From: jprocter <Jim Procter>
Date: Thu, 7 Sep 2006 11:39:37 +0000 (+0000)
Subject: This commit was manufactured by cvs2svn to create branch 'VamJalview'.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git

This commit was manufactured by cvs2svn to create branch 'VamJalview'.

Cherrypick from master 2006-09-07 11:39:36 UTC jimp 'added copy consensus sequence to consensus annotation popup menu':
    src/jalview/appletgui/Tooltip.java
    src/jalview/datamodel/.cvsignore
    src/jalview/datamodel/AlignmentView.java
    src/jalview/datamodel/CigarArray.java
    src/jalview/datamodel/CigarBase.java
    src/jalview/datamodel/CigarCigar.java
    src/jalview/datamodel/CigarSimple.java
    src/jalview/datamodel/ColumnSelection.java
    src/jalview/datamodel/DBRefSource.java
    src/jalview/datamodel/SeqCigar.java
    src/jalview/datamodel/UniprotProteinName.java
    src/jalview/gui/AnnotationExporter.java
    src/jalview/gui/DasSourceBrowser.java
    src/jalview/gui/Jalview2XML_V1.java
    src/jalview/io/AnnotationFile.java
    src/jalview/io/DBRefFetcher.java
    src/jalview/io/DasSequenceFeatureFetcher.java
    src/jalview/io/FeaturesFile.java
    src/jalview/io/JnetAnnotationMaker.java
    src/jalview/io/StockholmFile.java
    src/jalview/jbgui/GDasSourceBrowser.java
    src/jalview/schemabinding/version2/Alignment.java
    src/jalview/schemabinding/version2/AlignmentDescriptor.java
    src/jalview/schemabinding/version2/Annotation.java
    src/jalview/schemabinding/version2/AnnotationColours.java
    src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
    src/jalview/schemabinding/version2/AnnotationDescriptor.java
    src/jalview/schemabinding/version2/AnnotationElement.java
    src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
    src/jalview/schemabinding/version2/Colour.java
    src/jalview/schemabinding/version2/ColourDescriptor.java
    src/jalview/schemabinding/version2/DBRef.java
    src/jalview/schemabinding/version2/DBRefDescriptor.java
    src/jalview/schemabinding/version2/Feature.java
    src/jalview/schemabinding/version2/FeatureDescriptor.java
    src/jalview/schemabinding/version2/FeatureSettings.java
    src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
    src/jalview/schemabinding/version2/Features.java
    src/jalview/schemabinding/version2/FeaturesDescriptor.java
    src/jalview/schemabinding/version2/HiddenColumns.java
    src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
    src/jalview/schemabinding/version2/JGroup.java
    src/jalview/schemabinding/version2/JGroupDescriptor.java
    src/jalview/schemabinding/version2/JSeq.java
    src/jalview/schemabinding/version2/JSeqDescriptor.java
    src/jalview/schemabinding/version2/JalviewModel.java
    src/jalview/schemabinding/version2/JalviewModelDescriptor.java
    src/jalview/schemabinding/version2/JalviewModelSequence.java
    src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
    src/jalview/schemabinding/version2/JalviewUserColours.java
    src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
    src/jalview/schemabinding/version2/OtherData.java
    src/jalview/schemabinding/version2/OtherDataDescriptor.java
    src/jalview/schemabinding/version2/Pdbentry.java
    src/jalview/schemabinding/version2/PdbentryDescriptor.java
    src/jalview/schemabinding/version2/PdbentryItem.java
    src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
    src/jalview/schemabinding/version2/Pdbids.java
    src/jalview/schemabinding/version2/PdbidsDescriptor.java
    src/jalview/schemabinding/version2/Property.java
    src/jalview/schemabinding/version2/PropertyDescriptor.java
    src/jalview/schemabinding/version2/Sequence.java
    src/jalview/schemabinding/version2/SequenceDescriptor.java
    src/jalview/schemabinding/version2/SequenceSet.java
    src/jalview/schemabinding/version2/SequenceSetDescriptor.java
    src/jalview/schemabinding/version2/SequenceType.java
    src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
    src/jalview/schemabinding/version2/Setting.java
    src/jalview/schemabinding/version2/SettingDescriptor.java
    src/jalview/schemabinding/version2/ThresholdLine.java
    src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
    src/jalview/schemabinding/version2/Tree.java
    src/jalview/schemabinding/version2/TreeDescriptor.java
    src/jalview/schemabinding/version2/UserColourScheme.java
    src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
    src/jalview/schemabinding/version2/UserColours.java
    src/jalview/schemabinding/version2/UserColoursDescriptor.java
    src/jalview/schemabinding/version2/VAMSAS.java
    src/jalview/schemabinding/version2/VAMSASDescriptor.java
    src/jalview/schemabinding/version2/VamsasModel.java
    src/jalview/schemabinding/version2/VamsasModelDescriptor.java
    src/jalview/schemabinding/version2/Viewport.java
    src/jalview/schemabinding/version2/ViewportDescriptor.java
    src/jalview/util/ShiftList.java
    src/jalview/util/TableSorter.java
    src/jalview/ws/MsaWSThread.java
    src/jalview/ws/WSThread.java
    src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
    src/org/biojava/dasobert/das/DAS_Feature_Handler.java
    src/org/biojava/dasobert/das/FeatureThread.java
    src/org/biojava/dasobert/das2/Das2Capability.java
    src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
    src/org/biojava/dasobert/das2/Das2Source.java
    src/org/biojava/dasobert/das2/Das2SourceImpl.java
    src/org/biojava/dasobert/das2/DasSourceConverter.java
    src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
    src/org/biojava/dasobert/das2/io/DasSourceReader.java
    src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
    src/org/biojava/dasobert/dasregistry/Das1Source.java
    src/org/biojava/dasobert/dasregistry/Das2Validator.java
    src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
    src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
    src/org/biojava/dasobert/dasregistry/DasSource.java
    src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
    src/org/biojava/dasobert/eventmodel/FeatureEvent.java
    src/org/biojava/dasobert/eventmodel/FeatureListener.java
    src/org/biojava/dasobert/eventmodel/ObjectListener.java
    src/org/biojava/dasobert/eventmodel/SequenceEvent.java
    src/org/biojava/dasobert/eventmodel/SequenceListener.java
---

diff --git a/src/jalview/appletgui/Tooltip.java b/src/jalview/appletgui/Tooltip.java
new file mode 100755
index 0000000..389b012
--- /dev/null
+++ b/src/jalview/appletgui/Tooltip.java
@@ -0,0 +1,190 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
+package jalview.appletgui;
+
+import java.awt.*;
+import java.applet.*;
+import java.awt.event.*;
+import java.util.*;
+
+public class Tooltip extends Canvas implements MouseListener,
+    MouseMotionListener
+{
+
+        private String [] tip;
+        protected Component owner;
+
+        private Container mainContainer;
+        private LayoutManager mainLayout;
+
+        private boolean shown;
+
+        private final int VERTICAL_OFFSET = 20;
+        private final int HORIZONTAL_ENLARGE = 10;
+
+        int fontHeight = 0;
+
+        Image linkImage;
+
+        FontMetrics fm;
+
+
+
+        public Tooltip(String tip, Component owner)
+        {
+          this.owner = owner;
+          owner.addMouseListener(this);
+          owner.addMouseMotionListener(this);
+          setBackground(new Color(255, 255, 220));
+          setTip(tip);
+          java.net.URL url = getClass().getResource("/images/link.gif");
+          if (url != null)
+          {
+            linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
+          }
+        }
+
+
+        public void paint(Graphics g)
+        {
+                g.drawRect(0,0,getSize().width -1, getSize().height -1);
+                int lindex, x;
+                for(int i=0; i<tip.length; i++)
+                {
+                  x = 3;
+                  lindex = tip[i].indexOf("%LINK%");
+                  if(lindex!=-1)
+                  {
+                   if(lindex>0)
+                   {
+                     g.drawString(tip[i].substring(0, lindex), 3, (i+1)*fontHeight-3);
+                     x+=fm.stringWidth(tip[i].substring(0, lindex)+3);
+                   }
+                    g.drawImage(linkImage, x, i * fontHeight+1, this);
+                  }
+                  else
+                  g.drawString(tip[i], 3, (i+1)*fontHeight - 3);
+                }
+        }
+
+        private void addToolTip()
+        {
+                mainContainer.setLayout(null);
+                mainContainer.add(this, 0);
+                mainContainer.validate();
+                repaint();
+                shown = true;
+        }
+
+        void setTip(String tip)
+        {
+          fm = getFontMetrics(owner.getFont());
+          fontHeight = fm.getHeight();
+
+          int longestLine = 0;
+          StringTokenizer st = new StringTokenizer(tip, "\n");
+          this.tip = new String[st.countTokens()];
+          int index = 0;
+          while(st.hasMoreElements())
+          {
+            this.tip[index] = st.nextToken();
+            if(fm.stringWidth(this.tip[index])>longestLine)
+              longestLine = fm.stringWidth(this.tip[index]);
+            index ++;
+          }
+
+          setSize(longestLine + HORIZONTAL_ENLARGE,
+                  fontHeight*this.tip.length);
+        }
+
+        void setTipLocation(int x, int y)
+        {
+
+          setLocation((owner.getLocationOnScreen().x - mainContainer.getLocationOnScreen().x) +x,
+           (owner.getLocationOnScreen().y - mainContainer.getLocationOnScreen().y + VERTICAL_OFFSET)+y);
+
+
+
+        // correction, whole tool tip must be visible
+          if (mainContainer.getSize().width < (getLocation().x + getSize().width))
+          {
+            setLocation(mainContainer.getSize().width - getSize().width,
+                        getLocation().y);
+          }
+
+        }
+
+
+        private void removeToolTip() {
+                if (shown) {
+                        mainContainer.remove(0);
+                        mainContainer.setLayout(mainLayout);
+                        mainContainer.validate();
+                }
+                shown = false;
+        }
+
+        private void findMainContainer() {
+                Container parent = owner.getParent();
+                while (true) {
+                        if ((parent instanceof Applet) || (parent instanceof Frame)) {
+                                mainContainer = parent;
+                                break;
+                        } else {
+                                parent = parent.getParent();
+                        }
+                }
+                mainLayout = mainContainer.getLayout();
+        }
+
+        public void mouseEntered(MouseEvent me)
+        {     }
+
+        public void mouseExited(MouseEvent me)
+        {
+          removeToolTip();
+        }
+
+        public void mousePressed(MouseEvent me)
+        {
+          removeToolTip();
+        }
+
+        public void mouseReleased(MouseEvent me)
+        {}
+
+        public void mouseClicked(MouseEvent me)
+        {}
+
+        public void mouseMoved(MouseEvent me)
+        {
+          if (shown)
+            setTipLocation(me.getX(), me.getY());
+          else
+          {
+            findMainContainer();
+            addToolTip();
+            setTipLocation(me.getX(), me.getY());
+          }
+        }
+
+        public void mouseDragged(MouseEvent me)
+        {}
+}
diff --git a/src/jalview/datamodel/.cvsignore b/src/jalview/datamodel/.cvsignore
new file mode 100644
index 0000000..a4d99ef
--- /dev/null
+++ b/src/jalview/datamodel/.cvsignore
@@ -0,0 +1,5 @@
+.#Alignment.java.1.41
+.#Alignment.java.1.42
+.#Alignment.java.1.43
+.#Alignment.java.1.44
+.#AlignmentI.java.1.21
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
new file mode 100644
index 0000000..a76e90e
--- /dev/null
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -0,0 +1,434 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+
+
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+public class AlignmentView
+{
+    /**
+     * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
+     */
+    private SeqCigar[] sequences = null;
+  private int[] contigs = null;
+  private int width=0;
+  public AlignmentView(CigarArray seqcigararray)
+  {
+    if (!seqcigararray.isSeqCigarArray())
+      throw new Error("Implementation Error - can only make an alignment view from a CigarArray of sequences.");
+    //contigs = seqcigararray.applyDeletions();
+    contigs = seqcigararray.getDeletedRegions();
+    sequences = seqcigararray.getSeqCigarArray();
+    width = seqcigararray.getWidth(); // visible width
+  }
+
+  public void setSequences(SeqCigar[] sequences)
+  {
+    this.sequences = sequences;
+  }
+
+  public void setContigs(int[] contigs)
+  {
+    this.contigs = contigs;
+  }
+
+  public SeqCigar[] getSequences()
+  {
+    return sequences;
+  }
+  /**
+   * @see CigarArray.getDeletedRegions
+   * @return int[] { vis_start, sym_start, length }
+   */
+  public int[] getContigs()
+  {
+    return contigs;
+  }
+  /**
+   * get the full alignment and a columnselection object marking the hidden regions
+   * @param gapCharacter char
+   * @return Object[] { SequenceI[], ColumnSelection}
+   */
+  public Object[] getAlignmentAndColumnSelection(char gapCharacter) {
+    ColumnSelection colsel = new ColumnSelection();
+
+    return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel, contigs), colsel};
+  }
+  /**
+   * getSequenceStrings
+   *
+   * @param c char
+   * @return String[]
+   */
+  public String[] getSequenceStrings(char c)
+  {
+    String[] seqs=new String[sequences.length];
+    for (int n=0; n<sequences.length; n++) {
+      String fullseq = sequences[n].getSequenceString(c);
+      if (contigs != null)
+      {
+        seqs[n] = "";
+        int p = 0;
+        for (int h = 0; h < contigs.length; h += 3)
+        {
+          seqs[n] += fullseq.substring(p, contigs[h + 1]);
+          p = contigs[h + 1] + contigs[h + 2];
+        }
+        seqs[n] += fullseq.substring(p);
+      } else
+        seqs[n] = fullseq;
+    }
+    return seqs;
+  }
+  /**
+   *
+   * @return visible number of columns in alignment view
+   */
+  public int getWidth() {
+    return width;
+  }
+
+  protected void setWidth(int width) {
+    this.width = width;
+  }
+  /**
+   * get the contiguous subalignments in an alignment view.
+   * @param gapCharacter char
+   * @return SequenceI[][]
+   */
+  public SequenceI[][] getVisibleContigs(char gapCharacter) {
+    SequenceI[][] smsa;
+    int njobs = 1;
+    if (sequences==null || width<=0)
+      return null;
+    if (contigs != null && contigs.length > 0)
+    {
+      int start = 0;
+      njobs = 0;
+      int fwidth = width;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          njobs++;
+        }
+        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        njobs++;
+      }
+      smsa = new SequenceI[njobs][];
+      start = 0;
+      int j = 0;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if (contigs[contig + 1] - start > 0)
+        {
+          SequenceI mseq[] = new SequenceI[sequences.length];
+          for (int s = 0; s < mseq.length; s++)
+          {
+            mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+                contigs[contig + 1]);
+          }
+          smsa[j] = mseq;
+          j++;
+        }
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        SequenceI mseq[] = new SequenceI[sequences.length];
+        for (int s = 0; s < mseq.length; s++)
+        {
+          mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+              fwidth + 1);
+        }
+        smsa[j] = mseq;
+        j++;
+      }
+    }
+    else
+    {
+      smsa = new SequenceI[1][];
+      smsa[0] = new SequenceI[sequences.length];
+      for (int s = 0; s < sequences.length; s++)
+      {
+        smsa[0][s] = sequences[s].getSeq(gapCharacter);
+      }
+    }
+    return smsa;
+  }
+  /**
+   * return full msa and hidden regions with visible blocks replaced with new sub alignments
+   * @param nvismsa SequenceI[][]
+   * @param orders AlignmentOrder[] corresponding to each SequenceI[] block.
+   * @return Object[]
+   */
+  public Object[] getUpdatedView(SequenceI[][] nvismsa, AlignmentOrder[] orders, char gapCharacter) {
+    if (sequences == null || width <= 0)
+    {
+      throw new Error("empty view cannot be updated.");
+    }
+    if (nvismsa == null)
+      throw new Error(
+          "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
+    if (contigs != null && contigs.length > 0)
+    {
+      SequenceI[] alignment = new SequenceI[sequences.length];
+      ColumnSelection columnselection = new ColumnSelection();
+      if (contigs != null && contigs.length > 0)
+      {
+        int start = 0;
+        int nwidth = 0;
+        int owidth = width;
+        int j = 0;
+        for (int contig = 0; contig < contigs.length; contig += 3)
+        {
+          owidth += contigs[contig + 2]; // recover final column width
+          if (contigs[contig + 1] - start > 0)
+          {
+            int swidth = 0; // subalignment width
+            if (nvismsa[j] != null)
+            {
+              SequenceI mseq[] = nvismsa[j];
+              AlignmentOrder order=(orders==null) ? null : orders[j];
+              j++;
+              if (mseq.length!=sequences.length)
+                throw new Error("Mismatch between number of sequences in block "+j+" ("+mseq.length+") and the original view ("+sequences.length+")");
+              swidth = mseq[0].getLength(); // JBPNote: could ensure padded here.
+              for (int s = 0; s < mseq.length; s++)
+              {
+                if (alignment[s] == null)
+                {
+                  alignment[s] = mseq[s];
+                }
+                else
+                {
+                  alignment[s].setSequence(alignment[s].getSequence() +
+                                           mseq[s].getSequence());
+                  if (mseq[s].getStart() <= mseq[s].getEnd())
+                  {
+                    alignment[s].setEnd(mseq[s].getEnd());
+                  }
+                  if (order!=null) {
+                    order.updateSequence(mseq[s], alignment[s]);
+                  }
+                }
+              }
+            }
+            else
+            {
+              // recover original alignment block or place gaps
+              if (true)
+              {
+                // recover input data
+                for (int s = 0; s < sequences.length; s++)
+                {
+                  SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+                      contigs[contig + 1]);
+                  if (swidth < oseq.getLength())
+                  {
+                    swidth = oseq.getLength();
+                  }
+                  if (alignment[s] == null)
+                  {
+                    alignment[s] = oseq;
+                  }
+                  else
+                  {
+                    alignment[s].setSequence(alignment[s].getSequence() +
+                                             oseq.getSequence());
+                    if (oseq.getEnd() >= oseq.getStart())
+                    {
+                      alignment[s].setEnd(oseq.getEnd());
+                    }
+                  }
+                }
+
+              }
+              j++;
+            }
+            nwidth += swidth;
+          }
+          // advance to begining of visible region
+          start = contigs[contig + 1] + contigs[contig + 2];
+          // add hidden segment to right of next region
+          for (int s = 0; s < sequences.length; s++)
+          {
+            SequenceI hseq = sequences[s].getSeq(gapCharacter).getSubSequence(contigs[contig +
+                1], start);
+            if (alignment[s] == null)
+            {
+              alignment[s] = hseq;
+            }
+            else
+            {
+              alignment[s].setSequence(alignment[s].getSequence() +
+                                       hseq.getSequence());
+              if (hseq.getEnd() >= hseq.getStart())
+              {
+                alignment[s].setEnd(hseq.getEnd());
+              }
+            }
+          }
+          // mark hidden segment as hidden in the new alignment
+          columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
+          nwidth += contigs[contig + 2];
+        }
+        // Do final segment - if it exists
+        if (j < nvismsa.length)
+        {
+          int swidth = 0;
+          if (nvismsa[j] != null)
+          {
+            SequenceI mseq[] = nvismsa[j];
+            AlignmentOrder order = (orders!=null) ? orders[j] : null;
+            swidth = mseq[0].getLength();
+            for (int s = 0; s < mseq.length; s++)
+            {
+              if (alignment[s] == null)
+              {
+                alignment[s] = mseq[s];
+              }
+              else
+              {
+                alignment[s].setSequence(alignment[s].getSequence() +
+                                         mseq[s].getSequence());
+                if (mseq[s].getEnd() >= mseq[s].getStart())
+                {
+                  alignment[s].setEnd(mseq[s].getEnd());
+                }
+                if (order!=null) {
+                  order.updateSequence(mseq[s], alignment[s]);
+                }
+              }
+            }
+          }
+          else
+          {
+            if (start < owidth)
+            {
+              // recover input data or place gaps
+              if (true)
+              {
+                // recover input data
+                for (int s = 0; s < sequences.length; s++)
+                {
+                  SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+                      owidth + 1);
+                  if (swidth < oseq.getLength())
+                  {
+                    swidth = oseq.getLength();
+                  }
+                  if (alignment[s] == null)
+                  {
+                    alignment[s] = oseq;
+                  }
+                  else
+                  {
+                    alignment[s].setSequence(alignment[s].getSequence() +
+                                             oseq.getSequence());
+                    if (oseq.getEnd() >= oseq.getStart())
+                    {
+                      alignment[s].setEnd(oseq.getEnd());
+                    }
+                  }
+                }
+                nwidth += swidth;
+              }
+              else
+              {
+                // place gaps.
+                throw new Error("Padding not yet implemented.");
+              }
+            }
+          }
+        }
+      }
+      return new Object[] { alignment, columnselection};
+    } else {
+      if (nvismsa.length!=1)
+        throw new Error("Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="+nvismsa.length);
+      if (nvismsa[0]!=null)
+        return new Object[] { nvismsa[0], new ColumnSelection()};
+      else
+        return getAlignmentAndColumnSelection(gapCharacter);
+    }
+  }
+  /**
+   * returns simple array of start end positions of visible range on alignment.
+   * vis_start and vis_end are inclusive - use SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying alignment. 
+   * @return int[] { start_i, end_i } for 1<i<n visible regions.
+   */
+  public int[] getVisibleContigs() {
+    if (contigs != null && contigs.length > 0)
+    {
+      int start = 0;
+      int nvis = 0;
+      int fwidth = width;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          nvis++;
+        }
+        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        nvis++;
+      }
+      int viscontigs[] = new int[nvis*2];
+      nvis=0;
+      start=0;
+      for (int contig=0; contig<contigs.length; contig+=3) {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          viscontigs[nvis] = start;
+          viscontigs[nvis+1]=contigs[contig+1]-1; // end is inclusive
+          nvis+=2;
+        }
+        start = contigs[contig + 1] + contigs[contig + 2];              
+      }
+      if (start<fwidth) {
+        viscontigs[nvis] = start;
+        viscontigs[nvis+1]=fwidth; // end is inclusive
+        nvis+=2;
+      }
+      return viscontigs;
+    } else {
+      return new int[] { 0, width};
+    }
+  }
+}
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
new file mode 100644
index 0000000..9b60e56
--- /dev/null
+++ b/src/jalview/datamodel/CigarArray.java
@@ -0,0 +1,206 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class CigarArray extends CigarBase
+{
+    /**
+     * Do CIGAR operations on a set of sequences from many other cigars
+     * BAD THINGS WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY
+     * or a CIGARCIGAR is given a CIGARARRAY to insert gaps into.
+     */
+    /**
+     * array of subject cigars
+     */
+    public CigarSimple refCigars[]=null;
+    private boolean seqcigararray=false;
+  private CigarArray() {
+    super();
+  }
+
+  /**
+   * isSeqCigarArray()
+   * @return boolean true if all refCigars resolve to a SeqCigar or a CigarCigar
+   */
+  public boolean isSeqCigarArray()
+  {
+    return seqcigararray;
+  }
+  /**
+   * Apply CIGAR operations to several cigars in parallel
+   * will throw an error if any of cigar are actually CigarArrays.
+   * @param cigar Cigar[]
+   */
+  public CigarArray(CigarSimple[] cigars) {
+    super();
+    seqcigararray = true;
+    if (cigars != null && cigars.length > 0)
+    {
+      refCigars = new CigarSimple[cigars.length];
+      for (int c = 0; c < cigars.length; c++)
+      {
+        refCigars[c] = cigars[c];
+        if (! ( (cigars[c] instanceof SeqCigar)
+               || cigars[c] instanceof CigarCigar))
+        {
+          seqcigararray = false;
+        }
+      }
+    }
+  }
+  /**
+   * @see Cigar.getSequenceAndDeletions
+   * @param GapChar char
+   * @return Object[][]
+   */
+  protected Object[][] getArrayofSequenceAndDeletions(char GapChar) {
+      if (refCigars == null || refCigars.length == 0 || length == 0) {
+        return null;
+      }
+      Object[][] sqanddels = new Object[refCigars.length][];
+      for (int c=0; c<refCigars.length; c++) {
+        String refString = refCigars[c].getSequenceString(GapChar);
+        if (refString != null)
+        {
+          sqanddels[c] = getSequenceAndDeletions(refString, GapChar);
+        } else {
+          sqanddels[c] = null;
+        }
+      }
+      return sqanddels;
+    }
+  /**
+   * NOTE: this is an improper sequence string function
+   * @return String formed by newline concatenated results of applying CIGAR operations to each reference object in turn.
+   * @param GapChar char
+   * @return '\n' separated strings (empty results included as \n\n)
+   */
+  public String getSequenceString(char GapChar)
+  {
+    if (length==0 || refCigars==null)
+      return "";
+    StringBuffer seqStrings = new StringBuffer();
+    Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
+    for (int c=0; c<refCigars.length; c++) {
+      if (sqanddels[c]!=null) {
+        seqStrings.append( (String) sqanddels[c][0]);
+        sqanddels[c][0] = null;
+      }
+      seqStrings.append('\n');
+    }
+    return seqStrings.toString();
+  }
+  /**
+   * return string results of applying cigar string to all reference cigars
+   * @param GapChar char
+   * @return String[]
+   */
+  public String[] getSequenceStrings(char GapChar) {
+
+    if (length==0 || refCigars==null || refCigars.length==0)
+      return null;
+    Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
+    String[] seqs = new String[sqanddels.length];
+    for (int c=0; c<refCigars.length; c++) {
+      seqs[c] = (String) sqanddels[c][0];
+    }
+    return seqs;
+  }
+  /**
+   * Combines the CigarArray cigar operations with the operations in each
+   * reference cigar - creating a new reference cigar
+   * @return Cigar[]
+
+  public CigarBase[] getEditedCigars() {
+
+    return new CigarBase[] {};
+  }
+*/
+  /**
+   * applyDeletions
+   * edits underlying refCigars to propagate deleted regions, and removes deletion
+   * operations from CigarArray operation list.
+   * @return int[] position after deletion occured and range of deletion in cigarArray or null if none occured
+   */
+  public int[] applyDeletions()
+  {
+    java.util.Vector delpos=null;
+    if (length==0)
+      return null;
+    int cursor=0; // range counter for deletions
+    int vcursor=0; // visible column index
+    int offset=0; // shift in visible column index as deletions are made
+    int i=0;
+    while (i<length) {
+      if (operation[i]!=D) {
+        if (operation[i]==M)
+          cursor+=range[i];
+        vcursor+=range[i++];
+      }
+      else
+      {
+        if (delpos==null)
+          delpos=new java.util.Vector();
+        int delstart=cursor, delend=cursor+range[i]-1; // inclusive
+        delpos.addElement(new int[] { vcursor+offset, range[i]}); // index of right hand column after hidden region boundary
+        offset+=range[i]-1; // shift in visible column coordinates
+        System.arraycopy(operation, i+1, operation, i, length-i);
+        System.arraycopy(range, i+1, range, i, length-i);
+        length--;
+        /*        int dmax=0;
+         for (int s=0; s<refCigars.length; s++) {
+           int d = refCigars[s].deleteRange(delstart, delend);
+           if (d>dmax)
+             dmax=d;
+         }
+         offset+=dmax; // shift in visible column coordinates
+         */
+        for (int s=0; s<refCigars.length; s++) {
+          int d = refCigars[s].deleteRange(delstart, delend);
+        }
+
+      }
+    }
+    if (delpos!=null)
+    {
+      int[] pos=new int[delpos.size()*2];
+      for (int k = 0, l = delpos.size(); k < l; k++) {
+        int[] dr = ((int[]) delpos.elementAt(k));
+        pos[k*2] = dr[0];
+        pos[k*2+1] = dr[1];
+        delpos.setElementAt(null,k);
+      }
+      delpos=null;
+      return pos;
+    }
+    return null;
+  }
+  /**
+   *
+   * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does not resolve to set of seqCigars)
+   */
+  public SeqCigar[] getSeqCigarArray() {
+    if (!isSeqCigarArray())
+      return null;
+    SeqCigar[] sa = new SeqCigar[refCigars.length];
+    for (int i=0; i<refCigars.length; i++)
+      sa[i] = (SeqCigar) refCigars[i];
+    return sa;
+  }
+}
diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
new file mode 100644
index 0000000..a36bf76
--- /dev/null
+++ b/src/jalview/datamodel/CigarBase.java
@@ -0,0 +1,652 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.Vector;
+
+public abstract class CigarBase
+{
+  /**
+   * Base class for compact idiosyncratic representation of gaps and aligned residues
+   * Regards to Tom Oldfield for his DynamicArray class.
+   * 17th July 2006
+   * Not thread safe.
+   */
+  public CigarBase()
+  {
+    // nothing to be done (probably)
+  }
+
+  protected int length = 0;
+  protected int _inc_length = 10; // extension range for addition of new operations
+  protected char[] operation = null;
+  protected int[] range = null;
+  /**
+   * Range of Hidden residues in seq (translated as deleted in seq)
+   */
+  public static final char D = 'D'; /**
+  * Range of insertions to seq
+  */
+ public static final char I = 'I'; /**
+  * Range of aligned residues
+  */
+ public static final char M = 'M';
+  static protected final char _case_shift = 'a' - 'A';
+  /**
+   * Ugly function to get edited sequence string, start and end symbol positions and the deletion regions as an array of int pairs
+   * May return null for an empty cigar string.
+   * May return null for deletion ranges if there are none.
+   * @param reference - the symbol sequence to apply the cigar operations to (or null if no sequence)
+   * @param GapChar - the symbol to use for Insert operations
+   * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3] {start, end, col} or null} the gapped sequence, first and last residue index, and the deletion ranges on the reference sequence
+   */
+  public Object[] getSequenceAndDeletions(String reference, char GapChar)
+  {
+    int rlength=0;
+    int[][] deletions = new int[length][];
+    int[][] trunc_deletions = null;
+    StringBuffer sq = new StringBuffer();
+    int cursor = 0, alcursor=0,start = 0, startpos=0, end = 0, endpos=0, delcount = -1;
+    boolean consecutive_del = false;
+    if (length == 0)
+    {
+      return null;
+    }
+    if (reference!=null)
+      rlength=reference.length();
+    boolean modstart = true;
+    for (int i = 0; i < length; i++)
+    {
+      switch (operation[i])
+      {
+        case D:
+          if (!consecutive_del)
+          {
+            deletions[++delcount] = new int[]
+                {
+                cursor, 0, alcursor};
+          }
+          cursor += range[i];
+          deletions[delcount][1] = cursor - 1;
+          consecutive_del = true;
+          break;
+        case I:
+          consecutive_del = false;
+          for (int r = 0; r < range[i]; r++)
+          {
+            sq.append(GapChar);
+            alcursor++;
+          }
+          break;
+        case M:
+          consecutive_del = false;
+          if (modstart)
+          {
+            start = cursor;
+            startpos=alcursor;
+            modstart = false;
+          }
+          if (reference!=null) {
+            int sbend = cursor+range[i];
+            if (sbend>rlength) {
+              sq.append(reference.substring(cursor, rlength));
+              while (sbend-- >= rlength)
+              {
+                sq.append(GapChar);
+              }
+            } else {
+              sq.append(reference.substring(cursor, sbend));
+            }
+          }
+          alcursor+=range[i];
+          cursor += range[i];
+          end = cursor - 1;
+          endpos = alcursor;
+          break;
+        default:
+          throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
+      }
+    }
+    if (++delcount > 0)
+    {
+      trunc_deletions = new int[delcount][];
+      System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
+    }
+    deletions = null;
+    return new Object[]
+        {
+        ((reference!=null) ? sq.toString() : null),
+        new int[] {
+        start, startpos, end, endpos}, trunc_deletions};
+  }
+  protected void compact_operations() {
+    int i=1;
+    if (operation==null)
+      return;
+    char last = operation[0];
+    while (i<length) {
+      if (last==operation[i]) {
+        range[i-1]+=range[i];
+        int r = length-i;
+        if (r>0) {
+          System.arraycopy(range, i + 1, range, i, r);
+          System.arraycopy(operation, i + 1, operation, i, r);
+        }
+        length--;
+      } else {
+        last = operation[i++];
+      }
+    }
+  }
+  /**
+   * turn a cigar string into a series of operation range pairs
+   * @param cigarString String
+   * @return object[] {char[] operation, int[] range}
+   * @throws java.lang.Exception for improperly formated cigar strings or ones with unknown operations
+   */
+  public static Object[] parseCigarString(String cigarString)
+      throws Exception
+  {
+    int ops = 0;
+    for (int i = 0, l = cigarString.length(); i < l; i++)
+    {
+      char c = cigarString.charAt(i);
+      if (c == M || c == (M - _case_shift) || c == I || c == (I - _case_shift) ||
+          c == D || c == (D - _case_shift))
+      {
+        ops++;
+      }
+    }
+    char[] operation = new char[ops];
+    int[] range = new int[ops];
+    int op = 0;
+    int i = 0, l = cigarString.length();
+    while (i < l)
+    {
+      char c;
+      int j = i;
+      do
+      {
+        c = cigarString.charAt(j++);
+      }
+      while (c >= '0' && c <= '9' && j < l);
+      if (j >= l && c >= '0' && c <= '9')
+      {
+        throw new Exception("Unterminated cigar string.");
+      }
+      try
+      {
+        String rangeint = cigarString.substring(i, j - 1);
+        range[op] = Integer.parseInt(rangeint);
+        i = j;
+      }
+      catch (Exception e)
+      {
+        throw new Error("Implementation bug in parseCigarString");
+      }
+      if (c >= 'a' && c <= 'z')
+      {
+        c -= _case_shift;
+      }
+      if ( (c == M || c == I || c == D))
+      {
+        operation[op++] = c;
+      }
+      else
+      {
+        throw new Exception("Unexpected operation '" + c +
+                            "' in cigar string (position " + i + " in '" +
+                            cigarString + "'");
+      }
+    }
+    return new Object[]
+        {
+        operation, range};
+  }
+
+  /**
+   * add an operation to cigar string
+   * @param op char
+   * @param range int
+   */
+  public void addOperation(char op, int range)
+  {
+    if (op >= 'a' && op <= 'z')
+    {
+      op -= _case_shift;
+    }
+    if (op != M && op != D && op != I)
+    {
+      throw new Error("Implementation error. Invalid operation string.");
+    }
+    if (range<=0)
+      throw new Error("Invalid range string (must be non-zero positive number)");
+    int lngth = 0;
+    if (operation == null)
+    {
+      this.operation = new char[_inc_length];
+      this.range = new int[_inc_length];
+    }
+    if (length + 1 == operation.length)
+    {
+      char[] ops = this.operation;
+      this.operation = new char[length + 1 + _inc_length];
+      System.arraycopy(ops, 0, this.operation, 0, length);
+      ops = null;
+      int[] rng = this.range;
+      this.range = new int[length + 1 + _inc_length];
+      System.arraycopy(rng, 0, this.range, 0, length);
+      rng = null;
+    }
+    if ((length>0) && (operation[length-1]==op))
+      length--; // modify existing operation.
+    else
+      this.range[length]=0; // reset range
+    this.operation[length] = op;
+    this.range[length++] += range;
+  }
+
+  /**
+   * semi-efficient insert an operation on the current cigar string set at column pos (from 1)
+   * NOTE: Insertion operations simply extend width of cigar result - affecting registration of alignment
+   * Deletion ops will shorten length of result - and affect registration of alignment
+   * Match ops will also affect length of result - affecting registration of alignment
+   * (ie "10M".insert(4,I,3)->"4M3I3M") - (replace?)
+   * (ie "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment)
+   * (ie "5I5M".insert(4,I,3)->"8I5M") - real insertion
+   * (ie "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms changed to Ds
+   * (ie "10M".insert(4,M,3)->"13M")  - lengthens - Is changed to M, Ds changed to M.
+   * (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts sequence left by 1 residue and extends it by 3
+   * ( "10D5M".insert(-1,M,3)->"3M7D5M")
+   * ( "10D5M".insert(0,M,3)->"7D8M")
+   * ( "10D5M".insert(1,M,3)->"10D8M")
+   *
+   * ( "1M10D5M".insert(0,M,3)->"1M10D8M")
+   * ( "1M10D5M".insert(1,M,3)->"
+   *
+   * if pos is beyond width - I operations are added before the operation
+   * @param pos int -1, 0-length of visible region, or greater to append new ops (with insertions in between)
+   * @param op char
+   * @param range int
+  public void addOperationAt(int pos, char op, int range)
+  {
+    int cursor = -1; // mark the position for the current operation being edited.
+    int o = 0;
+    boolean last_d = false; // previous op was a deletion.
+    if (pos < -1)
+      throw new Error("pos<-1 is not supported.");
+    while (o<length) {
+      if (operation[o] != D)
+      {
+        if ( (cursor + this.range[o]) < pos)
+        {
+          cursor += this.range[o];
+          o++;
+          last_d=false;
+        }
+        else
+        {
+          break;
+        }
+      }
+      else {
+        last_d=true;
+        o++;
+      }
+    }
+    if (o==length) {
+      // must insert more operations before pos
+      if (pos-cursor>0)
+        addInsertion(pos-cursor);
+      // then just add the new operation. Regardless of what it is.
+      addOperation(op, range);
+    } else {
+      int diff = pos - cursor;
+
+      int e_length = length-o; // new edit operation array length.
+      // diff<0 - can only happen before first insertion or match. - affects op and all following
+      // dif==0 - only when at first position of existing op -
+      // diff>0 - must preserve some existing operations
+      int[] e_range = new int[e_length];
+      System.arraycopy(this.range, o, e_range, 0, e_length);
+      char[] e_op = new char[e_length];
+      System.arraycopy(this.operation, o, e_op, 0, e_length);
+      length = o; // can now use add_operation to extend list.
+      int e_o=0; // current operation being edited.
+      switch (op) {
+        case M:
+          switch (e_op[e_o])
+          {
+            case M:
+              if (last_d && diff <= 0)
+              {
+                // reduce D's, if possible
+                if (range<=this.range[o-1]) {
+                  this.range[o - 1] -= range;
+                } else {
+                  this.range[o-1]=0;
+                }
+                if (this.range[o-1]==0)
+                  o--; // lose this op.
+              }
+              e_range[e_o] += range; // just add more matched residues
+              break;
+            case I:
+              // change from insertion to match
+              if (last_d && diff<=0)
+              {
+                // reduce D's, if possible
+                if (range<=this.range[o-1]) {
+                  this.range[o - 1] -= range;
+                } else {
+                  this.range[o-1]=0;
+                }
+                if (this.range[o-1]==0)
+                  o--; // lose this op.
+              }
+              e_range[e_o]
+                    break;
+                default:
+                  throw new Inp
+                      }
+
+                      break;
+                case I:
+                  break;
+                case D:
+              }
+          break;
+        default:
+          throw new Error("Implementation Error: Unknown operation in addOperation!");
+      }
+      // finally, add remaining ops.
+      while (e_o<e_length) {
+        addOperation(e_op[e_o], e_range[e_o]);
+        e_o++;
+      }
+    }
+  }
+**/
+  /**
+   * Mark residues from start to end (inclusive) as deleted from the alignment, and removes any insertions.
+   * @param start int
+   * @param end int
+   * @return deleted int - number of symbols marked as deleted
+   */
+  public int deleteRange(int start, int end) {
+    int deleted=0;
+    if (length==0) {
+      // nothing to do here
+      return deleted;
+    }
+    if (start<0 || start>end)
+      throw new Error("Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");
+    // find beginning
+    int cursor = 0; // mark the position for the current operation being edited.
+    int rlength=1+end-start; // number of positions to delete
+    int oldlen=length;
+    int o = 0;
+    boolean editing=false;
+    char[] oldops = operation;
+    int[] oldrange = range;
+    length=0;
+    operation = null;
+    range = null;
+    compact_operations();
+    while (o<oldlen && cursor<=end && rlength>0) {
+      if (oldops[o] == D) {
+        // absorbed into new deleted region.
+        addDeleted(oldrange[o++]);
+        continue;
+      }
+
+      int remain = oldrange[o]; // number of op characters left to edit
+      if (!editing) {
+        if ( (cursor + remain) <= start)
+        {
+          addOperation(oldops[o],oldrange[o]);
+          cursor+=oldrange[o++];
+          continue; // next operation
+        }
+        editing=true;
+        // add operations before hidden region
+        if (start-cursor>0) {
+          addOperation(oldops[o], start- cursor);
+          remain -= start - cursor;
+        }
+      }
+      // start inserting new ops
+      if (o<oldlen && editing && rlength>0 && remain>0) {
+        switch (oldops[o]) {
+          case M:
+            if (rlength>remain) {
+              addDeleted(remain);
+              deleted+=remain;
+            } else {
+              deleted+=rlength;
+              addDeleted(rlength);
+              if (remain-rlength>0)
+                this.addOperation(M,remain-rlength); // add remaining back.
+              rlength=0;
+              remain=0;
+            }
+            break;
+          case I:
+            if (remain-rlength>0) {
+              // only remove some gaps
+              addInsertion(remain-rlength);
+              rlength=0;
+            }
+            break;
+          case D:
+            throw new Error("Implementation error."); // do nothing;
+          default:
+            throw new Error("Implementation Error! Unknown operation '"+oldops[o]+"'");
+        }
+        rlength-=remain;
+        remain = oldrange[++o]; // number of op characters left to edit
+      }
+    }
+    // add remaining
+    while (o<oldlen) {
+      addOperation(oldops[o],oldrange[o++]);
+    }
+    //if (cursor<(start+1)) {
+      // ran out of ops - nothing to do here ?
+     // addInsertion(start-cursor);
+    //}
+    return deleted;
+  }
+
+  /**
+   * Deleted regions mean that there will be discontinuous sequence numbering in the
+   * sequence returned by getSeq(char).
+   * @return true if there deletions
+   */
+  public boolean hasDeletedRegions()
+  {
+    for (int i = 0; i<length ; i++)
+    {
+      if (operation[i] == D)
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+  /**
+   * enumerate the ranges on seq that are marked as deleted in this cigar
+   * @return int[] { vis_start, sym_start, length }
+   */
+  public int[] getDeletedRegions() {
+    if (length==0)
+      return null;
+    Vector dr = new Vector();
+    int cursor=0, vcursor=0;
+    for (int i=0;i<length;i++) {
+      switch (operation[i]) {
+        case M:
+          cursor+=range[i];
+        case I:
+          vcursor+=range[i];
+          break;
+        case D:
+          dr.addElement(new int[] { vcursor, cursor, range[i]});
+          cursor+=range[i];
+      }
+    }
+    if (dr.size()==0)
+      return null;
+    int[] delregions = new int[dr.size()*3];
+    for (int i=0,l=dr.size(); i<l; i++) {
+      int[] reg = (int[]) dr.elementAt(i);
+      delregions[i*3] = reg[0];
+      delregions[i*3+1] = reg[1];
+      delregions[i*3+2] = reg[2];
+    }
+    return delregions;
+  }
+  /**
+   * sum of ranges in cigar string
+   * @return int number of residues hidden, matched, or gaps inserted into sequence
+   */
+  public int getFullWidth()
+  {
+    int w = 0;
+    if (range != null)
+    {
+      for (int i = 0; i < length; i++)
+      {
+        w += range[i];
+      }
+    }
+    return w;
+  }
+
+  /**
+   * Visible length of aligned sequence
+   * @return int length of including gaps and less hidden regions
+   */
+  public int getWidth()
+  {
+    int w = 0;
+    if (range != null)
+    {
+      for (int i = 0; i < length; i++)
+      {
+        if (operation[i] == M || operation[i] == I)
+        {
+          w += range[i];
+        }
+      }
+    }
+    return w;
+  }
+  /**
+   * mark a range of inserted residues
+   * @param range int
+   */
+  public void addInsertion(int range)
+  {
+    this.addOperation(I, range);
+  }
+
+  /**
+   * mark the next range residues as hidden (not aligned) or deleted
+   * @param range int
+   */
+  public void addDeleted(int range)
+  {
+    this.addOperation(D, range);
+  }
+
+  /**
+   * Modifies operation list to delete columns from start to end (inclusive)
+   * editing will remove insertion operations, and convert matches to deletions
+   * @param start alignment column
+   * @param end alignment column
+   * @return boolean true if residues were marked as deleted.
+  public boolean deleteRange(int start, int end)
+  {
+    boolean deleted = false;
+    int op = 0, prevop = -1, firstm = -1,
+        lastm = -1, postop = -1;
+    int width = 0; // zero'th column
+    if (length > 0)
+    {
+      // find operation bracketing start of the range
+      do
+      {
+        if (operation[op] != D)
+        {
+          width += range[prevop = op];
+        }
+        op++;
+      }
+      while (op < length && width < start);
+    }
+    if (width < start)
+    {
+      // run off end - add more operations up to deletion.
+      addInsertion(start - width);
+    }
+    else
+    {
+      // edit existing operations.
