    */
2889   public void changeColour(ColourSchemeI cs)
2890   {
2891     int threshold = 0;
2892
2893     if (cs != null)
2894     {
2895       if (viewport.getAbovePIDThreshold())
2896       {
2897         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2898                 "Background");
2899
2900         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2901
2902         viewport.setGlobalColourScheme(cs);
2903       }
2904       else
2905       {
2906         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2907       }
2908
2909       if (viewport.getConservationSelected())
2910       {
2911
2912         Alignment al = (Alignment) viewport.alignment;
2913         Conservation c = new Conservation("All",
2914                 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2915                         .getWidth() - 1);
2916
2917         c.calculate();
2918         c.verdict(false, viewport.ConsPercGaps);
2919
2920         cs.setConservation(c);
2921
2922         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2923                 cs, "Background"));
2924       }
2925       else
2926       {
2927         cs.setConservation(null);
2928       }
2929
2930       cs.setConsensus(viewport.hconsensus);
2931     }
2932
2933     viewport.setGlobalColourScheme(cs);
2934
2935     if (viewport.getColourAppliesToAllGroups())
2936     {
2937       Vector groups = viewport.alignment.getGroups();
2938
2939       for (int i = 0; i < groups.size(); i++)
2940       {
2941         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2942
2943         if (cs == null)
2944         {
2945           sg.cs = null;
2946           continue;
2947         }
2948
2949         if (cs instanceof ClustalxColourScheme)
2950         {
2951           sg.cs = new ClustalxColourScheme(sg
2952                   .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2953         }
2954         else if (cs instanceof UserColourScheme)
2955         {
2956           sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2957         }
2958         else
2959         {
2960           try
2961           {
2962             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2963           } catch (Exception ex)
2964           {
2965           }
2966         }
2967
2968         if (viewport.getAbovePIDThreshold()
2969                 || cs instanceof PIDColourScheme
2970                 || cs instanceof Blosum62ColourScheme)
2971         {
2972           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2973
2974           sg.cs.setConsensus(AAFrequency.calculate(sg
2975                   .getSequences(viewport.hiddenRepSequences), sg
2976                   .getStartRes(), sg.getEndRes() + 1));
2977         }
2978         else
2979         {
2980           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2981         }
2982
2983         if (viewport.getConservationSelected())
2984         {
2985           Conservation c = new Conservation("Group",
2986                   ResidueProperties.propHash, 3, sg
2987                           .getSequences(viewport.hiddenRepSequences), sg
2988                           .getStartRes(), sg.getEndRes() + 1);
2989           c.calculate();
2990           c.verdict(false, viewport.ConsPercGaps);
2991           sg.cs.setConservation(c);
2992         }
2993         else
2994         {
2995           sg.cs.setConservation(null);
2996         }
2997       }
2998     }
2999
3000     if (alignPanel.getOverviewPanel() != null)
3001     {
3002       alignPanel.getOverviewPanel().updateOverviewImage();
3003     }
3004
3005     alignPanel.paintAlignment(true);
3006   }
3007
3008   /**
3009    * DOCUMENT ME!
3010    *
3011    * @param e
3012    *          DOCUMENT ME!
3013    */
3014   protected void modifyPID_actionPerformed(ActionEvent e)
3015   {
3016     if (viewport.getAbovePIDThreshold()
3017             && viewport.globalColourScheme != null)
3018     {
3019       SliderPanel.setPIDSliderSource(alignPanel, viewport
3020               .getGlobalColourScheme(), "Background");
3021       SliderPanel.showPIDSlider();
3022     }
3023   }
3024
3025   /**
3026    * DOCUMENT ME!
3027    *
3028    * @param e
3029    *          DOCUMENT ME!
3030    */
3031   protected void modifyConservation_actionPerformed(ActionEvent e)
3032   {
3033     if (viewport.getConservationSelected()
3034             && viewport.globalColourScheme != null)
3035     {
3036       SliderPanel.setConservationSlider(alignPanel,
3037               viewport.globalColourScheme, "Background");
3038       SliderPanel.showConservationSlider();
3039     }
3040   }
3041
3042   /**
3043    * DOCUMENT ME!
3044    *
3045    * @param e
3046    *          DOCUMENT ME!
3047    */
3048   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3049   {
3050     viewport.setConservationSelected(conservationMenuItem.isSelected());
3051
3052     viewport.setAbovePIDThreshold(false);
3053     abovePIDThreshold.setSelected(false);
3054
3055     changeColour(viewport.getGlobalColourScheme());
3056
3057     modifyConservation_actionPerformed(null);
3058   }
3059
3060   /**
3061    * DOCUMENT ME!
3062    *
3063    * @param e
3064    *          DOCUMENT ME!
3065    */
3066   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3067   {
3068     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3069
3070     conservationMenuItem.setSelected(false);
3071     viewport.setConservationSelected(false);
3072
3073     changeColour(viewport.getGlobalColourScheme());
3074
3075     modifyPID_actionPerformed(null);
3076   }
3077
3078   /**
3079    * DOCUMENT ME!
3080    *
3081    * @param e
3082    *          DOCUMENT ME!
3083    */
3084   public void userDefinedColour_actionPerformed(ActionEvent e)
3085   {
3086     if (e.getActionCommand().equals("User Defined..."))
3087     {
3088       new UserDefinedColours(alignPanel, null);
3089     }
3090     else
3091     {
3092       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3093               .getUserColourSchemes().get(e.getActionCommand());
3094
3095       changeColour(udc);
3096     }
3097   }
3098
3099   public void updateUserColourMenu()
3100   {
3101
3102     Component[] menuItems = colourMenu.getMenuComponents();
3103     int i, iSize = menuItems.length;
3104     for (i = 0; i < iSize; i++)
3105     {
3106       if (menuItems[i].getName() != null
3107               && menuItems[i].getName().equals("USER_DEFINED"))
3108       {
3109         colourMenu.remove(menuItems[i]);
3110         iSize--;
3111       }
3112     }
3113     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3114     {
3115       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3116               .getUserColourSchemes().keys();
3117
3118       while (userColours.hasMoreElements())
3119       {
3120         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3121                 userColours.nextElement().toString());
3122         radioItem.setName("USER_DEFINED");
3123         radioItem.addMouseListener(new MouseAdapter()
3124         {
3125           public void mousePressed(MouseEvent evt)
3126           {
3127             if (evt.isControlDown()
3128                     || SwingUtilities.isRightMouseButton(evt))
3129             {
3130               radioItem
3131                       .removeActionListener(radioItem.getActionListeners()[0]);
3132
3133               int option = JOptionPane.showInternalConfirmDialog(
3134                       jalview.gui.Desktop.desktop,
3135                       "Remove from default list?",
3136                       "Remove user defined colour",
3137                       JOptionPane.YES_NO_OPTION);
3138               if (option == JOptionPane.YES_OPTION)
3139               {
3140                 jalview.gui.UserDefinedColours
3141                         .removeColourFromDefaults(radioItem.getText());
3142                 colourMenu.remove(radioItem);
3143               }
3144               else
3145               {
3146                 radioItem.addActionListener(new ActionListener()
3147                 {
3148                   public void actionPerformed(ActionEvent evt)
3149                   {
3150                     userDefinedColour_actionPerformed(evt);
3151                   }
3152                 });
3153               }
3154             }
3155           }
3156         });
3157         radioItem.addActionListener(new ActionListener()
3158         {
3159           public void actionPerformed(ActionEvent evt)
3160           {
3161             userDefinedColour_actionPerformed(evt);
3162           }
3163         });
3164
3165         colourMenu.insert(radioItem, 15);
3166         colours.add(radioItem);
3167       }
3168     }
3169   }
3170
3171   /**
3172    * DOCUMENT ME!
