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(editPane);
2325     Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
2326   }
2327
2328
2329   /**
2330    * DOCUMENT ME!
2331    *
2332    * @param e DOCUMENT ME!
2333    */
2334   public void overviewMenuItem_actionPerformed(ActionEvent e)
2335   {
2336     if (alignPanel.overviewPanel != null)
2337     {
2338       return;
2339     }
2340
2341     JInternalFrame frame = new JInternalFrame();
2342     OverviewPanel overview = new OverviewPanel(alignPanel);
2343     frame.setContentPane(overview);
2344     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2345                              frame.getWidth(), frame.getHeight());
2346     frame.pack();
2347     frame.setLayer(JLayeredPane.PALETTE_LAYER);
2348     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2349     {
2350       public void internalFrameClosed(
2351           javax.swing.event.InternalFrameEvent evt)
2352       {
2353         alignPanel.setOverviewPanel(null);
2354       }
2355       ;
2356     });
2357
2358     alignPanel.setOverviewPanel(overview);
2359   }
2360
2361   public void textColour_actionPerformed(ActionEvent e)
2362   {
2363     new TextColourChooser().chooseColour(alignPanel, null);
2364   }
2365
2366   /**
2367    * DOCUMENT ME!
2368    *
2369    * @param e DOCUMENT ME!
2370    */
2371   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2372   {
2373     changeColour(null);
2374   }
2375
2376   /**
2377    * DOCUMENT ME!
2378    *
2379    * @param e DOCUMENT ME!
2380    */
2381   public void clustalColour_actionPerformed(ActionEvent e)
2382   {
2383     changeColour(new ClustalxColourScheme(
2384         viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2385   }
2386
2387   /**
2388    * DOCUMENT ME!
2389    *
2390    * @param e DOCUMENT ME!
2391    */
2392   public void zappoColour_actionPerformed(ActionEvent e)
2393   {
2394     changeColour(new ZappoColourScheme());
2395   }
2396
2397   /**
2398    * DOCUMENT ME!
2399    *
2400    * @param e DOCUMENT ME!
2401    */
2402   public void taylorColour_actionPerformed(ActionEvent e)
2403   {
2404     changeColour(new TaylorColourScheme());
2405   }
2406
2407   /**
2408    * DOCUMENT ME!
2409    *
2410    * @param e DOCUMENT ME!
2411    */
2412   public void hydrophobicityColour_actionPerformed(ActionEvent e)
2413   {
2414     changeColour(new HydrophobicColourScheme());
2415   }
2416
2417   /**
2418    * DOCUMENT ME!
2419    *
2420    * @param e DOCUMENT ME!
2421    */
2422   public void helixColour_actionPerformed(ActionEvent e)
2423   {
2424     changeColour(new HelixColourScheme());
2425   }
2426
2427   /**
2428    * DOCUMENT ME!
2429    *
2430    * @param e DOCUMENT ME!
2431    */
2432   public void strandColour_actionPerformed(ActionEvent e)
2433   {
2434     changeColour(new StrandColourScheme());
2435   }
2436
2437   /**
2438    * DOCUMENT ME!
2439    *
2440    * @param e DOCUMENT ME!
2441    */
2442   public void turnColour_actionPerformed(ActionEvent e)
2443   {
2444     changeColour(new TurnColourScheme());
2445   }
2446
2447   /**
2448    * DOCUMENT ME!
2449    *
2450    * @param e DOCUMENT ME!
2451    */
2452   public void buriedColour_actionPerformed(ActionEvent e)
2453   {
2454     changeColour(new BuriedColourScheme());
2455   }
2456
2457   /**
2458    * DOCUMENT ME!
2459    *
2460    * @param e DOCUMENT ME!
2461    */
2462   public void nucleotideColour_actionPerformed(ActionEvent e)
2463   {
2464     changeColour(new NucleotideColourScheme());
2465   }
2466
2467   public void annotationColour_actionPerformed(ActionEvent e)
2468   {
2469     new AnnotationColourChooser(viewport, alignPanel);
2470   }
2471
2472
2473   /**
2474    * DOCUMENT ME!
2475    *
2476    * @param e DOCUMENT ME!
2477    */
2478   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2479   {
2480     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2481   }
2482
2483   /**
2484    * DOCUMENT ME!
2485    *
2486    * @param cs DOCUMENT ME!