+      op = prevop;
+      width -= range[prevop];
+      int[] oldrange = range;
+      char[] oldops = operation;
+      range = new int[oldrange.length];
+      operation = new char[oldops.length];
+      if (op < length)
+      {
+        do
+        {
+          if (operation[op] != D)
+          {
+            width += range[postop = op];
+          }
+          op++;
+        }
+        while (op < length && width <= end);
+      }
+    }
+    if (deleted == true)
+    {
+      addDeleted(end - start + 1);
+    }
+    return deleted;
+  }
+*/
+  /**
+   * Return an ENSEMBL style cigar string where D may indicates excluded parts of seq
+   * @return String of form ([0-9]+[IMD])+
+   */
+  public String getCigarstring()
+  {
+    StringBuffer cigarString = new StringBuffer();
+    for (int i = 0; i < length; i++)
+    {
+      cigarString.append("" + range[i]);
+      cigarString.append(operation[i]);
+    }
+    return cigarString.toString();
+  }
+}
diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
new file mode 100644
index 0000000..57848eb
--- /dev/null
+++ b/src/jalview/datamodel/CigarCigar.java
@@ -0,0 +1,50 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class CigarCigar
+    extends CigarSimple
+{
+  SeqCigar refCigar;
+    /**
+     * Apply CIGAR operations to the result of another cigar
+     * @param cigar Cigar
+     */
+    CigarCigar(SeqCigar cigar) {
+      super();
+      refCigar = cigar;
+    }
+  /**
+   *
+   * @return String formed by applying CIGAR operations to the reference object
+   * @param GapChar char
+   * @todo Implement this jalview.datamodel.Cigar method
+   */
+  public String getSequenceString(char GapChar)
+  {
+    if (length==0)
+      return "";
+    String refString = refCigar.getSequenceString(GapChar);
+    if (refString!=null) {
+      return (length==0) ? "" : (String) getSequenceAndDeletions(refString, GapChar)[0];
+    } else
+      return null;
+  }
+
+}
diff --git a/src/jalview/datamodel/CigarSimple.java b/src/jalview/datamodel/CigarSimple.java
new file mode 100644
index 0000000..c33da7a
--- /dev/null
+++ b/src/jalview/datamodel/CigarSimple.java
@@ -0,0 +1,43 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+public abstract class CigarSimple
+    extends CigarBase
+{
+    /**
+     * Return a symbol sequence with edits (gaps, insertions and deletions) applied
+     * @param GapChar char
+     * @return String
+     */
+    public abstract String getSequenceString(char GapChar);
+
+}
diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
new file mode 100644
index 0000000..2d22231
--- /dev/null
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -0,0 +1,728 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import jalview.util.ShiftList;
+
+import java.util.*;
+
+/**
+ * NOTE: Columns are zero based.
+ */
+public class ColumnSelection
+{
+    Vector selected = new Vector();
+
+    //Vector of int [] {startCol, endCol}
+    Vector hiddenColumns;
+
+    /**
+     * Add a column to the selection
+     *
+     * @param col index of column
+     */
+    public void addElement(int col)
+    {
+        Integer column = new Integer(col);
+        if (!selected.contains(column))
+        {
+            selected.addElement(column);
+        }
+    }
+
+    /**
+     * clears column selection
+     */
+    public void clear()
+    {
+        selected.removeAllElements();
+    }
+
+    /**
+     * removes col from selection
+     *
+     * @param col index of column to be removed
+     */
+    public void removeElement(int col)
+    {
+        Integer colInt = new Integer(col);
+
+        if (selected.contains(colInt))
+        {
+            selected.removeElement(colInt);
+        }
+    }
+
+    /**
+     * removes a range of columns from the selection
+     * @param start int - first column in range to be removed
+     * @param end int - last col
+     */
+    public void removeElements(int start, int end)
+    {
+      Integer colInt;
+      for(int i=start; i<end; i++)
+      {
+        colInt = new Integer(i);
+        if (selected.contains(colInt))
+        {
+            selected.removeElement(colInt);
+        }
+      }
+    }
+    /**
+     *
+     * @return Vector containing selected columns as Integers
+     */
+    public Vector getSelected()
+    {
+      return selected;
+    }
+
+    /**
+     *
+     * @param col index to search for in column selection
+     *
+     * @return true if Integer(col) is in selection.
+     */
+    public boolean contains(int col)
+    {
+        return selected.contains(new Integer(col));
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int columnAt(int i)
+    {
+        return ((Integer) selected.elementAt(i)).intValue();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int size()
+    {
+        return selected.size();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMax()
+    {
+        int max = -1;
+
+        for (int i = 0; i < selected.size(); i++)
+        {
+            if (columnAt(i) > max)
+            {
+                max = columnAt(i);
+            }
+        }
+
+        return max;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMin()
+    {
+        int min = 1000000000;
+
+        for (int i = 0; i < selected.size(); i++)
+        {
+            if (columnAt(i) < min)
+            {
+                min = columnAt(i);
+            }
+        }
+
+        return min;
+    }
+
+
+    /**
+     * propagate shift in alignment columns to column selection
+     *
+     * @param start beginning of edit
+     * @param left shift in edit (+ve for removal, or -ve for inserts)
+     */
+    public void compensateForEdit(int start, int change)
+    {
+        for (int i = 0; i < size(); i++)
+        {
+            int temp = columnAt(i);
+
+            if (temp >= start)
+            {
+                selected.setElementAt(new Integer(temp - change), i);
+            }
+        }
+
+        if(hiddenColumns!=null)
+        {
+          for(int i=0; i<hiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) hiddenColumns.elementAt(i);
+            if(region[0] > start)
+            {
+              region[0] -= change;
+              region[1] -= change;
+            }
+            if(region[0]<0)
+              region[0] = 0;
+            if(region[1] <0)
+             region[1] = 0;
+          }
+        }
+    }
+    /**
+     * propagate shift in alignment columns to column selection
+     * special version of compensateForEdit - allowing for edits within hidden regions
+     * @param start beginning of edit
+     * @param left shift in edit (+ve for removal, or -ve for inserts)
+     */
+    private void compensateForDelEdits(int start, int change)
+    {
+        for (int i = 0; i < size(); i++)
+        {
+            int temp = columnAt(i);
+
+            if (temp >= start)
+            {
+                selected.setElementAt(new Integer(temp - change), i);
+            }
+        }
+
+        if(hiddenColumns!=null)
+        {
+          for(int i=0; i<hiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) hiddenColumns.elementAt(i);
+            if(region[0] >= start)
+            {
+              region[0] -= change;
+            }
+            if (region[1]>= start) {
+              region[1] -=change;
+            }
+            if (region[1]<region[0]) {
+              hiddenColumns.removeElementAt(i--);
+            }
+
+            if(region[0]<0)
+              region[0] = 0;
+            if(region[1] <0)
+             region[1] = 0;
+          }
+        }
+    }
+    /**
+     * Adjust hidden column boundaries based on a series of column
+     * additions or deletions in visible regions.
+     * @param shiftrecord
+     * @return
+     */
+    public ShiftList compensateForEdits(ShiftList shiftrecord) {
+      if (shiftrecord!=null) {
+        Vector shifts = shiftrecord.shifts;
+        if (shifts!=null && shifts.size()>0) {
+          int shifted=0;
+          for (int i=0,j=shifts.size(); i<j; i++) {
+            int[] sh = (int[]) shifts.elementAt(i);
+            //compensateForEdit(shifted+sh[0], sh[1]);
+            compensateForDelEdits(shifted+sh[0], sh[1]);
+            shifted-=sh[1];
+          }
+        }
+        return shiftrecord.getInverse();
+      }
+      return null;
+    }
+    /**
+     * removes intersection of position,length ranges in deletions
+     * from the start,end regions marked in intervals.
+     * @param deletions
+     * @param intervals
+     * @return
+     */
+    private boolean pruneIntervalVector(Vector deletions, Vector intervals) {
+      boolean pruned=false;
+      int i=0,j=intervals.size()-1, s=0, t=deletions.size()-1;
+      int hr[]=(int[]) intervals.elementAt(i);
+      int sr[]=(int[]) deletions.elementAt(s);
+      while (i<=j && s<=t) {
+        boolean trailinghn=hr[1]>=sr[0];
+        if (!trailinghn) {
+          if (i<j)
+            hr=(int[]) intervals.elementAt(++i);
+          else
+            i++;
+          continue;
+        }
+        int endshift=sr[0]+sr[1]; // deletion ranges - -ve means an insert
+        if (endshift<hr[0] || endshift<sr[0]) { // leadinghc disjoint or not a deletion
+          if (s<t)
+            sr=(int[]) deletions.elementAt(++s);
+          else
+            s++;
+          continue;
+        }
+        boolean leadinghn=hr[0]>=sr[0];
+        boolean leadinghc=hr[0]<endshift;
+        boolean trailinghc=hr[1]<endshift;
+        if (leadinghn) {
+          if (trailinghc) {// deleted hidden region.
+            intervals.removeElementAt(i);
+            pruned=true;
+            j--;
+            if (i<=j)
+              hr=(int[]) intervals.elementAt(i);
+            continue;
+          }
+          if (leadinghc) {
+            hr[0]=endshift; // clip c terminal region
+            leadinghn=!leadinghn;
+            pruned=true;
+          }
+        }
+        if (!leadinghn) {
+          if (trailinghc) {
+            if (trailinghn) {
+              hr[1]=sr[0]-1;
+              pruned=true;
+            }
+          } else {
+            // sr contained in hr
+            if (s<t)
+              sr=(int[]) deletions.elementAt(++s);
+            else
+              s++;
+            continue;
+          }
+        }
+      }
+      return pruned; // true if any interval was removed or modified by operations.
+    }
+    private boolean pruneColumnList(Vector deletion, Vector list) {
+      int s=0,t=deletion.size();
+      int[] sr=(int[])list.elementAt(s++);
+      boolean pruned=false;
+      int i=0, j=list.size();
+      while (i<j && s<=t) {
+        int c=((Integer)list.elementAt(i++)).intValue();
+        if (sr[0]<=c) {
+          if (sr[1]+sr[0]>=c) { // sr[1] -ve means inseriton.
+            list.removeElementAt(--i);
+            j--;
+          } else {
+            if (s<t)
+              sr = (int[])deletion.elementAt(s);
+            s++;
+          }
+        }
+      }
+      return pruned;
+    }
+    /**
+     * remove any hiddenColumns or selected columns and shift remaining
+     * based on a series of position, range deletions.
+     * @param deletions
+     */
+    public void pruneDeletions(ShiftList deletions) {
+      if (deletions!=null) {
+        Vector shifts=deletions.shifts;
+        if (shifts!=null && shifts.size()>0) {
+          // delete any intervals intersecting.
+          if (hiddenColumns!=null) {
+            pruneIntervalVector(shifts, hiddenColumns);
+            if (hiddenColumns!=null && hiddenColumns.size()==0) {
+              hiddenColumns=null;
+            }
+          }
+          if (selected!=null && selected.size()>0) {
+            pruneColumnList(shifts, selected);
+            if (selected!=null && selected.size()==0)
+              selected=null;
+          }
+          // and shift the rest.
+          this.compensateForEdits(deletions);
+        }
+      }
+    }
+    /**
+     * This Method is used to return all the HiddenColumn regions
+     * less than the given index.
+     * @param end int
+     * @return Vector
+     */
+    public Vector getHiddenColumns()
+    {
+      return hiddenColumns;
+    }
+    /**
+     * Return absolute column index for a visible column index
+     * @param column int column index in alignment view
+     * @return alignment column index for column
+     */
+    public int adjustForHiddenColumns(int column)
+    {
+      int result = column;
+      if (hiddenColumns != null)
+      {
+        for (int i = 0; i < hiddenColumns.size(); i++)
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(i);
+          if (result >= region[0])
+          {
+            result += region[1] - region[0] + 1;
+          }
+        }
+      }
+      return result;
+    }
+
+    /**
+     * Use this method to find out where a visible column is in the alignment
+     * when hidden columns exist
+     * @param hiddenColumn int
+     * @return int
+     */
+    public int findColumnPosition(int hiddenColumn)
+    {
+      int result = hiddenColumn;
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        int gaps = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if (hiddenColumn > region[1])
+          {
+            result -= region[1]+1-region[0];
+          }
+          index++;
+        }
+        while (index < hiddenColumns.size());
+
+        result -= gaps;
+      }
+
+      return result;
+    }
+
+    /**
+     * Use this method to determine where the next hiddenRegion starts
+    */
+    public int findHiddenRegionPosition(int hiddenRegion)
+    {
+      int result = 0;
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        int gaps = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(hiddenRegion==0)
+          {
+            return region[0];
+          }
+
+            gaps +=  region[1] +1 - region[0];
+            result = region[1] +1;
+            index++;
+        }
+        while(index < hiddenRegion+1);
+
+        result -= gaps;
+      }
+
+      return result;
+    }
+
+    /**
+     * THis method returns the rightmost limit of a
+     * region of an alignment with hidden columns.
+     * In otherwords, the next hidden column.
+     * @param index int
+     */
+    public int getHiddenBoundaryRight(int alPos)
+    {
+      if (hiddenColumns != null)
+      {
+        int index = 0;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(alPos < region[0])
+            return region[0];
+
+          index++;
+        }
+        while(index < hiddenColumns.size());
+      }
+
+      return alPos;
+
+    }
+    /**
+     * THis method returns the rightmost limit of a
+     * region of an alignment with hidden columns.
+     * In otherwords, the next hidden column.
+     * @param index int
+     */
+    public int getHiddenBoundaryLeft(int alPos)
+    {
+      if (hiddenColumns != null)
+      {
+        int index = hiddenColumns.size()-1;
+        do
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(index);
+          if(alPos > region[1])
+            return region[1];
+
+          index--;
+        }
+        while(index >-1);
+      }
+
+      return alPos;
+
+    }
+
+    public void hideSelectedColumns()
+    {
+      while (size() > 0)
+      {
+        int column = ( (Integer) getSelected().firstElement()).intValue();
+        hideColumns(column);
+      }
+
+    }
+
+    public void hideColumns(int start, int end)
+    {
+      if(hiddenColumns==null)
+        hiddenColumns = new Vector();
+
+      boolean added = false;
+      boolean overlap = false;
+
+      for (int i = 0; i < hiddenColumns.size(); i++)
+      {
+        int[] region = (int[]) hiddenColumns.elementAt(i);
+        if ( start<=region[1] && end>=region[0])
+        {
+          hiddenColumns.removeElementAt(i);
+          overlap = true;
+          break;
+        }
+        else if (end < region[0] && start < region[0])
+        {
+          hiddenColumns.insertElementAt(new int[]
+                                        {start, end}, i);
+          added = true;
+          break;
+        }
+      }
+
+      if(overlap)
+      {
+         hideColumns(start, end);
+      }
+      else if (!added)
+        hiddenColumns.addElement(new int[] {start, end});
+
+    }
+
+    /**
+     * This method will find a range of selected columns
+     * around the column specified
+     * @param res int
+     */
+    public void hideColumns(int col)
+    {
+      // First find out range of columns to hide
+      int min = col, max = col+1;
+      while( contains(min) )
+      {  removeElement(min); min --;  }
+
+      while( contains(max) )
+      { removeElement(max);  max ++;  }
+
+      min++; max--;
+
+      hideColumns(min, max);
+    }
+
+    public void revealAllHiddenColumns()
+    {
+      if(hiddenColumns!=null)
+      {
+        for (int i = 0; i < hiddenColumns.size(); i++)
+        {
+          int[] region = (int[]) hiddenColumns.elementAt(i);
+          for (int j = region[0]; j < region[1]+1; j++)
+          {
+            addElement(j);
+          }
+        }
+      }
+
+      hiddenColumns = null;
+    }
+
+    public void revealHiddenColumns(int res)
+    {
+      for(int i=0; i<hiddenColumns.size(); i++)
+      {
+        int [] region = (int[])hiddenColumns.elementAt(i);
+        if( res == region[0])
+        {
+          for (int j = region[0]; j < region[1]+1; j++)
+          {
+            addElement(j);
+          }
+
+          hiddenColumns.removeElement(region);
+          break;
+        }
+      }
+      if(hiddenColumns.size()==0)
+        hiddenColumns = null;
+    }
+
+    public boolean isVisible(int column)
+    {
+      for(int i=0; i<hiddenColumns.size(); i++)
+      {
+        int [] region = (int[])hiddenColumns.elementAt(i);
+        if( column >= region[0] && column <= region[1])
+        {
+          return false;
+        }
+      }
+      return true;
+    }
+    /**
+     * Copy constructor
+     * @param copy
+     */
+    public ColumnSelection(ColumnSelection copy) {
+      if (copy!=null) {
+        if (copy.selected!=null) {
+          selected = new Vector();
+          for (int i=0,j=copy.selected.size(); i<j; i++) {
+            selected.setElementAt( ((Integer) copy.selected.elementAt(i)), i);
+          }
+        }
+        if (copy.hiddenColumns!=null) {
+          hiddenColumns=new Vector();
+          for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {
+            int[] rh,cp;
+            rh = (int[])copy.hiddenColumns.elementAt(i);
+            if (rh!=null) {
+              cp = new int[rh.length];
+              System.arraycopy(rh, 0, cp, 0, rh.length);
+              hiddenColumns.setElementAt(cp, i);
+            }
+          }
+        }
+      }
+    }
+
+  /**
+   * ColumnSelection
+   */
+  public ColumnSelection()
+  {
+  }
+
+  public String[] getVisibleSequenceStrings(int start, int end, SequenceI[] seqs) {
+    int i,iSize=seqs.length;
+    String selection[] = new String[iSize];
+    if (hiddenColumns!=null && hiddenColumns.size()>0)
+      {
+      for (i=0; i<iSize; i++) {
+        StringBuffer visibleSeq = new StringBuffer();
+        Vector regions = getHiddenColumns();
+
+        int blockStart = start, blockEnd=end;
+        int [] region;
+           int hideStart, hideEnd;
+
+           for (int j = 0; j < regions.size(); j++)
+           {
+             region = (int[]) regions.elementAt(j);
+             hideStart = region[0];
+             hideEnd = region[1];
+
+             if(hideStart < start)
+             {
+               continue;
+             }
+
+             blockStart = Math.min(blockStart, hideEnd+1);
+             blockEnd = Math.min(blockEnd, hideStart);
+
+             if(blockStart>blockEnd)
+             {
+                break;
+             }
+
+
+             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+             blockStart = hideEnd+1;
+             blockEnd = end;
+           }
+
+           if(end>blockStart)
+             visibleSeq.append(seqs[i].getSequence(blockStart, end));
+
+           selection[i] = visibleSeq.toString();
+        }
+      }
+      else
+      {
+        for(i=0; i<iSize; i++)
+        {
+        selection[i] = seqs[i].getSequence(start, end);
+        }
+      }
+      
+    return selection;
+    }
+  
+}
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
new file mode 100755
index 0000000..4830bc6
--- /dev/null
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -0,0 +1,47 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class DBRefSource
+{
+    /**
+     * UNIPROT Accession Number
+     */
+    public static String UNIPROT="UNIPROT";
+    /**
+     * UNIPROT Entry Name
+     */
+    public static String UP_NAME="UNIPROT_NAME";
+    /**
+     * PDB Entry Code
+     */
+    public static String PDB="PDB";
+    /**
+     * EMBL ID
+     */
+    public static String EMBL="EMBL";
+    /**
+     * EMBLCDS ID
+     */
+    public static String EMBLCDS="EMBLCDS";
+    /**
+     * PFAM ID
+     */
+    public static String PFAM="PFAM";
+    }
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
new file mode 100644
index 0000000..84da278
--- /dev/null
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -0,0 +1,602 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import jalview.analysis.*;
+import jalview.util.ShiftList;
+import java.util.Vector;
+
+public class SeqCigar
+    extends CigarSimple
+{
+    /**
+     * start(inclusive) and end(exclusive) of subsequence on refseq
+     */
+    private int start, end;
+  private SequenceI refseq = null;
+  /**
+   * Reference dataset sequence for the cigar string
+   * @return SequenceI
+   */
+  public SequenceI getRefSeq()
+  {
+    return refseq;
+  }
+  /**
+   *
+   * @return int start index of cigar ops on refSeq
+   */
+  public int getStart() {
+    return start;
+  }
+  /**
+   *
+   * @return int end index (exclusive) of cigar ops on refSeq
+   */
+  public int getEnd() {
+    return end;
+  }
+  /**
+   * Returns sequence as a string with cigar operations applied to it
+   * @return String
+   */
+  public String getSequenceString(char GapChar)
+  {
+    return (length == 0) ? "" :
+        (String) getSequenceAndDeletions(refseq.getSequence().substring(start, end), GapChar)[0];
+  }
+
+  /**
+   * recreates a gapped and edited version of RefSeq or null for an empty cigar string
+   * @return SequenceI
+   */
+  public SequenceI getSeq(char GapChar)
+  {
+    Sequence seq;
+    if (refseq == null || length == 0)
+    {
+      return null;
+    }
+    Object[] edit_result = getSequenceAndDeletions(refseq.getSequence().substring(start,end),
+        GapChar);
+    if (edit_result == null)
+    {
+      throw new Error(
+          "Implementation Error - unexpected null from getSequenceAndDeletions");
+    }
+    int bounds[] = (int[]) edit_result[1];
+    seq = new Sequence(refseq.getName(), (String) edit_result[0],
+                       refseq.getStart() + start+bounds[0],
+                       refseq.getStart() + start+((bounds[2]==0) ? -1 : bounds[2]));
+    // seq.checkValidRange(); probably not needed
+    seq.setDatasetSequence(refseq);
+    return seq;
+  }
+
+  /*
+     We don't allow this - refseq is given at construction time only
+   public void setSeq(SequenceI seq) {
+    this.seq = seq;
+     }
+   */
+  /**
+   * internal constructor - sets seq to a gapless sequence derived from seq
+   * and prepends any 'D' operations needed to get to the first residue of seq.
+   * @param seq SequenceI
+   * @param initialDeletion true to mark initial dataset sequence residues as deleted in subsequence
+   * @param _s index of first position in seq
+   * @param _e index after last position in (possibly gapped) seq
+   * @return true if gaps are present in seq
+   */
+  private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s, int _e)
+  {
+    boolean hasgaps = false;
+    if (seq == null)
+    {
+      throw new Error("Implementation Error - _setSeq(null,...)");
+    }
+    if (_s<0)
+      throw new Error("Implementation Error: _s="+_s);
+    String seq_string = seq.getSequence();
+    if (_e==0 || _e<_s || _e>seq_string.length())
+      _e=seq_string.length();
+    // resolve start and end positions relative to ungapped reference sequence
+    start = seq.findPosition(_s)-seq.getStart();
+    end = seq.findPosition(_e)-seq.getStart();
+    int l_ungapped = end-start;
+    // Find correct sequence to reference and correct start and end - if necessary
+    SequenceI ds = seq.getDatasetSequence();
+    if (ds == null)
+    {
+      // make a new dataset sequence
+      String ungapped = AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                                               new String(seq_string));
+      l_ungapped=ungapped.length();
+      // check that we haven't just duplicated an ungapped sequence.
+      if (l_ungapped == seq.getLength())
+      {
+        ds = seq;
+      }
+      else
+      {
+        ds = new Sequence(seq.getName(), ungapped,
+                          seq.getStart(),
+                          seq.getStart()+ungapped.length()-1);
+        // JBPNote: this would be consistent but may not be useful
+        //        seq.setDatasetSequence(ds);
+      }
+    }
+    // add in offset between seq and the dataset sequence
+    if (ds.getStart() < seq.getStart())
+    {
+      int offset=seq.getStart()-ds.getStart();
+      if (initialDeletion) {
+          // absolute cigar string
+          addDeleted(_s+offset);
+          start=0;
+          end+=offset;
+      } else {
+          // normal behaviour - just mark start and end subsequence
+          start+=offset;
+          end+=offset;
+
+      }
+
+    }
+
+    // any gaps to process ?
+    if (l_ungapped!=(_e-_s))
+      hasgaps=true;
+
+    this.refseq = ds;
+
+    // Check  offsets
+    if (end>ds.getLength()) {
+      throw new Error("SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
+//      end = ds.getLength();
+    }
+
+    return hasgaps;
+  }
+
+  /**
+   * directly initialise a cigar object with a sequence of range, operation pairs and a sequence to apply it to.
+   * operation and range should be relative to the seq.getStart()'th residue of the dataset seq resolved from seq.
+   * @param seq SequenceI
+   * @param operation char[]
+   * @param range int[]
+   */
+  public SeqCigar(SequenceI seq, char operation[], int range[])
+  {
+    super();
+    if (seq == null)
+    {
+      throw new Error("Implementation Bug. Null seq !");
+    }
+    if (operation.length != range.length)
+    {
+      throw new Error("Implementation Bug. Cigar Operation list!= range list");
+    }
+
+    if (operation != null)
+    {
+      this.operation = new char[operation.length + _inc_length];
+      this.range = new int[operation.length + _inc_length];
+
+      if (_setSeq(seq, false, 0, 0))
+      {
+        throw new Error("NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+      }
+      for (int i = this.length, j = 0; j < operation.length; i++, j++)
+      {
+        char op = operation[j];
+        if (op != M && op != I && op != D)
+        {
+          throw new Error(
+              "Implementation Bug. Cigar Operation '" + j + "' '" + op +
+              "' not one of '" + M + "', '" + I + "', or '" + D + "'.");
+        }
+        this.operation[i] = op;
+        this.range[i] = range[j];
+      }
+      this.length += operation.length;
+    }
+    else
+    {
+      this.operation = null;
+      this.range = null;
+      this.length = 0;
+      if (_setSeq(seq, false,0, 0))
+      {
+        throw new Error("NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+      }
+    }
+  }
+
+  /**
+   * add range matched residues to cigar string
+   * @param range int
+   */
+  public void addMatch(int range)
+  {
+    this.addOperation(M, range);
+  }
+  /**
+   * Adds
+   * insertion and match operations based on seq to the cigar up to
+   * the endpos column of seq.
+   *
+   * @param cigar CigarBase
+   * @param seq SequenceI
+   * @param startpos int
+   * @param endpos int
+   * @param initialDeletions if true then initial deletions will be added from start of seq to startpos
+   */
+  protected static void addSequenceOps(CigarBase cigar, SequenceI seq,
+                                       int startpos, int endpos, boolean initialDeletions)
+  {
+    char op = '\0';
+    int range = 0;
+    int p = 0, res = seq.getLength();
+
+    if (!initialDeletions)
+      p=startpos;
+
+
+    while (p <= endpos)
+    {
+      boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq.getCharAt(p)) : true;
+      if ( (startpos <= p) && (p <= endpos))
+      {
+        if (isGap)
+        {
+          if (range > 0 && op != I)
+          {
+            cigar.addOperation(op, range);
+            range = 0;
+          }
+          op = I;
+          range++;
+        }
+        else
+        {
+          if (range > 0 && op != M)
+          {
+            cigar.addOperation(op, range);
+            range = 0;
+          }
+          op = M;
+          range++;
+        }
+      }
+      else
+      {
+        if (!isGap)
+        {
+          if (range > 0 && op != D)
+          {
+            cigar.addOperation(op, range);
+            range = 0;
+          }
+          op = D;
+          range++;
+        }
+        else
+        {
+          // do nothing - insertions are not made in flanking regions
+        }
+      }
+      p++;
+    }
+    if (range > 0)
+    {
+      cigar.addOperation(op, range);
+    }
+  }
+
+  /**
+   * create a cigar string for given sequence
+   * @param seq SequenceI
+   */
+  public SeqCigar(SequenceI seq)
+  {
+    super();
+    if (seq == null)
+    {
+      throw new Error("Implementation error for new Cigar(SequenceI)");
+    }
+    _setSeq(seq, false, 0, 0);
+    // there is still work to do
+    addSequenceOps(this, seq, 0, seq.getLength()-1, false);
+  }
+
+  /**
+   * Create Cigar from a range of gaps and residues on a sequence object
+   * @param seq SequenceI
+   * @param start int - first column in range
+   * @param end int - last column in range
+   */
+  public SeqCigar(SequenceI seq, int start, int end)
+  {
+    super();
+    if (seq == null)
+    {
+      throw new Error("Implementation error for new Cigar(SequenceI)");
+    }
+    _setSeq(seq, false, start, end+1);
+    // there is still work to do
+    addSequenceOps(this, seq, start, end, false);
+  }
+
+  /**
+   * Create a cigar object from a cigar string like '[<I|D|M><range>]+'
+   * Will fail if the given seq already contains gaps (JBPNote: future implementation will fix)
+   * @param seq SequenceI object resolvable to a dataset sequence
+   * @param cigarString String
+   * @return Cigar
+   */
+  public static SeqCigar parseCigar(SequenceI seq, String cigarString)
+      throws Exception
+  {
+    Object[] opsandrange = parseCigarString(cigarString);
+    return new SeqCigar(seq, (char[]) opsandrange[0], (int[]) opsandrange[1]);
+  }
+
+  /**
+   * createAlignment
+   *
+   * @param alseqs SeqCigar[]
+   * @param gapCharacter char
+   * @return SequenceI[]
+   */
+  public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
+      char gapCharacter, ColumnSelection colsel, int[] segments)
+  {
+    SequenceI[] seqs = new SequenceI[alseqs.length];
+    StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
+    String[] alseqs_string=new String[alseqs.length];
+    Object[] gs_regions = new Object[alseqs.length];
+    for (int i = 0; i < alseqs.length; i++)
+    {
+      alseqs_string[i]=alseqs[i].getRefSeq().
+          getSequence().substring(alseqs[i].start,alseqs[i].end);
+      gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i], gapCharacter); // gapped sequence, {start, start col, end. endcol}, hidden regions {{start, end, col}})
+      if (gs_regions[i] == null)
+      {
+        throw new Error("Implementation error: " + i +
+                        "'th sequence Cigar has no operations.");
+      }
+      g_seqs[i] = new StringBuffer( (String) ( (Object[]) gs_regions[i])[0]); // the visible gapped sequence
+    }
+    // Now account for insertions. (well - deletions)
+    // this is complicated because we must keep track of shifted positions in each sequence
+    ShiftList shifts = new ShiftList();
+    for (int i = 0; i < alseqs.length; i++)
+    {
+      Object[] gs_region = ( (Object[]) ( (Object[]) gs_regions[i])[2]);
+      if (gs_region != null)
+
+      {
+        for (int hr = 0; hr < gs_region.length; hr++)
+        {
+          int[] region = (int[]) gs_region[hr];
+          char[] insert = new char[region[1] - region[0] + 1];
+          for (int s = 0; s < insert.length; s++)
+          {
+            insert[s] = gapCharacter;
+          }
+          int inspos = shifts.shift(region[2]); // resolve insertion position in current alignment frame of reference
+          for (int s = 0; s < alseqs.length; s++)
+          {
+            if (s != i)
+            {
+              if (g_seqs[s].length() <= inspos)
+              {
+                // prefix insertion with more gaps.
+                for (int l = inspos - g_seqs[s].length(); l > 0; l--)
+                {
+                  g_seqs[s].append(gapCharacter); // to debug - use a diffferent gap character here
+                }
+              }
+              g_seqs[s].insert(inspos, insert);
+            }
+            else
+            {
+              g_seqs[s].insert(inspos,
+                               alseqs_string[i].substring(region[0], region[1] + 1));
+            }
+          }
+          shifts.addShift(region[2], insert.length); // update shift in alignment frame of reference
+          if (segments==null)
+            // add a hidden column for this deletion
+            colsel.hideColumns(inspos, inspos+insert.length-1);
+        }
+      }
+    }
+    for (int i = 0; i < alseqs.length; i++)
+    {
+      int[] bounds = ( (int[]) ( (Object[]) gs_regions[i])[1]);
+      SequenceI ref = alseqs[i].getRefSeq();
+      seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
+                             ref.getStart() + alseqs[i].start+bounds[0],
+                             ref.getStart() + alseqs[i].start+(bounds[2]==0 ? -1 : bounds[2]));
+      seqs[i].setDatasetSequence(ref);
+    }
+    if (segments!=null) {
+      for (int i=0; i<segments.length; i+=3) {
+        //int start=shifts.shift(segments[i]-1)+1;
+        //int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
+        colsel.hideColumns(segments[i+1], segments[i+1]+segments[i+2]-1);
+      }
+    }
+    return seqs;
+  }
+
+  /**
+   * non rigorous testing
+   */
+  /**
+   *
+   * @param seq Sequence
+   * @param ex_cs_gapped String
+   * @return String
+   */
+  public static String testCigar_string(Sequence seq, String ex_cs_gapped)
+  {
+    SeqCigar c_sgapped = new SeqCigar(seq);
+    String cs_gapped = c_sgapped.getCigarstring();
+    if (!cs_gapped.equals(ex_cs_gapped))
+    {
+      System.err.println("Failed getCigarstring: incorect string '" + cs_gapped +
+                         "' != " + ex_cs_gapped);
+    }
+    return cs_gapped;
+  }
+
+  public static boolean testSeqRecovery(SeqCigar gen_sgapped,
+                                        SequenceI s_gapped)
+  {
+      // this is non-rigorous - start and end  recovery is not tested.
+    SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
+    if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
+    {
+      System.err.println("Couldn't reconstruct sequence.\n" +
+                         gen_sgapped_s.getSequence() + "\n" +
+                         s_gapped.getSequence());
+      return false;
+    }
+    return true;
+  }
+
+  public static void main(String argv[])
+      throws Exception
+  {
+    String o_seq;
+    Sequence s = new Sequence("MySeq",
+                              o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt",
+                              39, 80);
+    String orig_gapped;
+    Sequence s_gapped = new Sequence("MySeq",
+        orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
+                                     39, 80);
+    String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
+    s_gapped.setDatasetSequence(s);
+    String sub_gapped_s;
+    Sequence s_subsequence_gapped = new Sequence("MySeq",
+        sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
+                                                 43, 77);
+
+    s_subsequence_gapped.setDatasetSequence(s);
+    SeqCigar c_null = new SeqCigar(s);
+    String cs_null = c_null.getCigarstring();
+    if (!cs_null.equals("42M"))
+    {
+      System.err.println(
+          "Failed to recover ungapped sequence cigar operations:" +
+          ( (cs_null == "") ? "empty string" : cs_null));
+    }
+    testCigar_string(s_gapped, ex_cs_gapped);
+    SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
+    if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
+    {
+      System.err.println("Failed parseCigar(" + ex_cs_gapped +
+                         ")->getCigarString()->'" + gen_sgapped.getCigarstring() +
+                         "'");
+    }
+    testSeqRecovery(gen_sgapped, s_gapped);
+    // Test dataset resolution
+    SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
+    if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
+    {
+      System.err.println("Failed recovery for subsequence of dataset sequence");
+    }
+    // width functions
+    if (sub_gapped.getWidth() != sub_gapped_s.length())
+    {
+      System.err.println("Failed getWidth()");
+    }
+
+    sub_gapped.getFullWidth();
+    if (sub_gapped.hasDeletedRegions())
+    {
+      System.err.println("hasDeletedRegions is incorrect.");
+    }
+    // Test start-end region SeqCigar
+    SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
+    if (sub_se_gp.getWidth() != 41)
+    {
+      System.err.println(
+          "SeqCigar(seq, start, end) not properly clipped alignsequence.");
+    }
+    System.out.println("Original sequence align:\n" + sub_gapped_s +
+                       "\nReconstructed window from 8 to 48\n"
+                       + "XXXXXXXX" + sub_se_gp.getSequenceString('-') + "..."
+                       + "\nCigar String:" + sub_se_gp.getCigarstring() + "\n"
+        );
+    SequenceI ssgp = sub_se_gp.getSeq('-');
+    System.out.println("\t " + ssgp.getSequence());
+    for (int r = 0; r < 10; r++)
+    {
+      sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
+      int sl = sub_se_gp.getWidth();
+      int st = sl - 1 - r;
+      for (int rs = 0; rs < 10; rs++)
+      {
+        int e = st + rs;
+        sub_se_gp.deleteRange(st, e);
+        String ssgapedseq = sub_se_gp.getSeq('-').getSequence();
+        System.out.println(st + "," + e + "\t:" + ssgapedseq);
+        st -=3;
+      }
+    }
+    {
+      SeqCigar[] set = new SeqCigar[]
+          {
+          new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
+          new SeqCigar(s_gapped)};
+      Alignment al = new Alignment(set);
+      for (int i = 0; i < al.getHeight(); i++)
+      {
+        System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
+                           al.getSequenceAt(i).getStart() + "\t" +
+                           al.getSequenceAt(i).getEnd() + "\t" +
+                           al.getSequenceAt(i).getSequence());
+      }
+    }
+    {
+      System.out.println("Gapped.");
+      SeqCigar[] set = new SeqCigar[]
+          {
+          new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
+          new SeqCigar(s_gapped)};
+      set[0].deleteRange(20, 25);
+      Alignment al = new Alignment(set);
+      for (int i = 0; i < al.getHeight(); i++)
+      {
+        System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
+                           al.getSequenceAt(i).getStart() + "\t" +
+                           al.getSequenceAt(i).getEnd() + "\t" +
+                           al.getSequenceAt(i).getSequence());
+      }
+    }
+//    if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
+//      System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
+  }
+
+}
diff --git a/src/jalview/datamodel/UniprotProteinName.java b/src/jalview/datamodel/UniprotProteinName.java
new file mode 100755
index 0000000..6203a1f
--- /dev/null
+++ b/src/jalview/datamodel/UniprotProteinName.java
@@ -0,0 +1,38 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class UniprotProteinName
+{
+    /**
+   * internal content storage
+   */
+  private java.util.Vector names;
+
+  public void setName(java.util.Vector names)
+  {
+    this.names = names;
+  }
+
+  public java.util.Vector getName()
+  {
+    return names;
+  }
+
+}
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
new file mode 100755
index 0000000..d4975a6
--- /dev/null
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -0,0 +1,227 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
+package jalview.gui;
+
+import javax.swing.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+import jalview.io.*;
+import jalview.datamodel.AlignmentAnnotation;
+
+import java.awt.Color;
+import java.awt.FlowLayout;
+import javax.swing.BorderFactory;
+
+
+public class AnnotationExporter
+    extends JPanel
+{
+  JInternalFrame frame;
+  AlignmentPanel ap;
+  boolean features = true;
+  AlignmentAnnotation [] annotations;
+
+  public AnnotationExporter()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame,
+                             "",
+                             260, 125);
+  }
+
+  public void exportFeatures(AlignmentPanel ap)
+  {
+    this.ap = ap;
+    features = true;
+    frame.setTitle("Export Features");
+  }
+
+  public void exportAnnotations(AlignmentPanel ap,
+                                AlignmentAnnotation [] annotations)
+  {
+    this.ap = ap;
+    features = false;
+    GFFFormat.setVisible(false);
+    this.annotations = annotations;
+    frame.setTitle("Export Annotations");
+  }
+
+  public void toFile_actionPerformed(ActionEvent e)
+  {
+      JalviewFileChooser chooser = new JalviewFileChooser(
+      jalview.bin.Cache.getProperty( "LAST_DIRECTORY"));
+
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle(
+          features ? "Save Features to File" : "Save Annotation to File");
+      chooser.setToolTipText("Save");
+
+      int value = chooser.showSaveDialog(this);
+
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        String text = "No features found on alignment";
+        if (features)
+        {
+          if (GFFFormat.isSelected())
+            text = new FeaturesFile().printGFFFormat(
+                ap.av.alignment.getDataset().getSequencesArray(),
+                ap.av.featuresDisplayed);
+          else
+            text = new FeaturesFile().printJalviewFormat(
+                ap.av.alignment.getDataset().getSequencesArray(),
+                ap.av.featuresDisplayed);
+        }
+        else
+        {
+           text = new AnnotationFile().printAnnotations( annotations );
+        }
+
+        try
+        {
+          java.io.PrintWriter out = new java.io.PrintWriter(
+              new java.io.FileWriter(chooser.getSelectedFile()));
+
+          out.print(text);
+          out.close();
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+  }
+
+  public void toTextbox_actionPerformed(ActionEvent e)
+  {
+    String text = "No features found on alignment";
+    if(features)
+    {
+      if (GFFFormat.isSelected())
+        text = new FeaturesFile().printGFFFormat(
+            ap.av.alignment.getDataset().getSequencesArray(),
+            ap.av.featuresDisplayed);
+      else
+        text = new FeaturesFile().printJalviewFormat(
+            ap.av.alignment.getDataset().getSequencesArray(),
+                ap.av.featuresDisplayed);
+    }
+    else if(!features)
+    {
+      text = new AnnotationFile().printAnnotations( annotations );
+    }
+
+
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setText(text);
+    Desktop.addInternalFrame(cap,
+                             (features ?  "Features for - " : "Annotations for - ")
+                             + ap.alignFrame.getTitle(),
+                             600,
+                             500);
+
+
+  }
+
+  public void close_actionPerformed(ActionEvent e)
+  {
+    try{
+      frame.setClosed(true);
+    }catch(java.beans.PropertyVetoException ex)
+    {}
+  }
+
+
+
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(flowLayout1);
+    toFile.setText("to File");
+    toFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        toFile_actionPerformed(e);
+      }
+    });
+    toTextbox.setText("to Textbox");
+    toTextbox.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        toTextbox_actionPerformed(e);
+      }
+    });
+    close.setText("Close");
+    close.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        close_actionPerformed(e);
+      }
+    });
+    jalviewFormat.setOpaque(false);
+    jalviewFormat.setSelected(true);
+    jalviewFormat.setText("Jalview");
+    GFFFormat.setOpaque(false);
+    GFFFormat.setText("GFF");
+    jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
+    jLabel1.setText("Format: ");
+    this.setBackground(Color.white);
+    jPanel3.setBorder(BorderFactory.createEtchedBorder());
+    jPanel3.setOpaque(false);
+    jPanel1.setOpaque(false);
+    jPanel1.add(toFile);
+    jPanel1.add(toTextbox);
+    jPanel1.add(close);
+    jPanel3.add(jLabel1);
+    jPanel3.add(jalviewFormat);
+    jPanel3.add(GFFFormat);
+    buttonGroup.add(jalviewFormat);
+    buttonGroup.add(GFFFormat);
+    this.add(jPanel3, null);
+    this.add(jPanel1, null);
+  }
+
+  JPanel jPanel1 = new JPanel();
+  JButton toFile = new JButton();
+  JButton toTextbox = new JButton();
+  JButton close = new JButton();
+  ButtonGroup buttonGroup = new ButtonGroup();
+  JRadioButton jalviewFormat = new JRadioButton();
+  JRadioButton GFFFormat = new JRadioButton();
+  JLabel jLabel1 = new JLabel();
+  JPanel jPanel3 = new JPanel();
+  FlowLayout flowLayout1 = new FlowLayout();
+
+}
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
new file mode 100755
index 0000000..fc2b387
--- /dev/null
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -0,0 +1,810 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.jbgui.*;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.event.*;
+import jalview.util.TableSorter;
+import java.awt.event.*;
+import javax.swing.*;
+import java.util.*;
+
+
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import org.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.dasregistry.Das1Source;
+import java.awt.BorderLayout;
+
+public class DasSourceBrowser extends GDasSourceBrowser
+    implements Runnable, ListSelectionListener
+{
+  static DasSource[] dasSources = null;
+
+  Hashtable localSources = null;
+
+  Vector selectedSources;
+
+  String DEFAULT_REGISTRY = "http://das.sanger.ac.uk/registry/das1/sources/";
+
+  boolean loadingDasSources = false;
+
+
+  public DasSourceBrowser()
+  {
+    registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
+        DEFAULT_REGISTRY) );
+
+    setSelectedFromProperties();
+
+    displayFullDetails(null);
+    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+    filter1.addListSelectionListener(this);
+    filter2.addListSelectionListener(this);
+    filter3.addListSelectionListener(this);
+
+    //Ask to be notified of selection changes.