3173    *
3174    * @param e
3175    *          DOCUMENT ME!
3176    */
3177   public void PIDColour_actionPerformed(ActionEvent e)
3178   {
3179     changeColour(new PIDColourScheme());
3180   }
3181
3182   /**
3183    * DOCUMENT ME!
3184    *
3185    * @param e
3186    *          DOCUMENT ME!
3187    */
3188   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3189   {
3190     changeColour(new Blosum62ColourScheme());
3191   }
3192
3193   /**
3194    * DOCUMENT ME!
3195    *
3196    * @param e
3197    *          DOCUMENT ME!
3198    */
3199   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3200   {
3201     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3202     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3203             .getAlignment().getSequenceAt(0), null);
3204     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3205             viewport.alignment));
3206     alignPanel.paintAlignment(true);
3207   }
3208
3209   /**
3210    * DOCUMENT ME!
3211    *
3212    * @param e
3213    *          DOCUMENT ME!
3214    */
3215   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3216   {
3217     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3218     AlignmentSorter.sortByID(viewport.getAlignment());
3219     addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3220     alignPanel.paintAlignment(true);
3221   }
3222
3223   /**
3224    * DOCUMENT ME!
3225    *
3226    * @param e
3227    *          DOCUMENT ME!
3228    */
3229   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3230   {
3231     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3232     AlignmentSorter.sortByLength(viewport.getAlignment());
3233     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3234             viewport.alignment));
3235     alignPanel.paintAlignment(true);
3236   }
3237
3238   /**
3239    * DOCUMENT ME!
3240    *
3241    * @param e
3242    *          DOCUMENT ME!
3243    */
3244   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3245   {
3246     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3247     AlignmentSorter.sortByGroup(viewport.getAlignment());
3248     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3249             viewport.alignment));
3250
3251     alignPanel.paintAlignment(true);
3252   }
3253
3254   /**
3255    * DOCUMENT ME!
3256    *
3257    * @param e
3258    *          DOCUMENT ME!
3259    */
3260   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3261   {
3262     new RedundancyPanel(alignPanel, this);
3263   }
3264
3265   /**
3266    * DOCUMENT ME!
3267    *
3268    * @param e
3269    *          DOCUMENT ME!
3270    */
3271   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3272   {
3273     if ((viewport.getSelectionGroup() == null)
3274             || (viewport.getSelectionGroup().getSize() < 2))
3275     {
3276       JOptionPane.showInternalMessageDialog(this,
3277               "You must select at least 2 sequences.", "Invalid Selection",
3278               JOptionPane.WARNING_MESSAGE);
3279     }
3280     else
3281     {
3282       JInternalFrame frame = new JInternalFrame();
3283       frame.setContentPane(new PairwiseAlignPanel(viewport));
3284       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3285     }
3286   }
3287
3288   /**
3289    * DOCUMENT ME!
3290    *
3291    * @param e
3292    *          DOCUMENT ME!
3293    */
3294   public void PCAMenuItem_actionPerformed(ActionEvent e)
3295   {
3296     if (((viewport.getSelectionGroup() != null)
3297             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3298             .getSelectionGroup().getSize() > 0))
3299             || (viewport.getAlignment().getHeight() < 4))
3300     {
3301       JOptionPane.showInternalMessageDialog(this,
3302               "Principal component analysis must take\n"
3303                       + "at least 4 input sequences.",
3304               "Sequence selection insufficient",
3305               JOptionPane.WARNING_MESSAGE);
3306
3307       return;
3308     }
3309
3310     new PCAPanel(alignPanel);
3311   }
3312
3313   public void autoCalculate_actionPerformed(ActionEvent e)
3314   {
3315     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3316     if (viewport.autoCalculateConsensus)
3317     {
3318       viewport.firePropertyChange("alignment", null, viewport
3319               .getAlignment().getSequences());
3320     }
3321   }
3322
3323   /**
3324    * DOCUMENT ME!
3325    *
3326    * @param e
3327    *          DOCUMENT ME!
3328    */
3329   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3330   {
3331     NewTreePanel("AV", "PID", "Average distance tree using PID");
3332   }
3333
3334   /**
3335    * DOCUMENT ME!
3336    *
3337    * @param e
3338    *          DOCUMENT ME!
3339    */
3340   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3341   {
3342     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3343   }
3344
3345   /**
3346    * DOCUMENT ME!
3347    *
3348    * @param e
3349    *          DOCUMENT ME!
3350    */
3351   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3352   {
3353     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3354   }
3355
3356   /**
3357    * DOCUMENT ME!
3358    *
3359    * @param e
3360    *          DOCUMENT ME!
3361    */
3362   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3363   {
3364     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3365   }
3366
3367   /**
3368    * DOCUMENT ME!
3369    *
3370    * @param type
3371    *          DOCUMENT ME!
3372    * @param pwType
3373    *          DOCUMENT ME!
3374    * @param title
3375    *          DOCUMENT ME!