2487    */
2488   public void changeColour(ColourSchemeI cs)
2489   {
2490     int threshold = 0;
2491
2492     if(cs!=null)
2493     {
2494       if (viewport.getAbovePIDThreshold())
2495       {
2496         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2497                                                    "Background");
2498
2499         cs.setThreshold(threshold,
2500                         viewport.getIgnoreGapsConsensus());
2501
2502         viewport.setGlobalColourScheme(cs);
2503       }
2504       else
2505       {
2506         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2507       }
2508
2509       if (viewport.getConservationSelected())
2510       {
2511
2512         Alignment al = (Alignment) viewport.alignment;
2513         Conservation c = new Conservation("All",
2514                                           ResidueProperties.propHash, 3,
2515                                           al.getSequences(), 0,
2516                                           al.getWidth() - 1);
2517
2518         c.calculate();
2519         c.verdict(false, viewport.ConsPercGaps);
2520
2521         cs.setConservation(c);
2522
2523         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2524             "Background"));
2525       }
2526       else
2527       {
2528         cs.setConservation(null);
2529       }
2530
2531       cs.setConsensus(viewport.hconsensus);
2532     }
2533
2534     viewport.setGlobalColourScheme(cs);
2535
2536     if (viewport.getColourAppliesToAllGroups())
2537     {
2538       Vector groups = viewport.alignment.getGroups();
2539
2540       for (int i = 0; i < groups.size(); i++)
2541       {
2542         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2543
2544         if (cs == null)
2545         {
2546           sg.cs = null;
2547           continue;
2548         }
2549
2550         if (cs instanceof ClustalxColourScheme)
2551         {
2552           sg.cs = new ClustalxColourScheme(
2553               sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
2554         }
2555         else if (cs instanceof UserColourScheme)
2556         {
2557           sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2558         }
2559         else
2560         {
2561           try
2562           {
2563             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2564           }
2565           catch (Exception ex)
2566           {
2567           }
2568         }
2569
2570         if (viewport.getAbovePIDThreshold()
2571             || cs instanceof PIDColourScheme
2572             || cs instanceof Blosum62ColourScheme)
2573         {
2574          sg.cs.setThreshold(threshold,
2575                 viewport.getIgnoreGapsConsensus());
2576
2577          sg.cs.setConsensus(AAFrequency.calculate(
2578              sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
2579              sg.getEndRes()+1));
2580        }
2581         else
2582         {
2583           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2584         }
2585
2586
2587         if (viewport.getConservationSelected())
2588         {
2589           Conservation c = new Conservation("Group",
2590                                             ResidueProperties.propHash, 3,
2591                                             sg.getSequences(viewport.
2592               hiddenRepSequences),
2593                                             sg.getStartRes(),
2594                                             sg.getEndRes()+1);
2595           c.calculate();
2596           c.verdict(false, viewport.ConsPercGaps);
2597           sg.cs.setConservation(c);
2598         }
2599         else
2600         {
2601           sg.cs.setConservation(null);
2602       }
2603     }
2604     }
2605
2606     if (alignPanel.getOverviewPanel() != null)
2607     {
2608       alignPanel.getOverviewPanel().updateOverviewImage();
2609     }
2610
2611
2612
2613
2614     alignPanel.paintAlignment(true);
2615   }
2616
2617   /**
2618    * DOCUMENT ME!
2619    *
2620    * @param e DOCUMENT ME!
2621    */
2622   protected void modifyPID_actionPerformed(ActionEvent e)
2623   {
2624     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2625     {
2626       SliderPanel.setPIDSliderSource(alignPanel,
2627                                      viewport.getGlobalColourScheme(),
2628                                      "Background");
2629       SliderPanel.showPIDSlider();
2630     }
2631   }
2632
2633   /**
2634    * DOCUMENT ME!
2635    *
2636    * @param e DOCUMENT ME!
2637    */
2638   protected void modifyConservation_actionPerformed(ActionEvent e)
2639   {
2640     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2641     {
2642       SliderPanel.setConservationSlider(alignPanel,
2643                                         viewport.globalColourScheme,
2644                                         "Background");
2645       SliderPanel.showConservationSlider();
2646     }
2647   }
2648
2649   /**
2650    * DOCUMENT ME!
2651    *
2652    * @param e DOCUMENT ME!
2653    */
2654   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2655   {
2656     viewport.setConservationSelected(conservationMenuItem.isSelected());
2657
2658     viewport.setAbovePIDThreshold(false);
2659     abovePIDThreshold.setSelected(false);
2660
2661     changeColour(viewport.getGlobalColourScheme());
2662
2663     modifyConservation_actionPerformed(null);
2664   }
2665
2666   /**
2667    * DOCUMENT ME!
2668    *
2669    * @param e DOCUMENT ME!
2670    */
2671   public void abovePIDThreshold_actionPerformed(ActionEvent e)
2672   {
2673     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2674
2675     conservationMenuItem.setSelected(false);
2676     viewport.setConservationSelected(false);
2677
2678     changeColour(viewport.getGlobalColourScheme());
2679
2680     modifyPID_actionPerformed(null);
2681   }
2682
2683   /**
2684    * DOCUMENT ME!
2685    *
2686    * @param e DOCUMENT ME!
2687    */
2688   public void userDefinedColour_actionPerformed(ActionEvent e)
2689   {
2690     if (e.getActionCommand().equals("User Defined..."))