+    ListSelectionModel rowSM = table.getSelectionModel();
+    rowSM.addListSelectionListener(new ListSelectionListener()
+    {
+      public void valueChanged(ListSelectionEvent e)
+      {
+        ListSelectionModel lsm = (ListSelectionModel) e.getSource();
+        if (!lsm.isSelectionEmpty())
+        {
+          int selectedRow = lsm.getMinSelectionIndex();
+          displayFullDetails(table.getValueAt(selectedRow, 0).toString());
+        }
+      }
+    });
+
+    table.addMouseListener(new MouseAdapter()
+        {
+          public void mouseClicked(MouseEvent evt)
+          {
+            if(evt.getClickCount()==2
+               || SwingUtilities.isRightMouseButton(evt))
+              editRemoveLocalSource(evt);
+          }
+        });
+
+    if(dasSources!=null)
+    {
+       init();
+    }
+  }
+
+  public void paintComponent(java.awt.Graphics g)
+  {
+    if (dasSources == null && !loadingDasSources)
+    {
+      Thread worker = new Thread(this);
+      worker.start();
+    }
+  }
+
+  void init()
+  {
+    int dSize = dasSources.length;
+    Object[][] data = new Object[dSize][2];
+    for (int i = 0; i < dSize; i++)
+    {
+      data[i][0] = dasSources[i].getNickname();
+      data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
+          getNickname()));
+    }
+
+    refreshTableData(data);
+    setCapabilities(dasSources);
+
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            TableSorter sorter = (TableSorter)table.getModel();
+            sorter.setSortingStatus(1, TableSorter.DESCENDING);
+            sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
+          }
+        });
+
+    progressBar.setIndeterminate(false);
+    progressBar.setVisible(false);
+    addLocal.setVisible(true);
+    refresh.setVisible(true);
+  }
+
+
+  public void refreshTableData(Object[][] data)
+  {
+    TableSorter sorter = new TableSorter(new DASTableModel(data));
+    sorter.setTableHeader(table.getTableHeader());
+    table.setModel(sorter);
+  }
+
+  void displayFullDetails(String nickName)
+  {
+
+    StringBuffer text = new StringBuffer(
+        "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
+
+    if (nickName == null)
+    {
+      fullDetails.setText(text +
+                          "Select a DAS service from the table"
+                          + " to read a full description here.</font></html>");
+      return;
+    }
+
+    int dSize = dasSources.length;
+    for (int i = 0; i < dSize; i++)
+    {
+      if (!dasSources[i].getNickname().equals(nickName))
+        continue;
+
+      DasSource ds = dasSources[i];
+
+      text.append("<font color=\"#0000FF\">Id:</font> " + dasSources[i].getId() +
+                  "<br>");
+      text.append("<font color=\"#0000FF\">Nickname:</font> " +
+                  dasSources[i].getNickname() + "<br>");
+      text.append("<font color=\"#0000FF\">URL:</font> " + dasSources[i].getUrl() +
+                  "<br>");
+
+      text.append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
+                  +dasSources[i].getAdminemail()
+                  +"\">"+dasSources[i].getAdminemail()+"</a>" +
+                  "<br>");
+
+
+      text.append("<font color=\"#0000FF\">Registered at:</font> " + dasSources[i].getRegisterDate() +
+                        "<br>");
+
+      text.append("<font color=\"#0000FF\">Last successful test:</font> " + dasSources[i].getLeaseDate() +
+                        "<br>");
+
+      text.append("<font color=\"#0000FF\">Labels:</font> ");
+      for(int s=0; s<dasSources[i].getLabels().length; s++)
+      {
+        text.append( dasSources[i].getLabels()[s]);
+        if(s<dasSources[i].getLabels().length-1)
+          text.append(",");
+        text.append(" ");
+      }
+      text.append("<br>");
+
+
+
+      text.append("<font color=\"#0000FF\">Capabilities:</font> ");
+      String[] scap = dasSources[i].getCapabilities();
+      for (int j = 0; j < scap.length; j++)
+      {
+        text.append(scap[j]);
+        if (j < scap.length - 1)
+          text.append(", ");
+      }
+      text.append("<br>");
+
+      text.append("<font color=\"#0000FF\">Coordinates:</font> ");
+      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
+      for (int j = 0; j < dcs.length; j++)
+      {
+        text.append("(" + dcs[j].getUniqueId() + ") "
+                    + dcs[j].getCategory() + ", " + dcs[j].getName());
+        if (dcs[j].getNCBITaxId() != 0)
+          text.append(", " + dcs[j].getNCBITaxId());
+        if (dcs[j].getOrganismName().length() > 0)
+          text.append(", " + dcs[j].getOrganismName());
+
+        text.append("<br>");
+      }
+
+      text.append("<font color=\"#0000FF\">Description:</font> " +
+                  dasSources[i].getDescription() + "<br>");
+
+
+      if (dasSources[i].getHelperurl()!=null
+          && dasSources[i].getHelperurl().length() > 0)
+      {
+        text.append("<font color=\"#0000FF\"><a href=\"" +
+                    dasSources[i].getHelperurl()
+                    + "\">Go to site</a></font<br>");
+      }
+
+      text.append("</font></html>");
+
+      break;
+    }
+
+    fullDetails.setText(text.toString());
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        fullDetailsScrollpane.getVerticalScrollBar().setValue(0);
+      }
+    });
+  }
+
+
+  public void run()
+  {
+    loadingDasSources = true;
+
+    addLocal.setVisible(false);
+    refresh.setVisible(false);
+    progressBar.setVisible(true);
+    progressBar.setIndeterminate(true);
+
+    dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
+
+    appendLocalSources();
+
+    init();
+
+    loadingDasSources = false;
+
+  }
+
+  public Vector getSelectedSources()
+  {
+    Vector selected = new Vector();
+    for (int r = 0; r < selectedSources.size(); r++)
+    {
+        for (int i = 0; i < dasSources.length; i++)
+        {
+          if (dasSources[i].getNickname().equals(
+              selectedSources.elementAt(r)))
+          {
+            selected.addElement(dasSources[i]);
+            break;
+          }
+        }
+    }
+
+    return selected;
+  }
+
+  public DasSource[] getDASSource()
+  {
+    if(dasSources==null)
+    {
+     dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
+     appendLocalSources();
+    }
+
+    return dasSources;
+  }
+
+  public void refresh_actionPerformed(ActionEvent e)
+  {
+    saveProperties(jalview.bin.Cache.applicationProperties);
+
+    Thread worker = new Thread(this);
+    worker.start();
+  }
+
+  private void setCapabilities(DasSource[] sources)
+  {
+    Vector authority = new Vector();
+    Vector type = new Vector();
+    Vector label = new Vector();
+
+    authority.addElement("Any");
+    type.addElement("Any");
+    label.addElement("Any");
+
+    for (int i = 0; i < sources.length; i++)
+    {
+      DasSource ds = sources[i];
+
+      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
+
+      for (int j = 0; j < dcs.length; j++)
+      {
+        if (!type.contains(dcs[j].getCategory()))
+          type.addElement(dcs[j].getCategory());
+
+        if (!authority.contains(dcs[j].getName()))
+          authority.addElement(dcs[j].getName());
+      }
+
+      String[] slabels = ds.getLabels();
+      for (int s = 0; s < slabels.length; s++)
+      {
+        if (!label.contains(slabels[s]))
+        {
+          label.addElement(slabels[s]);
+        }
+      }
+
+    }
+
+    filter1.setListData(authority);
+    filter2.setListData(type);
+    filter3.setListData(label);
+
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        filter1.setSelectedIndex(0);
+        filter2.setSelectedIndex(0);
+        filter3.setSelectedIndex(0);
+      }
+    });
+  }
+
+  public void amendLocal(boolean newSource)
+  {
+    String url = "http://localhost:8080/", nickname = "";
+
+    if(!newSource)
+    {
+      int selectedRow = table.getSelectionModel().getMinSelectionIndex();
+      nickname = table.getValueAt(selectedRow, 0).toString();
+      url = ((DasSource)localSources.get(nickname)).getUrl();
+    }
+
+    JTextField nametf = new JTextField(nickname, 40);
+    JTextField urltf = new JTextField(url, 40);
+
+    JPanel panel = new JPanel(new BorderLayout());
+    JPanel pane12 = new JPanel(new BorderLayout());
+    pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER);
+    pane12.add(nametf, BorderLayout.EAST);
+    panel.add(pane12, BorderLayout.NORTH);
+    pane12 = new JPanel(new BorderLayout());
+    pane12.add(new JLabel("URL: "), BorderLayout.CENTER);
+    pane12.add(urltf, BorderLayout.EAST);
+    panel.add(pane12, BorderLayout.SOUTH);
+
+
+    int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+        panel, "Enter Nickname & URL of Local DAS Source",
+        JOptionPane.OK_CANCEL_OPTION);
+
+       if (reply != JOptionPane.OK_OPTION )
+       {
+           return;
+       }
+
+       if(!urltf.getText().endsWith("/"))
+         urltf.setText(urltf.getText()+"/");
+
+       Das1Source local = new Das1Source();
+
+       local.setUrl(urltf.getText());
+       local.setNickname(nametf.getText());
+
+
+       if(localSources==null)
+         localSources = new Hashtable();
+
+       localSources.put(local.getNickname(), local);
+
+       if(!newSource && !nickname.equals(nametf.getText()))
+       {
+         localSources.remove(nickname);
+       }
+
+       int size = dasSources.length;
+       int adjust = newSource ? 1 : 0;
+
+       Object[][] data = new Object[size+adjust][2];
+       for (int i = 0; i < size; i++)
+       {
+         if(!newSource && dasSources[i].getNickname().equals(nickname))
+         {
+           ((DasSource)dasSources[i]).setNickname(local.getNickname());
+           ((DasSource)dasSources[i]).setUrl(local.getUrl());
+           data[i][0] = local.getNickname();
+           data[i][1] = new Boolean(true);
+         }
+         else
+         {
+           data[i][0] = dasSources[i].getNickname();
+           data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
+               getNickname()));
+         }
+       }
+
+       if(newSource)
+       {
+         data[size][0] = local.getNickname();
+         data[size][1] = new Boolean(true);
+         selectedSources.add(local.getNickname());
+       }
+
+       DasSource [] tmp = new DasSource[size+adjust];
+
+       System.arraycopy(dasSources, 0, tmp, 0, size);
+
+       if(newSource)
+         tmp[size] = local;
+
+       dasSources = tmp;
+
+       refreshTableData(data);
+
+       SwingUtilities.invokeLater(new Runnable()
+       {
+         public void run()
+         {
+           scrollPane.getVerticalScrollBar().setValue(
+               scrollPane.getVerticalScrollBar().getMaximum()
+               );
+         }
+       });
+
+       displayFullDetails(local.getNickname());
+     }
+
+    public void editRemoveLocalSource(MouseEvent evt)
+    {
+      int selectedRow = table.getSelectionModel().getMinSelectionIndex();
+      if(selectedRow==-1)
+        return;
+
+      String nickname = table.getValueAt(selectedRow, 0).toString();
+
+      if (!localSources.containsKey(nickname))
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+        "You can only edit or remove local DAS Sources!",
+         "Public DAS source - not editable",
+         JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+
+
+      Object[] options = {"Edit", "Remove", "Cancel"};
+      int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+    "Do you want to edit or remove "+nickname+"?",
+    "Edit / Remove Local DAS Source",
+    JOptionPane.YES_NO_CANCEL_OPTION,
+    JOptionPane.QUESTION_MESSAGE,
+    null,
+    options,
+    options[2]);
+
+      switch(choice)
+      {
+        case 0: amendLocal(false);   break;
+        case 1:
+          localSources.remove(nickname);
+          selectedSources.remove(nickname);
+          Object[][] data = new Object[dasSources.length-1][2];
+          DasSource [] tmp = new DasSource[dasSources.length-1];
+          int index = 0;
+          for (int i = 0; i < dasSources.length; i++)
+          {
+            if (dasSources[i].getNickname().equals(nickname))
+            {
+              continue;
+            }
+            else
+            {
+              tmp[index] = dasSources[i];
+              data[index][0] = dasSources[i].getNickname();
+              data[index][1] = new Boolean(selectedSources.contains(dasSources[i].
+                  getNickname()));
+              index++;
+            }
+          }
+           dasSources = tmp;
+           refreshTableData(data);
+           SwingUtilities.invokeLater(new Runnable()
+           {
+             public void run()
+             {
+               scrollPane.getVerticalScrollBar().setValue(
+                   scrollPane.getVerticalScrollBar().getMaximum()
+                   );
+             }
+           });
+
+          break;
+      }
+    }
+
+    void appendLocalSources()
+    {
+      if(localSources==null)
+        return;
+
+      int size = dasSources!=null ? dasSources.length : 0;
+      int lsize = localSources.size();
+
+      Object[][] data = new Object[size+lsize][2];
+      for (int i = 0; i < size; i++)
+      {
+        data[i][0] = dasSources[i].getNickname();
+        data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
+            getNickname()));
+      }
+
+      DasSource [] tmp = new DasSource[size+lsize];
+      if(dasSources!=null)
+        System.arraycopy(dasSources, 0, tmp, 0, size);
+
+      Enumeration en = localSources.keys();
+      int index = size;
+      while(en.hasMoreElements())
+      {
+        String key = en.nextElement().toString();
+        data[index][0] = key;
+        data[index][1] = new Boolean(false);
+        tmp[index] = new Das1Source();
+        tmp[index].setNickname(key);
+        tmp[index].setUrl( ((DasSource)localSources.get(key)).getUrl() );
+
+        index++;
+      }
+
+      dasSources = tmp;
+
+      refreshTableData(data);
+  }
+
+  public void valueChanged(ListSelectionEvent evt)
+  {
+    //Called when the MainTable selection changes
+    if (evt.getValueIsAdjusting() )
+    {
+      return;
+    }
+
+
+    displayFullDetails(null);
+
+    // Filter the displayed data sources
+    int dSize = dasSources.length;
+
+
+    ArrayList names = new ArrayList();
+    ArrayList selected = new ArrayList();
+    DasSource ds;
+
+    //The features filter is not visible, but we must still
+    //filter the das source list here.
+    //July 2006 - only 6 sources fo not serve features
+    Object [] dummyFeatureList = new Object[]{"features"};
+
+    for (int i = 0; i < dSize; i++)
+    {
+      ds = dasSources[i];
+      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
+
+      if (dcs.length == 0 && ds.getCapabilities().length == 0
+          && filter1.getSelectedIndex() == 0
+          && filter2.getSelectedIndex() == 0
+          && filter3.getSelectedIndex() == 0)
+      {
+        //THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
+        //HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
+        //IS ADDED FROM THE REGISTRY
+        names.add(ds.getNickname());
+        selected.add(new Boolean(
+              selectedSources.contains(ds.getNickname())));
+        continue;
+      }
+
+
+      if (!selectedInList(dummyFeatureList, ds.getCapabilities())
+      ||  !selectedInList(filter3.getSelectedValues(),
+                          ds.getLabels()))
+      {
+        continue;
+      }
+
+      for (int j = 0; j < dcs.length; j++)
+      {
+        if (   selectedInList(filter1.getSelectedValues(),
+                           new String[]
+                           {dcs[j].getName()})
+            && selectedInList(filter2.getSelectedValues(),
+                              new String[]
+                              {dcs[j].getCategory()}))
+        {
+          names.add(ds.getNickname());
+          selected.add(new Boolean(
+              selectedSources.contains(ds.getNickname())));
+          break;
+        }
+      }
+    }
+
+    dSize = names.size();
+    Object[][] data = new Object[dSize][2];
+    for (int d = 0; d < dSize; d++)
+    {
+      data[d][0] = names.get(d);
+      data[d][1] = selected.get(d);
+    }
+
+    refreshTableData(data);
+  }
+
+  boolean selectedInList(Object [] selection, String[] items)
+  {
+    for (int i = 0; i < selection.length; i++)
+    {
+      if (selection[i].equals("Any") )
+        return true;
+
+      for (int j = 0; j < items.length; j++)
+      {
+        if (selection[i].equals(items[j]))
+          return true;
+      }
+    }
+
+    return false;
+  }
+
+  void setSelectedFromProperties()
+  {
+     String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
+     StringTokenizer st = new StringTokenizer(active, "\t");
+     selectedSources = new Vector();
+     while(st.hasMoreTokens())
+     {
+       selectedSources.addElement(st.nextToken());
+     }
+
+     String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
+     if(local!=null)
+     {
+       if(localSources == null)
+         localSources = new Hashtable();
+
+       st = new StringTokenizer(local, "\t");
+       while(st.hasMoreTokens())
+       {
+         String token = st.nextToken();
+         int bar = token.indexOf("|");
+         Das1Source source = new Das1Source();
+
+         source.setUrl(token.substring(bar + 1));
+         source.setNickname(token.substring(0, bar));
+
+         localSources.put(source.getNickname(), source);
+       }
+     }
+  }
+
+  public void reset_actionPerformed(ActionEvent e)
+  {
+    registryURL.setText(DEFAULT_REGISTRY);
+  }
+
+  public void saveProperties(Properties properties)
+  {
+    if (registryURL.getText() == null || registryURL.getText().length() < 1)
+      properties.remove("DAS_REGISTRY_URL");
+    else
+      properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());
+
+    StringBuffer sb = new StringBuffer();
+    for(int r=0; r<table.getModel().getRowCount(); r++)
+    {
+      if( ((Boolean)table.getValueAt(r,1)).booleanValue())
+      {
+        sb.append(table.getValueAt(r,0)+"\t");
+      }
+    }
+
+    properties.setProperty("DAS_ACTIVE_SOURCE", sb.toString() );
+
+    if(localSources!=null)
+    {
+      sb = new StringBuffer();
+      Enumeration en = localSources.keys();
+      while(en.hasMoreElements())
+      {
+        String token = en.nextElement().toString();
+        sb.append(token+"|"
+                  + ((DasSource)localSources.get(token)).getUrl()
+                  +"\t");
+      }
+
+      properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());
+    }
+
+  }
+
+  class DASTableModel
+      extends AbstractTableModel
+  {
+
+    public DASTableModel(Object[][] data)
+    {
+      this.data = data;
+    }
+
+    private String[] columnNames = new String[]  {"Nickname", "Use Source"};
+
+    private Object[][] data;
+
+    public int getColumnCount()
+    {
+      return columnNames.length;
+    }
+
+    public int getRowCount()
+    {
+      return data.length;
+    }
+
+    public String getColumnName(int col)
+    {
+      return columnNames[col];
+    }
+
+    public Object getValueAt(int row, int col)
+    {
+      return data[row][col];
+    }
+
+    /*
+     * JTable uses this method to determine the default renderer/
+     * editor for each cell.  If we didn't implement this method,
+     * then the last column would contain text ("true"/"false"),
+     * rather than a check box.
+     */
+    public Class getColumnClass(int c)
+    {
+      return getValueAt(0, c).getClass();
+    }
+
+    /*
+     * Don't need to implement this method unless your table's
+     * editable.
+     */
+    public boolean isCellEditable(int row, int col)
+    {
+      //Note that the data/cell address is constant,
+      //no matter where the cell appears onscreen.
+      return col == 1;
+
+    }
+
+    /*
+     * Don't need to implement this method unless your table's
+     * data can change.
+     */
+    public void setValueAt(Object value, int row, int col)
+    {
+      data[row][col] = value;
+      fireTableCellUpdated(row, col);
+
+      String name = getValueAt(row,0).toString();
+      boolean selected = ((Boolean)value).booleanValue();
+
+      if(selectedSources.contains(name) && !selected)
+        selectedSources.remove(name);
+
+      if(!selectedSources.contains(name) && selected)
+        selectedSources.add(name);
+    }
+  }
+}
+
+
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
new file mode 100755
index 0000000..8bce1e8
--- /dev/null
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -0,0 +1,485 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.schemes.*;
+
+import jalview.gui.*;
+
+import java.io.*;
+
+import java.net.*;
+
+import java.util.*;
+
+import java.util.jar.*;
+
+import javax.swing.*;
+
+import org.exolab.castor.xml.*;
+
+import jalview.binding.*;
+
+
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview2XML_V1
+{
+   jalview.schemes.UserColourScheme GetUserColourScheme(
+        JalviewModelSequence jms, String id)
+    {
+        UserColours[] uc = jms.getUserColours();
+        UserColours colours = null;
+
+        for (int i = 0; i < uc.length; i++)
+        {
+            if (uc[i].getId().equals(id))
+            {
+                colours = uc[i];
+
+                break;
+            }
+        }
+
+        int csize = colours.getUserColourScheme().getColourCount();
+        java.awt.Color[] newColours = new java.awt.Color[csize];
+
+        for (int i = 0; i < csize; i++)
+        {
+            newColours[i] = new java.awt.Color(Integer.parseInt(
+                        colours.getUserColourScheme().getColour(i).getRGB(), 16));
+        }
+
+        return new jalview.schemes.UserColourScheme(newColours);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     */
+    public AlignFrame LoadJalviewAlign(String file)
+    {
+
+        jalview.gui.AlignFrame af = null;
+
+        try
+        {
+            //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+            URL url = null;
+
+            if (file.startsWith("http://"))
+            {
+                url = new URL(file);
+            }
+
+            JarInputStream jin = null;
+            JarEntry jarentry = null;
+            int entryCount = 1;
+
+            do
+            {
+                if (url != null)
+                {
+                    jin = new JarInputStream(url.openStream());
+                }
+                else
+                {
+                    jin = new JarInputStream(new FileInputStream(file));
+                }
+
+                for (int i = 0; i < entryCount; i++)
+                {
+                    jarentry = jin.getNextJarEntry();
+                  }
+
+                  class NoDescIDResolver implements IDResolver
+                  {
+                    public Object resolve(String idref)
+                    {
+                      System.out.println(idref+" used");
+                      return null;
+                    }
+                  }
+
+
+                if (jarentry != null)
+                {
+                    InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+                    JalviewModel object = new JalviewModel();
+
+                    object = (JalviewModel) object.unmarshal(in);
+
+                    af = LoadFromObject(object);
+                    entryCount++;
+                }
+            }
+            while (jarentry != null);
+        }
+        catch(java.net.UnknownHostException ex)
+        {
+          ex.printStackTrace();
+          System.err.println("Couldn't locate Jalview XML file : " +
+              ex + "\n");
+           JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                    "Couldn't locate " + file,
+                                    "URL not found",
+                                    JOptionPane.WARNING_MESSAGE);
+
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+            System.err.println("Exception whilst loading jalview XML file : " +
+                ex + "\n");
+             JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                      "Error loading  " + file,
+                                      "Error loading Jalview file",
+                                      JOptionPane.WARNING_MESSAGE);
+
+        }
+
+        return af;
+    }
+
+    AlignFrame LoadFromObject(JalviewModel object)
+    {
+        Vector seqids = new Vector();
+        SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+        Sequence[] vamsasSeq = vamsasSet.getSequence();
+
+        JalviewModelSequence jms = object.getJalviewModelSequence();
+
+        //////////////////////////////////
+        //LOAD SEQUENCES
+        jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
+        JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+        for (int i = 0; i < vamsasSeq.length; i++)
+        {
+            jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
+                    vamsasSeq[i].getSequence());
+            jseqs[i].setStart(JSEQ[i].getStart());
+            jseqs[i].setEnd(JSEQ[i].getEnd());
+            jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
+            seqids.add(jseqs[i]);
+        }
+
+        ///SequenceFeatures are added to the DatasetSequence,
+        // so we must create the dataset before loading features
+        /////////////////////////////////
+        jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
+        al.setDataset(null);
+        /////////////////////////////////
+
+        for (int i = 0; i < vamsasSeq.length; i++)
+        {
+          if (JSEQ[i].getFeaturesCount() > 0)
+          {
+            Features[] features = JSEQ[i].getFeatures();
+            for (int f = 0; f < features.length; f++)
+            {
+              jalview.datamodel.SequenceFeature sf
+                  = new jalview.datamodel.SequenceFeature(features[f].getType(),
+                  features[f].getDescription(), features[f].getStatus(),
+                  features[f].getBegin(), features[f].getEnd(),
+                  null);
+
+              al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+            }
+          }
+          if (JSEQ[i].getPdbidsCount() > 0)
+          {
+            Pdbids[] ids = JSEQ[i].getPdbids();
+            for (int p = 0; p < ids.length; p++)
+            {
+              jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
+              entry.setId(ids[p].getId());
+              entry.setType(ids[p].getType());
+              al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+            }
+
+          }
+        }
+
+         /////////////////////////////////
+        //////////////////////////////////
+        //LOAD ANNOTATIONS
+        if (vamsasSet.getAnnotation() != null)
+        {
+            Annotation[] an = vamsasSet.getAnnotation();
+
+            for (int i = 0; i < an.length; i++)
+            {
+                AnnotationElement[] ae = an[i].getAnnotationElement();
+                jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
+
+                for (int aa = 0; aa < ae.length; aa++)
+                {
+                    anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
+                            ae[aa].getDescription(),
+                            ae[aa].getSecondaryStructure().charAt(0),
+                            ae[aa].getValue());
+                }
+
+                jalview.datamodel.AlignmentAnnotation jaa = null;
+
+                if (an[i].getGraph())
+                {
+                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+                            an[i].getDescription(), anot, 0, 0,
+                            jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
+                }
+                else
+                {
+                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+                            an[i].getDescription(), anot);
+                }
+
+                al.addAnnotation(jaa);
+            }
+        }
+
+
+        /////////////////////////////////
+        // LOAD VIEWPORT
+        Viewport[] views = jms.getViewport();
+        Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+
+        AlignFrame af = new AlignFrame(al);
+
+
+        //  af.changeColour() );
+        /////////////////////////
+        //LOAD GROUPS
+        if (jms.getJGroupCount() > 0)
+        {
+            JGroup[] groups = jms.getJGroup();
+
+            for (int i = 0; i < groups.length; i++)
+            {
+                ColourSchemeI cs = null;
+
+                if (groups[i].getColour() != null)
+                {
+                    if (groups[i].getColour().startsWith("ucs"))
+                    {
+                        cs = GetUserColourScheme(jms, groups[i].getColour());
+                    }
+                    else
+                    {
+                        cs = ColourSchemeProperty.getColour(al,
+                                groups[i].getColour());
+                    }
+
+                    if(cs!=null)
+                      cs.setThreshold(groups[i].getPidThreshold(), true);
+
+                }
+
+                Vector seqs = new Vector();
+                int[] ids = groups[i].getSeq();
+
+                for (int s = 0; s < ids.length; s++)
+                {
+                    seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
+                            ids[s]));
+                }
+
+                jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
+                        groups[i].getName(), cs, groups[i].getDisplayBoxes(),
+                        groups[i].getDisplayText(), groups[i].getColourText(),
+                        groups[i].getStart(), groups[i].getEnd());
+
+                sg.setOutlineColour(new java.awt.Color(
+                        groups[i].getOutlineColour()));
+
+                if (groups[i].getConsThreshold() != 0)
+                {
+                    jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
+                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,
+                            sg.getWidth() - 1);
+                    c.calculate();
+                    c.verdict(false, 25);
+                    sg.cs.setConservation(c);
+                }
+
+                al.addGroup(sg);
+            }
+        }
+
+
+
+        af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+            view.getHeight());
+        af.viewport.setStartRes(view.getStartRes());
+        af.viewport.setStartSeq(view.getStartSeq());
+        af.viewport.setShowAnnotation(view.getShowAnnotation());
+        af.viewport.showConservation = view.getShowConservation();
+        af.viewport.showQuality = view.getShowQuality();
+        af.viewport.showIdentity = view.getShowIdentity();
+        af.viewport.setAbovePIDThreshold(view.getPidSelected());
+        af.abovePIDThreshold.setSelected(view.getPidSelected());
+        af.viewport.setColourText(view.getShowColourText());
+        af.colourTextMenuItem.setSelected(view.getShowColourText());
+        af.viewport.setConservationSelected(view.getConservationSelected());
+        af.conservationMenuItem.setSelected(view.getConservationSelected());
+
+        af.viewport.setShowJVSuffix(view.getShowFullId());
+        af.seqLimits.setSelected(view.getShowFullId());
+
+        af.viewport.setFont(new java.awt.Font(view.getFontName(),
+                view.getFontStyle(), view.getFontSize()));
+        af.alignPanel.fontChanged();
+
+        af.viewport.setRenderGaps(view.getRenderGaps());
+        af.renderGapsMenuItem.setSelected(view.getRenderGaps());
+
+        af.viewport.setWrapAlignment(view.getWrapAlignment());
+        af.wrapMenuItem.setSelected(view.getWrapAlignment());
+
+
+        af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+
+        af.annotationPanelMenuItem.setState(view.getShowAnnotation());
+        af.viewport.setShowAnnotation(view.getShowAnnotation());
+        af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+
+
+        af.viewport.setShowBoxes(view.getShowBoxes());
+        af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
+        af.viewport.setShowText(view.getShowText());
+        af.viewTextMenuItem.setSelected(view.getShowText());
+
+        ColourSchemeI cs = null;
+
+        if (view.getBgColour() != null)
+        {
+            if (view.getBgColour().startsWith("ucs"))
+            {
+                cs = GetUserColourScheme(jms, view.getBgColour());
+            }
+            else
+            {
+                cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+            }
+
+            if(cs!=null)
+            {
+              cs.setThreshold(view.getPidThreshold(), true);
+              cs.setConsensus(af.viewport.vconsensus);
+            }
+        }
+
+        af.setColourSelected(view.getBgColour());
+        af.viewport.setGlobalColourScheme(cs);
+        af.viewport.setColourAppliesToAllGroups(false);
+        af.changeColour(cs);
+        if (view.getConservationSelected() && cs!=null)
+        {
+          cs.setConservationInc(view.getConsThreshold());
+        }
+
+        af.viewport.setColourAppliesToAllGroups(true);
+
+        if (view.getShowSequenceFeatures())
+        {
+           af.viewport.showSequenceFeatures = true;
+           af.showSeqFeatures.setSelected(true);
+        }
+
+        if(jms.getFeatureSettings()!=null)
+        {
+          af.viewport.featuresDisplayed = new Hashtable();
+          String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
+         for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
+         {
+           Setting setting = jms.getFeatureSettings().getSetting(fs);
+
+           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
+               new java.awt.Color(setting.getColour()));
+
+           renderOrder[fs] = setting.getType();
+
+           if(setting.getDisplay())
+             af.viewport.featuresDisplayed.put(
+                 setting.getType(), new Integer(setting.getColour()));
+         }
+         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+        }
+
+
+        Desktop.addInternalFrame(af, view.getTitle(),
+             view.getWidth(), view.getHeight());
+
+        //LOAD TREES
+        ///////////////////////////////////////
+        if (jms.getTreeCount() > 0)
+        {
+            try
+            {
+                for (int t = 0; t < jms.getTreeCount(); t++)
+                {
+
+                    Tree tree = jms.getTree(t);
+
+                    TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
+                                tree.getNewick()), tree.getTitle(),
+                                tree.getWidth(), tree.getHeight(),
+                                tree.getXpos(), tree.getYpos());
+
+                    tp.fitToWindow.setState(tree.getFitToWindow());
+                    tp.fitToWindow_actionPerformed(null);
+
+                    if(tree.getFontName()!=null)
+                      tp.setTreeFont(new java.awt.Font(tree.getFontName(),
+                                          tree.getFontStyle(),
+                                          tree.getFontSize()));
+                    else
+                      tp.setTreeFont(new java.awt.Font(view.getFontName(),
+                                            view.getFontStyle(),
+                                            tree.getFontSize()));
+
+                    tp.showPlaceholders(tree.getMarkUnlinked());
+                    tp.showBootstrap(tree.getShowBootstrap());
+                    tp.showDistances(tree.getShowDistances());
+
+                    tp.treeCanvas.threshold = tree.getThreshold();
+
+                    if (tree.getCurrentTree())
+                      af.viewport.setCurrentTree(tp.getTree());
+                }
+
+            }
+            catch (Exception ex)
+            {
+                ex.printStackTrace();
+            }
+
+        }
+
+        return af;
+    }
+}
+
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
new file mode 100755
index 0000000..08b5862
--- /dev/null
+++ b/src/jalview/io/AnnotationFile.java
@@ -0,0 +1,423 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
+package jalview.io;
+
+import java.io.*;
+import jalview.datamodel.*;
+import java.util.*;
+import jalview.schemes.UserColourScheme;
+import java.net.URL;
+
+
+public class AnnotationFile
+{
+
+  public String printAnnotations(AlignmentAnnotation [] annotations)
+  {
+    StringBuffer text = new StringBuffer(
+      "JALVIEW_ANNOTATION\n"
+      +"# Created: "
+      +new java.util.Date()+"\n\n");
+
+    AlignmentAnnotation row;
+    String comma;
+    String seqref = null;
+
+    StringBuffer colours = new StringBuffer();
+    StringBuffer graphLine = new StringBuffer();
+
+    Hashtable graphGroup = new Hashtable();
+
+    java.awt.Color color;
+
+    for(int i=0; i<annotations.length; i++)
+    {
+      row = annotations[i];
+      color = null;
+
+      if( row.sequenceRef == null)
+        seqref = null;
+
+      else if (seqref == null
+           || !seqref.equals(row.sequenceRef.getName()))
+      {
+        seqref = row.sequenceRef.getName();
+        text.append("\nSEQUENCE_REF\t" + seqref + "\n");
+      }
+
+
+      if( row.graph == AlignmentAnnotation.NO_GRAPH)
+      {
+          text.append("NO_GRAPH\t");
+      }
+      else
+      {
+        if( row.graph == AlignmentAnnotation.BAR_GRAPH)
+          text.append("BAR_GRAPH\t");
+        else if(row.graph == AlignmentAnnotation.LINE_GRAPH)
+          text.append("LINE_GRAPH\t");
+
+        if(row.getThreshold()!=null)
+            graphLine.append("GRAPHLINE\t"
+                             + row.label + "\t"
+                             + row.getThreshold().value + "\t"
+                             + row.getThreshold().label + "\t"
+                             + jalview.util.Format.getHexString(
+                                 row.getThreshold().colour)+"\n"
+                );
+
+          if(row.graphGroup>-1)
+          {
+            String key = String.valueOf(row.graphGroup);
+            if(graphGroup.containsKey(key))
+              graphGroup.put(key, graphGroup.get(key)
+                             +"\t"+row.label);
+            else
+              graphGroup.put(key, row.label);
+          }
+      }
+
+      text.append(row.label+"\t");
+
+      for(int j=0; j<row.annotations.length; j++)
+      {
+        if(row.annotations[j]!=null)
+        {
+          comma = "";
+          if (row.annotations[j].displayCharacter.length() > 0
+              && !row.annotations[j].displayCharacter.equals(" "))
+          {
+            text.append(row.annotations[j].displayCharacter);
+            comma = ",";
+          }
+          if (row.annotations[j].secondaryStructure!=' ')
+          {
+            text.append(comma + row.annotations[j].secondaryStructure);
+            comma = ",";
+          }
+          if (row.annotations[j].value!=0f)
+          {
+            color = row.annotations[j].colour;
+            text.append(comma + row.annotations[j].value);
+          }
+        }
+        text.append("|");
+      }
+
+      text.append("\n");
+
+      if(color!=null && color!=java.awt.Color.black)
+      {
+        colours.append("COLOUR\t"
+                       +row.label+"\t"
+                       +jalview.util.Format.getHexString(color)+"\n");
+      }
+
+    }
+
+    text.append("\n");
+
+    text.append(colours.toString());
+    text.append(graphLine.toString());
+    if(graphGroup.size()>0)
+    {
+      text.append("COMBINE\t");
+      Enumeration en = graphGroup.elements();
+      while(en.hasMoreElements())
+      {
+        text.append(en.nextElement()+"\n");
+      }
+    }
+
+    return text.toString();
+  }
+
+  public boolean readAnnotationFile(AlignmentI al, String file)
+  {
+    try
+    {
+      BufferedReader in = null;
+      java.io.InputStream is = getClass().getResourceAsStream("/" + file);
+      if (is != null)
+      {
+        in = new BufferedReader(new java.io.InputStreamReader(is));
+      }
+      else
+      {
+        try
+        {
+          URL url = new URL(file);
+          in = new BufferedReader(new InputStreamReader(url.openStream()));
+        }
+        catch (java.net.MalformedURLException ex)
+        {
+          in = new BufferedReader(new FileReader(file));
+        }
+      }
+
+      String line, label, description, token;
+      int graphStyle, index;
+      SequenceI refSeq = null;
+      int refSeqIndex = 1;
+      int existingAnnotations = 0;
+      if(al.getAlignmentAnnotation()!=null)
+       existingAnnotations = al.getAlignmentAnnotation().length;
+
+      int alWidth = al.getWidth();
+
+      StringTokenizer st;
+      Annotation[] annotations;
+      AlignmentAnnotation annotation = null;
+
+      // First confirm this is an Annotation file
+      boolean jvAnnotationFile = false;
+      while ( (line = in.readLine()) != null)
+      {
+        if (line.indexOf("#") == 0 )
+          continue;
+
+        if (line.indexOf("JALVIEW_ANNOTATION") > -1)
+        {
+          jvAnnotationFile = true;
+          break;
+        }
+      }
+
+      if(!jvAnnotationFile)
+      {
+        in.close();
+        return false;
+      }
+
+      while ( (line = in.readLine()) != null)
+      {
+        if(line.indexOf("#")==0
+           || line.indexOf("JALVIEW_ANNOTATION")>-1
+           || line.length()==0)
+          continue;
+
+        st = new StringTokenizer(line, "\t");
+        token = st.nextToken();
+        if(token.equalsIgnoreCase("COLOUR"))
+        {
+          colourAnnotations(al, st.nextToken(), st.nextToken());
+          continue;
+        }
+
+        if(token.equalsIgnoreCase("COMBINE") )
+        {
+          combineAnnotations(al, st);
+          continue;
+        }
+
+        if (token.equalsIgnoreCase("GRAPHLINE"))
+        {
+          addLine(al, st);
+          continue;
+        }
+
+
+        if(token.equalsIgnoreCase("SEQUENCE_REF") )
+        {
+          refSeq = al.findName(st.nextToken());
+          try{
+            refSeqIndex = Integer.parseInt(st.nextToken());
+          }
+          catch(Exception ex)
+          {
+            refSeqIndex = 1;
+          }
+
+          continue;
+        }
+
+
+        graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
+        label = description = st.nextToken();
+
+        line = st.nextToken();
+
+        st = new StringTokenizer(line, "|", true);
+        annotations = new Annotation[alWidth];
+
+        index = 0;
+        boolean emptyColumn = true;
+
+
+        while (st.hasMoreElements() && index<alWidth)
+        {
+          token = st.nextToken().trim();
+          if(token.equals("|"))
+          {
+            if(emptyColumn)
+              index++;
+
+            emptyColumn = true;
+          }
+          else
+          {
+            annotations[index++] = parseAnnotation(token);
+            emptyColumn = false;
+          }
+        }
+
+       annotation = new AlignmentAnnotation(label,
+                                          description,
+                                          annotations,
+                                          0,
+                                          0,
+                                          graphStyle);
+
+       if(refSeq!=null)
+       {
+         annotation.createSequenceMapping(refSeq, refSeqIndex, false);
+         refSeq.addAlignmentAnnotation(annotation);
+       }
+
+       al.addAnnotation(annotation);
+
+       al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);
+      }
+
+    }catch(Exception ex)
+    {
+      ex.printStackTrace();
+      System.out.println("Problem reading annotation file: "+ex);
+      return false;
+    }
+    return true;
+  }
+
+  Annotation parseAnnotation(String string)
+  {
+    String desc = "", displayChar="";
+    char ss = ' '; // secondaryStructure
+    float value = 0;
+    boolean parsedValue = false;
+    StringTokenizer st = new StringTokenizer(string, ",");
+    String token;
+    while(st.hasMoreTokens())
+    {
+      token = st.nextToken().trim();
+      if(token.length()==0)
+        continue;
+
+      if(!parsedValue)
+      {
+        try{
+          displayChar = token;
+          value = new Float(token).floatValue();
+          parsedValue = true;
+        }catch(NumberFormatException ex){}
+      }
+
+      if(token.equals("H") || token.equals("E"))
+      {
+        // Either this character represents a helix or sheet
+        // or an integer which can be displayed
+        ss = token.charAt(0);
+        if(displayChar.equals(token.substring(0,1)))
+          displayChar = "";
+      }
+      else if(desc.length()<1)
+        desc = token;
+
+    }
+
+    return new Annotation(displayChar, desc, ss, value);
+  }
+
+  void colourAnnotations(AlignmentI al, String label, String colour)
+  {
+    UserColourScheme ucs = new UserColourScheme(colour);
+    Annotation[] annotations;
+    for(int i=0; i<al.getAlignmentAnnotation().length; i++)
+    {
+      if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
+      {
+        annotations = al.getAlignmentAnnotation()[i].annotations;
+        for(int j=0; j<annotations.length; j++)
+        {
+          if(annotations[j]!=null)
+            annotations[j].colour = ucs.findColour("A");
+        }
+      }
+    }
+  }
+
+  void combineAnnotations(AlignmentI al, StringTokenizer st)
+  {
+    int graphGroup = -1;
+    String group = st.nextToken();
+    //First make sure we are not overwriting the graphIndex
+    for(int i=0; i<al.getAlignmentAnnotation().length; i++)
+    {
+      if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+      {
+        graphGroup = al.getAlignmentAnnotation()[i].graphGroup +1;
+        al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
+        break;
+      }
+    }
+
+    //Now update groups
+    while(st.hasMoreTokens())
+    {
+      group = st.nextToken();
+      for(int i=0; i<al.getAlignmentAnnotation().length; i++)
+      {
+        if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+        {
+          al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
+          break;
+        }
+      }
+    }
+  }
+
+  void addLine(AlignmentI al, StringTokenizer st)
+  {
+    String group = st.nextToken();
+    AlignmentAnnotation annotation = null;
+
+    for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+    {
+      if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+      {
+        annotation = al.getAlignmentAnnotation()[i];
+        break;
+      }
+    }
+
+    if(annotation==null)
+      return;
+    float value = new Float(st.nextToken()).floatValue();
+    String label = st.hasMoreTokens() ?  st.nextToken() : null;
+    java.awt.Color colour = null;
+    if(st.hasMoreTokens())
+    {
+      UserColourScheme ucs = new UserColourScheme(st.nextToken());
+      colour = ucs.findColour("A");
+    }
+
+    annotation.setThreshold(new GraphLine(value, label, colour));
+
+  }
+}
diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
new file mode 100644
index 0000000..805e78d
--- /dev/null
+++ b/src/jalview/io/DBRefFetcher.java
@@ -0,0 +1,362 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+package jalview.io;
+
+import jalview.datamodel.*;
+
+import jalview.gui.*;
+
+import java.io.*;
+
+import java.util.*;
+
+import org.exolab.castor.mapping.Mapping;
+
+import org.exolab.castor.xml.*;
+import jalview.analysis.AlignSeq;
+
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class DBRefFetcher implements Runnable
+{
+  AlignmentI align;
+  AlignmentI dataset;
+  AlignFrame af;
+  ArrayList unknownSequences;
+  CutAndPasteTransfer output = new CutAndPasteTransfer();
+  StringBuffer sbuffer = new StringBuffer();
+  boolean uniprotFlag = false;
+  boolean running = false;
+
+  public DBRefFetcher()
+  {}
+
+  public Vector getUniprotEntries(File file)
+  {
+    UniprotFile uni = new UniprotFile();
+    try
+    {
+      // 1. Load the mapping information from the file
+      Mapping map = new Mapping(uni.getClass().getClassLoader());
+      java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
+      map.loadMapping(url);
+
+      // 2. Unmarshal the data
+      Unmarshaller unmar = new Unmarshaller(uni);
+      unmar.setIgnoreExtraElements(true);
+      unmar.setMapping(map);
+   //   unmar.setDebug(true);
+
+      uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
+    }
+    catch (Exception e)
+    {
+      System.out.println("Error getUniprotEntries() "+e);
+    }
+
+
+    return uni.getUniprotEntries();
+  }
+
+  /**
+   * Creates a new SequenceFeatureFetcher object.
+   *
+   * @param align DOCUMENT ME!
+   * @param ap DOCUMENT ME!
+   */
+  public DBRefFetcher(AlignmentI align, AlignFrame af)
+  {
+    this.af = af;
+    unknownSequences = new ArrayList();
+    this.align = align;
+    this.dataset = align.getDataset();
+  }
+
+  public boolean fetchDBRefs(boolean waitTillFinished)
+  {
+    Thread thread = new Thread(this);
+    thread.start();
+    running = true;
+
+    if(waitTillFinished)
+    {
+      while(running)
+      {
+        try{
+          Thread.sleep(500);
+        }catch(Exception ex){}
+      }
+    }
+
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    long startTime = System.currentTimeMillis();
+    af.setProgressBar("Fetching db refs", startTime);
+    running = true;
+
+    try
+    {
+      int seqIndex = 0;
+      Vector sequences = dataset.getSequences();
+
+      while (seqIndex < sequences.size())
+      {
+        Vector ids = new Vector();
+
+        for (int i = 0; (seqIndex < sequences.size()) && (i < 50);
+             seqIndex++, i++)
+        {
+          Sequence sequence = (Sequence) sequences.get(seqIndex);
+          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {
+              jalview.datamodel.DBRefSource.UNIPROT});
+          if (uprefs!=null)
+          {
+            // we know the id for this entry, so don't note its ID in the unknownSequences list
+            for (int j=0,k=uprefs.length; j<k; j++)
+              ids.add(uprefs[j].getAccessionId());
+            unknownSequences.add(sequence);
+          } else {
+            if (!ids.contains(sequence.getName()))
+            {
+              ids.add(sequence.getName());
+              unknownSequences.add(sequence);
+            }
+          }
+        }
+
+        ///////////////////////////////////
+        ///READ FROM EBI
+        if (ids.size() > 0)
+        {
+          StringBuffer remainingIds = new StringBuffer("uniprot:");
+          for (int i = 0; i < ids.size(); i++)
+           {
+             if(ids.get(i).toString().indexOf("|")>-1)
+             {
+               remainingIds.append(ids.get(i).toString().substring(
+                   ids.get(i).toString().lastIndexOf("|") + 1));
+               uniprotFlag = true;
+             }
+             else
+               remainingIds.append(ids.get(i));
+
+             remainingIds.append(";");
+           }
+
+          EBIFetchClient ebi = new EBIFetchClient();
+          File file = ebi.fetchDataAsFile(remainingIds.toString(),
+                                          "xml", "raw");
+
+
+
+          if (file != null)
+          {
+            ReadUniprotFile(file, ids);
+          }
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    if (sbuffer.length() > 0)
+    {
+      output.setText(
+          "Your sequences have been matched to Uniprot. Some of the ids have been\n" +
+          "altered, most likely the start/end residue will have been updated.\n" +
+          "Save your alignment to maintain the updated id.\n\n" +
+          sbuffer.toString());
+      Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
+      // The above is the dataset, we must now find out the index
+      // of the viewed sequence
+
+    }
+
+    af.setProgressBar("DBRef search completed", startTime);
+   // promptBeforeBlast();
+
+   running = false;
+
+  }
+
+
+  void promptBeforeBlast()
+   {
+     // This must be outside the run() body as java 1.5
+     // will not return any value from the OptionPane to the expired thread.
+      if (unknownSequences.size() > 0)
+      {
+       // int reply = javax.swing.JOptionPane.showConfirmDialog(
+       //     Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences."