3376    */
3377   void NewTreePanel(String type, String pwType, String title)
3378   {
3379     TreePanel tp;
3380
3381     if (viewport.getSelectionGroup() != null)
3382     {
3383       if (viewport.getSelectionGroup().getSize() < 3)
3384       {
3385         JOptionPane
3386                 .showMessageDialog(
3387                         Desktop.desktop,
3388                         "You need to have more than two sequences selected to build a tree!",
3389                         "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3390         return;
3391       }
3392
3393       int s = 0;
3394       SequenceGroup sg = viewport.getSelectionGroup();
3395
3396       /* Decide if the selection is a column region */
3397       while (s < sg.getSize())
3398       {
3399         if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3400                 .getEndRes())
3401         {
3402           JOptionPane
3403                   .showMessageDialog(
3404                           Desktop.desktop,
3405                           "The selected region to create a tree may\nonly contain residues or gaps.\n"
3406                                   + "Try using the Pad function in the edit menu,\n"
3407                                   + "or one of the multiple sequence alignment web services.",
3408                           "Sequences in selection are not aligned",
3409                           JOptionPane.WARNING_MESSAGE);
3410
3411           return;
3412         }
3413       }
3414
3415       title = title + " on region";
3416       tp = new TreePanel(alignPanel, type, pwType);
3417     }
3418     else
3419     {
3420       // are the visible sequences aligned?
3421       if (!viewport.alignment.isAligned(false))
3422       {
3423         JOptionPane
3424                 .showMessageDialog(
3425                         Desktop.desktop,
3426                         "The sequences must be aligned before creating a tree.\n"
3427                                 + "Try using the Pad function in the edit menu,\n"
3428                                 + "or one of the multiple sequence alignment web services.",
3429                         "Sequences not aligned",
3430                         JOptionPane.WARNING_MESSAGE);
3431
3432         return;
3433       }
3434
3435       if (viewport.alignment.getHeight() < 2)
3436       {
3437         return;
3438       }
3439
3440       tp = new TreePanel(alignPanel, type, pwType);
3441     }
3442
3443     title += " from ";
3444
3445     if (viewport.viewName != null)
3446     {
3447       title += viewport.viewName + " of ";
3448     }
3449
3450     title += this.title;
3451
3452     Desktop.addInternalFrame(tp, title, 600, 500);
3453   }
3454
3455   /**
3456    * DOCUMENT ME!
3457    *
3458    * @param title
3459    *          DOCUMENT ME!
3460    * @param order
3461    *          DOCUMENT ME!
3462    */
3463   public void addSortByOrderMenuItem(String title,
3464           final AlignmentOrder order)
3465   {
3466     final JMenuItem item = new JMenuItem("by " + title);
3467     sort.add(item);
3468     item.addActionListener(new java.awt.event.ActionListener()
3469     {
3470       public void actionPerformed(ActionEvent e)
3471       {
3472         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3473
3474         // TODO: JBPNote - have to map order entries to curent SequenceI
3475         // pointers
3476         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3477
3478         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3479                 viewport.alignment));
3480
3481         alignPanel.paintAlignment(true);
3482       }
3483     });
3484   }
3485
3486   /**
3487    * Add a new sort by annotation score menu item
3488    *
3489    * @param sort
3490    *          the menu to add the option to
3491    * @param scoreLabel
3492    *          the label used to retrieve scores for each sequence on the
3493    *          alignment
3494    */
3495   public void addSortByAnnotScoreMenuItem(JMenu sort,
3496           final String scoreLabel)
3497   {
3498     final JMenuItem item = new JMenuItem(scoreLabel);
3499     sort.add(item);
3500     item.addActionListener(new java.awt.event.ActionListener()
3501     {
3502       public void actionPerformed(ActionEvent e)
3503       {
3504         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3505         AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3506                 .getAlignment());// ,viewport.getSelectionGroup());
3507         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3508                 viewport.alignment));
3509         alignPanel.paintAlignment(true);
3510       }
3511     });
3512   }
3513
3514   /**
3515    * last hash for alignment's annotation array - used to minimise cost of
3516    * rebuild.
3517    */
3518   protected int _annotationScoreVectorHash;
3519
3520   /**
3521    * search the alignment and rebuild the sort by annotation score submenu the
3522    * last alignment annotation vector hash is stored to minimize cost of
3523    * rebuilding in subsequence calls.
3524    *
3525    */
3526   public void buildSortByAnnotationScoresMenu()
3527   {
3528     if (viewport.alignment.getAlignmentAnnotation() == null)
3529     {
3530       return;
3531     }
3532
3533     if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3534     {
3535       sortByAnnotScore.removeAll();
3536       // almost certainly a quicker way to do this - but we keep it simple
3537       Hashtable scoreSorts = new Hashtable();
3538       AlignmentAnnotation aann[];
3539       Enumeration sq = viewport.alignment.getSequences().elements();
3540       while (sq.hasMoreElements())
3541       {
3542         aann = ((SequenceI) sq.nextElement()).getAnnotation();
3543         for (int i = 0; aann != null && i < aann.length; i++)
3544         {
3545           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3546           {
3547             scoreSorts.put(aann[i].label, aann[i].label);
3548           }
3549         }
3550       }
3551       Enumeration labels = scoreSorts.keys();
3552       while (labels.hasMoreElements())
3553       {
3554         addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3555                 .nextElement());
3556       }
3557       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3558       scoreSorts.clear();
3559
3560       _annotationScoreVectorHash = viewport.alignment
3561               .getAlignmentAnnotation().hashCode();
3562     }
3563   }
3564
3565   /**
3566    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3567    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3568    * call. Listeners are added to remove the menu item when the treePanel is
3569    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3570    * modified.
3571    *
3572    * @param treePanel
3573    *          Displayed tree window.
3574    * @param title
3575    *          SortBy menu item title.
3576    */
3577   public void buildTreeMenu()
3578   {
3579     sortByTreeMenu.removeAll();
3580
3581     Vector comps = (Vector) PaintRefresher.components.get(viewport
3582             .getSequenceSetId());
3583     Vector treePanels = new Vector();
3584     int i, iSize = comps.size();
3585     for (i = 0; i < iSize; i++)
3586     {
3587       if (comps.elementAt(i) instanceof TreePanel)
3588       {
3589         treePanels.add(comps.elementAt(i));
3590       }
3591     }
3592
3593     iSize = treePanels.size();
3594
3595     if (iSize < 1)
3596     {
3597       sortByTreeMenu.setVisible(false);
3598       return;
3599     }
3600
3601     sortByTreeMenu.setVisible(true);
3602
3603     for (i = 0; i < treePanels.size(); i++)
3604     {
3605       TreePanel tp = (TreePanel) treePanels.elementAt(i);
3606       final JMenuItem item = new JMenuItem(tp.getTitle());
3607       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3608       item.addActionListener(new java.awt.event.ActionListener()
3609       {
3610         public void actionPerformed(ActionEvent e)
3611         {
3612           SequenceI[] oldOrder = viewport.getAlignment()
3613                   .getSequencesArray();
3614           AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3615
3616           addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3617                   viewport.alignment));
3618
3619           alignPanel.paintAlignment(true);
3620         }
3621       });
3622
3623       sortByTreeMenu.add(item);
3624     }
3625   }
3626
3627   /**
3628    * Work out whether the whole set of sequences or just the selected set will
3629    * be submitted for multiple alignment.