2691     {
2692       new UserDefinedColours(alignPanel, null);
2693     }
2694     else
2695     {
2696       UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2697           getUserColourSchemes().get(e.getActionCommand());
2698
2699       changeColour(udc);
2700     }
2701   }
2702
2703   public void updateUserColourMenu()
2704   {
2705
2706     Component[] menuItems = colourMenu.getMenuComponents();
2707     int i, iSize = menuItems.length;
2708     for (i = 0; i < iSize; i++)
2709     {
2710       if (menuItems[i].getName() != null &&
2711           menuItems[i].getName().equals("USER_DEFINED"))
2712       {
2713         colourMenu.remove(menuItems[i]);
2714         iSize--;
2715       }
2716     }
2717     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2718     {
2719       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2720           getUserColourSchemes().keys();
2721
2722       while (userColours.hasMoreElements())
2723       {
2724         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
2725             userColours.
2726             nextElement().toString());
2727         radioItem.setName("USER_DEFINED");
2728         radioItem.addMouseListener(new MouseAdapter()
2729             {
2730               public void mousePressed(MouseEvent evt)
2731               {
2732                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2733                 {
2734                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2735
2736               int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
2737                   Desktop.desktop,
2738                       "Remove from default list?",
2739                       "Remove user defined colour",
2740                       JOptionPane.YES_NO_OPTION);
2741                   if(option == JOptionPane.YES_OPTION)
2742                   {
2743                 jalview.gui.UserDefinedColours.removeColourFromDefaults(
2744                     radioItem.getText());
2745                     colourMenu.remove(radioItem);
2746                   }
2747                   else
2748               {
2749                     radioItem.addActionListener(new ActionListener()
2750                     {
2751                       public void actionPerformed(ActionEvent evt)
2752                       {
2753                         userDefinedColour_actionPerformed(evt);
2754                       }
2755                     });
2756                 }
2757               }
2758           }
2759             });
2760         radioItem.addActionListener(new ActionListener()
2761         {
2762           public void actionPerformed(ActionEvent evt)
2763           {
2764             userDefinedColour_actionPerformed(evt);
2765           }
2766         });
2767
2768         colourMenu.insert(radioItem, 15);
2769         colours.add(radioItem);
2770       }
2771     }
2772   }
2773
2774   /**
2775    * DOCUMENT ME!
2776    *
2777    * @param e DOCUMENT ME!
2778    */
2779   public void PIDColour_actionPerformed(ActionEvent e)
2780   {
2781     changeColour(new PIDColourScheme());
2782   }
2783
2784   /**
2785    * DOCUMENT ME!
2786    *
2787    * @param e DOCUMENT ME!
2788    */
2789   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2790   {
2791     changeColour(new Blosum62ColourScheme());
2792   }
2793
2794   /**
2795    * DOCUMENT ME!
2796    *
2797    * @param e DOCUMENT ME!
2798    */
2799   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2800   {
2801     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2802     AlignmentSorter.sortByPID(viewport.getAlignment(),
2803                               viewport.getAlignment().getSequenceAt(0));
2804     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2805                                     viewport.alignment));
2806     alignPanel.paintAlignment(true);
2807   }
2808
2809   /**
2810    * DOCUMENT ME!
2811    *
2812    * @param e DOCUMENT ME!
2813    */
2814   public void sortIDMenuItem_actionPerformed(ActionEvent e)
2815   {
2816     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2817     AlignmentSorter.sortByID(viewport.getAlignment());
2818     addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2819     alignPanel.paintAlignment(true);
2820   }
2821
2822   /**
2823    * DOCUMENT ME!
2824    *
2825    * @param e DOCUMENT ME!
2826    */
2827   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2828   {
2829     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2830     AlignmentSorter.sortByGroup(viewport.getAlignment());
2831     addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2832
2833     alignPanel.paintAlignment(true);
2834   }
2835   /**
2836    * DOCUMENT ME!
2837    *
2838    * @param e DOCUMENT ME!
2839    */
2840   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2841   {
2842     new RedundancyPanel(alignPanel, this);
2843   }
2844
2845
2846   /**
2847    * DOCUMENT ME!
2848    *
2849    * @param e DOCUMENT ME!
2850    */
2851   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2852   {
2853     if ( (viewport.getSelectionGroup() == null) ||
2854         (viewport.getSelectionGroup().getSize() < 2))
2855     {
2856       JOptionPane.showInternalMessageDialog(this,
2857                                             "You must select at least 2 sequences.",
2858                                             "Invalid Selection",
2859                                             JOptionPane.WARNING_MESSAGE);
2860     }
2861     else
2862     {
2863       JInternalFrame frame = new JInternalFrame();
2864       frame.setContentPane(new PairwiseAlignPanel(viewport));
2865       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2866     }
2867   }
2868
2869   /**
2870    * DOCUMENT ME!
2871    *
2872    * @param e DOCUMENT ME!