+        //        +"\nPerform blast for unknown sequences?",
+        //            "Blast for Unidentified Sequences",
+        //             javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);
+     javax.swing.JOptionPane.showMessageDialog(
+    Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences.",
+            "Unidentified Sequences",
+             javax.swing.JOptionPane.WARNING_MESSAGE);
+
+
+      //  if(reply == javax.swing.JOptionPane.YES_OPTION)
+     //    new WSWUBlastClient(ap, align, unknownSequences);
+      }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param result DOCUMENT ME!
+   * @param out DOCUMENT ME!
+   * @param align DOCUMENT ME!
+   */
+  void ReadUniprotFile(File file, Vector ids)
+  {
+    if(!file.exists())
+      return;
+
+    SequenceI [] sequence = null;
+
+    Vector entries = getUniprotEntries(file);
+
+    int i, iSize = entries==null?0:entries.size();
+    UniprotEntry entry;
+    for (i = 0; i < iSize; i++)
+    {
+      entry = (UniprotEntry) entries.elementAt(i);
+      String idmatch = entry.getAccession().elementAt(0).toString();
+      sequence = dataset.findSequenceMatch(idmatch);
+
+      if (sequence.length==0)
+      {
+        //Sequence maybe Name, not Accession
+        idmatch = entry.getName().elementAt(0).toString();
+        sequence = dataset.findSequenceMatch(idmatch);
+      }
+
+      if(sequence.length>0)
+        ids.remove(sequence[0].getName());
+
+      else  if (sequence.length==0 && uniprotFlag)
+      {
+          StringBuffer upid = new StringBuffer("UniProt/Swiss-Prot|");
+          for(int u=0; u<entry.getAccession().size(); u++)
+            upid.append(entry.getAccession().elementAt(u)+"|");
+
+          sequence = dataset.findSequenceMatch(upid+idmatch);
+          ids.remove(idmatch);
+      }
+
+      if(sequence.length==0)
+      {
+        System.out.println(idmatch+" not found");
+        continue;
+      }
+
+      for(int m=0; m<sequence.length; m++)
+      {
+
+      sequence[m].addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
+                                       "0",
+                                       entry.getAccession().elementAt(0).toString()));
+
+      System.out.println("Adding dbref to "+sequence[m].getName()+" : "+
+                         entry.getAccession().elementAt(0).toString());
+
+      String nonGapped = AlignSeq.extractGaps("-. ", sequence[m].getSequence());
+
+      int absStart = entry.getUniprotSequence().getContent().indexOf(
+          nonGapped.toString());
+
+      if (absStart == -1)
+      {
+        // Is UniprotSequence contained in dataset sequence?
+        absStart = nonGapped.toString().indexOf(entry.getUniprotSequence().getContent());
+        if(absStart == -1)
+        {
+          sbuffer.append(sequence[m].getName() +
+                         " SEQUENCE NOT %100 MATCH \n");
+
+          continue;
+        }
+
+        if (entry.getFeature() != null)
+        {
+          Enumeration e = entry.getFeature().elements();
+          while (e.hasMoreElements())
+          {
+            SequenceFeature sf = (SequenceFeature) e.nextElement();
+            sf.setBegin(sf.getBegin() + absStart + 1);
+            sf.setEnd(sf.getEnd() + absStart + 1);
+          }
+
+          sbuffer.append(sequence[m].getName() +
+                         " HAS " + absStart +
+              " PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"
+                         + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
+          absStart = 0;
+        }
+
+      }
+
+      unknownSequences.remove(sequence);
+
+      int absEnd = absStart + nonGapped.toString().length();
+      absStart += 1;
+
+      Enumeration e = entry.getDbReference().elements();
+      Vector onlyPdbEntries = new Vector();
+      while(e.hasMoreElements())
+      {
+        PDBEntry pdb = (PDBEntry)e.nextElement();
+        if(!pdb.getType().equals(DBRefSource.PDB))
+          continue;
+
+        sequence[m].addDBRef(new DBRefEntry(DBRefSource.PDB,
+                                       "0",
+                                       pdb.getId()));
+
+        onlyPdbEntries.addElement(pdb);
+      }
+
+      sequence[m].setPDBId(onlyPdbEntries);
+
+      sequence[m].setStart(absStart);
+      sequence[m].setEnd(absEnd);
+
+
+      }
+    }
+  }
+}
+
+
diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
new file mode 100755
index 0000000..f78f943
--- /dev/null
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -0,0 +1,474 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+package jalview.io;
+
+import jalview.datamodel.*;
+
+import jalview.gui.*;
+
+import java.util.*;
+
+import java.net.URL;
+
+import org.biojava.dasobert.das.FeatureThread;
+import org.biojava.dasobert.eventmodel.FeatureEvent;
+import org.biojava.dasobert.eventmodel.FeatureListener;
+import org.biojava.dasobert.dasregistry.DasSource;
+
+import org.biojava.dasobert.das2.io.DasSourceReaderImpl;
+import org.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.das2.Das2Source;
+import org.biojava.dasobert.das2.DasSourceConverter;
+
+
+import jalview.bin.Cache;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class DasSequenceFeatureFetcher implements Runnable
+{
+  SequenceI [] sequences;
+  AlignFrame af;
+  StringBuffer sbuffer = new StringBuffer();
+  Vector selectedSources;
+
+  long startTime;
+  int threadsRunning = 0;
+
+
+  /**
+   * Creates a new SequenceFeatureFetcher object.
+   * Uses default
+   *
+   * @param align DOCUMENT ME!
+   * @param ap DOCUMENT ME!
+   */
+  public DasSequenceFeatureFetcher(SequenceI [] sequences,
+                                   final AlignFrame af,
+                                   Vector selectedSources)
+  {
+    this.selectedSources = selectedSources;
+    this.sequences = sequences;
+    this.af = af;
+
+    int uniprotCount = 0;
+    for (int i = 0; i < selectedSources.size(); i++)
+    {
+      DasSource source = (DasSource) selectedSources.elementAt(i);
+      DasCoordinateSystem[] coords = source.getCoordinateSystem();
+      for (int c = 0; c < coords.length; c++)
+      {
+        if (coords[c].getName().indexOf("UniProt")>-1)
+        {
+          uniprotCount++;
+          break;
+        }
+      }
+    }
+
+    int refCount = 0;
+    for(int i=0; i<sequences.length; i++)
+    {
+      DBRefEntry [] dbref = sequences[i].getDBRef();
+      if(dbref!=null)
+      {
+        for(int j=0; j<dbref.length; j++)
+        {
+          if(dbref[j].getSource()
+             .equals(jalview.datamodel.DBRefSource.UNIPROT))
+          {
+            refCount++;
+            break;
+          }
+        }
+      }
+    }
+
+    if(refCount<sequences.length && uniprotCount>0)
+    {
+
+     int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          "Do you want Jalview to find\n"
+         +"Uniprot Accession ids for given sequence names?",
+         "Find Uniprot Accession Ids",
+         JOptionPane.YES_NO_OPTION,
+         JOptionPane.QUESTION_MESSAGE);
+
+     if(reply == JOptionPane.YES_OPTION)
+     {
+       Thread thread = new Thread(new FetchDBRefs());
+       thread.start();
+     }
+     else
+      startFetching();
+    }
+    else
+      startFetching();
+
+  /* System.out.println("User selection is "   +
+                       ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)
+                      + " % Uniprot,  and "+refCount+" / " +sequences.length+" have uniprot accession");
+*/
+  }
+
+  void startFetching()
+  {
+    Thread thread = new Thread(this);
+    thread.start();
+  }
+
+  class FetchDBRefs implements Runnable
+  {
+    public void run()
+    {
+      new DBRefFetcher(
+             af.getViewport().getAlignment(), af).fetchDBRefs(true);
+      startFetching();
+    }
+  }
+
+
+  /**
+   * creates a jalview sequence feature from a das feature document
+   * @param dasfeature
+   * @return sequence feature object created using dasfeature information
+   */
+  SequenceFeature newSequenceFeature(Map dasfeature, String nickname)
+  {
+	  try {
+		/**
+	   * Different qNames for a DAS Feature - are string keys to the HashMaps in features
+	   * "METHOD") ||
+	   qName.equals("TYPE") ||
+	   qName.equals("START") ||
+	   qName.equals("END") ||
+	   qName.equals("NOTE") ||
+	   qName.equals("LINK") ||
+	   qName.equals("SCORE")
+	   */
+		  String desc = new String();
+		  if (dasfeature.containsKey("NOTE"))
+				desc+=(String) dasfeature.get("NOTE");
+
+
+                  int start = 0, end = 0;
+                  float score = 0f;
+
+                  try{ start = Integer.parseInt( dasfeature.get("START").toString()); }
+                  catch( Exception ex){}
+                  try{ end = Integer.parseInt( dasfeature.get("END").toString()); }
+                  catch (Exception ex){}
+                  try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }
+                  catch (Exception ex){}
+
+
+		  SequenceFeature f = new SequenceFeature(
+				  (String) dasfeature.get("TYPE"),
+				  desc,
+				  start,
+				  end,
+                                  score,
+				  nickname);
+
+                  if (dasfeature.containsKey("LINK"))
+                 {
+                      f.addLink(f.getType()+" "+f.begin+"_"+f.end
+                                +"|"+ dasfeature.get("LINK"));
+		  }
+                  // (String) dasfeature.get("ID"),
+                  ////  (String) dasfeature.get("METHOD"),
+				//  (String) dasfeature.get("SCORE"),
+				//  null
+		  	// );
+
+	  return f;
+	  }
+	  catch (Exception e) {
+            e.printStackTrace();
+		  Cache.log.debug("Failed to parse "+dasfeature.toString(), e);
+		  return null;
+	  }
+  }
+  /**
+   * fetch and add das features to a sequence using the given source URL and Id to create a feature request
+   * @param seq
+   * @param SourceUrl
+   * @param id
+   */
+  protected void createFeatureFetcher(final SequenceI seq,
+                                      final String sourceUrl,
+                                      String id,
+                                      String nickname)
+  {
+	  //////////////
+	  /// fetch DAS features
+          final Das1Source source = new Das1Source();
+          source.setUrl(sourceUrl);
+          source.setNickname(nickname);
+
+
+          Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
+                          sourceUrl);
+
+          if (id != null && id.length() > 0)
+          {
+            setThreadsRunning(+1);
+
+          //  int start=seq.getStart(), end = seq.getEnd();
+          /*  if(af.getViewport().getSelectionGroup()!=null)
+            {
+              SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());
+              start = tmp.findPosition(
+              af.getViewport().getSelectionGroup().getStartRes()
+                  );
+
+              end = tmp.findPosition(
+                 af.getViewport().getSelectionGroup().getEndRes()
+                 );
+            }*/
+
+            FeatureThread fetcher = new FeatureThread(id
+                                                   //  +  ":" + start + "," + end,
+                                                      , source);
+
+
+            fetcher.addFeatureListener(new FeatureListener()
+            {
+              public void comeBackLater(FeatureEvent e)
+              {
+                setThreadsRunning(-1);
+                Cache.log.debug("das source " + e.getDasSource().getNickname() +
+                                " asked us to come back in " + e.getComeBackLater() +
+                                " secs.");
+              }
+
+              public void newFeatures(FeatureEvent e)
+              {
+                setThreadsRunning(-1);
+                Das1Source ds = e.getDasSource();
+
+                Map[] features = e.getFeatures();
+                // add features to sequence
+                Cache.log.debug("das source " + ds.getUrl() + " returned " +
+                                features.length + " features");
+
+                if (features.length > 0)
+                {
+                  for (int i = 0; i < features.length; i++)
+                  {
+                      SequenceFeature f = newSequenceFeature(features[i],
+                        source.getNickname());
+
+                      seq.addSequenceFeature(f);
+                  }
+                }
+                else
+                {
+                  System.out.println("No features found for sequence " +seq.getName()
+                                     +" from: "+ e.getDasSource().getNickname());
+                }
+
+              }
+            }
+
+            );
+
+            //NOTE alignPanel listener will be called after the previous
+            //anonymous listener!!!
+            fetcher.addFeatureListener(af);
+
+            fetcher.start();
+	  }
+  }
+
+  synchronized void setThreadsRunning(int i)
+  {
+    threadsRunning += i;
+    if(threadsRunning<1)
+    {
+      af.setProgressBar("DAS Feature Fetching Complete", startTime);
+
+      if(af.featureSettings!=null)
+        af.featureSettings.setTableData();
+    }
+  }
+
+  /**
+   * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
+   */
+  public void run()
+  {
+    startTime = System.currentTimeMillis();
+    af.setProgressBar("Fetching DAS Sequence Features", startTime);
+
+    DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();
+
+    if(selectedSources==null || selectedSources.size()==0)
+    {
+      String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
+      StringTokenizer st = new StringTokenizer(active, "\t");
+      Vector selectedSources = new Vector();
+      String token;
+      while (st.hasMoreTokens())
+      {
+        token = st.nextToken();
+        for (int i = 0; i < sources.length; i++)
+        {
+          if (sources[i].getNickname().equals(token))
+          {
+            selectedSources.addElement(sources[i]);
+            break;
+          }
+        }
+      }
+    }
+
+    if(selectedSources == null || selectedSources.size()==0)
+    {
+      System.out.println("No DAS Sources active");
+      af.setProgressBar("No DAS Sources Active", startTime);
+      return;
+    }
+
+    try
+    {
+      int seqIndex = 0;
+      while (seqIndex < sequences.length)
+      {
+          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
+              new String[]  {
+              jalview.datamodel.DBRefSource.PDB,
+              jalview.datamodel.DBRefSource.UNIPROT});
+
+          for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)
+          {
+            DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);
+
+            if (uprefs != null)
+            {
+              // we know the id for this entry, so don't note its ID in the unknownSequences list
+              for (int j = 0;  j < uprefs.length; j++)
+              {
+
+                // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end
+                DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
+                for (int l=0; l<cs.length; l++)
+                {
+                  if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))
+                  {
+                    Cache.log.debug("Launched fetcher for coordinate system " +
+                                    cs[l].getName());
+
+
+                    createFeatureFetcher(sequences[seqIndex],
+                                         dasSource.getUrl(),
+                                          uprefs[j].getAccessionId(),
+                                         dasSource.getNickname());
+                  }
+                }
+              }
+            }
+            else
+            {
+              String id = null;
+              // try and use the name as the sequence id
+              if (sequences[seqIndex].getName().indexOf("|") > -1)
+              {
+                id = sequences[seqIndex].getName().substring(
+                    sequences[seqIndex].getName().lastIndexOf("|") + 1);
+              }
+              else
+              {
+                id = sequences[seqIndex].getName();
+              }
+              if (id != null)
+              {
+                // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references
+                createFeatureFetcher(sequences[seqIndex],
+                                     dasSource.getUrl(),
+                                     id,
+                                     dasSource.getNickname());
+              }
+            }
+          }
+
+          seqIndex++;
+    }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+
+  public static DasSource[] getDASSources()
+  {
+    DasSourceReaderImpl reader = new DasSourceReaderImpl();
+
+    String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
+        "http://das.sanger.ac.uk/registry/das1/sources/"
+      );
+
+    try
+    {
+      URL url = new URL(registryURL);
+
+      DasSource[] sources = reader.readDasSource(url);
+
+      List das1sources = new ArrayList();
+      for (int i = 0; i < sources.length; i++)
+      {
+        DasSource ds = sources[i];
+        if (ds instanceof Das2Source)
+        {
+          Das2Source d2s = (Das2Source) ds;
+          if (d2s.hasDas1Capabilities())
+          {
+            Das1Source d1s = DasSourceConverter.toDas1Source(d2s);
+            das1sources.add(d1s);
+          }
+
+        }
+        else if (ds instanceof Das1Source)
+        {
+          das1sources.add( (Das1Source) ds);
+        }
+      }
+
+      return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+      return null;
+    }
+
+  }
+}
+
+
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
new file mode 100755
index 0000000..c32fbc9
--- /dev/null
+++ b/src/jalview/io/FeaturesFile.java
@@ -0,0 +1,497 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+package jalview.io;
+
+import jalview.datamodel.*;
+
+import java.io.*;
+import java.util.*;
+import jalview.schemes.UserColourScheme;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeaturesFile extends AlignFile
+{
+    /**
+     * Creates a new FeaturesFile object.
+     */
+    public FeaturesFile()
+    {
+    }
+
+
+    /**
+     * Creates a new FeaturesFile object.
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public FeaturesFile(String inFile, String type)
+       throws IOException
+    {
+        super(inFile, type);
+    }
+
+    /**
+     * The Application can render HTML, but the applet will
+     * remove HTML tags and replace links with %LINK%
+     * Both need to read links in HTML however
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public boolean parse(AlignmentI align,
+                         Hashtable colours,
+                         boolean removeHTML)
+    {
+      return parse(align, colours, null, removeHTML);
+    }
+    /**
+     * The Application can render HTML, but the applet will
+     * remove HTML tags and replace links with %LINK%
+     * Both need to read links in HTML however
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public boolean parse(AlignmentI align,
+                         Hashtable colours,
+                         Hashtable featureLink,
+                         boolean removeHTML)
+    {
+      String line = null;
+      try
+      {
+        SequenceI seq = null;
+        String type, desc, token=null;
+
+        int index, start, end;
+        float score;
+        StringTokenizer st;
+        SequenceFeature sf;
+        String featureGroup = null, groupLink = null;
+        Hashtable typeLink = new Hashtable();
+
+        boolean GFFFile = true;
+
+        while ( (line = nextLine()) != null)
+        {
+          if(line.startsWith("#"))
+            continue;
+
+          st = new StringTokenizer(line, "\t");
+          if (st.countTokens()>1 && st.countTokens() < 4 )
+          {
+            GFFFile = false;
+            type = st.nextToken();
+            if (type.equalsIgnoreCase("startgroup"))
+            {
+              featureGroup = st.nextToken();
+              if (st.hasMoreElements())
+              {
+                groupLink = st.nextToken();
+                featureLink.put(featureGroup, groupLink);
+              }
+            }
+            else if (type.equalsIgnoreCase("endgroup"))
+            {
+              //We should check whether this is the current group,
+              //but at present theres no way of showing more than 1 group
+              st.nextToken();
+              featureGroup = null;
+              groupLink = null;
+            }
+            else
+            {
+              UserColourScheme ucs = new UserColourScheme(st.nextToken());
+              colours.put(type, ucs.findColour("A"));
+              if (st.hasMoreElements())
+              {
+                String link = st.nextToken();
+                typeLink.put(type, link);
+                if(featureLink==null)
+                  featureLink = new Hashtable();
+                featureLink.put(type, link);
+              }
+
+            }
+            continue;
+          }
+
+          while (st.hasMoreElements())
+          {
+
+            if(GFFFile)
+            {
+              // Still possible this is an old Jalview file,
+              // which does not have type colours at the beginning
+              token = st.nextToken();
+              seq = align.findName(token);
+              if(seq != null)
+              {
+                desc = st.nextToken();
+                type = st.nextToken();
+                start = Integer.parseInt(st.nextToken());
+                end = Integer.parseInt(st.nextToken());
+                try
+                {
+                  score =  new Float(st.nextToken()).floatValue();
+                }
+                catch (NumberFormatException ex)
+                {
+                  score = 0;
+                }
+
+                sf = new SequenceFeature(type, desc, start, end, score, null);
+
+                try
+                {
+                  sf.setValue("STRAND", st.nextToken());
+                  sf.setValue("FRAME", st.nextToken());
+                }
+                catch (Exception ex)
+                {}
+
+                if(st.hasMoreTokens())
+                {
+                  StringBuffer attributes = new StringBuffer();
+                  while (st.hasMoreTokens())
+                  {
+                    attributes.append("\t"+st.nextElement());
+                  }
+                  sf.setValue("ATTRIBUTES", attributes.toString());
+                }
+
+                seq.addSequenceFeature(sf);
+
+                break;
+              }
+            }
+
+            if(GFFFile && seq==null)
+            {
+              desc = token;
+            }
+            else
+              desc = st.nextToken();
+
+
+            token = st.nextToken();
+            if (!token.equals("ID_NOT_SPECIFIED"))
+            {
+              seq = align.findName(token);
+              st.nextToken();
+            }
+            else
+            {
+              try{
+                index = Integer.parseInt(st.nextToken());
+                seq = align.getSequenceAt(index);
+              }
+              catch(NumberFormatException ex)
+              {
+                seq = null;
+              }
+            }
+
+            if(seq==null)
+            {
+              System.out.println("Sequence not found: "+line);
+              break;
+            }
+
+            start = Integer.parseInt(st.nextToken());
+            end = Integer.parseInt(st.nextToken());
+
+            type = st.nextToken();
+
+            if (!colours.containsKey(type))
+            {
+              // Probably the old style groups file
+              UserColourScheme ucs = new UserColourScheme(type);
+              colours.put(type, ucs.findColour("A"));
+            }
+
+            sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
+
+            seq.addSequenceFeature(sf);
+
+            if(groupLink!=null && removeHTML)
+            {
+              sf.addLink(groupLink);
+              sf.description += "%LINK%";
+            }
+            if(typeLink.containsKey(type) && removeHTML)
+            {
+              sf.addLink(typeLink.get(type).toString());
+              sf.description += "%LINK%";
+            }
+
+            parseDescriptionHTML(sf, removeHTML);
+
+            //If we got here, its not a GFFFile
+            GFFFile = false;
+          }
+        }
+      }
+      catch (Exception ex)
+      {
+        System.out.println(line);
+        System.out.println("Error parsing feature file: " + ex +"\n"+line);
+        return false;
+      }
+
+      return true;
+    }
+
+    void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+    {
+      StringBuffer sb = new StringBuffer();
+      StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
+      String token,  link;
+      while(st.hasMoreElements())
+      {
+        token = st.nextToken("<>");
+        if(token.equalsIgnoreCase("html") || token.startsWith("/"))
+          continue;
+
+        if(token.startsWith("a href="))
+        {
+          link = token.substring(token.indexOf("\"")+1, token.length()-1);
+          String label = st.nextToken("<>");
+          sf.addLink(label+"|"+link);
+          sb.append(label+"%LINK%");
+        }
+        else if(token.equalsIgnoreCase("br"))
+          sb.append("\n");
+        else
+          sb.append(token);
+      }
+
+      if(removeHTML)
+        sf.description = sb.toString();
+  }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param len DOCUMENT ME!
+     * @param gaps DOCUMENT ME!
+     * @param displayId DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String printJalviewFormat(SequenceI [] seqs,
+                                     Hashtable visible)
+    {
+        StringBuffer out = new StringBuffer();
+        SequenceFeature [] next;
+
+        if(visible==null || visible.size()<1)
+          return "No Features Visible";
+
+        Enumeration en = visible.keys();
+        String type;
+        int color;
+        while( en.hasMoreElements() )
+        {
+          type = en.nextElement().toString();
+          color = Integer.parseInt( visible.get(type).toString() );
+          out.append(type + "\t"
+                     + jalview.util.Format.getHexString(
+                         new java.awt.Color(color)  )
+                     +"\n");
+        }
+
+        //Work out which groups are both present and visible
+        Vector groups = new Vector();
+        int groupIndex = 0;
+
+        for(int i=0; i<seqs.length; i++)
+        {
+          next = seqs[i].getSequenceFeatures();
+          if(next!=null)
+          {
+            for(int j=0; j<next.length; j++)
+            {
+              if (!visible.containsKey(next[j].type))
+                continue;
+
+              if (    next[j].featureGroup != null
+                  && !groups.contains(next[j].featureGroup))
+                groups.addElement(next[j].featureGroup);
+            }
+          }
+        }
+
+        String group = null;
+
+        do
+        {
+
+
+          if (groups.size() > 0 && groupIndex < groups.size())
+          {
+            group = groups.elementAt(groupIndex).toString();
+            out.append("\nSTARTGROUP\t" + group + "\n");
+          }
+          else
+            group = null;
+
+          for (int i = 0; i < seqs.length; i++)
+          {
+            next = seqs[i].getSequenceFeatures();
+            if (next != null)
+            {
+              for (int j = 0; j < next.length; j++)
+              {
+                if (!visible.containsKey(next[j].type))
+                  continue;
+
+                if (group != null
+                    && (next[j].featureGroup==null
+                        || !next[j].featureGroup.equals(group))
+                  )
+                  continue;
+
+                if(group==null && next[j].featureGroup!=null)
+                  continue;
+
+                if(next[j].description==null || next[j].description.equals(""))
+                  out.append(next[j].type+"\t");
+                else
+                {
+                  out.append(next[j].description+" ");
+                  if(next[j].links!=null)
+                    {
+                      for(int l=0; l<next[j].links.size(); l++)
+                      {
+                        String label = next[j].links.elementAt(l).toString();
+                        String href = label.substring(label.indexOf("|")+1);
+                        label = label.substring(0, label.indexOf("|"));
+
+                        if(next[j].description.indexOf(href)==-1)
+                        {
+                          out.append("<a href=\""
+                                     + href
+                                     + "\">"
+                                     + label
+                                     + "</a>");
+                        }
+                      }
+                    }
+                   out.append("\t");
+                }
+
+
+                out.append(  seqs[i].getName() + "\t-1\t"
+                           + next[j].begin + "\t"
+                           + next[j].end + "\t"
+                           + next[j].type + "\n"
+                    );
+              }
+            }
+          }
+
+          if(group!=null)
+          {
+            out.append("ENDGROUP\t"+group+"\n");
+            groupIndex++;
+          }
+          else
+            break;
+
+        }
+        while(groupIndex < groups.size()+1);
+
+
+      return out.toString();
+    }
+
+    public String printGFFFormat(SequenceI [] seqs, Hashtable visible)
+    {
+      StringBuffer out = new StringBuffer();
+      SequenceFeature [] next;
+      String source;
+
+      for(int i=0; i<seqs.length; i++)
+      {
+        if(seqs[i].getSequenceFeatures()!=null)
+        {
+          next = seqs[i].getSequenceFeatures();
+          for(int j=0; j<next.length; j++)
+          {
+            if(!visible.containsKey(next[j].type))
+              continue;
+
+            source = next[j].featureGroup;
+            if(source==null)
+              source = next[j].getDescription();
+
+            out.append(seqs[i].getName() + "\t"
+                       + source + "\t"
+                       + next[j].type  + "\t"
+                       + next[j].begin + "\t"
+                       + next[j].end   + "\t"
+                       + next[j].score + "\t"
+                      );
+
+            if(next[j].getValue("STRAND")!=null)
+              out.append(next[j].getValue("STRAND")+"\t");
+            else
+              out.append(".\t");
+
+            if(next[j].getValue("FRAME")!=null)
+              out.append(next[j].getValue("FRAME"));
+            else
+              out.append(".");
+
+            if(next[j].getValue("ATTRIBUTES")!=null)
+              out.append(next[j].getValue("ATTRIBUTES"));
+
+            out.append("\n");
+
+          }
+        }
+      }
+
+      return out.toString();
+    }
+
+    public void parse()
+    {
+      //IGNORED
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print()
+    {
+        return "USE printGFFFormat() or printJalviewFormat()";
+    }
+}
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
new file mode 100755
index 0000000..61f0ce1
--- /dev/null
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -0,0 +1,145 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/package jalview.io;
+
+import jalview.datamodel.*;
+
+public class JnetAnnotationMaker
+{
+  /**
+   * adds the annotation parsed by prediction to al.
+   * @param prediction JPredFile
+   * @param al AlignmentI
+   * @param FirstSeq int -
+   * @param noMsa boolean
+   */
+  public static void add_annotation(JPredFile prediction, AlignmentI al,
+                                    int FirstSeq, boolean noMsa)
+      throws Exception
+  {
+    int i = 0;
+    SequenceI[] preds = prediction.getSeqsAsArray();
+    // in the future we could search for the query
+    // sequence in the alignment before calling this function.
+    SequenceI seqRef = al.getSequenceAt(FirstSeq);
+    int width = preds[0].getSequence().length();
+    int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
+    if (gapmap.length != width)
+    {
+      throw (new Exception(
+          "Number of residues in supposed query sequence ('" +
+          al.getSequenceAt(FirstSeq).getName() + "'\n" +
+          al.getSequenceAt(FirstSeq).getSequence() +
+          ")\ndiffer from number of prediction sites in prediction (" + width +
+          ")"));
+    }
+
+    AlignmentAnnotation annot;
+    Annotation[] annotations = null;
+
+    int existingAnnotations = 0;
+    if(al.getAlignmentAnnotation()!=null)
+       existingAnnotations = al.getAlignmentAnnotation().length;
+
+
+    while (i < preds.length)
+    {
+      String id = preds[i].getName().toUpperCase();
+
+      if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
+          id.startsWith("JPRED"))
+      {
+        annotations = new Annotation[al.getWidth()];
+
+        if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
+            id.equals("JNETFREQ") || id.equals("JNETHMM") ||
+            id.equals("JNETALIGN") || id.equals("JPRED"))
+        {
+          for (int j = 0; j < width; j++)
+          {
+            annotations[gapmap[j]] = new Annotation("", "",
+                preds[i].getCharAt(j), 0);
+          }
+        }
+        else if (id.equals("JNETCONF"))
+        {
+          for (int j = 0; j < width; j++)
+          {
+            float value = new Float(preds[i].getCharAt(
+                j) + "").floatValue();
+            annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
+                j) + "", "", preds[i].getCharAt(j),
+                value);
+          }
+        }
+        else
+        {
+          for (int j = 0; j < width; j++)
+          {
+            annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
+                j) + "", "", ' ', 0);
+          }
+        }
+
+        if (id.equals("JNETCONF"))
+        {
+          annot = new AlignmentAnnotation(preds[i].getName(),
+                                          "JNet Output", annotations, 0f,
+                                          10f,
+                                          AlignmentAnnotation.BAR_GRAPH);
+        }
+        else
+        {
+          annot = new AlignmentAnnotation(preds[i].getName(),
+                                          "JNet Output", annotations);
+        }
+
+        if (seqRef != null)
+        {
+          annot.createSequenceMapping(seqRef, 1, true);
+          seqRef.addAlignmentAnnotation(annot);
+        }
+
+        al.addAnnotation(annot);
+        al.setAnnotationIndex(annot,
+                              al.getAlignmentAnnotation().
+                              length - existingAnnotations - 1);
+
+        if (noMsa)
+        {
+          al.deleteSequence(preds[i]);
+        }
+      }
+
+      i++;
+    }
+
+    //Hashtable scores = prediction.getScores();
+
+    /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
+                          "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
+
+      addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
+     "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
+
+      addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
+                          "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
+     */
+
+  }
+}
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
new file mode 100644
index 0000000..fd5fd44
--- /dev/null
+++ b/src/jalview/io/StockholmFile.java
@@ -0,0 +1,409 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+/*
+ * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
+ */
+package jalview.io;
+import java.io.*;
+import java.util.*;
+import jalview.datamodel.*;
+import com.stevesoft.pat.*;
+//import org.apache.log4j.*;
+
+/**
+ * This class is supposed to parse a Stockholm format file into Jalview
+ * @author bsb at sanger.ac.uk
+ * @version 0.3
+ */
+public class StockholmFile extends AlignFile
+{
+        //static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
+
+    public StockholmFile()
+    {
+    }
+
+
+    public StockholmFile(String inFile, String type) throws IOException
+    {
+        super(inFile, type);
+    }
+
+    public void initData()
+    {
+         super.initData();
+    }
+
+    /**
+     * Parse a file in Stockholm format into Jalview's data model. The file has
+     * to be passed at construction time
+     * @throws IOException If there is an error with the input file
+     */
+    public void parse() throws IOException
+    {
+        // --------------- Variable Definitions -------------------
+        String line;
+        String version;
+      //  String id;
+        Hashtable alAnn = new Hashtable(); // Alignment wide annotations
+        Hashtable seqAnn = new Hashtable(); // Sequence related annotations
+        Hashtable seqs = new Hashtable();
+        Regex p, r, rend, s, x;
+
+        // ------------------ Parsing File ----------------------
+        // First, we have to check that this file has STOCKHOLM format, i.e. the first line must match
+        r = new Regex("# STOCKHOLM ([\\d\\.]+)");
+        if(!r.search(nextLine()))
+        {
+            throw new IOException("This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
+        }
+        else
+        {
+            version = r.stringMatched(1);
+            //logger.debug("Stockholm version: " + version);
+        }
+
+//      We define some Regexes here that will be used regularily later
+        rend = new Regex("\\/\\/"); // Find the end of an alignment
+        p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in id/from/to
+        s = new Regex("(\\S+)\\s+(\\w{2})\\s+(.*)"); // Parses annotation subtype
+        r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
+        x = new Regex("(\\S+)\\s+(\\S+)"); //split id from sequence
+
+        rend.optimize();
+        p.optimize();
+        s.optimize();
+        r.optimize();
+        x.optimize();
+
+        while ( (line = nextLine()) != null)
+        {
+            if (line.length() == 0) continue;
+            if(rend.search(line))
+            {
+//              End of the alignment, pass stuff back
+
+                 this.noSeqs = seqs.size();
+                //logger.debug("Number of sequences: " + this.noSeqs);
+                Enumeration accs = seqs.keys();
+                while (accs.hasMoreElements())
+                {
+                    String acc = (String) accs.nextElement();
+                    //logger.debug("Processing sequence " + acc);
+                    String seq = (String) seqs.get(acc);
+                    if (maxLength < seq.length())
+                    {
+                        maxLength = seq.length();
+                    }
+                    int start = 1;
+                    int end = -1;
+                    String sid = acc;
+                    // Split accession in id and from/to
+                    if (p.search(acc))
+                    {
+                        sid = p.stringMatched(1);
+                        start = Integer.parseInt(p.stringMatched(2));
+                        end = Integer.parseInt(p.stringMatched(3));
+                    }
+                    //logger.debug(sid + ", " + start + ", " + end);
+
+                    Sequence seqO = new Sequence(sid, seq, start, end);
+                    Hashtable features = null;
+                    // We need to adjust the positions of all features to account for gaps
+                    try
+                    {
+                         features = (Hashtable) ((Hashtable) seqAnn.get(acc)).get("features");
+                    }
+                    catch (java.lang.NullPointerException e)
+                    {
+                       //loggerwarn("Getting Features for " + acc + ": " + e.getMessage());
+                       //continue;
+                    }
+                    // if we have features
+                    if (features != null)
+                    {
+                        Enumeration i = features.keys();
+                        while(i.hasMoreElements())
+                        {
+                            String type = i.nextElement().toString();
+                            Hashtable content = (Hashtable) features.get(type);
+
+                            Enumeration j = content.keys();
+                            while(j.hasMoreElements())
+                            {
+                                        String desc = j.nextElement().toString();
+                                        String ns = content.get(desc).toString();
+                                        char[] byChar = ns.toCharArray();
+                                        for (int k = 0; k < byChar.length; k++)
+                                        {
+                                                char c = byChar[k];
+                                                if (! (c == ' ' || c == '_' ||
+                                                       c == '-'))
+                                                {
+                                                  int new_pos = seqO.findPosition(k);
+                                                  SequenceFeature feat =
+                                                      new SequenceFeature(type,
+                                                      desc, new_pos, new_pos, 0f, null);
+
+                                                  seqO.addSequenceFeature(feat);
+                                                }
+                                        }
+                                }
+
+                        }
+
+                    }
+                    //logger.debug("Adding seq " + acc + " from "  + start + " to " + end + ": " + seq);
+                    this.seqs.addElement(seqO);
+                }
+            }
+            else if (!r.search(line))
+            {
+                //System.err.println("Found sequence line: " + line);
+
+                // Split sequence in sequence and accession parts
+                if(!x.search(line))
+                {
+                                //logger.error("Could not parse sequence line: " + line);
+                                throw new IOException("Could not parse sequence line: " + line);
+                }
+                String ns  = (String) seqs.get(x.stringMatched(1));
+                if (ns == null) ns = "";
+                ns += x.stringMatched(2);
+
+                seqs.put(x.stringMatched(1), ns);
+            }
+            else
+            {
+                String annType = r.stringMatched(1);
+                String annContent = r.stringMatched(2);
+
+                //System.err.println("type:" + annType + " content: " + annContent);
+
+                if (annType.equals("GF"))
+                {
+                    /* Generic per-File annotation, free text
+                     * Magic features:
+                     * #=GF NH <tree in New Hampshire eXtended format>
+                     * #=GF TN <Unique identifier for the next tree>
+                     * Pfam descriptions:
+                        7. DESCRIPTION OF FIELDS
+
+                           Compulsory fields:
+                           ------------------
+
+                           AC   Accession number:           Accession number in form PFxxxxx.version or PBxxxxxx.
+                           ID   Identification:             One word name for family.
+                           DE   Definition:                 Short description of family.
+                           AU   Author:                     Authors of the entry.
+                           SE   Source of seed:             The source suggesting the seed members belong to one family.
+                           GA   Gathering method:           Search threshold to build the full alignment.
+                           TC   Trusted Cutoff:             Lowest sequence score and domain score of match in the full alignment.
+                           NC   Noise Cutoff:               Highest sequence score and domain score of match not in full alignment.
+                           TP   Type:                       Type of family -- presently Family, Domain, Motif or Repeat.
+                           SQ   Sequence:                   Number of sequences in alignment.
+                           AM   Alignment Method        The order ls and fs hits are aligned to the model to build the full align.
+                           //                               End of alignment.
+
+                           Optional fields:
+                           ----------------
+
+                           DC   Database Comment:           Comment about database reference.
+                           DR   Database Reference:         Reference to external database.
+                           RC   Reference Comment:          Comment about literature reference.
+                           RN   Reference Number:           Reference Number.
+                           RM   Reference Medline:          Eight digit medline UI number.
+                           RT   Reference Title:            Reference Title.
+                           RA   Reference Author:           Reference Author
+                           RL   Reference Location:         Journal location.
+                           PI   Previous identifier:        Record of all previous ID lines.
+                           KW   Keywords:                   Keywords.
+                           CC   Comment:                    Comments.
+                           NE   Pfam accession:         Indicates a nested domain.
+                           NL   Location:                   Location of nested domains - sequence ID, start and end of insert.
+
+                           Obsolete fields:
+                           -----------
+                           AL   Alignment method of seed:   The method used to align the seed members.
+                     */
+                    // Let's save the annotations, maybe we'll be able to do something with them later...
+                    Regex an = new Regex("(\\w+)\\s*(.*)");
+                    if (an.search(annContent)) alAnn.put(an.stringMatched(1), an.stringMatched(2));
+                }
+                else if(annType.equals("GS"))
+                {
+                    // Generic per-Sequence annotation, free text
+                    /* Pfam uses these features:
+                        Feature                    Description
+                        ---------------------      -----------
+                        AC <accession>             ACcession number
+                        DE <freetext>              DEscription
+                        DR <db>; <accession>;      Database Reference
+                        OS <organism>              OrganiSm (species)
+                        OC <clade>                 Organism Classification (clade, etc.)
+                        LO <look>                  Look (Color, etc.)
+                    */
+                    if (s.search(annContent))
+                    {
+                        String acc = s.stringMatched(1);
+                        String type = s.stringMatched(2);
+                        String content = s.stringMatched(3);
+
+                        Hashtable ann;
+                        if (seqAnn.containsKey(acc))
+                        {
+                            ann = (Hashtable) seqAnn.get(acc);
+                        }
+                        else
+                        {
+                            ann = new Hashtable();
+                        }
+                        ann.put(type, content);
+                        seqAnn.put(acc, ann);
+                    }
+                    else
+                    {
+                        throw new IOException("Error parsing " + line);
+                    }
+                }
+                else if(annType.equals("GC"))
+                {
+                  System.out.println(annContent);
+                    // Generic per-Column annotation, exactly 1 char per column
+                }
+                else if(annType.equals("GR"))
+                {
+                    // Generic per-Sequence AND per-Column markup, exactly 1 char per column
+                    /*
+                        Feature   Description            Markup letters
+                        -------   -----------            --------------
+                        SS        Secondary Structure    [HGIEBTSCX]
+                        SA        Surface Accessibility  [0-9X]
+                                      (0=0%-10%; ...; 9=90%-100%)
+                        TM        TransMembrane          [Mio]
+                        PP        Posterior Probability  [0-9*]
+                                      (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00)
+                        LI        LIgand binding         [*]
+                        AS        Active Site            [*]
+                        IN        INtron (in or after)   [0-2]
+                     */
+                    if (s.search(annContent))
+                    {
+                        String acc = s.stringMatched(1);
+                        String type = s.stringMatched(2);
+                        String seq = s.stringMatched(3);
+                        String description = new String();
+
+                        // Check for additional information about the current annotation
+                        if (x.search(seq))
+                        {
+                            description = x.stringMatched(1);
+                            seq = x.stringMatched(2);
+                        }
+                        // sequence id with from-to fields
+
+                        Hashtable ann;
+                        // Get an object with all the annotations for this sequence
+                        if (seqAnn.containsKey(acc))
+                        {
+                            //logger.debug("Found annotations for " + acc);
+                            ann = (Hashtable) seqAnn.get(acc);
+                        }
+                        else
+                        {
+                            //logger.debug("Creating new annotations holder for " + acc);
+                            ann = new Hashtable();
+                            seqAnn.put(acc, ann);
+                        }
+
+                        Hashtable features;
+                        // Get an object with all the content for an annotation
+                        if (ann.containsKey("features"))
+                        {
+                            //logger.debug("Found features for " + acc);
+                            features = (Hashtable) ann.get("features");
+                        }
+                        else
+                        {
+                            //logger.debug("Creating new features holder for " + acc);
+                            features = new Hashtable();
+                            ann.put("features", features);
+                        }
+
+                        Hashtable content;
+                        if (features.containsKey(this.id2type(type)))
+                        {
+                            //logger.debug("Found content for " + this.id2type(type));
+                            content = (Hashtable) features.get(this.id2type(type));
+                        }
+                        else
+                        {
+                            //logger.debug("Creating new content holder for " + this.id2type(type));
+                            content = new Hashtable();
+                            features.put(this.id2type(type), content);
+                        }
+                        String ns = (String) content.get(description);
+                        if (ns == null) ns = "";
+                        ns += seq;
+                        content.put(description, seq);
+                    }
+                    else
+                    {
+                        throw new IOException("Error parsing " + line);
+                    }
+                }
+                else
+                {
+                    throw new IOException("Unknown annotation detected: " + annType + " " + annContent);
+                }
+            }
+        }
+    }
+
+    public static String print(SequenceI[] s)
+    {
+        return "not yet implemented";
+    }
+
+    public String print()
+    {
+        return print(getSeqsAsArray());
+    }
+
+    private String id2type(String id)
+    {
+        // GR ids
+        if (id.equals("SS")) return "secondary structure";
+        else if (id.equals("SA")) return "surface accessibility";
+        else if (id.equals("TM")) return "transmembrane";
+        else if (id.equals("PP")) return "posterior probability";
+        else if (id.equals("LI")) return "ligand binding";
+        else if (id.equals("AS")) return "active site";
+        else if (id.equals("IN")) return "intron";
+        else if (id.equals("IR")) return "interacting residue";
+        // GS ids
+        else if (id.equals("AC")) return "accession";
+        else if (id.equals("OS")) return "organism";
+        else if (id.equals("CL")) return "class";
+        else if (id.equals("DE")) return "description";
+        else if (id.equals("DR")) return "reference";
+        else if (id.equals("LO")) return "look";
+        else return null;
+    }
+}
diff --git a/src/jalview/jbgui/GDasSourceBrowser.java b/src/jalview/jbgui/GDasSourceBrowser.java
new file mode 100755
index 0000000..a3493d8
--- /dev/null
+++ b/src/jalview/jbgui/GDasSourceBrowser.java
@@ -0,0 +1,210 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import javax.swing.*;
+import javax.swing.border.TitledBorder;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.awt.*;
+import javax.swing.BorderFactory;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.event.HyperlinkEvent;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Insets;
+
+public class GDasSourceBrowser
+    extends JPanel
+{
+  public GDasSourceBrowser()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(gridBagLayout1);
+    refresh.setText("Refresh Available Sources");
+    refresh.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        refresh_actionPerformed(e);
+      }
+    });
+    progressBar.setPreferredSize(new Dimension(450, 20));
+    progressBar.setString("");
+    scrollPane.setBorder(titledBorder1);
+    scrollPane.setBorder(BorderFactory.createEtchedBorder());
+    fullDetailsScrollpane.setBorder(BorderFactory.createEtchedBorder());
+    fullDetails.addHyperlinkListener(new HyperlinkListener()
+    {
+      public void hyperlinkUpdate(HyperlinkEvent e)
+      {
+        fullDetails_hyperlinkUpdate(e);
+      }
+    });
+    fullDetails.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    fullDetails.setEditable(false);
+    registryLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    registryLabel.setHorizontalAlignment(SwingConstants.TRAILING);
+    registryLabel.setText("Use Registry");
+    addLocal.setText("Add Local Source");
+    addLocal.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        amendLocal(true);
+      }
+    });
+    jPanel1.setLayout(flowLayout1);
+    jPanel1.setMinimumSize(new Dimension(596, 30));
+    jPanel1.setPreferredSize(new Dimension(596, 30));
+    jScrollPane2.setBorder(titledBorder3);
+    jScrollPane3.setBorder(titledBorder4);
+    jScrollPane4.setBorder(titledBorder5);
+    titledBorder2.setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    titledBorder3.setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    titledBorder4.setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    filter1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    filter2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    filter3.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    table.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    reset.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    reset.setMargin(new Insets(2, 2, 2, 2));
+    reset.setText("Reset");
+    reset.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        reset_actionPerformed(e);
+      }
+    });
+    jPanel2.setLayout(borderLayout1);
+    borderLayout1.setHgap(5);
+    registryURL.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+    scrollPane.getViewport().add(table);
+    fullDetailsScrollpane.getViewport().add(fullDetails);
+    jScrollPane3.getViewport().add(filter2);
+    jScrollPane4.getViewport().add(filter3);
+    jPanel1.add(refresh, null);
+    jPanel1.add(addLocal, null);
+    jPanel1.add(progressBar, null);
+    jScrollPane2.getViewport().add(filter1);
+    this.add(jPanel1, new GridBagConstraints(0, 3, 3, 1, 1.0, 1.0
+                                             , GridBagConstraints.CENTER,
+                                             GridBagConstraints.HORIZONTAL,
+                                             new Insets(0, 0, 0, 0), 0, 0));
+    this.add(fullDetailsScrollpane, new GridBagConstraints(1, 0, 2, 1, 1.0, 1.0
+        , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+        new Insets(3, 0, 0, 3), 240, 130));
+    this.add(scrollPane, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0
+                                                , GridBagConstraints.CENTER,
+                                                GridBagConstraints.BOTH,
+                                                new Insets(3, 2, 0, 0), 150,
+                                                130));
+    jPanel2.add(registryLabel, java.awt.BorderLayout.WEST);
+    jPanel2.add(registryURL, java.awt.BorderLayout.CENTER);
+    jPanel2.add(reset, java.awt.BorderLayout.EAST);
+    this.add(jPanel2, new GridBagConstraints(0, 2, 3, 1, 0.0, 0.0
+                                             , GridBagConstraints.CENTER,
+                                             GridBagConstraints.HORIZONTAL,
+                                             new Insets(5, 10, 0, 10), 339, 0));
+    this.add(jScrollPane2, new GridBagConstraints(0, 1, 1, 1, 1.0, 1.0
+                                                  , GridBagConstraints.CENTER,
+                                                  GridBagConstraints.BOTH,
+                                                  new Insets(0, 0, 0, 60), 80,
+                                                  60));
+    this.add(jScrollPane4, new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0
+                                                  , GridBagConstraints.CENTER,
+                                                  GridBagConstraints.BOTH,
+                                                  new Insets(0, -80, 0, 0), 80,
+                                                  60));
+    this.add(jScrollPane3, new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0
+                                                  , GridBagConstraints.CENTER,
+                                                  GridBagConstraints.BOTH,
+                                                  new Insets(0, -60, 0, 80), 80,
+                                                  60));
+  }
+
+  protected JTable table = new JTable();
+  protected JEditorPane fullDetails = new JEditorPane("text/html", "");
+  TitledBorder titledBorder1 = new TitledBorder("Available DAS Sources");
+  protected JButton refresh = new JButton();
+  protected JProgressBar progressBar = new JProgressBar();
+  protected JScrollPane scrollPane = new JScrollPane();
+  TitledBorder titledBorder2 = new TitledBorder("Full Details");
+  protected JScrollPane fullDetailsScrollpane = new JScrollPane();
+  protected JList filter1 = new JList();
+  protected JList filter2 = new JList();
+  protected JList filter3 = new JList();
+  JScrollPane jScrollPane2 = new JScrollPane();
+  JScrollPane jScrollPane3 = new JScrollPane();
+  JScrollPane jScrollPane4 = new JScrollPane();
+  protected JTextField registryURL = new JTextField();
+  protected JLabel registryLabel = new JLabel();
+  protected JButton addLocal = new JButton();
+  JPanel jPanel1 = new JPanel();
+  FlowLayout flowLayout1 = new FlowLayout();
+  GridBagLayout gridBagLayout1 = new GridBagLayout();
+  TitledBorder titledBorder3 = new TitledBorder("Authority:");
+  TitledBorder titledBorder4 = new TitledBorder("Type:");
+  TitledBorder titledBorder5 = new TitledBorder("Label:");
+  JButton reset = new JButton();
+  JPanel jPanel2 = new JPanel();
+  BorderLayout borderLayout1 = new BorderLayout();
+  public void refresh_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void fullDetails_hyperlinkUpdate(HyperlinkEvent e)
+  {
+    try{
+
+      if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED)
+        jalview.util.BrowserLauncher.openURL(e.getURL().toString());
+    }
+    catch(Exception ex)
+    {
+      System.out.println(e.getURL());
+      ex.printStackTrace();
+    }
+  }
+
+  public void amendLocal(boolean newSource)
+  {
+
+  }
+
+  public void reset_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+}
diff --git a/src/jalview/schemabinding/version2/Alignment.java b/src/jalview/schemabinding/version2/Alignment.java
new file mode 100755
index 0000000..3b9d53b
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Alignment.java
@@ -0,0 +1,173 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Alignment.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Alignment implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _annotation
+     */
+    private jalview.schemabinding.version2.Annotation _annotation;
+
+    /**
+     * Field _sequenceSet
+     */
+    private jalview.schemabinding.version2.SequenceSet _sequenceSet;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Alignment() {
+        super();
+    } //-- jalview.schemabinding.version2.Alignment()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'annotation'.