3630    *
3631    */
3632   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3633   {
3634     // Now, check we have enough sequences
3635     AlignmentView msa = null;
3636
3637     if ((viewport.getSelectionGroup() != null)
3638             && (viewport.getSelectionGroup().getSize() > 1))
3639     {
3640       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3641       // some common interface!
3642       /*
3643        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3644        * SequenceI[sz = seqs.getSize(false)];
3645        *
3646        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3647        * seqs.getSequenceAt(i); }
3648        */
3649       msa = viewport.getAlignmentView(true);
3650     }
3651     else
3652     {
3653       /*
3654        * Vector seqs = viewport.getAlignment().getSequences();
3655        *
3656        * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3657        *
3658        * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3659        * seqs.elementAt(i); } }
3660        */
3661       msa = viewport.getAlignmentView(false);
3662     }
3663     return msa;
3664   }
3665
3666   /**
3667    * Decides what is submitted to a secondary structure prediction service: the
3668    * first sequence in the alignment, or in the current selection, or, if the
3669    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3670    * region or the whole alignment. (where the first sequence in the set is the
3671    * one that the prediction will be for).
3672    */
3673   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3674   {
3675     AlignmentView seqs = null;
3676
3677     if ((viewport.getSelectionGroup() != null)
3678             && (viewport.getSelectionGroup().getSize() > 0))
3679     {
3680       seqs = viewport.getAlignmentView(true);
3681     }
3682     else
3683     {
3684       seqs = viewport.getAlignmentView(false);
3685     }
3686     // limit sequences - JBPNote in future - could spawn multiple prediction
3687     // jobs
3688     // TODO: viewport.alignment.isAligned is a global state - the local
3689     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3690     if (!viewport.alignment.isAligned(false))
3691     {
3692       seqs.setSequences(new SeqCigar[]
3693       { seqs.getSequences()[0] });
3694       // TODO: if seqs.getSequences().length>1 then should really have warned
3695       // user!
3696
3697     }
3698     return seqs;
3699   }
3700
3701   /**
3702    * DOCUMENT ME!
3703    *
3704    * @param e
3705    *          DOCUMENT ME!
3706    */
3707   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3708   {
3709     // Pick the tree file
3710     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3711             .getProperty("LAST_DIRECTORY"));
3712     chooser.setFileView(new JalviewFileView());
3713     chooser.setDialogTitle("Select a newick-like tree file");
3714     chooser.setToolTipText("Load a tree file");
3715
3716     int value = chooser.showOpenDialog(null);
3717
3718     if (value == JalviewFileChooser.APPROVE_OPTION)
3719     {
3720       String choice = chooser.getSelectedFile().getPath();
3721       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3722       jalview.io.NewickFile fin = null;
3723       try
3724       {
3725         fin = new jalview.io.NewickFile(choice, "File");
3726         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3727       } catch (Exception ex)
3728       {
3729         JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3730                 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3731         ex.printStackTrace();
3732       }
3733       if (fin != null && fin.hasWarningMessage())
3734       {
3735         JOptionPane.showMessageDialog(Desktop.desktop, fin
3736                 .getWarningMessage(), "Possible problem with tree file",
3737                 JOptionPane.WARNING_MESSAGE);
3738       }
3739     }
3740   }
3741
3742   public TreePanel ShowNewickTree(NewickFile nf, String title)
3743   {
3744     return ShowNewickTree(nf, title, 600, 500, 4, 5);
3745   }
3746
3747   public TreePanel ShowNewickTree(NewickFile nf, String title,
3748           AlignmentView input)
3749   {
3750     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3751   }
3752
3753   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3754           int h, int x, int y)
3755   {
3756     return ShowNewickTree(nf, title, null, w, h, x, y);
3757   }
3758
3759   /**
3760    * Add a treeviewer for the tree extracted from a newick file object to the
3761    * current alignment view
3762    *
3763    * @param nf
3764    *          the tree
3765    * @param title
3766    *          tree viewer title
3767    * @param input
3768    *          Associated alignment input data (or null)
3769    * @param w
3770    *          width
3771    * @param h
3772    *          height
3773    * @param x
3774    *          position
3775    * @param y
3776    *          position
3777    * @return TreePanel handle
3778    */
3779   public TreePanel ShowNewickTree(NewickFile nf, String title,
3780           AlignmentView input, int w, int h, int x, int y)
3781   {
3782     TreePanel tp = null;
3783
3784     try
3785     {
3786       nf.parse();
3787
3788       if (nf.getTree() != null)
3789       {
3790         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3791
3792         tp.setSize(w, h);
3793
3794         if (x > 0 && y > 0)
3795         {
3796           tp.setLocation(x, y);
3797         }
3798
3799         Desktop.addInternalFrame(tp, title, w, h);
3800       }
3801     } catch (Exception ex)
3802     {
3803       ex.printStackTrace();
3804     }
3805
3806     return tp;
3807   }
3808
3809   private boolean buildingMenu = false;
3810
3811   /**
3812    * Generates menu items and listener event actions for web service clients
3813    *
3814    */
3815   public void BuildWebServiceMenu()
3816   {
3817     while (buildingMenu)
3818     {
3819       try
3820       {
3821         System.err.println("Waiting for building menu to finish.");
3822         Thread.sleep(10);
3823       } catch (Exception e)
3824       {
3825       }
3826       ;
3827     }
3828     buildingMenu = true;
3829     try
3830     {
3831       System.err
3832               .println("Building ws menu again " + Thread.currentThread());
3833       // TODO: add support for context dependent disabling of services based on
3834       // alignment and current selection
3835       // TODO: add additional serviceHandle parameter to specify abstract
3836       // handler
3837       // class independently of AbstractName
3838       // TODO: add in rediscovery GUI function to restart discoverer
3839       // TODO: group services by location as well as function and/or introduce
3840       // object broker mechanism.