2873    */
2874   public void PCAMenuItem_actionPerformed(ActionEvent e)
2875   {
2876     if ( ( (viewport.getSelectionGroup() != null) &&
2877           (viewport.getSelectionGroup().getSize() < 4) &&
2878           (viewport.getSelectionGroup().getSize() > 0)) ||
2879         (viewport.getAlignment().getHeight() < 4))
2880     {
2881       JOptionPane.showInternalMessageDialog(this,
2882                                             "Principal component analysis must take\n" +
2883                                             "at least 4 input sequences.",
2884                                             "Sequence selection insufficient",
2885                                             JOptionPane.WARNING_MESSAGE);
2886
2887       return;
2888     }
2889
2890      new PCAPanel(alignPanel);
2891   }
2892
2893
2894   public void autoCalculate_actionPerformed(ActionEvent e)
2895   {
2896     viewport.autoCalculateConsensus = autoCalculate.isSelected();
2897     if(viewport.autoCalculateConsensus)
2898     {
2899       viewport.firePropertyChange("alignment",
2900                                   null,
2901                                   viewport.getAlignment().getSequences());
2902     }
2903   }
2904
2905
2906   /**
2907    * DOCUMENT ME!
2908    *
2909    * @param e DOCUMENT ME!
2910    */
2911   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2912   {
2913     NewTreePanel("AV", "PID", "Average distance tree using PID");
2914   }
2915
2916   /**
2917    * DOCUMENT ME!
2918    *
2919    * @param e DOCUMENT ME!
2920    */
2921   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2922   {
2923     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2924   }
2925
2926   /**
2927    * DOCUMENT ME!
2928    *
2929    * @param e DOCUMENT ME!
2930    */
2931   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2932   {
2933     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2934   }
2935
2936   /**
2937    * DOCUMENT ME!
2938    *
2939    * @param e DOCUMENT ME!
2940    */
2941   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2942   {
2943     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2944   }
2945
2946   /**
2947    * DOCUMENT ME!
2948    *
2949    * @param type DOCUMENT ME!
2950    * @param pwType DOCUMENT ME!
2951    * @param title DOCUMENT ME!
2952    */
2953   void NewTreePanel(String type, String pwType, String title)
2954   {
2955     TreePanel tp;
2956
2957     if (viewport.getSelectionGroup() != null)
2958     {
2959       if (viewport.getSelectionGroup().getSize() < 3)
2960       {
2961         JOptionPane.showMessageDialog(Desktop.desktop,
2962                                       "You need to have more than two sequences selected to build a tree!",
2963                                       "Not enough sequences",
2964                                       JOptionPane.WARNING_MESSAGE);
2965         return;
2966       }
2967
2968       int s = 0;
2969       SequenceGroup sg = viewport.getSelectionGroup();
2970
2971       /* Decide if the selection is a column region */
2972       while (s < sg.getSize())
2973       {
2974         if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
2975             sg.getEndRes())
2976         {
2977           JOptionPane.showMessageDialog(Desktop.desktop,
2978                                         "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2979                                         "Try using the Pad function in the edit menu,\n" +
2980                                         "or one of the multiple sequence alignment web services.",
2981                                         "Sequences in selection are not aligned",
2982                                         JOptionPane.WARNING_MESSAGE);
2983
2984           return;
2985         }
2986       }
2987
2988       title = title + " on region";
2989       tp = new TreePanel(alignPanel, type, pwType);
2990     }
2991     else
2992     {
2993       //are the sequences aligned?
2994       if (!viewport.alignment.isAligned())
2995       {
2996         JOptionPane.showMessageDialog(Desktop.desktop,
2997                                       "The sequences must be aligned before creating a tree.\n" +
2998                                       "Try using the Pad function in the edit menu,\n" +
2999                                       "or one of the multiple sequence alignment web services.",
3000                                       "Sequences not aligned",
3001                                       JOptionPane.WARNING_MESSAGE);
3002
3003         return;
3004       }
3005
3006       if(viewport.alignment.getHeight()<2)
3007       {
3008         return;
3009       }
3010
3011       tp = new TreePanel(alignPanel, type, pwType);
3012     }
3013
3014     title += " from ";
3015
3016     if(viewport.viewName!=null)
3017     {
3018       title+= viewport.viewName+" of ";
3019     }
3020
3021     title += this.title;
3022
3023     Desktop.addInternalFrame(tp, title, 600, 500);
3024   }
3025
3026   /**
3027    * DOCUMENT ME!
3028    *
3029    * @param title DOCUMENT ME!
3030    * @param order DOCUMENT ME!
3031    */
3032   public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
3033   {
3034     final JMenuItem item = new JMenuItem("by " + title);
3035     sort.add(item);
3036     item.addActionListener(new java.awt.event.ActionListener()
3037     {
3038       public void actionPerformed(ActionEvent e)
3039       {
3040         SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
3041
3042         // TODO: JBPNote - have to map order entries to curent SequenceI pointers
3043         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3044
3045         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3046                                         viewport.alignment));
3047
3048         alignPanel.paintAlignment(true);
3049       }
3050     });
3051   }
3052   /**
3053    * Add a new sort by annotation score menu item
3054    * @param sort the menu to add the option to
3055    * @param scoreLabel the label used to retrieve scores for each sequence on the alignment
3056    */
3057   public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel)
3058   {
3059     final JMenuItem item = new JMenuItem(scoreLabel);
3060     sort.add(item);
3061     item.addActionListener(new java.awt.event.ActionListener()
3062     {
3063       public void actionPerformed(ActionEvent e)
3064       {
3065         SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
3066         AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
3067         addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
3068         alignPanel.paintAlignment(true);
3069       }
3070     });
3071   }
3072   /**
3073    * last hash for alignment's annotation array - used to minimise cost of rebuild.