+     * 
+     * @return Annotation
+     * @return the value of field 'annotation'.
+     */
+    public jalview.schemabinding.version2.Annotation getAnnotation()
+    {
+        return this._annotation;
+    } //-- jalview.schemabinding.version2.Annotation getAnnotation() 
+
+    /**
+     * Returns the value of field 'sequenceSet'.
+     * 
+     * @return SequenceSet
+     * @return the value of field 'sequenceSet'.
+     */
+    public jalview.schemabinding.version2.SequenceSet getSequenceSet()
+    {
+        return this._sequenceSet;
+    } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'annotation'.
+     * 
+     * @param annotation the value of field 'annotation'.
+     */
+    public void setAnnotation(jalview.schemabinding.version2.Annotation annotation)
+    {
+        this._annotation = annotation;
+    } //-- void setAnnotation(jalview.schemabinding.version2.Annotation) 
+
+    /**
+     * Sets the value of field 'sequenceSet'.
+     * 
+     * @param sequenceSet the value of field 'sequenceSet'.
+     */
+    public void setSequenceSet(jalview.schemabinding.version2.SequenceSet sequenceSet)
+    {
+        this._sequenceSet = sequenceSet;
+    } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Alignment) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alignment.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/AlignmentDescriptor.java b/src/jalview/schemabinding/version2/AlignmentDescriptor.java
new file mode 100755
index 0000000..b285229
--- /dev/null
+++ b/src/jalview/schemabinding/version2/AlignmentDescriptor.java
@@ -0,0 +1,243 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AlignmentDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AlignmentDescriptor() {
+        super();
+        nsURI = "www.vamsas.ac.uk/jalview/version2";
+        xmlName = "Alignment";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _annotation
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotation", "Annotation", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Alignment target = (Alignment) object;
+                return target.getAnnotation();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Alignment target = (Alignment) object;
+                    target.setAnnotation( (jalview.schemabinding.version2.Annotation) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Annotation();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _annotation
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _sequenceSet
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSet", "SequenceSet", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Alignment target = (Alignment) object;
+                return target.getSequenceSet();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Alignment target = (Alignment) object;
+                    target.setSequenceSet( (jalview.schemabinding.version2.SequenceSet) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.SequenceSet();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _sequenceSet
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.AlignmentDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Alignment.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
new file mode 100755
index 0000000..ec9b84c
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -0,0 +1,590 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Annotation.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Annotation implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _graph
+     */
+    private boolean _graph;
+
+    /**
+     * keeps track of state for field: _graph
+     */
+    private boolean _has_graph;
+
+    /**
+     * Field _graphType
+     */
+    private int _graphType;
+
+    /**
+     * keeps track of state for field: _graphType
+     */
+    private boolean _has_graphType;
+
+    /**
+     * Field _sequenceRef
+     */
+    private java.lang.String _sequenceRef;
+
+    /**
+     * Field _graphColour
+     */
+    private int _graphColour;
+
+    /**
+     * keeps track of state for field: _graphColour
+     */
+    private boolean _has_graphColour;
+
+    /**
+     * Field _graphGroup
+     */
+    private int _graphGroup;
+
+    /**
+     * keeps track of state for field: _graphGroup
+     */
+    private boolean _has_graphGroup;
+
+    /**
+     * Field _annotationElementList
+     */
+    private java.util.Vector _annotationElementList;
+
+    /**
+     * Field _label
+     */
+    private java.lang.String _label;
+
+    /**
+     * Field _description
+     */
+    private java.lang.String _description;
+
+    /**
+     * Field _thresholdLine
+     */
+    private jalview.schemabinding.version2.ThresholdLine _thresholdLine;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Annotation() {
+        super();
+        _annotationElementList = new Vector();
+    } //-- jalview.schemabinding.version2.Annotation()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addAnnotationElement
+     * 
+     * 
+     * 
+     * @param vAnnotationElement
+     */
+    public void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _annotationElementList.addElement(vAnnotationElement);
+    } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement) 
+
+    /**
+     * Method addAnnotationElement
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAnnotationElement
+     */
+    public void addAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _annotationElementList.insertElementAt(vAnnotationElement, index);
+    } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) 
+
+    /**
+     * Method deleteGraph
+     * 
+     */
+    public void deleteGraph()
+    {
+        this._has_graph= false;
+    } //-- void deleteGraph() 
+
+    /**
+     * Method deleteGraphColour
+     * 
+     */
+    public void deleteGraphColour()
+    {
+        this._has_graphColour= false;
+    } //-- void deleteGraphColour() 
+
+    /**
+     * Method deleteGraphGroup
+     * 
+     */
+    public void deleteGraphGroup()
+    {
+        this._has_graphGroup= false;
+    } //-- void deleteGraphGroup() 
+
+    /**
+     * Method deleteGraphType
+     * 
+     */
+    public void deleteGraphType()
+    {
+        this._has_graphType= false;
+    } //-- void deleteGraphType() 
+
+    /**
+     * Method enumerateAnnotationElement
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateAnnotationElement()
+    {
+        return _annotationElementList.elements();
+    } //-- java.util.Enumeration enumerateAnnotationElement() 
+
+    /**
+     * Method getAnnotationElement
+     * 
+     * 
+     * 
+     * @param index
+     * @return AnnotationElement
+     */
+    public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _annotationElementList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);
+    } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int) 
+
+    /**
+     * Method getAnnotationElement
+     * 
+     * 
+     * 
+     * @return AnnotationElement
+     */
+    public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()
+    {
+        int size = _annotationElementList.size();
+        jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.schemabinding.version2.AnnotationElement[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() 
+
+    /**
+     * Method getAnnotationElementCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getAnnotationElementCount()
+    {
+        return _annotationElementList.size();
+    } //-- int getAnnotationElementCount() 
+
+    /**
+     * Returns the value of field 'description'.
+     * 
+     * @return String
+     * @return the value of field 'description'.
+     */
+    public java.lang.String getDescription()
+    {
+        return this._description;
+    } //-- java.lang.String getDescription() 
+
+    /**
+     * Returns the value of field 'graph'.
+     * 
+     * @return boolean
+     * @return the value of field 'graph'.
+     */
+    public boolean getGraph()
+    {
+        return this._graph;
+    } //-- boolean getGraph() 
+
+    /**
+     * Returns the value of field 'graphColour'.
+     * 
+     * @return int
+     * @return the value of field 'graphColour'.
+     */
+    public int getGraphColour()
+    {
+        return this._graphColour;
+    } //-- int getGraphColour() 
+
+    /**
+     * Returns the value of field 'graphGroup'.
+     * 
+     * @return int
+     * @return the value of field 'graphGroup'.
+     */
+    public int getGraphGroup()
+    {
+        return this._graphGroup;
+    } //-- int getGraphGroup() 
+
+    /**
+     * Returns the value of field 'graphType'.
+     * 
+     * @return int
+     * @return the value of field 'graphType'.
+     */
+    public int getGraphType()
+    {
+        return this._graphType;
+    } //-- int getGraphType() 
+
+    /**
+     * Returns the value of field 'label'.
+     * 
+     * @return String
+     * @return the value of field 'label'.
+     */
+    public java.lang.String getLabel()
+    {
+        return this._label;
+    } //-- java.lang.String getLabel() 
+
+    /**
+     * Returns the value of field 'sequenceRef'.
+     * 
+     * @return String
+     * @return the value of field 'sequenceRef'.
+     */
+    public java.lang.String getSequenceRef()
+    {
+        return this._sequenceRef;
+    } //-- java.lang.String getSequenceRef() 
+
+    /**
+     * Returns the value of field 'thresholdLine'.
+     * 
+     * @return ThresholdLine
+     * @return the value of field 'thresholdLine'.
+     */
+    public jalview.schemabinding.version2.ThresholdLine getThresholdLine()
+    {
+        return this._thresholdLine;
+    } //-- jalview.schemabinding.version2.ThresholdLine getThresholdLine() 
+
+    /**
+     * Method hasGraph
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasGraph()
+    {
+        return this._has_graph;
+    } //-- boolean hasGraph() 
+
+    /**
+     * Method hasGraphColour
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasGraphColour()
+    {
+        return this._has_graphColour;
+    } //-- boolean hasGraphColour() 
+
+    /**
+     * Method hasGraphGroup
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasGraphGroup()
+    {
+        return this._has_graphGroup;
+    } //-- boolean hasGraphGroup() 
+
+    /**
+     * Method hasGraphType
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasGraphType()
+    {
+        return this._has_graphType;
+    } //-- boolean hasGraphType() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllAnnotationElement
+     * 
+     */
+    public void removeAllAnnotationElement()
+    {
+        _annotationElementList.removeAllElements();
+    } //-- void removeAllAnnotationElement() 
+
+    /**
+     * Method removeAnnotationElement
+     * 
+     * 
+     * 
+     * @param index
+     * @return AnnotationElement
+     */
+    public jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int index)
+    {
+        java.lang.Object obj = _annotationElementList.elementAt(index);
+        _annotationElementList.removeElementAt(index);
+        return (jalview.schemabinding.version2.AnnotationElement) obj;
+    } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int) 
+
+    /**
+     * Method setAnnotationElement
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAnnotationElement
+     */
+    public void setAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _annotationElementList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _annotationElementList.setElementAt(vAnnotationElement, index);
+    } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) 
+
+    /**
+     * Method setAnnotationElement
+     * 
+     * 
+     * 
+     * @param annotationElementArray
+     */
+    public void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement[] annotationElementArray)
+    {
+        //-- copy array
+        _annotationElementList.removeAllElements();
+        for (int i = 0; i < annotationElementArray.length; i++) {
+            _annotationElementList.addElement(annotationElementArray[i]);
+        }
+    } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement) 
+
+    /**
+     * Sets the value of field 'description'.
+     * 
+     * @param description the value of field 'description'.
+     */
+    public void setDescription(java.lang.String description)
+    {
+        this._description = description;
+    } //-- void setDescription(java.lang.String) 
+
+    /**
+     * Sets the value of field 'graph'.
+     * 
+     * @param graph the value of field 'graph'.
+     */
+    public void setGraph(boolean graph)
+    {
+        this._graph = graph;
+        this._has_graph = true;
+    } //-- void setGraph(boolean) 
+
+    /**
+     * Sets the value of field 'graphColour'.
+     * 
+     * @param graphColour the value of field 'graphColour'.
+     */
+    public void setGraphColour(int graphColour)
+    {
+        this._graphColour = graphColour;
+        this._has_graphColour = true;
+    } //-- void setGraphColour(int) 
+
+    /**
+     * Sets the value of field 'graphGroup'.
+     * 
+     * @param graphGroup the value of field 'graphGroup'.
+     */
+    public void setGraphGroup(int graphGroup)
+    {
+        this._graphGroup = graphGroup;
+        this._has_graphGroup = true;
+    } //-- void setGraphGroup(int) 
+
+    /**
+     * Sets the value of field 'graphType'.
+     * 
+     * @param graphType the value of field 'graphType'.
+     */
+    public void setGraphType(int graphType)
+    {
+        this._graphType = graphType;
+        this._has_graphType = true;
+    } //-- void setGraphType(int) 
+
+    /**
+     * Sets the value of field 'label'.
+     * 
+     * @param label the value of field 'label'.
+     */
+    public void setLabel(java.lang.String label)
+    {
+        this._label = label;
+    } //-- void setLabel(java.lang.String) 
+
+    /**
+     * Sets the value of field 'sequenceRef'.
+     * 
+     * @param sequenceRef the value of field 'sequenceRef'.
+     */
+    public void setSequenceRef(java.lang.String sequenceRef)
+    {
+        this._sequenceRef = sequenceRef;
+    } //-- void setSequenceRef(java.lang.String) 
+
+    /**
+     * Sets the value of field 'thresholdLine'.
+     * 
+     * @param thresholdLine the value of field 'thresholdLine'.
+     */
+    public void setThresholdLine(jalview.schemabinding.version2.ThresholdLine thresholdLine)
+    {
+        this._thresholdLine = thresholdLine;
+    } //-- void setThresholdLine(jalview.schemabinding.version2.ThresholdLine) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java
new file mode 100755
index 0000000..b2af2c4
--- /dev/null
+++ b/src/jalview/schemabinding/version2/AnnotationColours.java
@@ -0,0 +1,385 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class AnnotationColours.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AnnotationColours implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _aboveThreshold
+     */
+    private int _aboveThreshold;
+
+    /**
+     * keeps track of state for field: _aboveThreshold
+     */
+    private boolean _has_aboveThreshold;
+
+    /**
+     * Field _annotation
+     */
+    private java.lang.String _annotation;
+
+    /**
+     * Field _minColour
+     */
+    private int _minColour;
+
+    /**
+     * keeps track of state for field: _minColour
+     */
+    private boolean _has_minColour;
+
+    /**
+     * Field _maxColour
+     */
+    private int _maxColour;
+
+    /**
+     * keeps track of state for field: _maxColour
+     */
+    private boolean _has_maxColour;
+
+    /**
+     * Field _colourScheme
+     */
+    private java.lang.String _colourScheme;
+
+    /**
+     * Field _threshold
+     */
+    private float _threshold;
+
+    /**
+     * keeps track of state for field: _threshold
+     */
+    private boolean _has_threshold;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AnnotationColours() {
+        super();
+    } //-- jalview.schemabinding.version2.AnnotationColours()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method deleteAboveThreshold
+     * 
+     */
+    public void deleteAboveThreshold()
+    {
+        this._has_aboveThreshold= false;
+    } //-- void deleteAboveThreshold() 
+
+    /**
+     * Method deleteMaxColour
+     * 
+     */
+    public void deleteMaxColour()
+    {
+        this._has_maxColour= false;
+    } //-- void deleteMaxColour() 
+
+    /**
+     * Method deleteMinColour
+     * 
+     */
+    public void deleteMinColour()
+    {
+        this._has_minColour= false;
+    } //-- void deleteMinColour() 
+
+    /**
+     * Method deleteThreshold
+     * 
+     */
+    public void deleteThreshold()
+    {
+        this._has_threshold= false;
+    } //-- void deleteThreshold() 
+
+    /**
+     * Returns the value of field 'aboveThreshold'.
+     * 
+     * @return int
+     * @return the value of field 'aboveThreshold'.
+     */
+    public int getAboveThreshold()
+    {
+        return this._aboveThreshold;
+    } //-- int getAboveThreshold() 
+
+    /**
+     * Returns the value of field 'annotation'.
+     * 
+     * @return String
+     * @return the value of field 'annotation'.
+     */
+    public java.lang.String getAnnotation()
+    {
+        return this._annotation;
+    } //-- java.lang.String getAnnotation() 
+
+    /**
+     * Returns the value of field 'colourScheme'.
+     * 
+     * @return String
+     * @return the value of field 'colourScheme'.
+     */
+    public java.lang.String getColourScheme()
+    {
+        return this._colourScheme;
+    } //-- java.lang.String getColourScheme() 
+
+    /**
+     * Returns the value of field 'maxColour'.
+     * 
+     * @return int
+     * @return the value of field 'maxColour'.
+     */
+    public int getMaxColour()
+    {
+        return this._maxColour;
+    } //-- int getMaxColour() 
+
+    /**
+     * Returns the value of field 'minColour'.
+     * 
+     * @return int
+     * @return the value of field 'minColour'.
+     */
+    public int getMinColour()
+    {
+        return this._minColour;
+    } //-- int getMinColour() 
+
+    /**
+     * Returns the value of field 'threshold'.
+     * 
+     * @return float
+     * @return the value of field 'threshold'.
+     */
+    public float getThreshold()
+    {
+        return this._threshold;
+    } //-- float getThreshold() 
+
+    /**
+     * Method hasAboveThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasAboveThreshold()
+    {
+        return this._has_aboveThreshold;
+    } //-- boolean hasAboveThreshold() 
+
+    /**
+     * Method hasMaxColour
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasMaxColour()
+    {
+        return this._has_maxColour;
+    } //-- boolean hasMaxColour() 
+
+    /**
+     * Method hasMinColour
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasMinColour()
+    {
+        return this._has_minColour;
+    } //-- boolean hasMinColour() 
+
+    /**
+     * Method hasThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasThreshold()
+    {
+        return this._has_threshold;
+    } //-- boolean hasThreshold() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'aboveThreshold'.
+     * 
+     * @param aboveThreshold the value of field 'aboveThreshold'.
+     */
+    public void setAboveThreshold(int aboveThreshold)
+    {
+        this._aboveThreshold = aboveThreshold;
+        this._has_aboveThreshold = true;
+    } //-- void setAboveThreshold(int) 
+
+    /**
+     * Sets the value of field 'annotation'.
+     * 
+     * @param annotation the value of field 'annotation'.
+     */
+    public void setAnnotation(java.lang.String annotation)
+    {
+        this._annotation = annotation;
+    } //-- void setAnnotation(java.lang.String) 
+
+    /**
+     * Sets the value of field 'colourScheme'.
+     * 
+     * @param colourScheme the value of field 'colourScheme'.
+     */
+    public void setColourScheme(java.lang.String colourScheme)
+    {
+        this._colourScheme = colourScheme;
+    } //-- void setColourScheme(java.lang.String) 
+
+    /**
+     * Sets the value of field 'maxColour'.
+     * 
+     * @param maxColour the value of field 'maxColour'.
+     */
+    public void setMaxColour(int maxColour)
+    {
+        this._maxColour = maxColour;
+        this._has_maxColour = true;
+    } //-- void setMaxColour(int) 
+
+    /**
+     * Sets the value of field 'minColour'.
+     * 
+     * @param minColour the value of field 'minColour'.
+     */
+    public void setMinColour(int minColour)
+    {
+        this._minColour = minColour;
+        this._has_minColour = true;
+    } //-- void setMinColour(int) 
+
+    /**
+     * Sets the value of field 'threshold'.
+     * 
+     * @param threshold the value of field 'threshold'.
+     */
+    public void setThreshold(float threshold)
+    {
+        this._threshold = threshold;
+        this._has_threshold = true;
+    } //-- void setThreshold(float) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
new file mode 100755
index 0000000..c3c06e6
--- /dev/null
+++ b/src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
@@ -0,0 +1,406 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AnnotationColoursDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AnnotationColoursDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "AnnotationColours";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _aboveThreshold
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                if(!target.hasAboveThreshold())
+                    return null;
+                return new java.lang.Integer(target.getAboveThreshold());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteAboveThreshold();
+                        return;
+                    }
+                    target.setAboveThreshold( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _aboveThreshold
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _annotation
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                return target.getAnnotation();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    target.setAnnotation( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _annotation
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _minColour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                if(!target.hasMinColour())
+                    return null;
+                return new java.lang.Integer(target.getMinColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteMinColour();
+                        return;
+                    }
+                    target.setMinColour( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _minColour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _maxColour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                if(!target.hasMaxColour())
+                    return null;
+                return new java.lang.Integer(target.getMaxColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteMaxColour();
+                        return;
+                    }
+                    target.setMaxColour( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _maxColour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _colourScheme
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                return target.getColourScheme();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    target.setColourScheme( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _colourScheme
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _threshold
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationColours target = (AnnotationColours) object;
+                if(!target.hasThreshold())
+                    return null;
+                return new java.lang.Float(target.getThreshold());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationColours target = (AnnotationColours) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteThreshold();
+                        return;
+                    }
+                    target.setThreshold( ((java.lang.Float)value).floatValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _threshold
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            FloatValidator typeValidator = new FloatValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- jalview.schemabinding.version2.AnnotationColoursDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.AnnotationColours.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/AnnotationDescriptor.java
new file mode 100755
index 0000000..b2290fe
--- /dev/null
+++ b/src/jalview/schemabinding/version2/AnnotationDescriptor.java
@@ -0,0 +1,520 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AnnotationDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AnnotationDescriptor() {
+        super();
+        nsURI = "www.vamsas.ac.uk/jalview/version2";
+        xmlName = "Annotation";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _graph
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Annotation target = (Annotation) object;
+                if(!target.hasGraph())
+                    return null;
+                return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Annotation target = (Annotation) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setGraph( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _graph
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _graphType
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphType", "graphType", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Annotation target = (Annotation) object;
+                if(!target.hasGraphType())
+                    return null;
+                return new java.lang.Integer(target.getGraphType());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Annotation target = (Annotation) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteGraphType();
+                        return;
+                    }
+                    target.setGraphType( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _graphType
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _sequenceRef
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Annotation target = (Annotation) object;
+                return target.getSequenceRef();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Annotation target = (Annotation) object;
+                    target.setSequenceRef( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _sequenceRef
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _graphColour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Annotation target = (Annotation) object;
+                if(!target.hasGraphColour())
+                    return null;
+                return new java.lang.Integer(target.getGraphColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Annotation target = (Annotation) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteGraphColour();
+                        return;
+                    }
+                    target.setGraphColour( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _graphColour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _graphGroup
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Annotation target = (Annotation) object;
+                if(!target.hasGraphGroup())
+                    return null;
+                return new java.lang.Integer(target.getGraphGroup());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Annotation target = (Annotation) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteGraphGroup();
+                        return;
+                    }
+                    target.setGraphGroup( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _graphGroup
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _annotationElementList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Annotation target = (Annotation) object;
+                return target.getAnnotationElement();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Annotation target = (Annotation) object;
+                    target.addAnnotationElement( (jalview.schemabinding.version2.AnnotationElement) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.AnnotationElement();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _annotationElementList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _label
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Annotation target = (Annotation) object;
+                return target.getLabel();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Annotation target = (Annotation) object;
+                    target.setLabel( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _label
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _description
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Annotation target = (Annotation) object;
+                return target.getDescription();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Annotation target = (Annotation) object;
+                    target.setDescription( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _description
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _thresholdLine
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.ThresholdLine.class, "_thresholdLine", "thresholdLine", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Annotation target = (Annotation) object;
+                return target.getThresholdLine();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Annotation target = (Annotation) object;
+                    target.setThresholdLine( (jalview.schemabinding.version2.ThresholdLine) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.ThresholdLine();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _thresholdLine
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.AnnotationDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Annotation.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java
new file mode 100755
index 0000000..2507197
--- /dev/null
+++ b/src/jalview/schemabinding/version2/AnnotationElement.java
@@ -0,0 +1,359 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class AnnotationElement.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AnnotationElement implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _position
+     */
+    private int _position;
+
+    /**
+     * keeps track of state for field: _position
+     */
+    private boolean _has_position;
+
+    /**
+     * Field _colour
+     */
+    private int _colour;
+
+    /**
+     * keeps track of state for field: _colour
+     */
+    private boolean _has_colour;
+
+    /**
+     * Field _displayCharacter
+     */
+    private java.lang.String _displayCharacter;
+
+    /**
+     * Field _description
+     */
+    private java.lang.String _description;
+
+    /**
+     * Field _secondaryStructure
+     */
+    private java.lang.String _secondaryStructure;
+
+    /**
+     * Field _value
+     */
+    private float _value;
+
+    /**
+     * keeps track of state for field: _value
+     */
+    private boolean _has_value;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AnnotationElement() {
+        super();
+    } //-- jalview.schemabinding.version2.AnnotationElement()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method deleteColour
+     * 
+     */
+    public void deleteColour()
+    {
+        this._has_colour= false;
+    } //-- void deleteColour() 
+
+    /**
+     * Method deletePosition
+     * 
+     */
+    public void deletePosition()
+    {
+        this._has_position= false;
+    } //-- void deletePosition() 
+
+    /**
+     * Method deleteValue
+     * 
+     */
+    public void deleteValue()
+    {
+        this._has_value= false;
+    } //-- void deleteValue() 
+
+    /**
+     * Returns the value of field 'colour'.
+     * 
+     * @return int
+     * @return the value of field 'colour'.
+     */
+    public int getColour()
+    {
+        return this._colour;
+    } //-- int getColour() 
+
+    /**
+     * Returns the value of field 'description'.
+     * 
+     * @return String
+     * @return the value of field 'description'.
+     */
+    public java.lang.String getDescription()
+    {
+        return this._description;
+    } //-- java.lang.String getDescription() 
+
+    /**
+     * Returns the value of field 'displayCharacter'.
+     * 
+     * @return String
+     * @return the value of field 'displayCharacter'.
+     */
+    public java.lang.String getDisplayCharacter()
+    {
+        return this._displayCharacter;
+    } //-- java.lang.String getDisplayCharacter() 
+
+    /**
+     * Returns the value of field 'position'.
+     * 
+     * @return int
+     * @return the value of field 'position'.
+     */
+    public int getPosition()
+    {
+        return this._position;
+    } //-- int getPosition() 
+
+    /**
+     * Returns the value of field 'secondaryStructure'.
+     * 
+     * @return String
+     * @return the value of field 'secondaryStructure'.
+     */
+    public java.lang.String getSecondaryStructure()
+    {
+        return this._secondaryStructure;
+    } //-- java.lang.String getSecondaryStructure() 
+
+    /**
+     * Returns the value of field 'value'.
+     * 
+     * @return float
+     * @return the value of field 'value'.
+     */
+    public float getValue()
+    {
+        return this._value;
+    } //-- float getValue() 
+
+    /**
+     * Method hasColour
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasColour()
+    {
+        return this._has_colour;
+    } //-- boolean hasColour() 
+
+    /**
+     * Method hasPosition
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasPosition()
+    {
+        return this._has_position;
+    } //-- boolean hasPosition() 
+
+    /**
+     * Method hasValue
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasValue()
+    {
+        return this._has_value;
+    } //-- boolean hasValue() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'colour'.
+     * 
+     * @param colour the value of field 'colour'.
+     */
+    public void setColour(int colour)
+    {
+        this._colour = colour;
+        this._has_colour = true;
+    } //-- void setColour(int) 
+
+    /**
+     * Sets the value of field 'description'.
+     * 
+     * @param description the value of field 'description'.
+     */
+    public void setDescription(java.lang.String description)
+    {
+        this._description = description;
+    } //-- void setDescription(java.lang.String) 
+
+    /**
+     * Sets the value of field 'displayCharacter'.
+     * 
+     * @param displayCharacter the value of field 'displayCharacter'
+     */
+    public void setDisplayCharacter(java.lang.String displayCharacter)
+    {
+        this._displayCharacter = displayCharacter;
+    } //-- void setDisplayCharacter(java.lang.String) 
+
+    /**
+     * Sets the value of field 'position'.
+     * 
+     * @param position the value of field 'position'.
+     */
+    public void setPosition(int position)
+    {
+        this._position = position;
+        this._has_position = true;
+    } //-- void setPosition(int) 
+
+    /**
+     * Sets the value of field 'secondaryStructure'.
+     * 
+     * @param secondaryStructure the value of field
+     * 'secondaryStructure'.
+     */
+    public void setSecondaryStructure(java.lang.String secondaryStructure)
+    {
+        this._secondaryStructure = secondaryStructure;
+    } //-- void setSecondaryStructure(java.lang.String) 
+
+    /**
+     * Sets the value of field 'value'.
+     * 
+     * @param value the value of field 'value'.
+     */
+    public void setValue(float value)
+    {
+        this._value = value;
+        this._has_value = true;
+    } //-- void setValue(float) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationElement.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
new file mode 100755
index 0000000..0eab95b
--- /dev/null
+++ b/src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
@@ -0,0 +1,413 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AnnotationElementDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AnnotationElementDescriptor() {
+        super();
+        nsURI = "www.vamsas.ac.uk/jalview/version2";
+        xmlName = "annotationElement";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _position
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                if(!target.hasPosition())
+                    return null;
+                return new java.lang.Integer(target.getPosition());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setPosition( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _position
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _colour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                if(!target.hasColour())
+                    return null;
+                return new java.lang.Integer(target.getColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteColour();
+                        return;
+                    }
+                    target.setColour( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _colour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _displayCharacter
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                return target.getDisplayCharacter();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    target.setDisplayCharacter( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _displayCharacter
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _description
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                return target.getDescription();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    target.setDescription( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _description
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _secondaryStructure
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                return target.getSecondaryStructure();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    target.setSecondaryStructure( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _secondaryStructure
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setLength(1);
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _value
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_value", "value", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                if(!target.hasValue())
+                    return null;
+                return new java.lang.Float(target.getValue());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteValue();
+                        return;
+                    }
+                    target.setValue( ((java.lang.Float)value).floatValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _value
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            FloatValidator typeValidator = new FloatValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.AnnotationElementDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.AnnotationElement.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java
new file mode 100755
index 0000000..bcc4642
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Colour.java
@@ -0,0 +1,173 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Colour.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Colour implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _name
+     */
+    private java.lang.String _name;
+
+    /**
+     * Field _RGB
+     */
+    private java.lang.String _RGB;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Colour() {
+        super();
+    } //-- jalview.schemabinding.version2.Colour()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'name'.
+     * 
+     * @return String
+     * @return the value of field 'name'.
+     */
+    public java.lang.String getName()
+    {
+        return this._name;
+    } //-- java.lang.String getName() 
+
+    /**
+     * Returns the value of field 'RGB'.
+     * 
+     * @return String
+     * @return the value of field 'RGB'.
+     */
+    public java.lang.String getRGB()
+    {
+        return this._RGB;
+    } //-- java.lang.String getRGB() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'name'.
+     * 
+     * @param name the value of field 'name'.
+     */
+    public void setName(java.lang.String name)
+    {
+        this._name = name;
+    } //-- void setName(java.lang.String) 
+
+    /**
+     * Sets the value of field 'RGB'.
+     * 
+     * @param RGB the value of field 'RGB'.
+     */
+    public void setRGB(java.lang.String RGB)
+    {
+        this._RGB = RGB;
+    } //-- void setRGB(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.Colour.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/ColourDescriptor.java b/src/jalview/schemabinding/version2/ColourDescriptor.java
new file mode 100755
index 0000000..7aa3a82
--- /dev/null
+++ b/src/jalview/schemabinding/version2/ColourDescriptor.java
@@ -0,0 +1,243 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class ColourDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public ColourDescriptor() {
+        super();
+        xmlName = "colour";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _name
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Colour target = (Colour) object;
+                return target.getName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Colour target = (Colour) object;
+                    target.setName( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _name
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _RGB
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Colour target = (Colour) object;
+                return target.getRGB();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Colour target = (Colour) object;
+                    target.setRGB( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _RGB
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- jalview.schemabinding.version2.ColourDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Colour.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java
new file mode 100644
index 0000000..576a4ad
--- /dev/null
+++ b/src/jalview/schemabinding/version2/DBRef.java
@@ -0,0 +1,199 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class DBRef.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class DBRef implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _source
+     */
+    private java.lang.String _source;
+
+    /**
+     * Field _version
+     */
+    private java.lang.String _version;
+
+    /**
+     * Field _accessionId
+     */
+    private java.lang.String _accessionId;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public DBRef() {
+        super();
+    } //-- jalview.schemabinding.version2.DBRef()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'accessionId'.
+     * 
+     * @return String
+     * @return the value of field 'accessionId'.
+     */
+    public java.lang.String getAccessionId()
+    {
+        return this._accessionId;
+    } //-- java.lang.String getAccessionId() 
+
+    /**
+     * Returns the value of field 'source'.
+     * 
+     * @return String
+     * @return the value of field 'source'.
+     */
+    public java.lang.String getSource()
+    {
+        return this._source;
+    } //-- java.lang.String getSource() 
+
+    /**
+     * Returns the value of field 'version'.
+     * 
+     * @return String
+     * @return the value of field 'version'.
+     */
+    public java.lang.String getVersion()
+    {
+        return this._version;
+    } //-- java.lang.String getVersion() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'accessionId'.
+     * 
+     * @param accessionId the value of field 'accessionId'.
+     */
+    public void setAccessionId(java.lang.String accessionId)
+    {
+        this._accessionId = accessionId;
+    } //-- void setAccessionId(java.lang.String) 
+
+    /**
+     * Sets the value of field 'source'.
+     * 
+     * @param source the value of field 'source'.
+     */
+    public void setSource(java.lang.String source)
+    {
+        this._source = source;
+    } //-- void setSource(java.lang.String) 
+
+    /**
+     * Sets the value of field 'version'.
+     * 
+     * @param version the value of field 'version'.
+     */
+    public void setVersion(java.lang.String version)
+    {
+        this._version = version;
+    } //-- void setVersion(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/DBRefDescriptor.java b/src/jalview/schemabinding/version2/DBRefDescriptor.java
new file mode 100644
index 0000000..939d5b1
--- /dev/null
+++ b/src/jalview/schemabinding/version2/DBRefDescriptor.java
@@ -0,0 +1,278 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class DBRefDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public DBRefDescriptor() {
+        super();
+        nsURI = "www.vamsas.ac.uk/jalview/version2";
+        xmlName = "DBRef";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _source
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                DBRef target = (DBRef) object;
+                return target.getSource();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    DBRef target = (DBRef) object;
+                    target.setSource( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _source
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _version
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                DBRef target = (DBRef) object;
+                return target.getVersion();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    DBRef target = (DBRef) object;
+                    target.setVersion( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _version
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _accessionId
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                DBRef target = (DBRef) object;
+                return target.getAccessionId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    DBRef target = (DBRef) object;
+                    target.setAccessionId( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _accessionId
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- jalview.schemabinding.version2.DBRefDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.DBRef.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java
new file mode 100755
index 0000000..305e287
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Feature.java
@@ -0,0 +1,537 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Feature.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Feature implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _begin
+     */
+    private int _begin;
+
+    /**
+     * keeps track of state for field: _begin
+     */
+    private boolean _has_begin;
+
+    /**
+     * Field _end
+     */
+    private int _end;
+
+    /**
+     * keeps track of state for field: _end
+     */
+    private boolean _has_end;
+
+    /**
+     * Field _type
+     */
+    private java.lang.String _type;
+
+    /**
+     * Field _description
+     */
+    private java.lang.String _description;
+
+    /**
+     * Field _status
+     */
+    private java.lang.String _status;
+
+    /**
+     * Field _featureGroup
+     */
+    private java.lang.String _featureGroup;
+
+    /**
+     * Field _score
+     */
+    private float _score;
+
+    /**
+     * keeps track of state for field: _score
+     */
+    private boolean _has_score;
+
+    /**
+     * Field _otherDataList
+     */
+    private java.util.Vector _otherDataList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Feature() {
+        super();
+        _otherDataList = new Vector();
+    } //-- jalview.schemabinding.version2.Feature()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addOtherData
+     * 
+     * 
+     * 
+     * @param vOtherData
+     */
+    public void addOtherData(jalview.schemabinding.version2.OtherData vOtherData)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _otherDataList.addElement(vOtherData);
+    } //-- void addOtherData(jalview.schemabinding.version2.OtherData) 
+
+    /**
+     * Method addOtherData
+     * 
+     * 
+     * 
+     * @param index
+     * @param vOtherData
+     */
+    public void addOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _otherDataList.insertElementAt(vOtherData, index);
+    } //-- void addOtherData(int, jalview.schemabinding.version2.OtherData) 
+
+    /**
+     * Method deleteBegin
+     * 
+     */
+    public void deleteBegin()
+    {
+        this._has_begin= false;
+    } //-- void deleteBegin() 
+
+    /**
+     * Method deleteEnd
+     * 
+     */
+    public void deleteEnd()
+    {
+        this._has_end= false;
+    } //-- void deleteEnd() 
+
+    /**
+     * Method deleteScore
+     * 
+     */
+    public void deleteScore()
+    {
+        this._has_score= false;
+    } //-- void deleteScore() 
+
+    /**
+     * Method enumerateOtherData
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateOtherData()
+    {
+        return _otherDataList.elements();
+    } //-- java.util.Enumeration enumerateOtherData() 
+
+    /**
+     * Returns the value of field 'begin'.
+     * 
+     * @return int
+     * @return the value of field 'begin'.
+     */
+    public int getBegin()
+    {
+        return this._begin;
+    } //-- int getBegin() 
+
+    /**
+     * Returns the value of field 'description'.
+     * 
+     * @return String
+     * @return the value of field 'description'.
+     */
+    public java.lang.String getDescription()
+    {
+        return this._description;
+    } //-- java.lang.String getDescription() 
+
+    /**
+     * Returns the value of field 'end'.
+     * 
+     * @return int
+     * @return the value of field 'end'.
+     */
+    public int getEnd()
+    {
+        return this._end;
+    } //-- int getEnd() 
+
+    /**
+     * Returns the value of field 'featureGroup'.
+     * 
+     * @return String
+     * @return the value of field 'featureGroup'.
+     */
+    public java.lang.String getFeatureGroup()
+    {
+        return this._featureGroup;
+    } //-- java.lang.String getFeatureGroup() 
+
+    /**
+     * Method getOtherData
+     * 
+     * 
+     * 
+     * @param index
+     * @return OtherData
+     */
+    public jalview.schemabinding.version2.OtherData getOtherData(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _otherDataList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(index);
+    } //-- jalview.schemabinding.version2.OtherData getOtherData(int) 
+
+    /**
+     * Method getOtherData
+     * 
+     * 
+     * 
+     * @return OtherData
+     */
+    public jalview.schemabinding.version2.OtherData[] getOtherData()
+    {
+        int size = _otherDataList.size();
+        jalview.schemabinding.version2.OtherData[] mArray = new jalview.schemabinding.version2.OtherData[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.OtherData[] getOtherData() 
+
+    /**
+     * Method getOtherDataCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getOtherDataCount()
+    {
+        return _otherDataList.size();
+    } //-- int getOtherDataCount() 
+
+    /**
+     * Returns the value of field 'score'.
+     * 
+     * @return float
+     * @return the value of field 'score'.
+     */
+    public float getScore()
+    {
+        return this._score;
+    } //-- float getScore() 
+
+    /**
+     * Returns the value of field 'status'.
+     * 
+     * @return String
+     * @return the value of field 'status'.
+     */
+    public java.lang.String getStatus()
+    {
+        return this._status;
+    } //-- java.lang.String getStatus() 
+
+    /**
+     * Returns the value of field 'type'.
+     * 
+     * @return String
+     * @return the value of field 'type'.
+     */
+    public java.lang.String getType()
+    {
+        return this._type;
+    } //-- java.lang.String getType() 
+
+    /**
+     * Method hasBegin
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasBegin()
+    {
+        return this._has_begin;
+    } //-- boolean hasBegin() 
+
+    /**
+     * Method hasEnd
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasEnd()
+    {
+        return this._has_end;
+    } //-- boolean hasEnd() 
+
+    /**
+     * Method hasScore
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasScore()
+    {
+        return this._has_score;
+    } //-- boolean hasScore() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllOtherData
+     * 
+     */
+    public void removeAllOtherData()
+    {
+        _otherDataList.removeAllElements();
+    } //-- void removeAllOtherData() 
+
+    /**
+     * Method removeOtherData
+     * 
+     * 
+     * 
+     * @param index
+     * @return OtherData
+     */
+    public jalview.schemabinding.version2.OtherData removeOtherData(int index)
+    {
+        java.lang.Object obj = _otherDataList.elementAt(index);
+        _otherDataList.removeElementAt(index);
+        return (jalview.schemabinding.version2.OtherData) obj;
+    } //-- jalview.schemabinding.version2.OtherData removeOtherData(int) 
+
+    /**
+     * Sets the value of field 'begin'.
+     * 
+     * @param begin the value of field 'begin'.
+     */
+    public void setBegin(int begin)
+    {
+        this._begin = begin;
+        this._has_begin = true;
+    } //-- void setBegin(int) 
+
+    /**
+     * Sets the value of field 'description'.
+     * 
+     * @param description the value of field 'description'.
+     */
+    public void setDescription(java.lang.String description)
+    {
+        this._description = description;
+    } //-- void setDescription(java.lang.String) 
+
+    /**
+     * Sets the value of field 'end'.
+     * 
+     * @param end the value of field 'end'.
+     */
+    public void setEnd(int end)
+    {
+        this._end = end;
+        this._has_end = true;
+    } //-- void setEnd(int) 
+
+    /**
+     * Sets the value of field 'featureGroup'.
+     * 
+     * @param featureGroup the value of field 'featureGroup'.
+     */
+    public void setFeatureGroup(java.lang.String featureGroup)
+    {
+        this._featureGroup = featureGroup;
+    } //-- void setFeatureGroup(java.lang.String) 
+
+    /**
+     * Method setOtherData
+     * 
+     * 
+     * 
+     * @param index
+     * @param vOtherData
+     */
+    public void setOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _otherDataList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _otherDataList.setElementAt(vOtherData, index);
+    } //-- void setOtherData(int, jalview.schemabinding.version2.OtherData) 
+
+    /**
+     * Method setOtherData
+     * 
+     * 
+     * 
+     * @param otherDataArray
+     */
+    public void setOtherData(jalview.schemabinding.version2.OtherData[] otherDataArray)
+    {
+        //-- copy array
+        _otherDataList.removeAllElements();
+        for (int i = 0; i < otherDataArray.length; i++) {
+            _otherDataList.addElement(otherDataArray[i]);
+        }
+    } //-- void setOtherData(jalview.schemabinding.version2.OtherData) 
+
+    /**
+     * Sets the value of field 'score'.