3841       Vector wsmenu = new Vector();
3842       final IProgressIndicator af = this;
3843       if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
3844               && Discoverer.services != null
3845               && (Discoverer.services.size() > 0))
3846       {
3847         // TODO: refactor to allow list of AbstractName/Handler bindings to be
3848         // stored or retrieved from elsewhere
3849         Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3850         Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3851         Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3852         // TODO: move GUI generation code onto service implementation - so a
3853         // client instance attaches itself to the GUI with method call like
3854         // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3855         // alignframe)
3856         if (msaws != null)
3857         {
3858           // Add any Multiple Sequence Alignment Services
3859           final JMenu msawsmenu = new JMenu("Alignment");
3860           for (int i = 0, j = msaws.size(); i < j; i++)
3861           {
3862             final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3863                     .get(i);
3864             jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3865                     .getServiceClient(sh);
3866             impl.attachWSMenuEntry(msawsmenu, this);
3867
3868           }
3869           wsmenu.add(msawsmenu);
3870         }
3871         if (secstrpr != null)
3872         {
3873           // Add any secondary structure prediction services
3874           final JMenu secstrmenu = new JMenu(
3875                   "Secondary Structure Prediction");
3876           for (int i = 0, j = secstrpr.size(); i < j; i++)
3877           {
3878             final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3879                     .get(i);
3880             jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3881                     .getServiceClient(sh);
3882             impl.attachWSMenuEntry(secstrmenu, this);
3883           }
3884           wsmenu.add(secstrmenu);
3885         }
3886         if (seqsrch != null)
3887         {
3888           // Add any sequence search services
3889           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3890           for (int i = 0, j = seqsrch.size(); i < j; i++)
3891           {
3892             final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3893                     .elementAt(i);
3894             jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3895                     .getServiceClient(sh);
3896             impl.attachWSMenuEntry(seqsrchmenu, this);
3897           }
3898           wsmenu.add(seqsrchmenu);
3899         }
3900       }
3901
3902       // TODO: move into separate menu builder class.
3903       if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
3904       {
3905         Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
3906         if (jws2servs != null)
3907         {
3908           if (jws2servs.hasServices())
3909           {
3910             JMenu jws2men = new JMenu("Jalview 2 Services");
3911             jws2servs.attachWSMenuEntry(jws2men, this);
3912             for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
3913             {
3914               wsmenu.add(jws2men.getMenuComponent(i));
3915             }
3916           }
3917         }
3918       }
3919       resetWebServiceMenu();
3920       // finally, add the whole shebang onto the webservices menu
3921       if (wsmenu.size() > 0)
3922       {
3923         for (int i = 0, j = wsmenu.size(); i < j; i++)
3924         {
3925           webService.add((JMenu) wsmenu.get(i));
3926         }
3927       }
3928       else
3929       {
3930         this.webService.add(this.webServiceNoServices);
3931       }
3932     } catch (Exception e)
3933     {
3934     }
3935     ;
3936     buildingMenu = false;
3937   }
3938
3939   /**
3940    * empty the web service menu and add any ad-hoc functions not dynamically
3941    * discovered.
3942    *
3943    */
3944   private void resetWebServiceMenu()
3945   {
3946     webService.removeAll();
3947     build_fetchdbmenu(webService);
3948     build_urlServiceMenu(webService);
3949   }
3950
3951   /**
3952    * construct any groupURL type service menu entries.
3953    *
3954    * @param webService
3955    */
3956   private void build_urlServiceMenu(JMenu webService)
3957   {
3958     if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
3959     {
3960       jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
3961               webService, this);
3962     }
3963   }
3964
3965   /*
3966    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3967    * chooser = new JalviewFileChooser(jalview.bin.Cache.
3968    * getProperty("LAST_DIRECTORY"));
3969    *
3970    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3971    * to Vamsas file"); chooser.setToolTipText("Export");
3972    *
3973    * int value = chooser.showSaveDialog(this);
3974    *
3975    * if (value == JalviewFileChooser.APPROVE_OPTION) {
3976    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3977    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3978    * chooser.getSelectedFile().getAbsolutePath(), this); } }
3979    */
3980   /**
3981    * prototype of an automatically enabled/disabled analysis function
3982    *
3983    */
3984   protected void setShowProductsEnabled()
3985   {
3986     SequenceI[] selection = viewport.getSequenceSelection();
3987     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3988             viewport.getAlignment().getDataset()))
3989     {
3990       showProducts.setEnabled(true);
3991
3992     }
3993     else
3994     {
3995       showProducts.setEnabled(false);
3996     }
3997   }
3998
3999   /**
4000    * search selection for sequence xRef products and build the show products
4001    * menu.
4002    *
4003    * @param selection
4004    * @param dataset
4005    * @return true if showProducts menu should be enabled.
4006    */
4007   public boolean canShowProducts(SequenceI[] selection,
4008           boolean isRegionSelection, Alignment dataset)
4009   {
4010     boolean showp = false;
4011     try
4012     {
4013       showProducts.removeAll();
4014       final boolean dna = viewport.getAlignment().isNucleotide();
4015       final Alignment ds = dataset;
4016       String[] ptypes = (selection == null || selection.length == 0) ? null
4017               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4018       // Object[] prods =
4019       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4020       // selection, dataset, true);
4021       final SequenceI[] sel = selection;
4022       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4023       {
4024         showp = true;
4025         final boolean isRegSel = isRegionSelection;
4026         final AlignFrame af = this;
4027         final String source = ptypes[t];
4028         JMenuItem xtype = new JMenuItem(ptypes[t]);
4029         xtype.addActionListener(new ActionListener()
4030         {
4031
4032           public void actionPerformed(ActionEvent e)
4033           {
4034             // TODO: new thread for this call with vis-delay
4035             af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4036                     isRegSel, dna, source);
4037           }
4038
4039         });
4040         showProducts.add(xtype);
4041       }
4042       showProducts.setVisible(showp);
4043       showProducts.setEnabled(showp);
4044     } catch (Exception e)
4045     {
4046       jalview.bin.Cache.log
4047               .warn(
4048                       "canTranslate threw an exception - please report to help@jalview.org",
4049                       e);
4050       return false;
4051     }
4052     return showp;
4053   }
4054
4055   protected void showProductsFor(SequenceI[] sel, Alignment ds,
4056           boolean isRegSel, boolean dna, String source)
4057   {
4058     final boolean fisRegSel = isRegSel;
4059     final boolean fdna = dna;
4060     final String fsrc = source;
4061     final AlignFrame ths = this;
4062     final SequenceI[] fsel = sel;
4063     Runnable foo = new Runnable()
4064     {
4065
4066       public void run()
4067       {
4068         final long sttime = System.currentTimeMillis();
4069         ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4070         try
4071         {
4072           Alignment ds = ths.getViewport().alignment.getDataset(); // update
4073           // our local
4074           // dataset
4075           // reference
4076           Alignment prods = CrossRef
4077                   .findXrefSequences(fsel, fdna, fsrc, ds);
4078           if (prods != null)
4079           {
4080             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4081             for (int s = 0; s < sprods.length; s++)
4082             {
4083               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4084               if (ds.getSequences() == null
4085                       || !ds.getSequences().contains(