3074    */
3075   protected int _annotationScoreVectorHash;
3076   /**
3077    * search the alignment and rebuild the sort by annotation score submenu
3078    * the last alignment annotation vector hash is stored to minimize
3079    * cost of rebuilding in subsequence calls.
3080    *
3081    */
3082   public void buildSortByAnnotationScoresMenu()
3083   {
3084     if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash)
3085     {
3086       sortByAnnotScore.removeAll();
3087       // almost certainly a quicker way to do this - but we keep it simple
3088       Hashtable scoreSorts=new Hashtable();
3089       AlignmentAnnotation aann[] = viewport.alignment.getAlignmentAnnotation();
3090       for (int i=0;i<aann.length; i++)
3091       {
3092         if (aann[i].hasScore() && aann[i].sequenceRef!=null)
3093         {
3094           scoreSorts.put(aann[i].label, aann[i].label);
3095         }
3096       }
3097       Enumeration labels = scoreSorts.keys();
3098       while (labels.hasMoreElements())
3099       {
3100         addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels.nextElement());
3101       }
3102       sortByAnnotScore.setVisible(scoreSorts.size()>0);
3103       scoreSorts.clear();
3104     }
3105   }
3106
3107   /**
3108    * Maintain the Order by->Displayed Tree menu.
3109    * Creates a new menu item for a TreePanel with an appropriate
3110    * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
3111    * to remove the menu item when the treePanel is closed, and adjust
3112    * the tree leaf to sequence mapping when the alignment is modified.
3113    * @param treePanel Displayed tree window.
3114    * @param title SortBy menu item title.
3115    */
3116   public void buildTreeMenu()
3117   {
3118     sortByTreeMenu.removeAll();
3119
3120     Vector comps = (Vector) PaintRefresher.components.get(viewport.
3121         getSequenceSetId());
3122     Vector treePanels = new Vector();
3123     int i, iSize = comps.size();
3124     for(i=0; i<iSize; i++)
3125     {
3126       if(comps.elementAt(i) instanceof TreePanel)
3127       {
3128         treePanels.add(comps.elementAt(i));
3129       }
3130     }
3131
3132     iSize = treePanels.size();
3133
3134     if(iSize<1)
3135     {
3136       sortByTreeMenu.setVisible(false);
3137       return;
3138     }
3139
3140     sortByTreeMenu.setVisible(true);
3141
3142     for(i=0; i<treePanels.size(); i++)
3143     {
3144       TreePanel tp = (TreePanel)treePanels.elementAt(i);
3145       final JMenuItem item = new JMenuItem(tp.getTitle());
3146       final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
3147       item.addActionListener(new java.awt.event.ActionListener()
3148       {
3149         public void actionPerformed(ActionEvent e)
3150         {
3151           SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3152           AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3153
3154           addHistoryItem(new OrderCommand("Tree Sort",
3155                                           oldOrder,
3156                                           viewport.alignment));
3157
3158           alignPanel.paintAlignment(true);
3159         }
3160       });
3161
3162       sortByTreeMenu.add(item);
3163     }
3164   }
3165
3166   /**
3167    * Work out whether the whole set of sequences
3168    * or just the selected set will be submitted for multiple alignment.
3169    *
3170    */
3171   private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3172   {
3173     // Now, check we have enough sequences
3174     AlignmentView msa = null;
3175
3176     if ( (viewport.getSelectionGroup() != null) &&
3177         (viewport.getSelectionGroup().getSize() > 1))
3178     {
3179       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
3180       /*SequenceGroup seqs = viewport.getSelectionGroup();
3181       int sz;
3182       msa = new SequenceI[sz = seqs.getSize(false)];
3183
3184       for (int i = 0; i < sz; i++)
3185       {
3186         msa[i] = (SequenceI) seqs.getSequenceAt(i);
3187       } */
3188       msa = viewport.getAlignmentView(true);
3189     }
3190     else
3191     {
3192       /*Vector seqs = viewport.getAlignment().getSequences();
3193
3194       if (seqs.size() > 1)
3195       {
3196         msa = new SequenceI[seqs.size()];
3197
3198         for (int i = 0; i < seqs.size(); i++)
3199         {
3200           msa[i] = (SequenceI) seqs.elementAt(i);
3201         }
3202       }*/
3203       msa = viewport.getAlignmentView(false);
3204     }
3205     return msa;
3206   }
3207
3208   /**
3209    * Decides what is submitted to a secondary structure prediction service,
3210    * the currently selected sequence, or the currently selected alignment
3211    * (where the first sequence in the set is the one that the prediction
3212    * will be for).