+     * 
+     * @param score the value of field 'score'.
+     */
+    public void setScore(float score)
+    {
+        this._score = score;
+        this._has_score = true;
+    } //-- void setScore(float) 
+
+    /**
+     * Sets the value of field 'status'.
+     * 
+     * @param status the value of field 'status'.
+     */
+    public void setStatus(java.lang.String status)
+    {
+        this._status = status;
+    } //-- void setStatus(java.lang.String) 
+
+    /**
+     * Sets the value of field 'type'.
+     * 
+     * @param type the value of field 'type'.
+     */
+    public void setType(java.lang.String type)
+    {
+        this._type = type;
+    } //-- void setType(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/FeatureDescriptor.java b/src/jalview/schemabinding/version2/FeatureDescriptor.java
new file mode 100755
index 0000000..d0b9372
--- /dev/null
+++ b/src/jalview/schemabinding/version2/FeatureDescriptor.java
@@ -0,0 +1,477 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class FeatureDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public FeatureDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "feature";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _begin
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Feature target = (Feature) object;
+                if(!target.hasBegin())
+                    return null;
+                return new java.lang.Integer(target.getBegin());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Feature target = (Feature) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setBegin( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _begin
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _end
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Feature target = (Feature) object;
+                if(!target.hasEnd())
+                    return null;
+                return new java.lang.Integer(target.getEnd());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Feature target = (Feature) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setEnd( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _end
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _type
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Feature target = (Feature) object;
+                return target.getType();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Feature target = (Feature) object;
+                    target.setType( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _type
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _description
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Feature target = (Feature) object;
+                return target.getDescription();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Feature target = (Feature) object;
+                    target.setDescription( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _description
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _status
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Feature target = (Feature) object;
+                return target.getStatus();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Feature target = (Feature) object;
+                    target.setStatus( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _status
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _featureGroup
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Feature target = (Feature) object;
+                return target.getFeatureGroup();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Feature target = (Feature) object;
+                    target.setFeatureGroup( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _featureGroup
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _score
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Feature target = (Feature) object;
+                if(!target.hasScore())
+                    return null;
+                return new java.lang.Float(target.getScore());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Feature target = (Feature) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteScore();
+                        return;
+                    }
+                    target.setScore( ((java.lang.Float)value).floatValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _score
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            FloatValidator typeValidator = new FloatValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _otherDataList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Feature target = (Feature) object;
+                return target.getOtherData();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Feature target = (Feature) object;
+                    target.addOtherData( (jalview.schemabinding.version2.OtherData) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.OtherData();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _otherDataList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.FeatureDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Feature.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java
new file mode 100755
index 0000000..c20a83c
--- /dev/null
+++ b/src/jalview/schemabinding/version2/FeatureSettings.java
@@ -0,0 +1,274 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class FeatureSettings.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureSettings implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _settingList
+     */
+    private java.util.Vector _settingList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public FeatureSettings() {
+        super();
+        _settingList = new Vector();
+    } //-- jalview.schemabinding.version2.FeatureSettings()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addSetting
+     * 
+     * 
+     * 
+     * @param vSetting
+     */
+    public void addSetting(jalview.schemabinding.version2.Setting vSetting)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _settingList.addElement(vSetting);
+    } //-- void addSetting(jalview.schemabinding.version2.Setting) 
+
+    /**
+     * Method addSetting
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSetting
+     */
+    public void addSetting(int index, jalview.schemabinding.version2.Setting vSetting)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _settingList.insertElementAt(vSetting, index);
+    } //-- void addSetting(int, jalview.schemabinding.version2.Setting) 
+
+    /**
+     * Method enumerateSetting
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateSetting()
+    {
+        return _settingList.elements();
+    } //-- java.util.Enumeration enumerateSetting() 
+
+    /**
+     * Method getSetting
+     * 
+     * 
+     * 
+     * @param index
+     * @return Setting
+     */
+    public jalview.schemabinding.version2.Setting getSetting(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _settingList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.Setting) _settingList.elementAt(index);
+    } //-- jalview.schemabinding.version2.Setting getSetting(int) 
+
+    /**
+     * Method getSetting
+     * 
+     * 
+     * 
+     * @return Setting
+     */
+    public jalview.schemabinding.version2.Setting[] getSetting()
+    {
+        int size = _settingList.size();
+        jalview.schemabinding.version2.Setting[] mArray = new jalview.schemabinding.version2.Setting[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.Setting) _settingList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.Setting[] getSetting() 
+
+    /**
+     * Method getSettingCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getSettingCount()
+    {
+        return _settingList.size();
+    } //-- int getSettingCount() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllSetting
+     * 
+     */
+    public void removeAllSetting()
+    {
+        _settingList.removeAllElements();
+    } //-- void removeAllSetting() 
+
+    /**
+     * Method removeSetting
+     * 
+     * 
+     * 
+     * @param index
+     * @return Setting
+     */
+    public jalview.schemabinding.version2.Setting removeSetting(int index)
+    {
+        java.lang.Object obj = _settingList.elementAt(index);
+        _settingList.removeElementAt(index);
+        return (jalview.schemabinding.version2.Setting) obj;
+    } //-- jalview.schemabinding.version2.Setting removeSetting(int) 
+
+    /**
+     * Method setSetting
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSetting
+     */
+    public void setSetting(int index, jalview.schemabinding.version2.Setting vSetting)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _settingList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _settingList.setElementAt(vSetting, index);
+    } //-- void setSetting(int, jalview.schemabinding.version2.Setting) 
+
+    /**
+     * Method setSetting
+     * 
+     * 
+     * 
+     * @param settingArray
+     */
+    public void setSetting(jalview.schemabinding.version2.Setting[] settingArray)
+    {
+        //-- copy array
+        _settingList.removeAllElements();
+        for (int i = 0; i < settingArray.length; i++) {
+            _settingList.addElement(settingArray[i]);
+        }
+    } //-- void setSetting(jalview.schemabinding.version2.Setting) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.FeatureSettings.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
new file mode 100755
index 0000000..219037e
--- /dev/null
+++ b/src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
@@ -0,0 +1,208 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class FeatureSettingsDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public FeatureSettingsDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "FeatureSettings";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _settingList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Setting.class, "_settingList", "setting", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                FeatureSettings target = (FeatureSettings) object;
+                return target.getSetting();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    FeatureSettings target = (FeatureSettings) object;
+                    target.addSetting( (jalview.schemabinding.version2.Setting) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Setting();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _settingList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.FeatureSettingsDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.FeatureSettings.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java
new file mode 100755
index 0000000..72321c6
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Features.java
@@ -0,0 +1,118 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Features.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Features extends Feature 
+implements java.io.Serializable
+{
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Features() {
+        super();
+    } //-- jalview.schemabinding.version2.Features()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Features) Unmarshaller.unmarshal(jalview.schemabinding.version2.Features.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/FeaturesDescriptor.java
new file mode 100755
index 0000000..5eea818
--- /dev/null
+++ b/src/jalview/schemabinding/version2/FeaturesDescriptor.java
@@ -0,0 +1,166 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class FeaturesDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class FeaturesDescriptor extends FeatureDescriptor {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public FeaturesDescriptor() {
+        super();
+        setExtendsWithoutFlatten(new FeatureDescriptor());
+        nsURI = "www.jalview.org";
+        xmlName = "features";
+    } //-- jalview.schemabinding.version2.FeaturesDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return super.getExtends();
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        if (identity == null)
+            return super.getIdentity();
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Features.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java
new file mode 100644
index 0000000..5b83e64
--- /dev/null
+++ b/src/jalview/schemabinding/version2/HiddenColumns.java
@@ -0,0 +1,227 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class HiddenColumns.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class HiddenColumns implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _start
+     */
+    private int _start;
+
+    /**
+     * keeps track of state for field: _start
+     */
+    private boolean _has_start;
+
+    /**
+     * Field _end
+     */
+    private int _end;
+
+    /**
+     * keeps track of state for field: _end
+     */
+    private boolean _has_end;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public HiddenColumns() {
+        super();
+    } //-- jalview.schemabinding.version2.HiddenColumns()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method deleteEnd
+     * 
+     */
+    public void deleteEnd()
+    {
+        this._has_end= false;
+    } //-- void deleteEnd() 
+
+    /**
+     * Method deleteStart
+     * 
+     */
+    public void deleteStart()
+    {
+        this._has_start= false;
+    } //-- void deleteStart() 
+
+    /**
+     * Returns the value of field 'end'.
+     * 
+     * @return int
+     * @return the value of field 'end'.
+     */
+    public int getEnd()
+    {
+        return this._end;
+    } //-- int getEnd() 
+
+    /**
+     * Returns the value of field 'start'.
+     * 
+     * @return int
+     * @return the value of field 'start'.
+     */
+    public int getStart()
+    {
+        return this._start;
+    } //-- int getStart() 
+
+    /**
+     * Method hasEnd
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasEnd()
+    {
+        return this._has_end;
+    } //-- boolean hasEnd() 
+
+    /**
+     * Method hasStart
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasStart()
+    {
+        return this._has_start;
+    } //-- boolean hasStart() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'end'.
+     * 
+     * @param end the value of field 'end'.
+     */
+    public void setEnd(int end)
+    {
+        this._end = end;
+        this._has_end = true;
+    } //-- void setEnd(int) 
+
+    /**
+     * Sets the value of field 'start'.
+     * 
+     * @param start the value of field 'start'.
+     */
+    public void setStart(int start)
+    {
+        this._start = start;
+        this._has_start = true;
+    } //-- void setStart(int) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
new file mode 100644
index 0000000..df99628
--- /dev/null
+++ b/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
@@ -0,0 +1,252 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class HiddenColumnsDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public HiddenColumnsDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "hiddenColumns";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _start
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                HiddenColumns target = (HiddenColumns) object;
+                if(!target.hasStart())
+                    return null;
+                return new java.lang.Integer(target.getStart());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    HiddenColumns target = (HiddenColumns) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteStart();
+                        return;
+                    }
+                    target.setStart( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _start
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _end
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                HiddenColumns target = (HiddenColumns) object;
+                if(!target.hasEnd())
+                    return null;
+                return new java.lang.Integer(target.getEnd());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    HiddenColumns target = (HiddenColumns) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteEnd();
+                        return;
+                    }
+                    target.setEnd( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _end
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- jalview.schemabinding.version2.HiddenColumnsDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.HiddenColumns.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
new file mode 100755
index 0000000..f3fe3e9
--- /dev/null
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -0,0 +1,750 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class JGroup.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JGroup implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _start
+     */
+    private int _start;
+
+    /**
+     * keeps track of state for field: _start
+     */
+    private boolean _has_start;
+
+    /**
+     * Field _end
+     */
+    private int _end;
+
+    /**
+     * keeps track of state for field: _end
+     */
+    private boolean _has_end;
+
+    /**
+     * Field _name
+     */
+    private java.lang.String _name;
+
+    /**
+     * Field _colour
+     */
+    private java.lang.String _colour;
+
+    /**
+     * Field _consThreshold
+     */
+    private int _consThreshold;
+
+    /**
+     * keeps track of state for field: _consThreshold
+     */
+    private boolean _has_consThreshold;
+
+    /**
+     * Field _pidThreshold
+     */
+    private int _pidThreshold;
+
+    /**
+     * keeps track of state for field: _pidThreshold
+     */
+    private boolean _has_pidThreshold;
+
+    /**
+     * Field _outlineColour
+     */
+    private int _outlineColour;
+
+    /**
+     * keeps track of state for field: _outlineColour
+     */
+    private boolean _has_outlineColour;
+
+    /**
+     * Field _displayBoxes
+     */
+    private boolean _displayBoxes;
+
+    /**
+     * keeps track of state for field: _displayBoxes
+     */
+    private boolean _has_displayBoxes;
+
+    /**
+     * Field _displayText
+     */
+    private boolean _displayText;
+
+    /**
+     * keeps track of state for field: _displayText
+     */
+    private boolean _has_displayText;
+
+    /**
+     * Field _colourText
+     */
+    private boolean _colourText;
+
+    /**
+     * keeps track of state for field: _colourText
+     */
+    private boolean _has_colourText;
+
+    /**
+     * Field _seqList
+     */
+    private java.util.Vector _seqList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JGroup() {
+        super();
+        _seqList = new Vector();
+    } //-- jalview.schemabinding.version2.JGroup()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addSeq
+     * 
+     * 
+     * 
+     * @param vSeq
+     */
+    public void addSeq(int vSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _seqList.addElement(new java.lang.Integer(vSeq));
+    } //-- void addSeq(int) 
+
+    /**
+     * Method addSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSeq
+     */
+    public void addSeq(int index, int vSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
+    } //-- void addSeq(int, int) 
+
+    /**
+     * Method deleteColourText
+     * 
+     */
+    public void deleteColourText()
+    {
+        this._has_colourText= false;
+    } //-- void deleteColourText() 
+
+    /**
+     * Method deleteConsThreshold
+     * 
+     */
+    public void deleteConsThreshold()
+    {
+        this._has_consThreshold= false;
+    } //-- void deleteConsThreshold() 
+
+    /**
+     * Method deleteDisplayBoxes
+     * 
+     */
+    public void deleteDisplayBoxes()
+    {
+        this._has_displayBoxes= false;
+    } //-- void deleteDisplayBoxes() 
+
+    /**
+     * Method deleteDisplayText
+     * 
+     */
+    public void deleteDisplayText()
+    {
+        this._has_displayText= false;
+    } //-- void deleteDisplayText() 
+
+    /**
+     * Method deleteEnd
+     * 
+     */
+    public void deleteEnd()
+    {
+        this._has_end= false;
+    } //-- void deleteEnd() 
+
+    /**
+     * Method deleteOutlineColour
+     * 
+     */
+    public void deleteOutlineColour()
+    {
+        this._has_outlineColour= false;
+    } //-- void deleteOutlineColour() 
+
+    /**
+     * Method deletePidThreshold
+     * 
+     */
+    public void deletePidThreshold()
+    {
+        this._has_pidThreshold= false;
+    } //-- void deletePidThreshold() 
+
+    /**
+     * Method deleteStart
+     * 
+     */
+    public void deleteStart()
+    {
+        this._has_start= false;
+    } //-- void deleteStart() 
+
+    /**
+     * Method enumerateSeq
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateSeq()
+    {
+        return _seqList.elements();
+    } //-- java.util.Enumeration enumerateSeq() 
+
+    /**
+     * Returns the value of field 'colour'.
+     * 
+     * @return String
+     * @return the value of field 'colour'.
+     */
+    public java.lang.String getColour()
+    {
+        return this._colour;
+    } //-- java.lang.String getColour() 
+
+    /**
+     * Returns the value of field 'colourText'.
+     * 
+     * @return boolean
+     * @return the value of field 'colourText'.
+     */
+    public boolean getColourText()
+    {
+        return this._colourText;
+    } //-- boolean getColourText() 
+
+    /**
+     * Returns the value of field 'consThreshold'.
+     * 
+     * @return int
+     * @return the value of field 'consThreshold'.
+     */
+    public int getConsThreshold()
+    {
+        return this._consThreshold;
+    } //-- int getConsThreshold() 
+
+    /**
+     * Returns the value of field 'displayBoxes'.
+     * 
+     * @return boolean
+     * @return the value of field 'displayBoxes'.
+     */
+    public boolean getDisplayBoxes()
+    {
+        return this._displayBoxes;
+    } //-- boolean getDisplayBoxes() 
+
+    /**
+     * Returns the value of field 'displayText'.
+     * 
+     * @return boolean
+     * @return the value of field 'displayText'.
+     */
+    public boolean getDisplayText()
+    {
+        return this._displayText;
+    } //-- boolean getDisplayText() 
+
+    /**
+     * Returns the value of field 'end'.
+     * 
+     * @return int
+     * @return the value of field 'end'.
+     */
+    public int getEnd()
+    {
+        return this._end;
+    } //-- int getEnd() 
+
+    /**
+     * Returns the value of field 'name'.
+     * 
+     * @return String
+     * @return the value of field 'name'.
+     */
+    public java.lang.String getName()
+    {
+        return this._name;
+    } //-- java.lang.String getName() 
+
+    /**
+     * Returns the value of field 'outlineColour'.
+     * 
+     * @return int
+     * @return the value of field 'outlineColour'.
+     */
+    public int getOutlineColour()
+    {
+        return this._outlineColour;
+    } //-- int getOutlineColour() 
+
+    /**
+     * Returns the value of field 'pidThreshold'.
+     * 
+     * @return int
+     * @return the value of field 'pidThreshold'.
+     */
+    public int getPidThreshold()
+    {
+        return this._pidThreshold;
+    } //-- int getPidThreshold() 
+
+    /**
+     * Method getSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @return int
+     */
+    public int getSeq(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _seqList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return ((java.lang.Integer)_seqList.elementAt(index)).intValue();
+    } //-- int getSeq(int) 
+
+    /**
+     * Method getSeq
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int[] getSeq()
+    {
+        int size = _seqList.size();
+        int[] mArray = new int[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();
+        }
+        return mArray;
+    } //-- int[] getSeq() 
+
+    /**
+     * Method getSeqCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getSeqCount()
+    {
+        return _seqList.size();
+    } //-- int getSeqCount() 
+
+    /**
+     * Returns the value of field 'start'.
+     * 
+     * @return int
+     * @return the value of field 'start'.
+     */
+    public int getStart()
+    {
+        return this._start;
+    } //-- int getStart() 
+
+    /**
+     * Method hasColourText
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasColourText()
+    {
+        return this._has_colourText;
+    } //-- boolean hasColourText() 
+
+    /**
+     * Method hasConsThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasConsThreshold()
+    {
+        return this._has_consThreshold;
+    } //-- boolean hasConsThreshold() 
+
+    /**
+     * Method hasDisplayBoxes
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasDisplayBoxes()
+    {
+        return this._has_displayBoxes;
+    } //-- boolean hasDisplayBoxes() 
+
+    /**
+     * Method hasDisplayText
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasDisplayText()
+    {
+        return this._has_displayText;
+    } //-- boolean hasDisplayText() 
+
+    /**
+     * Method hasEnd
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasEnd()
+    {
+        return this._has_end;
+    } //-- boolean hasEnd() 
+
+    /**
+     * Method hasOutlineColour
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasOutlineColour()
+    {
+        return this._has_outlineColour;
+    } //-- boolean hasOutlineColour() 
+
+    /**
+     * Method hasPidThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasPidThreshold()
+    {
+        return this._has_pidThreshold;
+    } //-- boolean hasPidThreshold() 
+
+    /**
+     * Method hasStart
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasStart()
+    {
+        return this._has_start;
+    } //-- boolean hasStart() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllSeq
+     * 
+     */
+    public void removeAllSeq()
+    {
+        _seqList.removeAllElements();
+    } //-- void removeAllSeq() 
+
+    /**
+     * Method removeSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @return int
+     */
+    public int removeSeq(int index)
+    {
+        java.lang.Object obj = _seqList.elementAt(index);
+        _seqList.removeElementAt(index);
+        return ((java.lang.Integer)obj).intValue();
+    } //-- int removeSeq(int) 
+
+    /**
+     * Sets the value of field 'colour'.
+     * 
+     * @param colour the value of field 'colour'.
+     */
+    public void setColour(java.lang.String colour)
+    {
+        this._colour = colour;
+    } //-- void setColour(java.lang.String) 
+
+    /**
+     * Sets the value of field 'colourText'.
+     * 
+     * @param colourText the value of field 'colourText'.
+     */
+    public void setColourText(boolean colourText)
+    {
+        this._colourText = colourText;
+        this._has_colourText = true;
+    } //-- void setColourText(boolean) 
+
+    /**
+     * Sets the value of field 'consThreshold'.
+     * 
+     * @param consThreshold the value of field 'consThreshold'.
+     */
+    public void setConsThreshold(int consThreshold)
+    {
+        this._consThreshold = consThreshold;
+        this._has_consThreshold = true;
+    } //-- void setConsThreshold(int) 
+
+    /**
+     * Sets the value of field 'displayBoxes'.
+     * 
+     * @param displayBoxes the value of field 'displayBoxes'.
+     */
+    public void setDisplayBoxes(boolean displayBoxes)
+    {
+        this._displayBoxes = displayBoxes;
+        this._has_displayBoxes = true;
+    } //-- void setDisplayBoxes(boolean) 
+
+    /**
+     * Sets the value of field 'displayText'.
+     * 
+     * @param displayText the value of field 'displayText'.
+     */
+    public void setDisplayText(boolean displayText)
+    {
+        this._displayText = displayText;
+        this._has_displayText = true;
+    } //-- void setDisplayText(boolean) 
+
+    /**
+     * Sets the value of field 'end'.
+     * 
+     * @param end the value of field 'end'.
+     */
+    public void setEnd(int end)
+    {
+        this._end = end;
+        this._has_end = true;
+    } //-- void setEnd(int) 
+
+    /**
+     * Sets the value of field 'name'.
+     * 
+     * @param name the value of field 'name'.
+     */
+    public void setName(java.lang.String name)
+    {
+        this._name = name;
+    } //-- void setName(java.lang.String) 
+
+    /**
+     * Sets the value of field 'outlineColour'.
+     * 
+     * @param outlineColour the value of field 'outlineColour'.
+     */
+    public void setOutlineColour(int outlineColour)
+    {
+        this._outlineColour = outlineColour;
+        this._has_outlineColour = true;
+    } //-- void setOutlineColour(int) 
+
+    /**
+     * Sets the value of field 'pidThreshold'.
+     * 
+     * @param pidThreshold the value of field 'pidThreshold'.
+     */
+    public void setPidThreshold(int pidThreshold)
+    {
+        this._pidThreshold = pidThreshold;
+        this._has_pidThreshold = true;
+    } //-- void setPidThreshold(int) 
+
+    /**
+     * Method setSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSeq
+     */
+    public void setSeq(int index, int vSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _seqList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _seqList.setElementAt(new java.lang.Integer(vSeq), index);
+    } //-- void setSeq(int, int) 
+
+    /**
+     * Method setSeq
+     * 
+     * 
+     * 
+     * @param seqArray
+     */
+    public void setSeq(int[] seqArray)
+    {
+        //-- copy array
+        _seqList.removeAllElements();
+        for (int i = 0; i < seqArray.length; i++) {
+            _seqList.addElement(new java.lang.Integer(seqArray[i]));
+        }
+    } //-- void setSeq(int) 
+
+    /**
+     * Sets the value of field 'start'.
+     * 
+     * @param start the value of field 'start'.
+     */
+    public void setStart(int start)
+    {
+        this._start = start;
+        this._has_start = true;
+    } //-- void setStart(int) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/JGroupDescriptor.java b/src/jalview/schemabinding/version2/JGroupDescriptor.java
new file mode 100755
index 0000000..231c631
--- /dev/null
+++ b/src/jalview/schemabinding/version2/JGroupDescriptor.java
@@ -0,0 +1,614 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class JGroupDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JGroupDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "JGroup";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _start
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                if(!target.hasStart())
+                    return null;
+                return new java.lang.Integer(target.getStart());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteStart();
+                        return;
+                    }
+                    target.setStart( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _start
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _end
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                if(!target.hasEnd())
+                    return null;
+                return new java.lang.Integer(target.getEnd());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteEnd();
+                        return;
+                    }
+                    target.setEnd( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _end
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _name
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                return target.getName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    target.setName( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _name
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _colour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                return target.getColour();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    target.setColour( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _colour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _consThreshold
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                if(!target.hasConsThreshold())
+                    return null;
+                return new java.lang.Integer(target.getConsThreshold());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteConsThreshold();
+                        return;
+                    }
+                    target.setConsThreshold( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _consThreshold
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _pidThreshold
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                if(!target.hasPidThreshold())
+                    return null;
+                return new java.lang.Integer(target.getPidThreshold());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deletePidThreshold();
+                        return;
+                    }
+                    target.setPidThreshold( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _pidThreshold
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _outlineColour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_outlineColour", "outlineColour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                if(!target.hasOutlineColour())
+                    return null;
+                return new java.lang.Integer(target.getOutlineColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteOutlineColour();
+                        return;
+                    }
+                    target.setOutlineColour( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _outlineColour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _displayBoxes
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                if(!target.hasDisplayBoxes())
+                    return null;
+                return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteDisplayBoxes();
+                        return;
+                    }
+                    target.setDisplayBoxes( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _displayBoxes
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _displayText
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayText", "displayText", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                if(!target.hasDisplayText())
+                    return null;
+                return (target.getDisplayText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteDisplayText();
+                        return;
+                    }
+                    target.setDisplayText( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _displayText
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _colourText
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourText", "colourText", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                if(!target.hasColourText())
+                    return null;
+                return (target.getColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteColourText();
+                        return;
+                    }
+                    target.setColourText( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _colourText
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _seqList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JGroup target = (JGroup) object;
+                return target.getSeq();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JGroup target = (JGroup) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.addSeq( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setRequired(true);
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _seqList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.JGroupDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.JGroup.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
new file mode 100755
index 0000000..19e2e6d
--- /dev/null
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -0,0 +1,841 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class JSeq.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JSeq implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _colour
+     */
+    private int _colour;
+
+    /**
+     * keeps track of state for field: _colour
+     */
+    private boolean _has_colour;
+
+    /**
+     * Field _start
+     */
+    private int _start;
+
+    /**
+     * keeps track of state for field: _start
+     */
+    private boolean _has_start;
+
+    /**
+     * Field _end
+     */
+    private int _end;
+
+    /**
+     * keeps track of state for field: _end
+     */
+    private boolean _has_end;
+
+    /**
+     * Field _id
+     */
+    private int _id;
+
+    /**
+     * keeps track of state for field: _id
+     */
+    private boolean _has_id;
+
+    /**
+     * Field _hidden
+     */
+    private boolean _hidden;
+
+    /**
+     * keeps track of state for field: _hidden
+     */
+    private boolean _has_hidden;
+
+    /**
+     * Field _featuresList
+     */
+    private java.util.Vector _featuresList;
+
+    /**
+     * Field _pdbidsList
+     */
+    private java.util.Vector _pdbidsList;
+
+    /**
+     * Field _hiddenSequencesList
+     */
+    private java.util.Vector _hiddenSequencesList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JSeq() {
+        super();
+        _featuresList = new Vector();
+        _pdbidsList = new Vector();
+        _hiddenSequencesList = new Vector();
+    } //-- jalview.schemabinding.version2.JSeq()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addFeatures
+     * 
+     * 
+     * 
+     * @param vFeatures
+     */
+    public void addFeatures(jalview.schemabinding.version2.Features vFeatures)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _featuresList.addElement(vFeatures);
+    } //-- void addFeatures(jalview.schemabinding.version2.Features) 
+
+    /**
+     * Method addFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @param vFeatures
+     */
+    public void addFeatures(int index, jalview.schemabinding.version2.Features vFeatures)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _featuresList.insertElementAt(vFeatures, index);
+    } //-- void addFeatures(int, jalview.schemabinding.version2.Features) 
+
+    /**
+     * Method addHiddenSequences
+     * 
+     * 
+     * 
+     * @param vHiddenSequences
+     */
+    public void addHiddenSequences(int vHiddenSequences)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
+    } //-- void addHiddenSequences(int) 
+
+    /**
+     * Method addHiddenSequences
+     * 
+     * 
+     * 
+     * @param index
+     * @param vHiddenSequences
+     */
+    public void addHiddenSequences(int index, int vHiddenSequences)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences), index);
+    } //-- void addHiddenSequences(int, int) 
+
+    /**
+     * Method addPdbids
+     * 
+     * 
+     * 
+     * @param vPdbids
+     */
+    public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _pdbidsList.addElement(vPdbids);
+    } //-- void addPdbids(jalview.schemabinding.version2.Pdbids) 
+
+    /**
+     * Method addPdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @param vPdbids
+     */
+    public void addPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _pdbidsList.insertElementAt(vPdbids, index);
+    } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids) 
+
+    /**
+     * Method deleteColour
+     * 
+     */
+    public void deleteColour()
+    {
+        this._has_colour= false;
+    } //-- void deleteColour() 
+
+    /**
+     * Method deleteEnd
+     * 
+     */
+    public void deleteEnd()
+    {
+        this._has_end= false;
+    } //-- void deleteEnd() 
+
+    /**
+     * Method deleteHidden
+     * 
+     */
+    public void deleteHidden()
+    {
+        this._has_hidden= false;
+    } //-- void deleteHidden() 
+
+    /**
+     * Method deleteId
+     * 
+     */
+    public void deleteId()
+    {
+        this._has_id= false;
+    } //-- void deleteId() 
+
+    /**
+     * Method deleteStart
+     * 
+     */
+    public void deleteStart()
+    {
+        this._has_start= false;
+    } //-- void deleteStart() 
+
+    /**
+     * Method enumerateFeatures
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateFeatures()
+    {
+        return _featuresList.elements();
+    } //-- java.util.Enumeration enumerateFeatures() 
+
+    /**
+     * Method enumerateHiddenSequences
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateHiddenSequences()
+    {
+        return _hiddenSequencesList.elements();
+    } //-- java.util.Enumeration enumerateHiddenSequences() 
+
+    /**
+     * Method enumeratePdbids
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumeratePdbids()
+    {
+        return _pdbidsList.elements();
+    } //-- java.util.Enumeration enumeratePdbids() 
+
+    /**
+     * Returns the value of field 'colour'.
+     * 
+     * @return int
+     * @return the value of field 'colour'.
+     */
+    public int getColour()
+    {
+        return this._colour;
+    } //-- int getColour() 
+
+    /**
+     * Returns the value of field 'end'.
+     * 
+     * @return int
+     * @return the value of field 'end'.
+     */
+    public int getEnd()
+    {
+        return this._end;
+    } //-- int getEnd() 
+
+    /**
+     * Method getFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @return Features
+     */
+    public jalview.schemabinding.version2.Features getFeatures(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _featuresList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);
+    } //-- jalview.schemabinding.version2.Features getFeatures(int) 
+
+    /**
+     * Method getFeatures
+     * 
+     * 
+     * 
+     * @return Features
+     */
+    public jalview.schemabinding.version2.Features[] getFeatures()
+    {
+        int size = _featuresList.size();
+        jalview.schemabinding.version2.Features[] mArray = new jalview.schemabinding.version2.Features[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.Features[] getFeatures() 
+
+    /**
+     * Method getFeaturesCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getFeaturesCount()
+    {
+        return _featuresList.size();
+    } //-- int getFeaturesCount() 
+
+    /**
+     * Returns the value of field 'hidden'.
+     * 
+     * @return boolean
+     * @return the value of field 'hidden'.
+     */
+    public boolean getHidden()
+    {
+        return this._hidden;
+    } //-- boolean getHidden() 
+
+    /**
+     * Method getHiddenSequences
+     * 
+     * 
+     * 
+     * @param index
+     * @return int
+     */
+    public int getHiddenSequences(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _hiddenSequencesList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();
+    } //-- int getHiddenSequences(int) 
+
+    /**
+     * Method getHiddenSequences
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int[] getHiddenSequences()
+    {
+        int size = _hiddenSequencesList.size();
+        int[] mArray = new int[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();
+        }
+        return mArray;
+    } //-- int[] getHiddenSequences() 
+
+    /**
+     * Method getHiddenSequencesCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getHiddenSequencesCount()
+    {
+        return _hiddenSequencesList.size();
+    } //-- int getHiddenSequencesCount() 
+
+    /**
+     * Returns the value of field 'id'.
+     * 
+     * @return int
+     * @return the value of field 'id'.
+     */
+    public int getId()
+    {
+        return this._id;
+    } //-- int getId() 
+
+    /**
+     * Method getPdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @return Pdbids
+     */
+    public jalview.schemabinding.version2.Pdbids getPdbids(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _pdbidsList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);
+    } //-- jalview.schemabinding.version2.Pdbids getPdbids(int) 
+
+    /**
+     * Method getPdbids
+     * 
+     * 
+     * 
+     * @return Pdbids
+     */
+    public jalview.schemabinding.version2.Pdbids[] getPdbids()
+    {
+        int size = _pdbidsList.size();
+        jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.version2.Pdbids[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.Pdbids[] getPdbids() 
+
+    /**
+     * Method getPdbidsCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getPdbidsCount()
+    {
+        return _pdbidsList.size();
+    } //-- int getPdbidsCount() 
+
+    /**
+     * Returns the value of field 'start'.
+     * 
+     * @return int
+     * @return the value of field 'start'.
+     */
+    public int getStart()
+    {
+        return this._start;
+    } //-- int getStart() 
+
+    /**
+     * Method hasColour
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasColour()
+    {
+        return this._has_colour;
+    } //-- boolean hasColour() 
+
+    /**
+     * Method hasEnd
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasEnd()
+    {
+        return this._has_end;
+    } //-- boolean hasEnd() 
+
+    /**
+     * Method hasHidden
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasHidden()
+    {
+        return this._has_hidden;
+    } //-- boolean hasHidden() 
+
+    /**
+     * Method hasId
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasId()
+    {
+        return this._has_id;
+    } //-- boolean hasId() 
+
+    /**
+     * Method hasStart
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasStart()
+    {
+        return this._has_start;
+    } //-- boolean hasStart() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllFeatures
+     * 
+     */
+    public void removeAllFeatures()
+    {
+        _featuresList.removeAllElements();
+    } //-- void removeAllFeatures() 
+
+    /**
+     * Method removeAllHiddenSequences
+     * 
+     */
+    public void removeAllHiddenSequences()
+    {
+        _hiddenSequencesList.removeAllElements();
+    } //-- void removeAllHiddenSequences() 
+
+    /**
+     * Method removeAllPdbids
+     * 
+     */
+    public void removeAllPdbids()
+    {
+        _pdbidsList.removeAllElements();
+    } //-- void removeAllPdbids() 
+
+    /**
+     * Method removeFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @return Features
+     */
+    public jalview.schemabinding.version2.Features removeFeatures(int index)
+    {
+        java.lang.Object obj = _featuresList.elementAt(index);
+        _featuresList.removeElementAt(index);
+        return (jalview.schemabinding.version2.Features) obj;
+    } //-- jalview.schemabinding.version2.Features removeFeatures(int) 
+
+    /**
+     * Method removeHiddenSequences
+     * 
+     * 
+     * 
+     * @param index
+     * @return int
+     */
+    public int removeHiddenSequences(int index)
+    {
+        java.lang.Object obj = _hiddenSequencesList.elementAt(index);
+        _hiddenSequencesList.removeElementAt(index);
+        return ((java.lang.Integer)obj).intValue();
+    } //-- int removeHiddenSequences(int) 
+
+    /**
+     * Method removePdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @return Pdbids
+     */
+    public jalview.schemabinding.version2.Pdbids removePdbids(int index)
+    {
+        java.lang.Object obj = _pdbidsList.elementAt(index);
+        _pdbidsList.removeElementAt(index);
+        return (jalview.schemabinding.version2.Pdbids) obj;
+    } //-- jalview.schemabinding.version2.Pdbids removePdbids(int) 
+
+    /**
+     * Sets the value of field 'colour'.
+     * 
+     * @param colour the value of field 'colour'.
+     */
+    public void setColour(int colour)
+    {
+        this._colour = colour;
+        this._has_colour = true;
+    } //-- void setColour(int) 
+
+    /**
+     * Sets the value of field 'end'.
+     * 
+     * @param end the value of field 'end'.
+     */
+    public void setEnd(int end)
+    {
+        this._end = end;
+        this._has_end = true;
+    } //-- void setEnd(int) 
+
+    /**
+     * Method setFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @param vFeatures
+     */
+    public void setFeatures(int index, jalview.schemabinding.version2.Features vFeatures)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _featuresList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _featuresList.setElementAt(vFeatures, index);
+    } //-- void setFeatures(int, jalview.schemabinding.version2.Features) 
+
+    /**
+     * Method setFeatures
+     * 
+     * 
+     * 
+     * @param featuresArray
+     */
+    public void setFeatures(jalview.schemabinding.version2.Features[] featuresArray)
+    {
+        //-- copy array
+        _featuresList.removeAllElements();
+        for (int i = 0; i < featuresArray.length; i++) {
+            _featuresList.addElement(featuresArray[i]);
+        }
+    } //-- void setFeatures(jalview.schemabinding.version2.Features) 
+
+    /**
+     * Sets the value of field 'hidden'.
+     * 
+     * @param hidden the value of field 'hidden'.
+     */
+    public void setHidden(boolean hidden)
+    {
+        this._hidden = hidden;
+        this._has_hidden = true;
+    } //-- void setHidden(boolean) 
+
+    /**
+     * Method setHiddenSequences
+     * 
+     * 
+     * 
+     * @param index
+     * @param vHiddenSequences
+     */
+    public void setHiddenSequences(int index, int vHiddenSequences)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _hiddenSequencesList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences), index);
+    } //-- void setHiddenSequences(int, int) 
+
+    /**
+     * Method setHiddenSequences
+     * 
+     * 
+     * 
+     * @param hiddenSequencesArray
+     */
+    public void setHiddenSequences(int[] hiddenSequencesArray)
+    {
+        //-- copy array
+        _hiddenSequencesList.removeAllElements();
+        for (int i = 0; i < hiddenSequencesArray.length; i++) {
+            _hiddenSequencesList.addElement(new java.lang.Integer(hiddenSequencesArray[i]));
+        }
+    } //-- void setHiddenSequences(int) 
+
+    /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(int id)
+    {
+        this._id = id;
+        this._has_id = true;
+    } //-- void setId(int) 
+
+    /**
+     * Method setPdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @param vPdbids
+     */
+    public void setPdbids(int index, jalview.schemabinding.version2.Pdbids vPdbids)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _pdbidsList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _pdbidsList.setElementAt(vPdbids, index);
+    } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids) 
+
+    /**
+     * Method setPdbids
+     * 
+     * 
+     * 
+     * @param pdbidsArray
+     */
+    public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray)
+    {
+        //-- copy array
+        _pdbidsList.removeAllElements();
+        for (int i = 0; i < pdbidsArray.length; i++) {
+            _pdbidsList.addElement(pdbidsArray[i]);
+        }
+    } //-- void setPdbids(jalview.schemabinding.version2.Pdbids) 
+
+    /**
+     * Sets the value of field 'start'.
+     * 
+     * @param start the value of field 'start'.
+     */
+    public void setStart(int start)
+    {
+        this._start = start;
+        this._has_start = true;
+    } //-- void setStart(int) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/JSeqDescriptor.java b/src/jalview/schemabinding/version2/JSeqDescriptor.java
new file mode 100755
index 0000000..eef74d2
--- /dev/null
+++ b/src/jalview/schemabinding/version2/JSeqDescriptor.java
@@ -0,0 +1,488 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class JSeqDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JSeqDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "JSeq";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _colour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if(!target.hasColour())
+                    return null;
+                return new java.lang.Integer(target.getColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteColour();
+                        return;
+                    }
+                    target.setColour( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _colour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _start
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if(!target.hasStart())
+                    return null;
+                return new java.lang.Integer(target.getStart());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setStart( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _start
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _end
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if(!target.hasEnd())
+                    return null;
+                return new java.lang.Integer(target.getEnd());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setEnd( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _end
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _id
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if(!target.hasId())
+                    return null;
+                return new java.lang.Integer(target.getId());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setId( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _hidden
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if(!target.hasHidden())
+                    return null;
+                return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteHidden();
+                        return;
+                    }
+                    target.setHidden( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _hidden
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _featuresList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                return target.getFeatures();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.addFeatures( (jalview.schemabinding.version2.Features) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Features();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _featuresList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _pdbidsList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                return target.getPdbids();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.addPdbids( (jalview.schemabinding.version2.Pdbids) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Pdbids();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _pdbidsList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _hiddenSequencesList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                return target.getHiddenSequences();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.addHiddenSequences( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _hiddenSequencesList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.JSeqDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.JSeq.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java
new file mode 100755
index 0000000..fe8deef
--- /dev/null
+++ b/src/jalview/schemabinding/version2/JalviewModel.java
@@ -0,0 +1,227 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Date;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class JalviewModel.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JalviewModel implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _creationDate
+     */
+    private java.util.Date _creationDate;
+
+    /**
+     * Field _version
+     */
+    private java.lang.String _version;
+
+    /**
+     * Field _vamsasModel
+     */
+    private jalview.schemabinding.version2.VamsasModel _vamsasModel;
+
+    /**
+     * Field _jalviewModelSequence
+     */
+    private jalview.schemabinding.version2.JalviewModelSequence _jalviewModelSequence;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JalviewModel() {
+        super();
+    } //-- jalview.schemabinding.version2.JalviewModel()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'creationDate'.
+     * 
+     * @return Date
+     * @return the value of field 'creationDate'.
+     */
+    public java.util.Date getCreationDate()
+    {
+        return this._creationDate;
+    } //-- java.util.Date getCreationDate() 
+
+    /**
+     * Returns the value of field 'jalviewModelSequence'.
+     * 
+     * @return JalviewModelSequence
+     * @return the value of field 'jalviewModelSequence'.
+     */
+    public jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence()
+    {
+        return this._jalviewModelSequence;
+    } //-- jalview.schemabinding.version2.JalviewModelSequence getJalviewModelSequence() 
+
+    /**
+     * Returns the value of field 'vamsasModel'.
+     * 
+     * @return VamsasModel
+     * @return the value of field 'vamsasModel'.
+     */
+    public jalview.schemabinding.version2.VamsasModel getVamsasModel()
+    {
+        return this._vamsasModel;
+    } //-- jalview.schemabinding.version2.VamsasModel getVamsasModel() 
+
+    /**
+     * Returns the value of field 'version'.
+     * 
+     * @return String
+     * @return the value of field 'version'.
+     */
+    public java.lang.String getVersion()
+    {
+        return this._version;
+    } //-- java.lang.String getVersion() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'creationDate'.
+     * 
+     * @param creationDate the value of field 'creationDate'.
+     */
+    public void setCreationDate(java.util.Date creationDate)
+    {
+        this._creationDate = creationDate;
+    } //-- void setCreationDate(java.util.Date) 
+
+    /**
+     * Sets the value of field 'jalviewModelSequence'.
+     * 
+     * @param jalviewModelSequence the value of field
+     * 'jalviewModelSequence'.
+     */
+    public void setJalviewModelSequence(jalview.schemabinding.version2.JalviewModelSequence jalviewModelSequence)
+    {
+        this._jalviewModelSequence = jalviewModelSequence;
+    } //-- void setJalviewModelSequence(jalview.schemabinding.version2.JalviewModelSequence) 
+
+    /**
+     * Sets the value of field 'vamsasModel'.
+     * 
+     * @param vamsasModel the value of field 'vamsasModel'.
+     */
+    public void setVamsasModel(jalview.schemabinding.version2.VamsasModel vamsasModel)
+    {
+        this._vamsasModel = vamsasModel;
+    } //-- void setVamsasModel(jalview.schemabinding.version2.VamsasModel) 
+
+    /**
+     * Sets the value of field 'version'.
+     * 
+     * @param version the value of field 'version'.