4086                               sprods[s].getDatasetSequence()))
4087                 ds.addSequence(sprods[s].getDatasetSequence());
4088               sprods[s].updatePDBIds();
4089             }
4090             Alignment al = new Alignment(sprods);
4091             AlignedCodonFrame[] cf = prods.getCodonFrames();
4092             al.setDataset(ds);
4093             for (int s = 0; cf != null && s < cf.length; s++)
4094             {
4095               al.addCodonFrame(cf[s]);
4096               cf[s] = null;
4097             }
4098             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4099                     DEFAULT_HEIGHT);
4100             String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4101                     + " for " + ((fisRegSel) ? "selected region of " : "")
4102                     + getTitle();
4103             Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4104                     DEFAULT_HEIGHT);
4105           }
4106           else
4107           {
4108             System.err.println("No Sequences generated for xRef type "
4109                     + fsrc);
4110           }
4111         } catch (Exception e)
4112         {
4113           jalview.bin.Cache.log.error(
4114                   "Exception when finding crossreferences", e);
4115         } catch (OutOfMemoryError e)
4116         {
4117           new OOMWarning("whilst fetching crossreferences", e);
4118         } catch (Error e)
4119         {
4120           jalview.bin.Cache.log.error("Error when finding crossreferences",
4121                   e);
4122         }
4123         ths.setProgressBar("Finished searching for sequences from " + fsrc,
4124                 sttime);
4125       }
4126
4127     };
4128     Thread frunner = new Thread(foo);
4129     frunner.start();
4130   }
4131
4132   public boolean canShowTranslationProducts(SequenceI[] selection,
4133           AlignmentI alignment)
4134   {
4135     // old way
4136     try
4137     {
4138       return (jalview.analysis.Dna.canTranslate(selection, viewport
4139               .getViewAsVisibleContigs(true)));
4140     } catch (Exception e)
4141     {
4142       jalview.bin.Cache.log
4143               .warn(
4144                       "canTranslate threw an exception - please report to help@jalview.org",
4145                       e);
4146       return false;
4147     }
4148   }
4149
4150   public void showProducts_actionPerformed(ActionEvent e)
4151   {
4152     // /////////////////////////////
4153     // Collect Data to be translated/transferred
4154
4155     SequenceI[] selection = viewport.getSequenceSelection();
4156     AlignmentI al = null;
4157     try
4158     {
4159       al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4160               .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4161               viewport.getAlignment().getDataset());
4162     } catch (Exception ex)
4163     {
4164       al = null;
4165       jalview.bin.Cache.log.debug("Exception during translation.", ex);
4166     }
4167     if (al == null)
4168     {
4169       JOptionPane
4170               .showMessageDialog(
4171                       Desktop.desktop,
4172                       "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4173                       "Translation Failed", JOptionPane.WARNING_MESSAGE);
4174     }
4175     else
4176     {
4177       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4178       Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4179               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4180     }
4181   }
4182
4183   public void showTranslation_actionPerformed(ActionEvent e)
4184   {
4185     // /////////////////////////////
4186     // Collect Data to be translated/transferred
4187
4188     SequenceI[] selection = viewport.getSequenceSelection();
4189     String[] seqstring = viewport.getViewAsString(true);
4190     AlignmentI al = null;
4191     try
4192     {
4193       al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4194               viewport.getViewAsVisibleContigs(true), viewport
4195                       .getGapCharacter(), viewport.alignment
4196                       .getAlignmentAnnotation(), viewport.alignment
4197                       .getWidth(), viewport.getAlignment().getDataset());
4198     } catch (Exception ex)
4199     {
4200       al = null;
4201       jalview.bin.Cache.log.debug("Exception during translation.", ex);
4202     }
4203     if (al == null)
4204     {
4205       JOptionPane
4206               .showMessageDialog(
4207                       Desktop.desktop,
4208                       "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4209                       "Translation Failed", JOptionPane.WARNING_MESSAGE);
4210     }
4211     else
4212     {
4213       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4214       Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4215               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4216     }
4217   }
4218
4219   /**
4220    * Try to load a features file onto the alignment.
4221    *
4222    * @param file
4223    *          contents or path to retrieve file
4224    * @param type
4225    *          access mode of file (see jalview.io.AlignFile)
4226    * @return true if features file was parsed corectly.
4227    */
4228   public boolean parseFeaturesFile(String file, String type)
4229   {
4230     boolean featuresFile = false;
4231     try
4232     {
4233       featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4234               .getDataset(), alignPanel.seqPanel.seqCanvas
4235               .getFeatureRenderer().featureColours, false);
4236     } catch (Exception ex)
4237     {
4238       ex.printStackTrace();
4239     }
4240
4241     if (featuresFile)
4242     {
4243       viewport.showSequenceFeatures = true;
4244       showSeqFeatures.setSelected(true);
4245       if (alignPanel.seqPanel.seqCanvas.fr != null)
4246       {
4247         // update the min/max ranges where necessary
4248         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4249       }
4250       if (featureSettings != null)
4251       {
4252         featureSettings.setTableData();
4253       }
4254       alignPanel.paintAlignment(true);
4255     }
4256
4257     return featuresFile;
4258   }
4259
4260   public void dragEnter(DropTargetDragEvent evt)
4261   {
4262   }
4263
4264   public void dragExit(DropTargetEvent evt)
4265   {
4266   }
4267
4268   public void dragOver(DropTargetDragEvent evt)
4269   {
4270   }
4271
4272   public void dropActionChanged(DropTargetDragEvent evt)
4273   {
4274   }
4275
4276   public void drop(DropTargetDropEvent evt)
4277   {
4278     Transferable t = evt.getTransferable();
4279     java.util.List files = null;
4280
4281     try
4282     {
4283       DataFlavor uriListFlavor = new DataFlavor(
4284               "text/uri-list;class=java.lang.String");
4285       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4286       {
4287         // Works on Windows and MacOSX
4288         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4289         files = (java.util.List) t
4290                 .getTransferData(DataFlavor.javaFileListFlavor);
4291       }
4292       else if (t.isDataFlavorSupported(uriListFlavor))
4293       {
4294         // This is used by Unix drag system
4295         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4296         String data = (String) t.getTransferData(uriListFlavor);
4297         files = new java.util.ArrayList(1);
4298         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4299                 data, "\r\n"); st.hasMoreTokens();)
4300         {
4301           String s = st.nextToken();
4302           if (s.startsWith("#"))
4303           {
4304             // the line is a comment (as per the RFC 2483)
4305             continue;
4306           }
4307
4308           java.net.URI uri = new java.net.URI(s);
4309           // check to see if we can handle this kind of URI
4310           if (uri.getScheme().toLowerCase().startsWith("http"))
4311           {
4312             files.add(uri.toString());
4313           }
4314           else
4315           {
4316             // otherwise preserve old behaviour: catch all for file objects
4317             java.io.File file = new java.io.File(uri);
4318             files.add(file.toString());
4319           }
4320         }
4321       }
4322     } catch (Exception e)
4323     {
4324       e.printStackTrace();
4325     }
4326     if (files != null)
4327     {
4328       try
4329       {
4330
4331         for (int i = 0; i < files.size(); i++)
4332         {
4333           loadJalviewDataFile(files.get(i).toString());
4334         }
4335       } catch (Exception ex)
4336       {
4337         ex.printStackTrace();
4338       }
4339     }
4340   }
4341
4342   /**
4343    * Attempt to load a "dropped" file or URL string: First by testing whether
4344    * it's and Annotation file, then a JNet file, and finally a features file. If
4345    * all are false then the user may have dropped an alignment file onto this
4346    * AlignFrame.