3213    */
3214   AlignmentView gatherSeqOrMsaForSecStrPrediction()
3215   {
3216    AlignmentView seqs = null;
3217
3218     if ( (viewport.getSelectionGroup() != null) &&
3219         (viewport.getSelectionGroup().getSize() > 0))
3220     {
3221       seqs = viewport.getAlignmentView(true);
3222     }
3223     else
3224     {
3225       seqs = viewport.getAlignmentView(false);
3226     }
3227     // limit sequences - JBPNote in future - could spawn multiple prediction jobs
3228     // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3229     if (!viewport.alignment.isAligned())
3230     {
3231       seqs.setSequences(new SeqCigar[]
3232                         {seqs.getSequences()[0]});
3233     }
3234     return seqs;
3235   }
3236   /**
3237    * DOCUMENT ME!
3238    *
3239    * @param e DOCUMENT ME!
3240    */
3241   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3242   {
3243     // Pick the tree file
3244     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3245         getProperty(
3246             "LAST_DIRECTORY"));
3247     chooser.setFileView(new JalviewFileView());
3248     chooser.setDialogTitle("Select a newick-like tree file");
3249     chooser.setToolTipText("Load a tree file");
3250
3251     int value = chooser.showOpenDialog(null);
3252
3253     if (value == JalviewFileChooser.APPROVE_OPTION)
3254     {
3255       String choice = chooser.getSelectedFile().getPath();
3256       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3257
3258       try
3259       {
3260         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
3261             "File");
3262         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3263       }
3264       catch (Exception ex)
3265       {
3266         JOptionPane.showMessageDialog(Desktop.desktop,
3267                                       "Problem reading tree file",
3268                                       ex.getMessage(),
3269                                       JOptionPane.WARNING_MESSAGE);
3270         ex.printStackTrace();
3271       }
3272     }
3273   }
3274
3275
3276   public TreePanel ShowNewickTree(NewickFile nf, String title)
3277   {
3278     return ShowNewickTree(nf,title,600,500,4,5);
3279   }
3280
3281   public TreePanel ShowNewickTree(NewickFile nf, String title,
3282                                   AlignmentView input)
3283   {
3284     return ShowNewickTree(nf,title, input, 600,500,4,5);
3285   }
3286
3287   public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
3288                                   int x, int y)
3289   {
3290     return ShowNewickTree(nf, title, null, w, h, x, y);
3291   }
3292   /**
3293    * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
3294    *
3295    * @param nf the tree
3296    * @param title tree viewer title
3297    * @param input Associated alignment input data (or null)
3298    * @param w width
3299    * @param h height
3300    * @param x position
3301    * @param y position
3302    * @return TreePanel handle
3303    */
3304   public TreePanel ShowNewickTree(NewickFile nf, String title,
3305                                   AlignmentView input, int w, int h, int x,
3306                                   int y)
3307   {
3308     TreePanel tp = null;
3309
3310     try
3311     {
3312       nf.parse();
3313
3314       if (nf.getTree() != null)
3315       {
3316         tp = new TreePanel(alignPanel,
3317                            "FromFile",
3318                            title,
3319                            nf, input);
3320
3321         tp.setSize(w,h);
3322
3323         if(x>0 && y>0)
3324         {
3325           tp.setLocation(x,y);
3326         }
3327
3328
3329         Desktop.addInternalFrame(tp, title, w, h);
3330       }
3331     }
3332     catch (Exception ex)
3333     {
3334       ex.printStackTrace();
3335     }
3336
3337     return tp;
3338   }
3339
3340
3341   /**
3342    * Generates menu items and listener event actions for web service clients
3343    *
3344    */
3345   public void BuildWebServiceMenu()
3346   {
3347     if ( (Discoverer.services != null)
3348         && (Discoverer.services.size() > 0))
3349     {
3350       Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3351       Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3352       Vector wsmenu = new Vector();
3353       final AlignFrame af = this;
3354       if (msaws != null)
3355       {
3356         // Add any Multiple Sequence Alignment Services
3357         final JMenu msawsmenu = new JMenu("Alignment");
3358         for (int i = 0, j = msaws.size(); i < j; i++)
3359         {
3360           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
3361               get(i);
3362           final JMenuItem method = new JMenuItem(sh.getName());
3363           method.addActionListener(new ActionListener()
3364           {
3365             public void actionPerformed(ActionEvent e)
3366             {
3367               AlignmentView msa = gatherSequencesForAlignment();
3368               new jalview.ws.MsaWSClient(sh, title, msa,
3369                                          false, true,
3370                                          viewport.getAlignment().getDataset(),
3371                                          af);
3372
3373             }
3374
3375           });
3376           msawsmenu.add(method);
3377           // Deal with services that we know accept partial alignments.
3378           if (sh.getName().indexOf("lustal") > -1)
3379           {
3380             // We know that ClustalWS can accept partial alignments for refinement.