+     */
+    public void setVersion(java.lang.String version)
+    {
+        this._version = version;
+    } //-- void setVersion(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModel.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/JalviewModelDescriptor.java
new file mode 100755
index 0000000..ad2dc13
--- /dev/null
+++ b/src/jalview/schemabinding/version2/JalviewModelDescriptor.java
@@ -0,0 +1,324 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class JalviewModelDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JalviewModelDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "JalviewModel";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _creationDate
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class, "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewModel target = (JalviewModel) object;
+                return target.getCreationDate();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewModel target = (JalviewModel) object;
+                    target.setCreationDate( (java.util.Date) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new java.util.Date();
+            }
+        } );
+        desc.setHandler( new org.exolab.castor.xml.handlers.DateFieldHandler(handler));
+        desc.setImmutable(true);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _creationDate
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _version
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewModel target = (JalviewModel) object;
+                return target.getVersion();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewModel target = (JalviewModel) object;
+                    target.setVersion( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _version
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _vamsasModel
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewModel target = (JalviewModel) object;
+                return target.getVamsasModel();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewModel target = (JalviewModel) object;
+                    target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.VamsasModel();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _vamsasModel
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _jalviewModelSequence
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JalviewModelSequence.class, "_jalviewModelSequence", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewModel target = (JalviewModel) object;
+                return target.getJalviewModelSequence();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewModel target = (JalviewModel) object;
+                    target.setJalviewModelSequence( (jalview.schemabinding.version2.JalviewModelSequence) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.JalviewModelSequence();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setContainer(true);
+        desc.setClassDescriptor(new jalview.schemabinding.version2.JalviewModelSequenceDescriptor());
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _jalviewModelSequence
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.JalviewModelDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.JalviewModel.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
new file mode 100755
index 0000000..45f486b
--- /dev/null
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -0,0 +1,904 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class JalviewModelSequence.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JalviewModelSequence implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _JSeqList
+     */
+    private java.util.Vector _JSeqList;
+
+    /**
+     * Field _JGroupList
+     */
+    private java.util.Vector _JGroupList;
+
+    /**
+     * Field _viewportList
+     */
+    private java.util.Vector _viewportList;
+
+    /**
+     * Field _userColoursList
+     */
+    private java.util.Vector _userColoursList;
+
+    /**
+     * Field _treeList
+     */
+    private java.util.Vector _treeList;
+
+    /**
+     * Field _featureSettings
+     */
+    private jalview.schemabinding.version2.FeatureSettings _featureSettings;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JalviewModelSequence() {
+        super();
+        _JSeqList = new Vector();
+        _JGroupList = new Vector();
+        _viewportList = new Vector();
+        _userColoursList = new Vector();
+        _treeList = new Vector();
+    } //-- jalview.schemabinding.version2.JalviewModelSequence()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addJGroup
+     * 
+     * 
+     * 
+     * @param vJGroup
+     */
+    public void addJGroup(jalview.schemabinding.version2.JGroup vJGroup)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _JGroupList.addElement(vJGroup);
+    } //-- void addJGroup(jalview.schemabinding.version2.JGroup) 
+
+    /**
+     * Method addJGroup
+     * 
+     * 
+     * 
+     * @param index
+     * @param vJGroup
+     */
+    public void addJGroup(int index, jalview.schemabinding.version2.JGroup vJGroup)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _JGroupList.insertElementAt(vJGroup, index);
+    } //-- void addJGroup(int, jalview.schemabinding.version2.JGroup) 
+
+    /**
+     * Method addJSeq
+     * 
+     * 
+     * 
+     * @param vJSeq
+     */
+    public void addJSeq(jalview.schemabinding.version2.JSeq vJSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _JSeqList.addElement(vJSeq);
+    } //-- void addJSeq(jalview.schemabinding.version2.JSeq) 
+
+    /**
+     * Method addJSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @param vJSeq
+     */
+    public void addJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _JSeqList.insertElementAt(vJSeq, index);
+    } //-- void addJSeq(int, jalview.schemabinding.version2.JSeq) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param vTree
+     */
+    public void addTree(jalview.schemabinding.version2.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.addElement(vTree);
+    } //-- void addTree(jalview.schemabinding.version2.Tree) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void addTree(int index, jalview.schemabinding.version2.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.insertElementAt(vTree, index);
+    } //-- void addTree(int, jalview.schemabinding.version2.Tree) 
+
+    /**
+     * Method addUserColours
+     * 
+     * 
+     * 
+     * @param vUserColours
+     */
+    public void addUserColours(jalview.schemabinding.version2.UserColours vUserColours)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _userColoursList.addElement(vUserColours);
+    } //-- void addUserColours(jalview.schemabinding.version2.UserColours) 
+
+    /**
+     * Method addUserColours
+     * 
+     * 
+     * 
+     * @param index
+     * @param vUserColours
+     */
+    public void addUserColours(int index, jalview.schemabinding.version2.UserColours vUserColours)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _userColoursList.insertElementAt(vUserColours, index);
+    } //-- void addUserColours(int, jalview.schemabinding.version2.UserColours) 
+
+    /**
+     * Method addViewport
+     * 
+     * 
+     * 
+     * @param vViewport
+     */
+    public void addViewport(jalview.schemabinding.version2.Viewport vViewport)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _viewportList.addElement(vViewport);
+    } //-- void addViewport(jalview.schemabinding.version2.Viewport) 
+
+    /**
+     * Method addViewport
+     * 
+     * 
+     * 
+     * @param index
+     * @param vViewport
+     */
+    public void addViewport(int index, jalview.schemabinding.version2.Viewport vViewport)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _viewportList.insertElementAt(vViewport, index);
+    } //-- void addViewport(int, jalview.schemabinding.version2.Viewport) 
+
+    /**
+     * Method enumerateJGroup
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateJGroup()
+    {
+        return _JGroupList.elements();
+    } //-- java.util.Enumeration enumerateJGroup() 
+
+    /**
+     * Method enumerateJSeq
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateJSeq()
+    {
+        return _JSeqList.elements();
+    } //-- java.util.Enumeration enumerateJSeq() 
+
+    /**
+     * Method enumerateTree
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateTree()
+    {
+        return _treeList.elements();
+    } //-- java.util.Enumeration enumerateTree() 
+
+    /**
+     * Method enumerateUserColours
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateUserColours()
+    {
+        return _userColoursList.elements();
+    } //-- java.util.Enumeration enumerateUserColours() 
+
+    /**
+     * Method enumerateViewport
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateViewport()
+    {
+        return _viewportList.elements();
+    } //-- java.util.Enumeration enumerateViewport() 
+
+    /**
+     * Returns the value of field 'featureSettings'.
+     * 
+     * @return FeatureSettings
+     * @return the value of field 'featureSettings'.
+     */
+    public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
+    {
+        return this._featureSettings;
+    } //-- jalview.schemabinding.version2.FeatureSettings getFeatureSettings() 
+
+    /**
+     * Method getJGroup
+     * 
+     * 
+     * 
+     * @param index
+     * @return JGroup
+     */
+    public jalview.schemabinding.version2.JGroup getJGroup(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _JGroupList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);
+    } //-- jalview.schemabinding.version2.JGroup getJGroup(int) 
+
+    /**
+     * Method getJGroup
+     * 
+     * 
+     * 
+     * @return JGroup
+     */
+    public jalview.schemabinding.version2.JGroup[] getJGroup()
+    {
+        int size = _JGroupList.size();
+        jalview.schemabinding.version2.JGroup[] mArray = new jalview.schemabinding.version2.JGroup[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.JGroup[] getJGroup() 
+
+    /**
+     * Method getJGroupCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getJGroupCount()
+    {
+        return _JGroupList.size();
+    } //-- int getJGroupCount() 
+
+    /**
+     * Method getJSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @return JSeq
+     */
+    public jalview.schemabinding.version2.JSeq getJSeq(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _JSeqList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);
+    } //-- jalview.schemabinding.version2.JSeq getJSeq(int) 
+
+    /**
+     * Method getJSeq
+     * 
+     * 
+     * 
+     * @return JSeq
+     */
+    public jalview.schemabinding.version2.JSeq[] getJSeq()
+    {
+        int size = _JSeqList.size();
+        jalview.schemabinding.version2.JSeq[] mArray = new jalview.schemabinding.version2.JSeq[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.JSeq[] getJSeq() 
+
+    /**
+     * Method getJSeqCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getJSeqCount()
+    {
+        return _JSeqList.size();
+    } //-- int getJSeqCount() 
+
+    /**
+     * Method getTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return Tree
+     */
+    public jalview.schemabinding.version2.Tree getTree(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);
+    } //-- jalview.schemabinding.version2.Tree getTree(int) 
+
+    /**
+     * Method getTree
+     * 
+     * 
+     * 
+     * @return Tree
+     */
+    public jalview.schemabinding.version2.Tree[] getTree()
+    {
+        int size = _treeList.size();
+        jalview.schemabinding.version2.Tree[] mArray = new jalview.schemabinding.version2.Tree[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.Tree[] getTree() 
+
+    /**
+     * Method getTreeCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getTreeCount()
+    {
+        return _treeList.size();
+    } //-- int getTreeCount() 
+
+    /**
+     * Method getUserColours
+     * 
+     * 
+     * 
+     * @param index
+     * @return UserColours
+     */
+    public jalview.schemabinding.version2.UserColours getUserColours(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _userColoursList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.UserColours) _userColoursList.elementAt(index);
+    } //-- jalview.schemabinding.version2.UserColours getUserColours(int) 
+
+    /**
+     * Method getUserColours
+     * 
+     * 
+     * 
+     * @return UserColours
+     */
+    public jalview.schemabinding.version2.UserColours[] getUserColours()
+    {
+        int size = _userColoursList.size();
+        jalview.schemabinding.version2.UserColours[] mArray = new jalview.schemabinding.version2.UserColours[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.UserColours) _userColoursList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.UserColours[] getUserColours() 
+
+    /**
+     * Method getUserColoursCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getUserColoursCount()
+    {
+        return _userColoursList.size();
+    } //-- int getUserColoursCount() 
+
+    /**
+     * Method getViewport
+     * 
+     * 
+     * 
+     * @param index
+     * @return Viewport
+     */
+    public jalview.schemabinding.version2.Viewport getViewport(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _viewportList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(index);
+    } //-- jalview.schemabinding.version2.Viewport getViewport(int) 
+
+    /**
+     * Method getViewport
+     * 
+     * 
+     * 
+     * @return Viewport
+     */
+    public jalview.schemabinding.version2.Viewport[] getViewport()
+    {
+        int size = _viewportList.size();
+        jalview.schemabinding.version2.Viewport[] mArray = new jalview.schemabinding.version2.Viewport[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.Viewport[] getViewport() 
+
+    /**
+     * Method getViewportCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getViewportCount()
+    {
+        return _viewportList.size();
+    } //-- int getViewportCount() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllJGroup
+     * 
+     */
+    public void removeAllJGroup()
+    {
+        _JGroupList.removeAllElements();
+    } //-- void removeAllJGroup() 
+
+    /**
+     * Method removeAllJSeq
+     * 
+     */
+    public void removeAllJSeq()
+    {
+        _JSeqList.removeAllElements();
+    } //-- void removeAllJSeq() 
+
+    /**
+     * Method removeAllTree
+     * 
+     */
+    public void removeAllTree()
+    {
+        _treeList.removeAllElements();
+    } //-- void removeAllTree() 
+
+    /**
+     * Method removeAllUserColours
+     * 
+     */
+    public void removeAllUserColours()
+    {
+        _userColoursList.removeAllElements();
+    } //-- void removeAllUserColours() 
+
+    /**
+     * Method removeAllViewport
+     * 
+     */
+    public void removeAllViewport()
+    {
+        _viewportList.removeAllElements();
+    } //-- void removeAllViewport() 
+
+    /**
+     * Method removeJGroup
+     * 
+     * 
+     * 
+     * @param index
+     * @return JGroup
+     */
+    public jalview.schemabinding.version2.JGroup removeJGroup(int index)
+    {
+        java.lang.Object obj = _JGroupList.elementAt(index);
+        _JGroupList.removeElementAt(index);
+        return (jalview.schemabinding.version2.JGroup) obj;
+    } //-- jalview.schemabinding.version2.JGroup removeJGroup(int) 
+
+    /**
+     * Method removeJSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @return JSeq
+     */
+    public jalview.schemabinding.version2.JSeq removeJSeq(int index)
+    {
+        java.lang.Object obj = _JSeqList.elementAt(index);
+        _JSeqList.removeElementAt(index);
+        return (jalview.schemabinding.version2.JSeq) obj;
+    } //-- jalview.schemabinding.version2.JSeq removeJSeq(int) 
+
+    /**
+     * Method removeTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return Tree
+     */
+    public jalview.schemabinding.version2.Tree removeTree(int index)
+    {
+        java.lang.Object obj = _treeList.elementAt(index);
+        _treeList.removeElementAt(index);
+        return (jalview.schemabinding.version2.Tree) obj;
+    } //-- jalview.schemabinding.version2.Tree removeTree(int) 
+
+    /**
+     * Method removeUserColours
+     * 
+     * 
+     * 
+     * @param index
+     * @return UserColours
+     */
+    public jalview.schemabinding.version2.UserColours removeUserColours(int index)
+    {
+        java.lang.Object obj = _userColoursList.elementAt(index);
+        _userColoursList.removeElementAt(index);
+        return (jalview.schemabinding.version2.UserColours) obj;
+    } //-- jalview.schemabinding.version2.UserColours removeUserColours(int) 
+
+    /**
+     * Method removeViewport
+     * 
+     * 
+     * 
+     * @param index
+     * @return Viewport
+     */
+    public jalview.schemabinding.version2.Viewport removeViewport(int index)
+    {
+        java.lang.Object obj = _viewportList.elementAt(index);
+        _viewportList.removeElementAt(index);
+        return (jalview.schemabinding.version2.Viewport) obj;
+    } //-- jalview.schemabinding.version2.Viewport removeViewport(int) 
+
+    /**
+     * Sets the value of field 'featureSettings'.
+     * 
+     * @param featureSettings the value of field 'featureSettings'.
+     */
+    public void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings featureSettings)
+    {
+        this._featureSettings = featureSettings;
+    } //-- void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings) 
+
+    /**
+     * Method setJGroup
+     * 
+     * 
+     * 
+     * @param index
+     * @param vJGroup
+     */
+    public void setJGroup(int index, jalview.schemabinding.version2.JGroup vJGroup)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _JGroupList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _JGroupList.setElementAt(vJGroup, index);
+    } //-- void setJGroup(int, jalview.schemabinding.version2.JGroup) 
+
+    /**
+     * Method setJGroup
+     * 
+     * 
+     * 
+     * @param JGroupArray
+     */
+    public void setJGroup(jalview.schemabinding.version2.JGroup[] JGroupArray)
+    {
+        //-- copy array
+        _JGroupList.removeAllElements();
+        for (int i = 0; i < JGroupArray.length; i++) {
+            _JGroupList.addElement(JGroupArray[i]);
+        }
+    } //-- void setJGroup(jalview.schemabinding.version2.JGroup) 
+
+    /**
+     * Method setJSeq
+     * 
+     * 
+     * 
+     * @param index
+     * @param vJSeq
+     */
+    public void setJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _JSeqList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _JSeqList.setElementAt(vJSeq, index);
+    } //-- void setJSeq(int, jalview.schemabinding.version2.JSeq) 
+
+    /**
+     * Method setJSeq
+     * 
+     * 
+     * 
+     * @param JSeqArray
+     */
+    public void setJSeq(jalview.schemabinding.version2.JSeq[] JSeqArray)
+    {
+        //-- copy array
+        _JSeqList.removeAllElements();
+        for (int i = 0; i < JSeqArray.length; i++) {
+            _JSeqList.addElement(JSeqArray[i]);
+        }
+    } //-- void setJSeq(jalview.schemabinding.version2.JSeq) 
+
+    /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void setTree(int index, jalview.schemabinding.version2.Tree vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _treeList.setElementAt(vTree, index);
+    } //-- void setTree(int, jalview.schemabinding.version2.Tree) 
+
+    /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param treeArray
+     */
+    public void setTree(jalview.schemabinding.version2.Tree[] treeArray)
+    {
+        //-- copy array
+        _treeList.removeAllElements();
+        for (int i = 0; i < treeArray.length; i++) {
+            _treeList.addElement(treeArray[i]);
+        }
+    } //-- void setTree(jalview.schemabinding.version2.Tree) 
+
+    /**
+     * Method setUserColours
+     * 
+     * 
+     * 
+     * @param index
+     * @param vUserColours
+     */
+    public void setUserColours(int index, jalview.schemabinding.version2.UserColours vUserColours)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _userColoursList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _userColoursList.setElementAt(vUserColours, index);
+    } //-- void setUserColours(int, jalview.schemabinding.version2.UserColours) 
+
+    /**
+     * Method setUserColours
+     * 
+     * 
+     * 
+     * @param userColoursArray
+     */
+    public void setUserColours(jalview.schemabinding.version2.UserColours[] userColoursArray)
+    {
+        //-- copy array
+        _userColoursList.removeAllElements();
+        for (int i = 0; i < userColoursArray.length; i++) {
+            _userColoursList.addElement(userColoursArray[i]);
+        }
+    } //-- void setUserColours(jalview.schemabinding.version2.UserColours) 
+
+    /**
+     * Method setViewport
+     * 
+     * 
+     * 
+     * @param index
+     * @param vViewport
+     */
+    public void setViewport(int index, jalview.schemabinding.version2.Viewport vViewport)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _viewportList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _viewportList.setElementAt(vViewport, index);
+    } //-- void setViewport(int, jalview.schemabinding.version2.Viewport) 
+
+    /**
+     * Method setViewport
+     * 
+     * 
+     * 
+     * @param viewportArray
+     */
+    public void setViewport(jalview.schemabinding.version2.Viewport[] viewportArray)
+    {
+        //-- copy array
+        _viewportList.removeAllElements();
+        for (int i = 0; i < viewportArray.length; i++) {
+            _viewportList.addElement(viewportArray[i]);
+        }
+    } //-- void setViewport(jalview.schemabinding.version2.Viewport) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
new file mode 100755
index 0000000..7f5bd43
--- /dev/null
+++ b/src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
@@ -0,0 +1,383 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class JalviewModelSequenceDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JalviewModelSequenceDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _JSeqList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewModelSequence target = (JalviewModelSequence) object;
+                return target.getJSeq();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewModelSequence target = (JalviewModelSequence) object;
+                    target.addJSeq( (jalview.schemabinding.version2.JSeq) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.JSeq();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setRequired(true);
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _JSeqList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _JGroupList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JGroup.class, "_JGroupList", "JGroup", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewModelSequence target = (JalviewModelSequence) object;
+                return target.getJGroup();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewModelSequence target = (JalviewModelSequence) object;
+                    target.addJGroup( (jalview.schemabinding.version2.JGroup) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.JGroup();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _JGroupList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _viewportList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Viewport.class, "_viewportList", "Viewport", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewModelSequence target = (JalviewModelSequence) object;
+                return target.getViewport();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewModelSequence target = (JalviewModelSequence) object;
+                    target.addViewport( (jalview.schemabinding.version2.Viewport) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Viewport();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setRequired(true);
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _viewportList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _userColoursList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColours.class, "_userColoursList", "UserColours", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewModelSequence target = (JalviewModelSequence) object;
+                return target.getUserColours();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewModelSequence target = (JalviewModelSequence) object;
+                    target.addUserColours( (jalview.schemabinding.version2.UserColours) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.UserColours();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _userColoursList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _treeList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewModelSequence target = (JalviewModelSequence) object;
+                return target.getTree();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewModelSequence target = (JalviewModelSequence) object;
+                    target.addTree( (jalview.schemabinding.version2.Tree) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Tree();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _treeList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _featureSettings
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.FeatureSettings.class, "_featureSettings", "FeatureSettings", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewModelSequence target = (JalviewModelSequence) object;
+                return target.getFeatureSettings();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewModelSequence target = (JalviewModelSequence) object;
+                    target.setFeatureSettings( (jalview.schemabinding.version2.FeatureSettings) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.FeatureSettings();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _featureSettings
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.JalviewModelSequenceDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.JalviewModelSequence.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java
new file mode 100755
index 0000000..7963596
--- /dev/null
+++ b/src/jalview/schemabinding/version2/JalviewUserColours.java
@@ -0,0 +1,300 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class JalviewUserColours.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JalviewUserColours implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _schemeName
+     */
+    private java.lang.String _schemeName;
+
+    /**
+     * Field _colourList
+     */
+    private java.util.Vector _colourList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JalviewUserColours() {
+        super();
+        _colourList = new Vector();
+    } //-- jalview.schemabinding.version2.JalviewUserColours()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addColour
+     * 
+     * 
+     * 
+     * @param vColour
+     */
+    public void addColour(jalview.schemabinding.version2.Colour vColour)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _colourList.addElement(vColour);
+    } //-- void addColour(jalview.schemabinding.version2.Colour) 
+
+    /**
+     * Method addColour
+     * 
+     * 
+     * 
+     * @param index
+     * @param vColour
+     */
+    public void addColour(int index, jalview.schemabinding.version2.Colour vColour)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _colourList.insertElementAt(vColour, index);
+    } //-- void addColour(int, jalview.schemabinding.version2.Colour) 
+
+    /**
+     * Method enumerateColour
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateColour()
+    {
+        return _colourList.elements();
+    } //-- java.util.Enumeration enumerateColour() 
+
+    /**
+     * Method getColour
+     * 
+     * 
+     * 
+     * @param index
+     * @return Colour
+     */
+    public jalview.schemabinding.version2.Colour getColour(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _colourList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);
+    } //-- jalview.schemabinding.version2.Colour getColour(int) 
+
+    /**
+     * Method getColour
+     * 
+     * 
+     * 
+     * @return Colour
+     */
+    public jalview.schemabinding.version2.Colour[] getColour()
+    {
+        int size = _colourList.size();
+        jalview.schemabinding.version2.Colour[] mArray = new jalview.schemabinding.version2.Colour[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.Colour[] getColour() 
+
+    /**
+     * Method getColourCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getColourCount()
+    {
+        return _colourList.size();
+    } //-- int getColourCount() 
+
+    /**
+     * Returns the value of field 'schemeName'.
+     * 
+     * @return String
+     * @return the value of field 'schemeName'.
+     */
+    public java.lang.String getSchemeName()
+    {
+        return this._schemeName;
+    } //-- java.lang.String getSchemeName() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllColour
+     * 
+     */
+    public void removeAllColour()
+    {
+        _colourList.removeAllElements();
+    } //-- void removeAllColour() 
+
+    /**
+     * Method removeColour
+     * 
+     * 
+     * 
+     * @param index
+     * @return Colour
+     */
+    public jalview.schemabinding.version2.Colour removeColour(int index)
+    {
+        java.lang.Object obj = _colourList.elementAt(index);
+        _colourList.removeElementAt(index);
+        return (jalview.schemabinding.version2.Colour) obj;
+    } //-- jalview.schemabinding.version2.Colour removeColour(int) 
+
+    /**
+     * Method setColour
+     * 
+     * 
+     * 
+     * @param index
+     * @param vColour
+     */
+    public void setColour(int index, jalview.schemabinding.version2.Colour vColour)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _colourList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _colourList.setElementAt(vColour, index);
+    } //-- void setColour(int, jalview.schemabinding.version2.Colour) 
+
+    /**
+     * Method setColour
+     * 
+     * 
+     * 
+     * @param colourArray
+     */
+    public void setColour(jalview.schemabinding.version2.Colour[] colourArray)
+    {
+        //-- copy array
+        _colourList.removeAllElements();
+        for (int i = 0; i < colourArray.length; i++) {
+            _colourList.addElement(colourArray[i]);
+        }
+    } //-- void setColour(jalview.schemabinding.version2.Colour) 
+
+    /**
+     * Sets the value of field 'schemeName'.
+     * 
+     * @param schemeName the value of field 'schemeName'.
+     */
+    public void setSchemeName(java.lang.String schemeName)
+    {
+        this._schemeName = schemeName;
+    } //-- void setSchemeName(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
new file mode 100755
index 0000000..661d102
--- /dev/null
+++ b/src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
@@ -0,0 +1,244 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class JalviewUserColoursDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JalviewUserColoursDescriptor() {
+        super();
+        nsURI = "www.jalview.org/colours";
+        xmlName = "JalviewUserColours";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _schemeName
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_schemeName", "schemeName", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewUserColours target = (JalviewUserColours) object;
+                return target.getSchemeName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewUserColours target = (JalviewUserColours) object;
+                    target.setSchemeName( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _schemeName
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _colourList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JalviewUserColours target = (JalviewUserColours) object;
+                return target.getColour();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JalviewUserColours target = (JalviewUserColours) object;
+                    target.addColour( (jalview.schemabinding.version2.Colour) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Colour();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _colourList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.JalviewUserColoursDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.JalviewUserColours.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java
new file mode 100644
index 0000000..47423eb
--- /dev/null
+++ b/src/jalview/schemabinding/version2/OtherData.java
@@ -0,0 +1,173 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class OtherData.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class OtherData implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _key
+     */
+    private java.lang.String _key;
+
+    /**
+     * Field _value
+     */
+    private java.lang.String _value;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public OtherData() {
+        super();
+    } //-- jalview.schemabinding.version2.OtherData()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'key'.
+     * 
+     * @return String
+     * @return the value of field 'key'.
+     */
+    public java.lang.String getKey()
+    {
+        return this._key;
+    } //-- java.lang.String getKey() 
+
+    /**
+     * Returns the value of field 'value'.
+     * 
+     * @return String
+     * @return the value of field 'value'.
+     */
+    public java.lang.String getValue()
+    {
+        return this._value;
+    } //-- java.lang.String getValue() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'key'.
+     * 
+     * @param key the value of field 'key'.
+     */
+    public void setKey(java.lang.String key)
+    {
+        this._key = key;
+    } //-- void setKey(java.lang.String) 
+
+    /**
+     * Sets the value of field 'value'.
+     * 
+     * @param value the value of field 'value'.
+     */
+    public void setValue(java.lang.String value)
+    {
+        this._value = value;
+    } //-- void setValue(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/OtherDataDescriptor.java
new file mode 100644
index 0000000..f6ec794
--- /dev/null
+++ b/src/jalview/schemabinding/version2/OtherDataDescriptor.java
@@ -0,0 +1,246 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class OtherDataDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public OtherDataDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "otherData";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _key
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                OtherData target = (OtherData) object;
+                return target.getKey();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    OtherData target = (OtherData) object;
+                    target.setKey( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _key
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _value
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                OtherData target = (OtherData) object;
+                return target.getValue();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    OtherData target = (OtherData) object;
+                    target.setValue( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _value
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- jalview.schemabinding.version2.OtherDataDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.OtherData.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java
new file mode 100755
index 0000000..93c2748
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Pdbentry.java
@@ -0,0 +1,352 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Pdbentry.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Pdbentry implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _id
+     */
+    private java.lang.String _id;
+
+    /**
+     * Field _type
+     */
+    private java.lang.String _type;
+
+    /**
+     * Field _file
+     */
+    private java.lang.String _file;
+
+    /**
+     * Field _items
+     */
+    private java.util.Vector _items;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Pdbentry() {
+        super();
+        _items = new Vector();
+    } //-- jalview.schemabinding.version2.Pdbentry()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addPdbentryItem
+     * 
+     * 
+     * 
+     * @param vPdbentryItem
+     */
+    public void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _items.addElement(vPdbentryItem);
+    } //-- void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem) 
+
+    /**
+     * Method addPdbentryItem
+     * 
+     * 
+     * 
+     * @param index
+     * @param vPdbentryItem
+     */
+    public void addPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _items.insertElementAt(vPdbentryItem, index);
+    } //-- void addPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem) 
+
+    /**
+     * Method enumeratePdbentryItem
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumeratePdbentryItem()
+    {
+        return _items.elements();
+    } //-- java.util.Enumeration enumeratePdbentryItem() 
+
+    /**
+     * Returns the value of field 'file'.
+     * 
+     * @return String
+     * @return the value of field 'file'.
+     */
+    public java.lang.String getFile()
+    {
+        return this._file;
+    } //-- java.lang.String getFile() 
+
+    /**
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
+
+    /**
+     * Method getPdbentryItem
+     * 
+     * 
+     * 
+     * @param index
+     * @return PdbentryItem
+     */
+    public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _items.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);
+    } //-- jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int) 
+
+    /**
+     * Method getPdbentryItem
+     * 
+     * 
+     * 
+     * @return PdbentryItem
+     */
+    public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()
+    {
+        int size = _items.size();
+        jalview.schemabinding.version2.PdbentryItem[] mArray = new jalview.schemabinding.version2.PdbentryItem[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem() 
+
+    /**
+     * Method getPdbentryItemCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getPdbentryItemCount()
+    {
+        return _items.size();
+    } //-- int getPdbentryItemCount() 
+
+    /**
+     * Returns the value of field 'type'.
+     * 
+     * @return String
+     * @return the value of field 'type'.
+     */
+    public java.lang.String getType()
+    {
+        return this._type;
+    } //-- java.lang.String getType() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllPdbentryItem
+     * 
+     */
+    public void removeAllPdbentryItem()
+    {
+        _items.removeAllElements();
+    } //-- void removeAllPdbentryItem() 
+
+    /**
+     * Method removePdbentryItem
+     * 
+     * 
+     * 
+     * @param index
+     * @return PdbentryItem
+     */
+    public jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int index)
+    {
+        java.lang.Object obj = _items.elementAt(index);
+        _items.removeElementAt(index);
+        return (jalview.schemabinding.version2.PdbentryItem) obj;
+    } //-- jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int) 
+
+    /**
+     * Sets the value of field 'file'.
+     * 
+     * @param file the value of field 'file'.
+     */
+    public void setFile(java.lang.String file)
+    {
+        this._file = file;
+    } //-- void setFile(java.lang.String) 
+
+    /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(java.lang.String id)
+    {
+        this._id = id;
+    } //-- void setId(java.lang.String) 
+
+    /**
+     * Method setPdbentryItem
+     * 
+     * 
+     * 
+     * @param index
+     * @param vPdbentryItem
+     */
+    public void setPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _items.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _items.setElementAt(vPdbentryItem, index);
+    } //-- void setPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem) 
+
+    /**
+     * Method setPdbentryItem
+     * 
+     * 
+     * 
+     * @param pdbentryItemArray
+     */
+    public void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem[] pdbentryItemArray)
+    {
+        //-- copy array
+        _items.removeAllElements();
+        for (int i = 0; i < pdbentryItemArray.length; i++) {
+            _items.addElement(pdbentryItemArray[i]);
+        }
+    } //-- void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem) 
+
+    /**
+     * Sets the value of field 'type'.
+     * 
+     * @param type the value of field 'type'.
+     */
+    public void setType(java.lang.String type)
+    {
+        this._type = type;
+    } //-- void setType(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbentry.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/PdbentryDescriptor.java
new file mode 100755
index 0000000..61a9eda
--- /dev/null
+++ b/src/jalview/schemabinding/version2/PdbentryDescriptor.java
@@ -0,0 +1,315 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class PdbentryDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public PdbentryDescriptor() {
+        super();
+        xmlName = "pdbentry";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _id
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Pdbentry target = (Pdbentry) object;
+                return target.getId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Pdbentry target = (Pdbentry) object;
+                    target.setId( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _type
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Pdbentry target = (Pdbentry) object;
+                return target.getType();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Pdbentry target = (Pdbentry) object;
+                    target.setType( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _type
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _file
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Pdbentry target = (Pdbentry) object;
+                return target.getFile();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Pdbentry target = (Pdbentry) object;
+                    target.setFile( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _file
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _items
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (String)null, org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Pdbentry target = (Pdbentry) object;
+                return target.getPdbentryItem();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Pdbentry target = (Pdbentry) object;
+                    target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.PdbentryItem();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setContainer(true);
+        desc.setClassDescriptor(new jalview.schemabinding.version2.PdbentryItemDescriptor());
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _items
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.PdbentryDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Pdbentry.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java
new file mode 100755
index 0000000..6f64036
--- /dev/null
+++ b/src/jalview/schemabinding/version2/PdbentryItem.java
@@ -0,0 +1,197 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.Serializable;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class PdbentryItem.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class PdbentryItem implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _propertyList
+     */
+    private java.util.Vector _propertyList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public PdbentryItem() {
+        super();
+        _propertyList = new Vector();
+    } //-- jalview.schemabinding.version2.PdbentryItem()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addProperty
+     * 
+     * 
+     * 
+     * @param vProperty
+     */
+    public void addProperty(jalview.schemabinding.version2.Property vProperty)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _propertyList.addElement(vProperty);
+    } //-- void addProperty(jalview.schemabinding.version2.Property) 
+
+    /**
+     * Method addProperty
+     * 
+     * 
+     * 
+     * @param index
+     * @param vProperty
+     */
+    public void addProperty(int index, jalview.schemabinding.version2.Property vProperty)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _propertyList.insertElementAt(vProperty, index);
+    } //-- void addProperty(int, jalview.schemabinding.version2.Property) 
+
+    /**
+     * Method enumerateProperty
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateProperty()
+    {
+        return _propertyList.elements();
+    } //-- java.util.Enumeration enumerateProperty() 
+
+    /**
+     * Method getProperty
+     * 
+     * 
+     * 
+     * @param index
+     * @return Property
+     */
+    public jalview.schemabinding.version2.Property getProperty(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _propertyList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.Property) _propertyList.elementAt(index);
+    } //-- jalview.schemabinding.version2.Property getProperty(int) 
+
+    /**
+     * Method getProperty
+     * 
+     * 
+     * 
+     * @return Property
+     */
+    public jalview.schemabinding.version2.Property[] getProperty()
+    {
+        int size = _propertyList.size();
+        jalview.schemabinding.version2.Property[] mArray = new jalview.schemabinding.version2.Property[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.Property) _propertyList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.Property[] getProperty() 
+
+    /**
+     * Method getPropertyCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getPropertyCount()
+    {
+        return _propertyList.size();
+    } //-- int getPropertyCount() 
+
+    /**
+     * Method removeAllProperty
+     * 
+     */
+    public void removeAllProperty()
+    {
+        _propertyList.removeAllElements();
+    } //-- void removeAllProperty() 
+
+    /**
+     * Method removeProperty
+     * 
+     * 
+     * 
+     * @param index
+     * @return Property
+     */
+    public jalview.schemabinding.version2.Property removeProperty(int index)
+    {
+        java.lang.Object obj = _propertyList.elementAt(index);
+        _propertyList.removeElementAt(index);
+        return (jalview.schemabinding.version2.Property) obj;
+    } //-- jalview.schemabinding.version2.Property removeProperty(int) 
+
+    /**
+     * Method setProperty
+     * 
+     * 
+     * 
+     * @param index
+     * @param vProperty
+     */
+    public void setProperty(int index, jalview.schemabinding.version2.Property vProperty)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _propertyList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _propertyList.setElementAt(vProperty, index);
+    } //-- void setProperty(int, jalview.schemabinding.version2.Property) 
+
+    /**
+     * Method setProperty
+     * 
+     * 
+     * 
+     * @param propertyArray
+     */
+    public void setProperty(jalview.schemabinding.version2.Property[] propertyArray)
+    {
+        //-- copy array
+        _propertyList.removeAllElements();
+        for (int i = 0; i < propertyArray.length; i++) {
+            _propertyList.addElement(propertyArray[i]);
+        }
+    } //-- void setProperty(jalview.schemabinding.version2.Property) 
+
+}
diff --git a/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
new file mode 100755
index 0000000..d9d36c0
--- /dev/null
+++ b/src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
@@ -0,0 +1,208 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class PdbentryItemDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public PdbentryItemDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "pdbentry";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _propertyList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                PdbentryItem target = (PdbentryItem) object;
+                return target.getProperty();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    PdbentryItem target = (PdbentryItem) object;
+                    target.addProperty( (jalview.schemabinding.version2.Property) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Property();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _propertyList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.PdbentryItemDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.PdbentryItem.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java
new file mode 100755
index 0000000..53b2e91
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Pdbids.java
@@ -0,0 +1,118 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Pdbids.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Pdbids extends Pdbentry 
+implements java.io.Serializable
+{
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Pdbids() {
+        super();
+    } //-- jalview.schemabinding.version2.Pdbids()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Pdbids) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/PdbidsDescriptor.java
new file mode 100755
index 0000000..607f122
--- /dev/null
+++ b/src/jalview/schemabinding/version2/PdbidsDescriptor.java
@@ -0,0 +1,166 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class PdbidsDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class PdbidsDescriptor extends PdbentryDescriptor {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public PdbidsDescriptor() {
+        super();
+        setExtendsWithoutFlatten(new PdbentryDescriptor());
+        nsURI = "www.jalview.org";
+        xmlName = "pdbids";
+    } //-- jalview.schemabinding.version2.PdbidsDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return super.getExtends();
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        if (identity == null)
+            return super.getIdentity();
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Pdbids.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java
new file mode 100755
index 0000000..338dd90
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Property.java
@@ -0,0 +1,173 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Property.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Property implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _name
+     */
+    private java.lang.String _name;
+
+    /**
+     * Field _value
+     */
+    private java.lang.String _value;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Property() {
+        super();
+    } //-- jalview.schemabinding.version2.Property()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'name'.
+     * 
+     * @return String
+     * @return the value of field 'name'.
+     */
+    public java.lang.String getName()
+    {
+        return this._name;
+    } //-- java.lang.String getName() 
+
+    /**
+     * Returns the value of field 'value'.
+     * 
+     * @return String
+     * @return the value of field 'value'.
+     */
+    public java.lang.String getValue()
+    {
+        return this._value;
+    } //-- java.lang.String getValue() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'name'.
+     * 
+     * @param name the value of field 'name'.
+     */
+    public void setName(java.lang.String name)
+    {
+        this._name = name;
+    } //-- void setName(java.lang.String) 
+
+    /**
+     * Sets the value of field 'value'.
+     * 
+     * @param value the value of field 'value'.
+     */
+    public void setValue(java.lang.String value)
+    {
+        this._value = value;
+    } //-- void setValue(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.Property.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/PropertyDescriptor.java b/src/jalview/schemabinding/version2/PropertyDescriptor.java
new file mode 100755
index 0000000..e22704c
--- /dev/null
+++ b/src/jalview/schemabinding/version2/PropertyDescriptor.java
@@ -0,0 +1,246 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class PropertyDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public PropertyDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "property";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _name
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Property target = (Property) object;
+                return target.getName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Property target = (Property) object;
+                    target.setName( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _name
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _value
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Property target = (Property) object;
+                return target.getValue();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Property target = (Property) object;
+                    target.setValue( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _value
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- jalview.schemabinding.version2.PropertyDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Property.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
new file mode 100755
index 0000000..993ad23
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -0,0 +1,276 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Sequence.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Sequence extends jalview.schemabinding.version2.SequenceType 
+implements java.io.Serializable
+{
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _DBRefList
+     */
+    private java.util.Vector _DBRefList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Sequence() {
+        super();
+        _DBRefList = new Vector();
+    } //-- jalview.schemabinding.version2.Sequence()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addDBRef
+     * 
+     * 
+     * 
+     * @param vDBRef
+     */
+    public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _DBRefList.addElement(vDBRef);
+    } //-- void addDBRef(jalview.schemabinding.version2.DBRef) 
+
+    /**
+     * Method addDBRef
+     * 
+     * 
+     * 
+     * @param index
+     * @param vDBRef
+     */
+    public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _DBRefList.insertElementAt(vDBRef, index);
+    } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef) 
+
+    /**
+     * Method enumerateDBRef
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateDBRef()
+    {
+        return _DBRefList.elements();
+    } //-- java.util.Enumeration enumerateDBRef() 
+
+    /**
+     * Method getDBRef
+     * 
+     * 
+     * 
+     * @param index
+     * @return DBRef
+     */
+    public jalview.schemabinding.version2.DBRef getDBRef(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _DBRefList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);
+    } //-- jalview.schemabinding.version2.DBRef getDBRef(int) 
+
+    /**
+     * Method getDBRef
+     * 
+     * 
+     * 
+     * @return DBRef
+     */
+    public jalview.schemabinding.version2.DBRef[] getDBRef()
+    {
+        int size = _DBRefList.size();
+        jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.version2.DBRef[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.DBRef[] getDBRef() 
+
+    /**
+     * Method getDBRefCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getDBRefCount()
+    {
+        return _DBRefList.size();
+    } //-- int getDBRefCount() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllDBRef
+     * 
+     */
+    public void removeAllDBRef()
+    {
+        _DBRefList.removeAllElements();
+    } //-- void removeAllDBRef() 
+
+    /**
+     * Method removeDBRef
+     * 
+     * 
+     * 
+     * @param index
+     * @return DBRef
+     */
+    public jalview.schemabinding.version2.DBRef removeDBRef(int index)
+    {
+        java.lang.Object obj = _DBRefList.elementAt(index);
+        _DBRefList.removeElementAt(index);
+        return (jalview.schemabinding.version2.DBRef) obj;
+    } //-- jalview.schemabinding.version2.DBRef removeDBRef(int) 
+
+    /**
+     * Method setDBRef
+     * 
+     * 
+     * 
+     * @param index
+     * @param vDBRef
+     */
+    public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _DBRefList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _DBRefList.setElementAt(vDBRef, index);
+    } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef) 
+
+    /**
+     * Method setDBRef
+     * 
+     * 
+     * 
+     * @param DBRefArray
+     */
+    public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)
+    {
+        //-- copy array
+        _DBRefList.removeAllElements();
+        for (int i = 0; i < DBRefArray.length; i++) {
+            _DBRefList.addElement(DBRefArray[i]);
+        }
+    } //-- void setDBRef(jalview.schemabinding.version2.DBRef) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Sequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/SequenceDescriptor.java b/src/jalview/schemabinding/version2/SequenceDescriptor.java
new file mode 100755
index 0000000..555284a
--- /dev/null
+++ b/src/jalview/schemabinding/version2/SequenceDescriptor.java
@@ -0,0 +1,211 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class SequenceDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class SequenceDescriptor extends jalview.schemabinding.version2.SequenceTypeDescriptor {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public SequenceDescriptor() {
+        super();
+        setExtendsWithoutFlatten(new jalview.schemabinding.version2.SequenceTypeDescriptor());
+        nsURI = "www.vamsas.ac.uk/jalview/version2";
+        xmlName = "Sequence";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _DBRefList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Sequence target = (Sequence) object;
+                return target.getDBRef();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Sequence target = (Sequence) object;
+                    target.addDBRef( (jalview.schemabinding.version2.DBRef) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.DBRef();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _DBRefList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.SequenceDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return super.getExtends();
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        if (identity == null)
+            return super.getIdentity();
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Sequence.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
new file mode 100755
index 0000000..187139d
--- /dev/null
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -0,0 +1,504 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class SequenceSet.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class SequenceSet implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _gapChar
+     */
+    private java.lang.String _gapChar;
+
+    /**
+     * Field _aligned
+     */
+    private boolean _aligned;
+
+    /**
+     * keeps track of state for field: _aligned
+     */
+    private boolean _has_aligned;
+
+    /**
+     * Field _sequenceList
+     */
+    private java.util.Vector _sequenceList;
+
+    /**
+     * Field _annotationList
+     */
+    private java.util.Vector _annotationList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public SequenceSet() {
+        super();
+        _sequenceList = new Vector();
+        _annotationList = new Vector();
+    } //-- jalview.schemabinding.version2.SequenceSet()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addAnnotation
+     * 
+     * 
+     * 
+     * @param vAnnotation
+     */
+    public void addAnnotation(jalview.schemabinding.version2.Annotation vAnnotation)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _annotationList.addElement(vAnnotation);
+    } //-- void addAnnotation(jalview.schemabinding.version2.Annotation) 
+
+    /**
+     * Method addAnnotation
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAnnotation
+     */
+    public void addAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _annotationList.insertElementAt(vAnnotation, index);
+    } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation) 
+
+    /**
+     * Method addSequence
+     * 
+     * 
+     * 
+     * @param vSequence
+     */
+    public void addSequence(jalview.schemabinding.version2.Sequence vSequence)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _sequenceList.addElement(vSequence);
+    } //-- void addSequence(jalview.schemabinding.version2.Sequence) 
+
+    /**
+     * Method addSequence
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSequence
+     */
+    public void addSequence(int index, jalview.schemabinding.version2.Sequence vSequence)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _sequenceList.insertElementAt(vSequence, index);
+    } //-- void addSequence(int, jalview.schemabinding.version2.Sequence) 
+
+    /**
+     * Method deleteAligned
+     * 
+     */
+    public void deleteAligned()
+    {
+        this._has_aligned= false;
+    } //-- void deleteAligned() 
+
+    /**
+     * Method enumerateAnnotation
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateAnnotation()
+    {
+        return _annotationList.elements();
+    } //-- java.util.Enumeration enumerateAnnotation() 
+
+    /**
+     * Method enumerateSequence
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateSequence()
+    {
+        return _sequenceList.elements();
+    } //-- java.util.Enumeration enumerateSequence() 
+
+    /**
+     * Returns the value of field 'aligned'.
+     * 
+     * @return boolean
+     * @return the value of field 'aligned'.
+     */
+    public boolean getAligned()
+    {
+        return this._aligned;
+    } //-- boolean getAligned() 
+
+    /**
+     * Method getAnnotation
+     * 
+     * 
+     * 
+     * @param index
+     * @return Annotation
+     */
+    public jalview.schemabinding.version2.Annotation getAnnotation(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _annotationList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);
+    } //-- jalview.schemabinding.version2.Annotation getAnnotation(int) 
+
+    /**
+     * Method getAnnotation
+     * 
+     * 
+     * 
+     * @return Annotation
+     */
+    public jalview.schemabinding.version2.Annotation[] getAnnotation()
+    {
+        int size = _annotationList.size();
+        jalview.schemabinding.version2.Annotation[] mArray = new jalview.schemabinding.version2.Annotation[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.Annotation[] getAnnotation() 
+
+    /**
+     * Method getAnnotationCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getAnnotationCount()
+    {
+        return _annotationList.size();
+    } //-- int getAnnotationCount() 
+
+    /**
+     * Returns the value of field 'gapChar'.
+     * 
+     * @return String
+     * @return the value of field 'gapChar'.