4347    *
4348    * @param file
4349    *          either a filename or a URL string.
4350    */
4351   public void loadJalviewDataFile(String file)
4352   {
4353     try
4354     {
4355       String protocol = jalview.io.FormatAdapter.FILE;
4356       String f = file.toLowerCase();
4357       if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4358               || f.indexOf("file:") == 0)
4359       {
4360         protocol = jalview.io.FormatAdapter.URL;
4361       }
4362
4363       boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4364               viewport.alignment, file, protocol);
4365
4366       if (!isAnnotation)
4367       {
4368         // try to see if its a JNet 'concise' style annotation file *before* we
4369         // try to parse it as a features file
4370         String format = new IdentifyFile().Identify(file, protocol);
4371         if (format.equalsIgnoreCase("JnetFile"))
4372         {
4373           jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4374                   protocol);
4375           new JnetAnnotationMaker().add_annotation(predictions, viewport
4376                   .getAlignment(), 0, false);
4377           isAnnotation = true;
4378         }
4379         else
4380         {
4381           // try to parse it as a features file
4382           boolean isGroupsFile = parseFeaturesFile(file, protocol);
4383           // if it wasn't a features file then we just treat it as a general
4384           // alignment file to load into the current view.
4385           if (!isGroupsFile)
4386           {
4387             new FileLoader().LoadFile(viewport, file, protocol, format);
4388           }
4389           else
4390           {
4391             alignPanel.paintAlignment(true);
4392           }
4393         }
4394       }
4395       if (isAnnotation)
4396       {
4397
4398         alignPanel.adjustAnnotationHeight();
4399         viewport.updateSequenceIdColours();
4400         buildSortByAnnotationScoresMenu();
4401         alignPanel.paintAlignment(true);
4402       }
4403     } catch (Exception ex)
4404     {
4405       ex.printStackTrace();
4406     }
4407   }
4408
4409   public void tabSelectionChanged(int index)
4410   {
4411     if (index > -1)
4412     {
4413       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4414       viewport = alignPanel.av;
4415       setMenusFromViewport(viewport);
4416     }
4417   }
4418
4419   public void tabbedPane_mousePressed(MouseEvent e)
4420   {
4421     if (SwingUtilities.isRightMouseButton(e))
4422     {
4423       String reply = JOptionPane.showInternalInputDialog(this,
4424               "Enter View Name", "Edit View Name",
4425               JOptionPane.QUESTION_MESSAGE);
4426
4427       if (reply != null)
4428       {
4429         viewport.viewName = reply;
4430         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4431       }
4432     }
4433   }
4434
4435   public AlignViewport getCurrentView()
4436   {
4437     return viewport;
4438   }
4439
4440   /**
4441    * Open the dialog for regex description parsing.
4442    */
4443   protected void extractScores_actionPerformed(ActionEvent e)
4444   {
4445     ParseProperties pp = new jalview.analysis.ParseProperties(
4446             viewport.alignment);
4447     // TODO: verify regex and introduce GUI dialog for version 2.5
4448     // if (pp.getScoresFromDescription("col", "score column ",
4449     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4450     // true)>0)
4451     if (pp.getScoresFromDescription("description column",
4452             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4453     {
4454       buildSortByAnnotationScoresMenu();
4455     }
4456   }
4457
4458   /*
4459    * (non-Javadoc)
4460    *
4461    * @see
4462    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4463    * )
4464    */
4465   protected void showDbRefs_actionPerformed(ActionEvent e)
4466   {
4467     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4468   }
4469
4470   /*
4471    * (non-Javadoc)
4472    *
4473    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4474    * ActionEvent)
4475    */
4476   protected void showNpFeats_actionPerformed(ActionEvent e)
4477   {
4478     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4479   }
4480
4481   /**
4482    * find the viewport amongst the tabs in this alignment frame and close that
4483    * tab
4484    *
4485    * @param av
4486    */
4487   public boolean closeView(AlignViewport av)
4488   {
4489     if (viewport == av)
4490     {
4491       this.closeMenuItem_actionPerformed(false);
4492       return true;
4493     }
4494     Component[] comp = tabbedPane.getComponents();
4495     for (int i = 0; comp != null && i < comp.length; i++)
4496     {
4497       if (comp[i] instanceof AlignmentPanel)
4498       {
4499         if (((AlignmentPanel) comp[i]).av == av)
4500         {
4501           // close the view.
4502           closeView((AlignmentPanel) comp[i]);
4503           return true;
4504         }
4505       }
4506     }
4507     return false;
4508   }
4509
4510   protected void build_fetchdbmenu(JMenu webService)
4511   {
4512     // Temporary hack - DBRef Fetcher always top level ws entry.
