src/jalview/gui/AlignFrame.java

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