3381             final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
3382             methodR.addActionListener(new ActionListener()
3383             {
3384               public void actionPerformed(ActionEvent e)
3385               {
3386                 AlignmentView msa = gatherSequencesForAlignment();
3387                 new jalview.ws.MsaWSClient(sh, title, msa,
3388                                            true, true,
3389                                            viewport.getAlignment().getDataset(),
3390                                            af);
3391
3392               }
3393
3394             });
3395             msawsmenu.add(methodR);
3396
3397           }
3398         }
3399         wsmenu.add(msawsmenu);
3400       }
3401       if (secstrpr != null)
3402       {
3403         // Add any secondary structure prediction services
3404         final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3405         for (int i = 0, j = secstrpr.size(); i < j; i++)
3406         {
3407           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3408               secstrpr.get(i);
3409           final JMenuItem method = new JMenuItem(sh.getName());
3410           method.addActionListener(new ActionListener()
3411           {
3412             public void actionPerformed(ActionEvent e)
3413             {
3414               AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3415               if (msa.getSequences().length == 1)
3416               {
3417                 // Single Sequence prediction
3418                 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3419               }
3420               else
3421               {
3422                 if (msa.getSequences().length > 1)
3423                 {
3424                   // Sequence profile based prediction
3425                   new jalview.ws.JPredClient(sh,
3426                       title, true, msa, af, true);
3427                 }
3428               }
3429             }
3430           });
3431           secstrmenu.add(method);
3432         }
3433         wsmenu.add(secstrmenu);
3434       }
3435       resetWebServiceMenu();
3436       for (int i = 0, j = wsmenu.size(); i < j; i++)
3437       {
3438         webService.add( (JMenu) wsmenu.get(i));
3439       }
3440     }
3441     else
3442     {
3443       resetWebServiceMenu();
3444       this.webService.add(this.webServiceNoServices);
3445     }
3446     // TODO: add in rediscovery function
3447     // TODO: reduce code redundancy.
3448     // TODO: group services by location as well as function.
3449   }
3450
3451
3452   /**
3453    * empty the web service menu and add any ad-hoc functions
3454    * not dynamically discovered.
3455    *
3456    */
3457   private void resetWebServiceMenu()
3458   {
3459     webService.removeAll();
3460     // Temporary hack - DBRef Fetcher always top level ws entry.
3461     JMenuItem rfetch = new JMenuItem("Fetch DB References");
3462     rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences");
3463     webService.add(rfetch);
3464     rfetch.addActionListener(new ActionListener() {
3465
3466       public void actionPerformed(ActionEvent e)
3467       {
3468         new jalview.io.DBRefFetcher(
3469                 alignPanel.av.getSequenceSelection(),
3470                 alignPanel.alignFrame).fetchDBRefs(false);
3471       }
3472
3473     });
3474   }
3475
3476  /* public void vamsasStore_actionPerformed(ActionEvent e)
3477   {
3478     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3479         getProperty("LAST_DIRECTORY"));
3480
3481     chooser.setFileView(new JalviewFileView());
3482     chooser.setDialogTitle("Export to Vamsas file");
3483     chooser.setToolTipText("Export");
3484
3485     int value = chooser.showSaveDialog(this);
3486
3487     if (value == JalviewFileChooser.APPROVE_OPTION)
3488     {
3489       jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3490       //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
3491       vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3492     }
3493   }*/
3494
3495
3496
3497 public void showTranslation_actionPerformed(ActionEvent e)
3498 {
3499   ///////////////////////////////
3500   // Collect Data to be translated/transferred
3501
3502   SequenceI [] selection = viewport.getSequenceSelection();
3503   String [] seqstring = viewport.getViewAsString(true);
3504   AlignmentI al  = null;
3505   try {
3506     al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
3507         viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
3508         viewport.alignment.getWidth());
3509   } catch (Exception ex) {
3510     al = null;
3511     jalview.bin.Cache.log.debug("Exception during translation.",ex);
3512   }
3513   if (al==null)
3514   {
3515     JOptionPane.showMessageDialog(Desktop.desktop,
3516         "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
3517         "Translation Failed",
3518         JOptionPane.WARNING_MESSAGE);
3519   } else {
3520     AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3521     Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3522                              DEFAULT_WIDTH,
3523                              DEFAULT_HEIGHT);
3524   }
3525 }
3526
3527 /**
3528  * DOCUMENT ME!
3529  *
3530  * @param String DOCUMENT ME!
3531  */
3532 public boolean parseFeaturesFile(String file, String type)
3533 {
3534     boolean featuresFile = false;
3535     try
3536     {
3537       featuresFile = new FeaturesFile(file,
3538           type).parse(viewport.alignment.getDataset(),
3539                                          alignPanel.seqPanel.seqCanvas.
3540                                          getFeatureRenderer().featureColours,
3541                                          false);
3542     }
3543     catch(Exception ex)
3544     {
3545       ex.printStackTrace();
3546     }
3547
3548     if(featuresFile)
3549     {
3550       viewport.showSequenceFeatures = true;
3551       showSeqFeatures.setSelected(true);
3552       alignPanel.paintAlignment(true);
3553     }
3554
3555     return featuresFile;
3556 }
3557
3558 public void dragEnter(DropTargetDragEvent evt)
3559 {}
3560
3561 public void dragExit(DropTargetEvent evt)
3562 {}
3563
3564 public void dragOver(DropTargetDragEvent evt)
3565 {}
3566
3567 public void dropActionChanged(DropTargetDragEvent evt)
3568 {}
3569
3570 public void drop(DropTargetDropEvent evt)
3571 {
3572     Transferable t = evt.getTransferable();
3573     java.util.List files = null;
3574
3575     try
3576     {
3577       DataFlavor uriListFlavor = new DataFlavor(
3578           "text/uri-list;class=java.lang.String");
3579       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3580       {
3581         //Works on Windows and MacOSX
3582         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3583         files = (java.util.List) t.getTransferData(DataFlavor.