4513     // TODO We probably want to store a sequence database checklist in
4514     // preferences and have checkboxes.. rather than individual sources selected
4515     // here
4516     JMenu rfetch = new JMenu("Fetch DB References");
4517     rfetch
4518             .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4519     webService.add(rfetch);
4520
4521     JMenuItem fetchr = new JMenuItem("Standard Databases");
4522     fetchr
4523             .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4524     fetchr.addActionListener(new ActionListener()
4525     {
4526
4527       public void actionPerformed(ActionEvent e)
4528       {
4529         new Thread(new Runnable()
4530         {
4531
4532           public void run()
4533           {
4534             new jalview.ws.DBRefFetcher(alignPanel.av
4535                     .getSequenceSelection(), alignPanel.alignFrame)
4536                     .fetchDBRefs(false);
4537           }
4538         }).start();
4539
4540       }
4541
4542     });
4543     rfetch.add(fetchr);
4544     JMenu dfetch = new JMenu();
4545     rfetch.add(dfetch);
4546     jalview.ws.SequenceFetcher sf = SequenceFetcher
4547             .getSequenceFetcherSingleton(this);
4548     String[] otherdb = sf.getOrderedSupportedSources();
4549     // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4550     // jalview.util.QuickSort.sort(otherdb, otherdb);
4551     int comp = 0, mcomp = 15;
4552     String mname = null;
4553     if (otherdb != null && otherdb.length > 0)
4554     {
4555       for (int i = 0; i < otherdb.length; i++)
4556       {
4557         String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4558         if (mname == null)
4559         {
4560           mname = "from '" + dbname + "'";
4561         }
4562         fetchr = new JMenuItem(otherdb[i]);
4563         final String[] dassource = new String[]
4564         { otherdb[i] };
4565         fetchr.addActionListener(new ActionListener()
4566         {
4567
4568           public void actionPerformed(ActionEvent e)
4569           {
4570             new Thread(new Runnable()
4571             {
4572
4573               public void run()
4574               {
4575                 new jalview.ws.DBRefFetcher(alignPanel.av
4576                         .getSequenceSelection(), alignPanel.alignFrame,
4577                         dassource).fetchDBRefs(false);
4578               }
4579             }).start();
4580           }
4581
4582         });
4583         fetchr.setToolTipText("Retrieve from " + dbname);
4584         dfetch.add(fetchr);
4585         if (comp++ == mcomp || i == (otherdb.length - 1))
4586         {
4587           dfetch.setText(mname + " to '" + dbname + "'");
4588           rfetch.add(dfetch);
4589           dfetch = new JMenu();
4590           mname = null;
4591           comp = 0;
4592         }
4593       }
4594     }
4595   }
4596
4597   /**
4598    * Left justify the whole alignment.
4599    */
4600   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4601   {
4602     AlignmentI al = viewport.getAlignment();
4603     al.justify(false);
4604     viewport.firePropertyChange("alignment", null, al);
4605   }
4606
4607   /**
4608    * Right justify the whole alignment.
4609    */
4610   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4611   {
4612     AlignmentI al = viewport.getAlignment();
4613     al.justify(true);
4614     viewport.firePropertyChange("alignment", null, al);
4615   }
4616
4617   public void setShowSeqFeatures(boolean b)
4618   {
4619     showSeqFeatures.setSelected(true);
4620     viewport.setShowSequenceFeatures(true);
4621   }
4622
4623   /*
4624    * (non-Javadoc)
4625    *
4626    * @see
4627    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4628    * awt.event.ActionEvent)
4629    */
4630   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4631   {
4632     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
4633     alignPanel.paintAlignment(true);
4634   }
4635
4636   /*
4637    * (non-Javadoc)
4638    *
4639    * @see
4640    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4641    * .ActionEvent)
4642    */
4643   protected void showGroupConsensus_actionPerformed(ActionEvent e)
4644   {
4645     viewport.setShowGroupConsensus(showGroupConsensus.getState());
4646     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4647
4648   }
4649
4650   /*
4651    * (non-Javadoc)
4652    *
4653    * @see
4654    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4655    * .event.ActionEvent)
4656    */
4657   protected void showGroupConservation_actionPerformed(ActionEvent e)
4658   {
4659     viewport.setShowGroupConservation(showGroupConservation.getState());
4660     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4661   }
4662
4663   /*
4664    * (non-Javadoc)
4665    *
4666    * @see
4667    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
4668    * .event.ActionEvent)
4669    */
4670   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
4671   {
4672     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
4673     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4674   }
4675
4676   /*
4677    * (non-Javadoc)
4678    *
4679    * @see
4680    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
4681    * .event.ActionEvent)
4682    */
4683   protected void showSequenceLogo_actionPerformed(ActionEvent e)
4684   {
4685     viewport.setShowSequenceLogo(showSequenceLogo.getState());
4686     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4687   }
4688
4689   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
4690   {
4691     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4692   }
4693
4694   /*
4695    * (non-Javadoc)
4696    *
4697    * @see
4698    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4699    * .event.ActionEvent)
4700    */
4701   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4702   {
4703     if (viewport.getSelectionGroup() != null)
4704     {
4705       SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4706               viewport.getSequenceSelection(), viewport.getAlignmentView(
4707                       true).getSequenceStrings(viewport.getGapCharacter()),
4708               viewport.alignment.getGroups());
4709       viewport.alignment.deleteAllGroups();
4710       viewport.sequenceColours = null;
4711       viewport.setSelectionGroup(null);
4712       // set view properties for each group
4713       for (int g = 0; g < gps.length; g++)
4714       {
4715         gps[g].setShowNonconserved(viewport.getShowUnconserved());
4716         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
4717         viewport.alignment.addGroup(gps[g]);
4718         Color col = new Color((int) (Math.random() * 255), (int) (Math
4719                 .random() * 255), (int) (Math.random() * 255));
4720         col = col.brighter();
4721         for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4722                 .hasMoreElements(); viewport.setSequenceColour(
4723                 (SequenceI) sq.nextElement(), col))
4724           ;
4725       }
4726       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4727       alignPanel.updateAnnotation();
4728       alignPanel.paintAlignment(true);
4729     }
4730   }
4731 }
4732
4733 class PrintThread extends Thread
4734 {
4735   AlignmentPanel ap;
4736
4737   public PrintThread(AlignmentPanel ap)
4738   {
4739     this.ap = ap;
4740   }
4741
4742   static PageFormat pf;
4743
4744   public void run()
4745   {
4746     PrinterJob printJob = PrinterJob.getPrinterJob();
4747
4748     if (pf != null)
4749     {
4750       printJob.setPrintable(ap, pf);
4751     }
4752     else
4753     {
4754       printJob.setPrintable(ap);
4755     }
4756
4757     if (printJob.printDialog())
4758     {
4759       try
4760       {
4761         printJob.print();
4762       } catch (Exception PrintException)
4763       {
4764         PrintException.printStackTrace();
4765       }
4766     }
4767   }
4768 }