3584             javaFileListFlavor);
3585       }
3586       else if (t.isDataFlavorSupported(uriListFlavor))
3587       {
3588         // This is used by Unix drag system
3589         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3590         String data = (String) t.getTransferData(uriListFlavor);
3591         files = new java.util.ArrayList(1);
3592         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3593             data,
3594             "\r\n");
3595              st.hasMoreTokens(); )
3596         {
3597           String s = st.nextToken();
3598           if (s.startsWith("#"))
3599           {
3600             // the line is a comment (as per the RFC 2483)
3601             continue;
3602           }
3603
3604           java.net.URI uri = new java.net.URI(s);
3605           java.io.File file = new java.io.File(uri);
3606           files.add(file);
3607         }
3608       }
3609     }
3610     catch (Exception e)
3611     {
3612       e.printStackTrace();
3613     }
3614     if (files != null)
3615     {
3616       try
3617       {
3618
3619         for (int i = 0; i < files.size(); i++)
3620         {
3621           loadJalviewDataFile(files.get(i).toString());
3622         }
3623       }
3624       catch (Exception ex)
3625       {
3626         ex.printStackTrace();
3627       }
3628     }
3629 }
3630
3631   // This method will attempt to load a "dropped" file first by testing
3632   // whether its and Annotation file, then features file. If both are
3633   // false then the user may have dropped an alignment file onto this
3634   // AlignFrame
3635    public void loadJalviewDataFile(String file)
3636   {
3637     try
3638     {
3639       String protocol = "File";
3640
3641       if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3642       {
3643         protocol = "URL";
3644       }
3645
3646       boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3647           alignment, file, protocol);
3648
3649       if (!isAnnotation)
3650       {
3651         boolean isGroupsFile = parseFeaturesFile(file,protocol);
3652         if (!isGroupsFile)
3653         {
3654           String format = new IdentifyFile().Identify(file, protocol);
3655
3656           if(format.equalsIgnoreCase("JnetFile"))
3657           {
3658             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3659                 file, protocol);
3660             new JnetAnnotationMaker().add_annotation(predictions,
3661                 viewport.getAlignment(),
3662                 0, false);
3663             alignPanel.adjustAnnotationHeight();
3664             alignPanel.paintAlignment(true);
3665           }
3666           else
3667           {
3668             new FileLoader().LoadFile(viewport, file, protocol, format);
3669         }
3670       }
3671       }
3672       else
3673       {
3674         // (isAnnotation)
3675         alignPanel.adjustAnnotationHeight();
3676       }
3677
3678     }
3679     catch (Exception ex)
3680     {
3681       ex.printStackTrace();
3682     }
3683   }
3684
3685   public void tabSelectionChanged(int index)
3686   {
3687     if (index > -1)
3688     {
3689       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3690       viewport = alignPanel.av;
3691       setMenusFromViewport(viewport);
3692     }
3693   }
3694
3695   public void tabbedPane_mousePressed(MouseEvent e)
3696   {
3697     if(SwingUtilities.isRightMouseButton(e))
3698     {
3699       String reply = JOptionPane.showInternalInputDialog(this,
3700           "Enter View Name",
3701           "Edit View Name",
3702           JOptionPane.QUESTION_MESSAGE);
3703
3704       if (reply != null)
3705       {
3706         viewport.viewName = reply;
3707         tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3708       }
3709     }
3710   }
3711
3712
3713   public AlignViewport getCurrentView()
3714   {
3715     return viewport;
3716   }
3717
3718
3719   /**
3720    * Open the dialog for regex description parsing.
3721    */
3722   protected void extractScores_actionPerformed(ActionEvent e)
3723   {
3724     ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment);
3725     if (pp.getScoresFromDescription("col", "score column ", "\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)")>0)
3726     {
3727       buildSortByAnnotationScoresMenu();
3728     }
3729   }
3730 }
3731
3732 class PrintThread
3733     extends Thread
3734 {
3735   AlignmentPanel ap;
3736   public PrintThread(AlignmentPanel ap)
3737   {
3738    this.ap = ap;
3739   }
3740   static PageFormat pf;
3741   public void run()
3742   {
3743     PrinterJob printJob = PrinterJob.getPrinterJob();
3744
3745     if (pf != null)
3746     {
3747       printJob.setPrintable(ap, pf);
3748     }
3749     else
3750     {
3751       printJob.setPrintable(ap);
3752     }
3753
3754     if (printJob.printDialog())
3755     {
3756       try
3757       {
3758         printJob.print();
3759       }
3760       catch (Exception PrintException)
3761       {
3762         PrintException.printStackTrace();
3763       }
3764     }
3765   }
3766 }