+     */
+    public java.lang.String getGapChar()
+    {
+        return this._gapChar;
+    } //-- java.lang.String getGapChar() 
+
+    /**
+     * Method getSequence
+     * 
+     * 
+     * 
+     * @param index
+     * @return Sequence
+     */
+    public jalview.schemabinding.version2.Sequence getSequence(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _sequenceList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);
+    } //-- jalview.schemabinding.version2.Sequence getSequence(int) 
+
+    /**
+     * Method getSequence
+     * 
+     * 
+     * 
+     * @return Sequence
+     */
+    public jalview.schemabinding.version2.Sequence[] getSequence()
+    {
+        int size = _sequenceList.size();
+        jalview.schemabinding.version2.Sequence[] mArray = new jalview.schemabinding.version2.Sequence[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.Sequence[] getSequence() 
+
+    /**
+     * Method getSequenceCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getSequenceCount()
+    {
+        return _sequenceList.size();
+    } //-- int getSequenceCount() 
+
+    /**
+     * Method hasAligned
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasAligned()
+    {
+        return this._has_aligned;
+    } //-- boolean hasAligned() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllAnnotation
+     * 
+     */
+    public void removeAllAnnotation()
+    {
+        _annotationList.removeAllElements();
+    } //-- void removeAllAnnotation() 
+
+    /**
+     * Method removeAllSequence
+     * 
+     */
+    public void removeAllSequence()
+    {
+        _sequenceList.removeAllElements();
+    } //-- void removeAllSequence() 
+
+    /**
+     * Method removeAnnotation
+     * 
+     * 
+     * 
+     * @param index
+     * @return Annotation
+     */
+    public jalview.schemabinding.version2.Annotation removeAnnotation(int index)
+    {
+        java.lang.Object obj = _annotationList.elementAt(index);
+        _annotationList.removeElementAt(index);
+        return (jalview.schemabinding.version2.Annotation) obj;
+    } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int) 
+
+    /**
+     * Method removeSequence
+     * 
+     * 
+     * 
+     * @param index
+     * @return Sequence
+     */
+    public jalview.schemabinding.version2.Sequence removeSequence(int index)
+    {
+        java.lang.Object obj = _sequenceList.elementAt(index);
+        _sequenceList.removeElementAt(index);
+        return (jalview.schemabinding.version2.Sequence) obj;
+    } //-- jalview.schemabinding.version2.Sequence removeSequence(int) 
+
+    /**
+     * Sets the value of field 'aligned'.
+     * 
+     * @param aligned the value of field 'aligned'.
+     */
+    public void setAligned(boolean aligned)
+    {
+        this._aligned = aligned;
+        this._has_aligned = true;
+    } //-- void setAligned(boolean) 
+
+    /**
+     * Method setAnnotation
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAnnotation
+     */
+    public void setAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _annotationList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _annotationList.setElementAt(vAnnotation, index);
+    } //-- void setAnnotation(int, jalview.schemabinding.version2.Annotation) 
+
+    /**
+     * Method setAnnotation
+     * 
+     * 
+     * 
+     * @param annotationArray
+     */
+    public void setAnnotation(jalview.schemabinding.version2.Annotation[] annotationArray)
+    {
+        //-- copy array
+        _annotationList.removeAllElements();
+        for (int i = 0; i < annotationArray.length; i++) {
+            _annotationList.addElement(annotationArray[i]);
+        }
+    } //-- void setAnnotation(jalview.schemabinding.version2.Annotation) 
+
+    /**
+     * Sets the value of field 'gapChar'.
+     * 
+     * @param gapChar the value of field 'gapChar'.
+     */
+    public void setGapChar(java.lang.String gapChar)
+    {
+        this._gapChar = gapChar;
+    } //-- void setGapChar(java.lang.String) 
+
+    /**
+     * Method setSequence
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSequence
+     */
+    public void setSequence(int index, jalview.schemabinding.version2.Sequence vSequence)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _sequenceList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _sequenceList.setElementAt(vSequence, index);
+    } //-- void setSequence(int, jalview.schemabinding.version2.Sequence) 
+
+    /**
+     * Method setSequence
+     * 
+     * 
+     * 
+     * @param sequenceArray
+     */
+    public void setSequence(jalview.schemabinding.version2.Sequence[] sequenceArray)
+    {
+        //-- copy array
+        _sequenceList.removeAllElements();
+        for (int i = 0; i < sequenceArray.length; i++) {
+            _sequenceList.addElement(sequenceArray[i]);
+        }
+    } //-- void setSequence(jalview.schemabinding.version2.Sequence) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
new file mode 100755
index 0000000..1e6c7b5
--- /dev/null
+++ b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
@@ -0,0 +1,323 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class SequenceSetDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public SequenceSetDescriptor() {
+        super();
+        nsURI = "www.vamsas.ac.uk/jalview/version2";
+        xmlName = "SequenceSet";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _gapChar
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                return target.getGapChar();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    target.setGapChar( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _gapChar
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _aligned
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                if(!target.hasAligned())
+                    return null;
+                return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteAligned();
+                        return;
+                    }
+                    target.setAligned( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _aligned
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _sequenceList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                return target.getSequence();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    target.addSequence( (jalview.schemabinding.version2.Sequence) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Sequence();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setRequired(true);
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _sequenceList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _annotationList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                return target.getAnnotation();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Annotation();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _annotationList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.SequenceSetDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.SequenceSet.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java
new file mode 100755
index 0000000..d413e2d
--- /dev/null
+++ b/src/jalview/schemabinding/version2/SequenceType.java
@@ -0,0 +1,225 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class SequenceType.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class SequenceType implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _id
+     */
+    private java.lang.String _id;
+
+    /**
+     * Field _description
+     */
+    private java.lang.String _description;
+
+    /**
+     * Field _sequence
+     */
+    private java.lang.String _sequence;
+
+    /**
+     * Field _name
+     */
+    private java.lang.String _name;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public SequenceType() {
+        super();
+    } //-- jalview.schemabinding.version2.SequenceType()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'description'.
+     * 
+     * @return String
+     * @return the value of field 'description'.
+     */
+    public java.lang.String getDescription()
+    {
+        return this._description;
+    } //-- java.lang.String getDescription() 
+
+    /**
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
+
+    /**
+     * Returns the value of field 'name'.
+     * 
+     * @return String
+     * @return the value of field 'name'.
+     */
+    public java.lang.String getName()
+    {
+        return this._name;
+    } //-- java.lang.String getName() 
+
+    /**
+     * Returns the value of field 'sequence'.
+     * 
+     * @return String
+     * @return the value of field 'sequence'.
+     */
+    public java.lang.String getSequence()
+    {
+        return this._sequence;
+    } //-- java.lang.String getSequence() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'description'.
+     * 
+     * @param description the value of field 'description'.
+     */
+    public void setDescription(java.lang.String description)
+    {
+        this._description = description;
+    } //-- void setDescription(java.lang.String) 
+
+    /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(java.lang.String id)
+    {
+        this._id = id;
+    } //-- void setId(java.lang.String) 
+
+    /**
+     * Sets the value of field 'name'.
+     * 
+     * @param name the value of field 'name'.
+     */
+    public void setName(java.lang.String name)
+    {
+        this._name = name;
+    } //-- void setName(java.lang.String) 
+
+    /**
+     * Sets the value of field 'sequence'.
+     * 
+     * @param sequence the value of field 'sequence'.
+     */
+    public void setSequence(java.lang.String sequence)
+    {
+        this._sequence = sequence;
+    } //-- void setSequence(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceType.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
new file mode 100755
index 0000000..9977ea3
--- /dev/null
+++ b/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
@@ -0,0 +1,325 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class SequenceTypeDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public SequenceTypeDescriptor() {
+        super();
+        nsURI = "www.vamsas.ac.uk/jalview/version2";
+        xmlName = "SequenceType";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _id
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceType target = (SequenceType) object;
+                return target.getId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceType target = (SequenceType) object;
+                    target.setId( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _description
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceType target = (SequenceType) object;
+                return target.getDescription();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceType target = (SequenceType) object;
+                    target.setDescription( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _description
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _sequence
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceType target = (SequenceType) object;
+                return target.getSequence();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceType target = (SequenceType) object;
+                    target.setSequence( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _sequence
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _name
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceType target = (SequenceType) object;
+                return target.getName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceType target = (SequenceType) object;
+                    target.setName( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _name
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.SequenceTypeDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.SequenceType.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java
new file mode 100755
index 0000000..668ef9d
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Setting.java
@@ -0,0 +1,253 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Setting.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Setting implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _type
+     */
+    private java.lang.String _type;
+
+    /**
+     * Field _colour
+     */
+    private int _colour;
+
+    /**
+     * keeps track of state for field: _colour
+     */
+    private boolean _has_colour;
+
+    /**
+     * Field _display
+     */
+    private boolean _display;
+
+    /**
+     * keeps track of state for field: _display
+     */
+    private boolean _has_display;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Setting() {
+        super();
+    } //-- jalview.schemabinding.version2.Setting()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method deleteColour
+     * 
+     */
+    public void deleteColour()
+    {
+        this._has_colour= false;
+    } //-- void deleteColour() 
+
+    /**
+     * Method deleteDisplay
+     * 
+     */
+    public void deleteDisplay()
+    {
+        this._has_display= false;
+    } //-- void deleteDisplay() 
+
+    /**
+     * Returns the value of field 'colour'.
+     * 
+     * @return int
+     * @return the value of field 'colour'.
+     */
+    public int getColour()
+    {
+        return this._colour;
+    } //-- int getColour() 
+
+    /**
+     * Returns the value of field 'display'.
+     * 
+     * @return boolean
+     * @return the value of field 'display'.
+     */
+    public boolean getDisplay()
+    {
+        return this._display;
+    } //-- boolean getDisplay() 
+
+    /**
+     * Returns the value of field 'type'.
+     * 
+     * @return String
+     * @return the value of field 'type'.
+     */
+    public java.lang.String getType()
+    {
+        return this._type;
+    } //-- java.lang.String getType() 
+
+    /**
+     * Method hasColour
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasColour()
+    {
+        return this._has_colour;
+    } //-- boolean hasColour() 
+
+    /**
+     * Method hasDisplay
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasDisplay()
+    {
+        return this._has_display;
+    } //-- boolean hasDisplay() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'colour'.
+     * 
+     * @param colour the value of field 'colour'.
+     */
+    public void setColour(int colour)
+    {
+        this._colour = colour;
+        this._has_colour = true;
+    } //-- void setColour(int) 
+
+    /**
+     * Sets the value of field 'display'.
+     * 
+     * @param display the value of field 'display'.
+     */
+    public void setDisplay(boolean display)
+    {
+        this._display = display;
+        this._has_display = true;
+    } //-- void setDisplay(boolean) 
+
+    /**
+     * Sets the value of field 'type'.
+     * 
+     * @param type the value of field 'type'.
+     */
+    public void setType(java.lang.String type)
+    {
+        this._type = type;
+    } //-- void setType(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.Setting.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/SettingDescriptor.java b/src/jalview/schemabinding/version2/SettingDescriptor.java
new file mode 100755
index 0000000..6cadc16
--- /dev/null
+++ b/src/jalview/schemabinding/version2/SettingDescriptor.java
@@ -0,0 +1,290 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class SettingDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public SettingDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "setting";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _type
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Setting target = (Setting) object;
+                return target.getType();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Setting target = (Setting) object;
+                    target.setType( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _type
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _colour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Setting target = (Setting) object;
+                if(!target.hasColour())
+                    return null;
+                return new java.lang.Integer(target.getColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Setting target = (Setting) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setColour( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _colour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _display
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Setting target = (Setting) object;
+                if(!target.hasDisplay())
+                    return null;
+                return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Setting target = (Setting) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setDisplay( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _display
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- jalview.schemabinding.version2.SettingDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Setting.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java
new file mode 100755
index 0000000..85854c1
--- /dev/null
+++ b/src/jalview/schemabinding/version2/ThresholdLine.java
@@ -0,0 +1,253 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class ThresholdLine.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ThresholdLine implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _label
+     */
+    private java.lang.String _label;
+
+    /**
+     * Field _value
+     */
+    private float _value;
+
+    /**
+     * keeps track of state for field: _value
+     */
+    private boolean _has_value;
+
+    /**
+     * Field _colour
+     */
+    private int _colour;
+
+    /**
+     * keeps track of state for field: _colour
+     */
+    private boolean _has_colour;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public ThresholdLine() {
+        super();
+    } //-- jalview.schemabinding.version2.ThresholdLine()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method deleteColour
+     * 
+     */
+    public void deleteColour()
+    {
+        this._has_colour= false;
+    } //-- void deleteColour() 
+
+    /**
+     * Method deleteValue
+     * 
+     */
+    public void deleteValue()
+    {
+        this._has_value= false;
+    } //-- void deleteValue() 
+
+    /**
+     * Returns the value of field 'colour'.
+     * 
+     * @return int
+     * @return the value of field 'colour'.
+     */
+    public int getColour()
+    {
+        return this._colour;
+    } //-- int getColour() 
+
+    /**
+     * Returns the value of field 'label'.
+     * 
+     * @return String
+     * @return the value of field 'label'.
+     */
+    public java.lang.String getLabel()
+    {
+        return this._label;
+    } //-- java.lang.String getLabel() 
+
+    /**
+     * Returns the value of field 'value'.
+     * 
+     * @return float
+     * @return the value of field 'value'.
+     */
+    public float getValue()
+    {
+        return this._value;
+    } //-- float getValue() 
+
+    /**
+     * Method hasColour
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasColour()
+    {
+        return this._has_colour;
+    } //-- boolean hasColour() 
+
+    /**
+     * Method hasValue
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasValue()
+    {
+        return this._has_value;
+    } //-- boolean hasValue() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'colour'.
+     * 
+     * @param colour the value of field 'colour'.
+     */
+    public void setColour(int colour)
+    {
+        this._colour = colour;
+        this._has_colour = true;
+    } //-- void setColour(int) 
+
+    /**
+     * Sets the value of field 'label'.
+     * 
+     * @param label the value of field 'label'.
+     */
+    public void setLabel(java.lang.String label)
+    {
+        this._label = label;
+    } //-- void setLabel(java.lang.String) 
+
+    /**
+     * Sets the value of field 'value'.
+     * 
+     * @param value the value of field 'value'.
+     */
+    public void setValue(float value)
+    {
+        this._value = value;
+        this._has_value = true;
+    } //-- void setValue(float) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
new file mode 100755
index 0000000..9241003
--- /dev/null
+++ b/src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
@@ -0,0 +1,288 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class ThresholdLineDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public ThresholdLineDescriptor() {
+        super();
+        nsURI = "www.vamsas.ac.uk/jalview/version2";
+        xmlName = "thresholdLine";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _label
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                ThresholdLine target = (ThresholdLine) object;
+                return target.getLabel();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    ThresholdLine target = (ThresholdLine) object;
+                    target.setLabel( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _label
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _value
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                ThresholdLine target = (ThresholdLine) object;
+                if(!target.hasValue())
+                    return null;
+                return new java.lang.Float(target.getValue());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    ThresholdLine target = (ThresholdLine) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteValue();
+                        return;
+                    }
+                    target.setValue( ((java.lang.Float)value).floatValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _value
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            FloatValidator typeValidator = new FloatValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _colour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                ThresholdLine target = (ThresholdLine) object;
+                if(!target.hasColour())
+                    return null;
+                return new java.lang.Integer(target.getColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    ThresholdLine target = (ThresholdLine) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteColour();
+                        return;
+                    }
+                    target.setColour( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _colour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- jalview.schemabinding.version2.ThresholdLineDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.ThresholdLine.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java
new file mode 100755
index 0000000..96b2e18
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Tree.java
@@ -0,0 +1,835 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Tree.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Tree implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _width
+     */
+    private int _width;
+
+    /**
+     * keeps track of state for field: _width
+     */
+    private boolean _has_width;
+
+    /**
+     * Field _height
+     */
+    private int _height;
+
+    /**
+     * keeps track of state for field: _height
+     */
+    private boolean _has_height;
+
+    /**
+     * Field _xpos
+     */
+    private int _xpos;
+
+    /**
+     * keeps track of state for field: _xpos
+     */
+    private boolean _has_xpos;
+
+    /**
+     * Field _ypos
+     */
+    private int _ypos;
+
+    /**
+     * keeps track of state for field: _ypos
+     */
+    private boolean _has_ypos;
+
+    /**
+     * Field _fontName
+     */
+    private java.lang.String _fontName;
+
+    /**
+     * Field _fontSize
+     */
+    private int _fontSize;
+
+    /**
+     * keeps track of state for field: _fontSize
+     */
+    private boolean _has_fontSize;
+
+    /**
+     * Field _fontStyle
+     */
+    private int _fontStyle;
+
+    /**
+     * keeps track of state for field: _fontStyle
+     */
+    private boolean _has_fontStyle;
+
+    /**
+     * Field _threshold
+     */
+    private float _threshold;
+
+    /**
+     * keeps track of state for field: _threshold
+     */
+    private boolean _has_threshold;
+
+    /**
+     * Field _showBootstrap
+     */
+    private boolean _showBootstrap;
+
+    /**
+     * keeps track of state for field: _showBootstrap
+     */
+    private boolean _has_showBootstrap;
+
+    /**
+     * Field _showDistances
+     */
+    private boolean _showDistances;
+
+    /**
+     * keeps track of state for field: _showDistances
+     */
+    private boolean _has_showDistances;
+
+    /**
+     * Field _markUnlinked
+     */
+    private boolean _markUnlinked;
+
+    /**
+     * keeps track of state for field: _markUnlinked
+     */
+    private boolean _has_markUnlinked;
+
+    /**
+     * Field _fitToWindow
+     */
+    private boolean _fitToWindow;
+
+    /**
+     * keeps track of state for field: _fitToWindow
+     */
+    private boolean _has_fitToWindow;
+
+    /**
+     * Field _currentTree
+     */
+    private boolean _currentTree;
+
+    /**
+     * keeps track of state for field: _currentTree
+     */
+    private boolean _has_currentTree;
+
+    /**
+     * Field _title
+     */
+    private java.lang.String _title;
+
+    /**
+     * Field _newick
+     */
+    private java.lang.String _newick;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Tree() {
+        super();
+    } //-- jalview.schemabinding.version2.Tree()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method deleteCurrentTree
+     * 
+     */
+    public void deleteCurrentTree()
+    {
+        this._has_currentTree= false;
+    } //-- void deleteCurrentTree() 
+
+    /**
+     * Method deleteFitToWindow
+     * 
+     */
+    public void deleteFitToWindow()
+    {
+        this._has_fitToWindow= false;
+    } //-- void deleteFitToWindow() 
+
+    /**
+     * Method deleteFontSize
+     * 
+     */
+    public void deleteFontSize()
+    {
+        this._has_fontSize= false;
+    } //-- void deleteFontSize() 
+
+    /**
+     * Method deleteFontStyle
+     * 
+     */
+    public void deleteFontStyle()
+    {
+        this._has_fontStyle= false;
+    } //-- void deleteFontStyle() 
+
+    /**
+     * Method deleteHeight
+     * 
+     */
+    public void deleteHeight()
+    {
+        this._has_height= false;
+    } //-- void deleteHeight() 
+
+    /**
+     * Method deleteMarkUnlinked
+     * 
+     */
+    public void deleteMarkUnlinked()
+    {
+        this._has_markUnlinked= false;
+    } //-- void deleteMarkUnlinked() 
+
+    /**
+     * Method deleteShowBootstrap
+     * 
+     */
+    public void deleteShowBootstrap()
+    {
+        this._has_showBootstrap= false;
+    } //-- void deleteShowBootstrap() 
+
+    /**
+     * Method deleteShowDistances
+     * 
+     */
+    public void deleteShowDistances()
+    {
+        this._has_showDistances= false;
+    } //-- void deleteShowDistances() 
+
+    /**
+     * Method deleteThreshold
+     * 
+     */
+    public void deleteThreshold()
+    {
+        this._has_threshold= false;
+    } //-- void deleteThreshold() 
+
+    /**
+     * Method deleteWidth
+     * 
+     */
+    public void deleteWidth()
+    {
+        this._has_width= false;
+    } //-- void deleteWidth() 
+
+    /**
+     * Method deleteXpos
+     * 
+     */
+    public void deleteXpos()
+    {
+        this._has_xpos= false;
+    } //-- void deleteXpos() 
+
+    /**
+     * Method deleteYpos
+     * 
+     */
+    public void deleteYpos()
+    {
+        this._has_ypos= false;
+    } //-- void deleteYpos() 
+
+    /**
+     * Returns the value of field 'currentTree'.
+     * 
+     * @return boolean
+     * @return the value of field 'currentTree'.
+     */
+    public boolean getCurrentTree()
+    {
+        return this._currentTree;
+    } //-- boolean getCurrentTree() 
+
+    /**
+     * Returns the value of field 'fitToWindow'.
+     * 
+     * @return boolean
+     * @return the value of field 'fitToWindow'.
+     */
+    public boolean getFitToWindow()
+    {
+        return this._fitToWindow;
+    } //-- boolean getFitToWindow() 
+
+    /**
+     * Returns the value of field 'fontName'.
+     * 
+     * @return String
+     * @return the value of field 'fontName'.
+     */
+    public java.lang.String getFontName()
+    {
+        return this._fontName;
+    } //-- java.lang.String getFontName() 
+
+    /**
+     * Returns the value of field 'fontSize'.
+     * 
+     * @return int
+     * @return the value of field 'fontSize'.
+     */
+    public int getFontSize()
+    {
+        return this._fontSize;
+    } //-- int getFontSize() 
+
+    /**
+     * Returns the value of field 'fontStyle'.
+     * 
+     * @return int
+     * @return the value of field 'fontStyle'.
+     */
+    public int getFontStyle()
+    {
+        return this._fontStyle;
+    } //-- int getFontStyle() 
+
+    /**
+     * Returns the value of field 'height'.
+     * 
+     * @return int
+     * @return the value of field 'height'.
+     */
+    public int getHeight()
+    {
+        return this._height;
+    } //-- int getHeight() 
+
+    /**
+     * Returns the value of field 'markUnlinked'.
+     * 
+     * @return boolean
+     * @return the value of field 'markUnlinked'.
+     */
+    public boolean getMarkUnlinked()
+    {
+        return this._markUnlinked;
+    } //-- boolean getMarkUnlinked() 
+
+    /**
+     * Returns the value of field 'newick'.
+     * 
+     * @return String
+     * @return the value of field 'newick'.
+     */
+    public java.lang.String getNewick()
+    {
+        return this._newick;
+    } //-- java.lang.String getNewick() 
+
+    /**
+     * Returns the value of field 'showBootstrap'.
+     * 
+     * @return boolean
+     * @return the value of field 'showBootstrap'.
+     */
+    public boolean getShowBootstrap()
+    {
+        return this._showBootstrap;
+    } //-- boolean getShowBootstrap() 
+
+    /**
+     * Returns the value of field 'showDistances'.
+     * 
+     * @return boolean
+     * @return the value of field 'showDistances'.
+     */
+    public boolean getShowDistances()
+    {
+        return this._showDistances;
+    } //-- boolean getShowDistances() 
+
+    /**
+     * Returns the value of field 'threshold'.
+     * 
+     * @return float
+     * @return the value of field 'threshold'.
+     */
+    public float getThreshold()
+    {
+        return this._threshold;
+    } //-- float getThreshold() 
+
+    /**
+     * Returns the value of field 'title'.
+     * 
+     * @return String
+     * @return the value of field 'title'.
+     */
+    public java.lang.String getTitle()
+    {
+        return this._title;
+    } //-- java.lang.String getTitle() 
+
+    /**
+     * Returns the value of field 'width'.
+     * 
+     * @return int
+     * @return the value of field 'width'.
+     */
+    public int getWidth()
+    {
+        return this._width;
+    } //-- int getWidth() 
+
+    /**
+     * Returns the value of field 'xpos'.
+     * 
+     * @return int
+     * @return the value of field 'xpos'.
+     */
+    public int getXpos()
+    {
+        return this._xpos;
+    } //-- int getXpos() 
+
+    /**
+     * Returns the value of field 'ypos'.
+     * 
+     * @return int
+     * @return the value of field 'ypos'.
+     */
+    public int getYpos()
+    {
+        return this._ypos;
+    } //-- int getYpos() 
+
+    /**
+     * Method hasCurrentTree
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasCurrentTree()
+    {
+        return this._has_currentTree;
+    } //-- boolean hasCurrentTree() 
+
+    /**
+     * Method hasFitToWindow
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasFitToWindow()
+    {
+        return this._has_fitToWindow;
+    } //-- boolean hasFitToWindow() 
+
+    /**
+     * Method hasFontSize
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasFontSize()
+    {
+        return this._has_fontSize;
+    } //-- boolean hasFontSize() 
+
+    /**
+     * Method hasFontStyle
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasFontStyle()
+    {
+        return this._has_fontStyle;
+    } //-- boolean hasFontStyle() 
+
+    /**
+     * Method hasHeight
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasHeight()
+    {
+        return this._has_height;
+    } //-- boolean hasHeight() 
+
+    /**
+     * Method hasMarkUnlinked
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasMarkUnlinked()
+    {
+        return this._has_markUnlinked;
+    } //-- boolean hasMarkUnlinked() 
+
+    /**
+     * Method hasShowBootstrap
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowBootstrap()
+    {
+        return this._has_showBootstrap;
+    } //-- boolean hasShowBootstrap() 
+
+    /**
+     * Method hasShowDistances
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowDistances()
+    {
+        return this._has_showDistances;
+    } //-- boolean hasShowDistances() 
+
+    /**
+     * Method hasThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasThreshold()
+    {
+        return this._has_threshold;
+    } //-- boolean hasThreshold() 
+
+    /**
+     * Method hasWidth
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasWidth()
+    {
+        return this._has_width;
+    } //-- boolean hasWidth() 
+
+    /**
+     * Method hasXpos
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasXpos()
+    {
+        return this._has_xpos;
+    } //-- boolean hasXpos() 
+
+    /**
+     * Method hasYpos
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasYpos()
+    {
+        return this._has_ypos;
+    } //-- boolean hasYpos() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'currentTree'.
+     * 
+     * @param currentTree the value of field 'currentTree'.
+     */
+    public void setCurrentTree(boolean currentTree)
+    {
+        this._currentTree = currentTree;
+        this._has_currentTree = true;
+    } //-- void setCurrentTree(boolean) 
+
+    /**
+     * Sets the value of field 'fitToWindow'.
+     * 
+     * @param fitToWindow the value of field 'fitToWindow'.
+     */
+    public void setFitToWindow(boolean fitToWindow)
+    {
+        this._fitToWindow = fitToWindow;
+        this._has_fitToWindow = true;
+    } //-- void setFitToWindow(boolean) 
+
+    /**
+     * Sets the value of field 'fontName'.
+     * 
+     * @param fontName the value of field 'fontName'.
+     */
+    public void setFontName(java.lang.String fontName)
+    {
+        this._fontName = fontName;
+    } //-- void setFontName(java.lang.String) 
+
+    /**
+     * Sets the value of field 'fontSize'.
+     * 
+     * @param fontSize the value of field 'fontSize'.
+     */
+    public void setFontSize(int fontSize)
+    {
+        this._fontSize = fontSize;
+        this._has_fontSize = true;
+    } //-- void setFontSize(int) 
+
+    /**
+     * Sets the value of field 'fontStyle'.
+     * 
+     * @param fontStyle the value of field 'fontStyle'.
+     */
+    public void setFontStyle(int fontStyle)
+    {
+        this._fontStyle = fontStyle;
+        this._has_fontStyle = true;
+    } //-- void setFontStyle(int) 
+
+    /**
+     * Sets the value of field 'height'.
+     * 
+     * @param height the value of field 'height'.
+     */
+    public void setHeight(int height)
+    {
+        this._height = height;
+        this._has_height = true;
+    } //-- void setHeight(int) 
+
+    /**
+     * Sets the value of field 'markUnlinked'.
+     * 
+     * @param markUnlinked the value of field 'markUnlinked'.
+     */
+    public void setMarkUnlinked(boolean markUnlinked)
+    {
+        this._markUnlinked = markUnlinked;
+        this._has_markUnlinked = true;
+    } //-- void setMarkUnlinked(boolean) 
+
+    /**
+     * Sets the value of field 'newick'.
+     * 
+     * @param newick the value of field 'newick'.
+     */
+    public void setNewick(java.lang.String newick)
+    {
+        this._newick = newick;
+    } //-- void setNewick(java.lang.String) 
+
+    /**
+     * Sets the value of field 'showBootstrap'.
+     * 
+     * @param showBootstrap the value of field 'showBootstrap'.
+     */
+    public void setShowBootstrap(boolean showBootstrap)
+    {
+        this._showBootstrap = showBootstrap;
+        this._has_showBootstrap = true;
+    } //-- void setShowBootstrap(boolean) 
+
+    /**
+     * Sets the value of field 'showDistances'.
+     * 
+     * @param showDistances the value of field 'showDistances'.
+     */
+    public void setShowDistances(boolean showDistances)
+    {
+        this._showDistances = showDistances;
+        this._has_showDistances = true;
+    } //-- void setShowDistances(boolean) 
+
+    /**
+     * Sets the value of field 'threshold'.
+     * 
+     * @param threshold the value of field 'threshold'.
+     */
+    public void setThreshold(float threshold)
+    {
+        this._threshold = threshold;
+        this._has_threshold = true;
+    } //-- void setThreshold(float) 
+
+    /**
+     * Sets the value of field 'title'.
+     * 
+     * @param title the value of field 'title'.
+     */
+    public void setTitle(java.lang.String title)
+    {
+        this._title = title;
+    } //-- void setTitle(java.lang.String) 
+
+    /**
+     * Sets the value of field 'width'.
+     * 
+     * @param width the value of field 'width'.
+     */
+    public void setWidth(int width)
+    {
+        this._width = width;
+        this._has_width = true;
+    } //-- void setWidth(int) 
+
+    /**
+     * Sets the value of field 'xpos'.
+     * 
+     * @param xpos the value of field 'xpos'.
+     */
+    public void setXpos(int xpos)
+    {
+        this._xpos = xpos;
+        this._has_xpos = true;
+    } //-- void setXpos(int) 
+
+    /**
+     * Sets the value of field 'ypos'.
+     * 
+     * @param ypos the value of field 'ypos'.
+     */
+    public void setYpos(int ypos)
+    {
+        this._ypos = ypos;
+        this._has_ypos = true;
+    } //-- void setYpos(int) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/TreeDescriptor.java b/src/jalview/schemabinding/version2/TreeDescriptor.java
new file mode 100755
index 0000000..5232c12
--- /dev/null
+++ b/src/jalview/schemabinding/version2/TreeDescriptor.java
@@ -0,0 +1,777 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class TreeDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public TreeDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "tree";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _width
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasWidth())
+                    return null;
+                return new java.lang.Integer(target.getWidth());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteWidth();
+                        return;
+                    }
+                    target.setWidth( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _width
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _height
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasHeight())
+                    return null;
+                return new java.lang.Integer(target.getHeight());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteHeight();
+                        return;
+                    }
+                    target.setHeight( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _height
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _xpos
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasXpos())
+                    return null;
+                return new java.lang.Integer(target.getXpos());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteXpos();
+                        return;
+                    }
+                    target.setXpos( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _xpos
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _ypos
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasYpos())
+                    return null;
+                return new java.lang.Integer(target.getYpos());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteYpos();
+                        return;
+                    }
+                    target.setYpos( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _ypos
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _fontName
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                return target.getFontName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    target.setFontName( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _fontName
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _fontSize
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasFontSize())
+                    return null;
+                return new java.lang.Integer(target.getFontSize());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteFontSize();
+                        return;
+                    }
+                    target.setFontSize( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _fontSize
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _fontStyle
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasFontStyle())
+                    return null;
+                return new java.lang.Integer(target.getFontStyle());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteFontStyle();
+                        return;
+                    }
+                    target.setFontStyle( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _fontStyle
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _threshold
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasThreshold())
+                    return null;
+                return new java.lang.Float(target.getThreshold());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteThreshold();
+                        return;
+                    }
+                    target.setThreshold( ((java.lang.Float)value).floatValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _threshold
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            FloatValidator typeValidator = new FloatValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showBootstrap
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasShowBootstrap())
+                    return null;
+                return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowBootstrap();
+                        return;
+                    }
+                    target.setShowBootstrap( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showBootstrap
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showDistances
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasShowDistances())
+                    return null;
+                return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowDistances();
+                        return;
+                    }
+                    target.setShowDistances( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showDistances
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _markUnlinked
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasMarkUnlinked())
+                    return null;
+                return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteMarkUnlinked();
+                        return;
+                    }
+                    target.setMarkUnlinked( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _markUnlinked
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _fitToWindow
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasFitToWindow())
+                    return null;
+                return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteFitToWindow();
+                        return;
+                    }
+                    target.setFitToWindow( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _fitToWindow
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _currentTree
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                if(!target.hasCurrentTree())
+                    return null;
+                return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteCurrentTree();
+                        return;
+                    }
+                    target.setCurrentTree( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _currentTree
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _title
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                return target.getTitle();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    target.setTitle( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _title
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _newick
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                return target.getNewick();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    target.setNewick( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _newick
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.TreeDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Tree.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java
new file mode 100755
index 0000000..00bc181
--- /dev/null
+++ b/src/jalview/schemabinding/version2/UserColourScheme.java
@@ -0,0 +1,118 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class UserColourScheme.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class UserColourScheme extends JalviewUserColours 
+implements java.io.Serializable
+{
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public UserColourScheme() {
+        super();
+    } //-- jalview.schemabinding.version2.UserColourScheme()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.UserColourScheme) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColourScheme.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
new file mode 100755
index 0000000..cf86a11
--- /dev/null
+++ b/src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
@@ -0,0 +1,166 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class UserColourSchemeDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class UserColourSchemeDescriptor extends JalviewUserColoursDescriptor {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public UserColourSchemeDescriptor() {
+        super();
+        setExtendsWithoutFlatten(new JalviewUserColoursDescriptor());
+        nsURI = "www.jalview.org";
+        xmlName = "UserColourScheme";
+    } //-- jalview.schemabinding.version2.UserColourSchemeDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return super.getExtends();
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        if (identity == null)
+            return super.getIdentity();
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.UserColourScheme.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java
new file mode 100755
index 0000000..28f2b39
--- /dev/null
+++ b/src/jalview/schemabinding/version2/UserColours.java
@@ -0,0 +1,173 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class UserColours.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class UserColours implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _id
+     */
+    private java.lang.String _id;
+
+    /**
+     * Field _userColourScheme
+     */
+    private jalview.schemabinding.version2.UserColourScheme _userColourScheme;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public UserColours() {
+        super();
+    } //-- jalview.schemabinding.version2.UserColours()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
+
+    /**
+     * Returns the value of field 'userColourScheme'.
+     * 
+     * @return UserColourScheme
+     * @return the value of field 'userColourScheme'.
+     */
+    public jalview.schemabinding.version2.UserColourScheme getUserColourScheme()
+    {
+        return this._userColourScheme;
+    } //-- jalview.schemabinding.version2.UserColourScheme getUserColourScheme() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(java.lang.String id)
+    {
+        this._id = id;
+    } //-- void setId(java.lang.String) 
+
+    /**
+     * Sets the value of field 'userColourScheme'.
+     * 
+     * @param userColourScheme the value of field 'userColourScheme'
+     */
+    public void setUserColourScheme(jalview.schemabinding.version2.UserColourScheme userColourScheme)
+    {
+        this._userColourScheme = userColourScheme;
+    } //-- void setUserColourScheme(jalview.schemabinding.version2.UserColourScheme) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.UserColours.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/UserColoursDescriptor.java
new file mode 100755
index 0000000..6c42d0b
--- /dev/null
+++ b/src/jalview/schemabinding/version2/UserColoursDescriptor.java
@@ -0,0 +1,245 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class UserColoursDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public UserColoursDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "UserColours";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _id
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                UserColours target = (UserColours) object;
+                return target.getId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    UserColours target = (UserColours) object;
+                    target.setId( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _userColourScheme
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColourScheme.class, "_userColourScheme", "UserColourScheme", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                UserColours target = (UserColours) object;
+                return target.getUserColourScheme();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    UserColours target = (UserColours) object;
+                    target.setUserColourScheme( (jalview.schemabinding.version2.UserColourScheme) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.UserColourScheme();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _userColourScheme
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.UserColoursDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.UserColours.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
new file mode 100755
index 0000000..9550690
--- /dev/null
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -0,0 +1,576 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class VAMSAS.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class VAMSAS implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _alignmentList
+     */
+    private java.util.Vector _alignmentList;
+
+    /**
+     * Field _treeList
+     */
+    private java.util.Vector _treeList;
+
+    /**
+     * Field _sequenceSetList
+     */
+    private java.util.Vector _sequenceSetList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public VAMSAS() {
+        super();
+        _alignmentList = new Vector();
+        _treeList = new Vector();
+        _sequenceSetList = new Vector();
+    } //-- jalview.schemabinding.version2.VAMSAS()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addAlignment
+     * 
+     * 
+     * 
+     * @param vAlignment
+     */
+    public void addAlignment(jalview.schemabinding.version2.Alignment vAlignment)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _alignmentList.addElement(vAlignment);
+    } //-- void addAlignment(jalview.schemabinding.version2.Alignment) 
+
+    /**
+     * Method addAlignment
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAlignment
+     */
+    public void addAlignment(int index, jalview.schemabinding.version2.Alignment vAlignment)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _alignmentList.insertElementAt(vAlignment, index);
+    } //-- void addAlignment(int, jalview.schemabinding.version2.Alignment) 
+
+    /**
+     * Method addSequenceSet
+     * 
+     * 
+     * 
+     * @param vSequenceSet
+     */
+    public void addSequenceSet(jalview.schemabinding.version2.SequenceSet vSequenceSet)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _sequenceSetList.addElement(vSequenceSet);
+    } //-- void addSequenceSet(jalview.schemabinding.version2.SequenceSet) 
+
+    /**
+     * Method addSequenceSet
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSequenceSet
+     */
+    public void addSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _sequenceSetList.insertElementAt(vSequenceSet, index);
+    } //-- void addSequenceSet(int, jalview.schemabinding.version2.SequenceSet) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param vTree
+     */
+    public void addTree(java.lang.String vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.addElement(vTree);
+    } //-- void addTree(java.lang.String) 
+
+    /**
+     * Method addTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void addTree(int index, java.lang.String vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _treeList.insertElementAt(vTree, index);
+    } //-- void addTree(int, java.lang.String) 
+
+    /**
+     * Method enumerateAlignment
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateAlignment()
+    {
+        return _alignmentList.elements();
+    } //-- java.util.Enumeration enumerateAlignment() 
+
+    /**
+     * Method enumerateSequenceSet
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateSequenceSet()
+    {
+        return _sequenceSetList.elements();
+    } //-- java.util.Enumeration enumerateSequenceSet() 
+
+    /**
+     * Method enumerateTree
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateTree()
+    {
+        return _treeList.elements();
+    } //-- java.util.Enumeration enumerateTree() 
+
+    /**
+     * Method getAlignment
+     * 
+     * 
+     * 
+     * @param index
+     * @return Alignment
+     */
+    public jalview.schemabinding.version2.Alignment getAlignment(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _alignmentList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.Alignment) _alignmentList.elementAt(index);
+    } //-- jalview.schemabinding.version2.Alignment getAlignment(int) 
+
+    /**
+     * Method getAlignment
+     * 
+     * 
+     * 
+     * @return Alignment
+     */
+    public jalview.schemabinding.version2.Alignment[] getAlignment()
+    {
+        int size = _alignmentList.size();
+        jalview.schemabinding.version2.Alignment[] mArray = new jalview.schemabinding.version2.Alignment[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.Alignment) _alignmentList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.Alignment[] getAlignment() 
+
+    /**
+     * Method getAlignmentCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getAlignmentCount()
+    {
+        return _alignmentList.size();
+    } //-- int getAlignmentCount() 
+
+    /**
+     * Method getSequenceSet
+     * 
+     * 
+     * 
+     * @param index
+     * @return SequenceSet
+     */
+    public jalview.schemabinding.version2.SequenceSet getSequenceSet(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _sequenceSetList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);
+    } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet(int) 
+
+    /**
+     * Method getSequenceSet
+     * 
+     * 
+     * 
+     * @return SequenceSet
+     */
+    public jalview.schemabinding.version2.SequenceSet[] getSequenceSet()
+    {
+        int size = _sequenceSetList.size();
+        jalview.schemabinding.version2.SequenceSet[] mArray = new jalview.schemabinding.version2.SequenceSet[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.SequenceSet) _sequenceSetList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.SequenceSet[] getSequenceSet() 
+
+    /**
+     * Method getSequenceSetCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getSequenceSetCount()
+    {
+        return _sequenceSetList.size();
+    } //-- int getSequenceSetCount() 
+
+    /**
+     * Method getTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return String
+     */
+    public java.lang.String getTree(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (String)_treeList.elementAt(index);
+    } //-- java.lang.String getTree(int) 
+
+    /**
+     * Method getTree
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String[] getTree()
+    {
+        int size = _treeList.size();
+        java.lang.String[] mArray = new java.lang.String[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (String)_treeList.elementAt(index);
+        }
+        return mArray;
+    } //-- java.lang.String[] getTree() 
+
+    /**
+     * Method getTreeCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getTreeCount()
+    {
+        return _treeList.size();
+    } //-- int getTreeCount() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAlignment
+     * 
+     * 
+     * 
+     * @param index
+     * @return Alignment
+     */
+    public jalview.schemabinding.version2.Alignment removeAlignment(int index)
+    {
+        java.lang.Object obj = _alignmentList.elementAt(index);
+        _alignmentList.removeElementAt(index);
+        return (jalview.schemabinding.version2.Alignment) obj;
+    } //-- jalview.schemabinding.version2.Alignment removeAlignment(int) 
+
+    /**
+     * Method removeAllAlignment
+     * 
+     */
+    public void removeAllAlignment()
+    {
+        _alignmentList.removeAllElements();
+    } //-- void removeAllAlignment() 
+
+    /**
+     * Method removeAllSequenceSet
+     * 
+     */
+    public void removeAllSequenceSet()
+    {
+        _sequenceSetList.removeAllElements();
+    } //-- void removeAllSequenceSet() 
+
+    /**
+     * Method removeAllTree
+     * 
+     */
+    public void removeAllTree()
+    {
+        _treeList.removeAllElements();
+    } //-- void removeAllTree() 
+
+    /**
+     * Method removeSequenceSet
+     * 
+     * 
+     * 
+     * @param index
+     * @return SequenceSet
+     */
+    public jalview.schemabinding.version2.SequenceSet removeSequenceSet(int index)
+    {
+        java.lang.Object obj = _sequenceSetList.elementAt(index);
+        _sequenceSetList.removeElementAt(index);
+        return (jalview.schemabinding.version2.SequenceSet) obj;
+    } //-- jalview.schemabinding.version2.SequenceSet removeSequenceSet(int) 
+
+    /**
+     * Method removeTree
+     * 
+     * 
+     * 
+     * @param index
+     * @return String
+     */
+    public java.lang.String removeTree(int index)
+    {
+        java.lang.Object obj = _treeList.elementAt(index);
+        _treeList.removeElementAt(index);
+        return (String)obj;
+    } //-- java.lang.String removeTree(int) 
+
+    /**
+     * Method setAlignment
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAlignment
+     */
+    public void setAlignment(int index, jalview.schemabinding.version2.Alignment vAlignment)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _alignmentList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _alignmentList.setElementAt(vAlignment, index);
+    } //-- void setAlignment(int, jalview.schemabinding.version2.Alignment) 
+
+    /**
+     * Method setAlignment
+     * 
+     * 
+     * 
+     * @param alignmentArray
+     */
+    public void setAlignment(jalview.schemabinding.version2.Alignment[] alignmentArray)
+    {
+        //-- copy array
+        _alignmentList.removeAllElements();
+        for (int i = 0; i < alignmentArray.length; i++) {
+            _alignmentList.addElement(alignmentArray[i]);
+        }
+    } //-- void setAlignment(jalview.schemabinding.version2.Alignment) 
+
+    /**
+     * Method setSequenceSet
+     * 
+     * 
+     * 
+     * @param index
+     * @param vSequenceSet
+     */
+    public void setSequenceSet(int index, jalview.schemabinding.version2.SequenceSet vSequenceSet)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _sequenceSetList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _sequenceSetList.setElementAt(vSequenceSet, index);
+    } //-- void setSequenceSet(int, jalview.schemabinding.version2.SequenceSet) 
+
+    /**
+     * Method setSequenceSet
+     * 
+     * 
+     * 
+     * @param sequenceSetArray
+     */
+    public void setSequenceSet(jalview.schemabinding.version2.SequenceSet[] sequenceSetArray)
+    {
+        //-- copy array
+        _sequenceSetList.removeAllElements();
+        for (int i = 0; i < sequenceSetArray.length; i++) {
+            _sequenceSetList.addElement(sequenceSetArray[i]);
+        }
+    } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet) 
+
+    /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param index
+     * @param vTree
+     */
+    public void setTree(int index, java.lang.String vTree)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _treeList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _treeList.setElementAt(vTree, index);
+    } //-- void setTree(int, java.lang.String) 
+
+    /**
+     * Method setTree
+     * 
+     * 
+     * 
+     * @param treeArray
+     */
+    public void setTree(java.lang.String[] treeArray)
+    {
+        //-- copy array
+        _treeList.removeAllElements();
+        for (int i = 0; i < treeArray.length; i++) {
+            _treeList.addElement(treeArray[i]);
+        }
+    } //-- void setTree(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.VAMSAS.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/VAMSASDescriptor.java
new file mode 100755
index 0000000..02140e0
--- /dev/null
+++ b/src/jalview/schemabinding/version2/VAMSASDescriptor.java
@@ -0,0 +1,282 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class VAMSASDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public VAMSASDescriptor() {
+        super();
+        nsURI = "www.vamsas.ac.uk/jalview/version2";
+        xmlName = "VAMSAS";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _alignmentList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alignment.class, "_alignmentList", "Alignment", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                VAMSAS target = (VAMSAS) object;
+                return target.getAlignment();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    VAMSAS target = (VAMSAS) object;
+                    target.addAlignment( (jalview.schemabinding.version2.Alignment) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.Alignment();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _alignmentList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _treeList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                VAMSAS target = (VAMSAS) object;
+                return target.getTree();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    VAMSAS target = (VAMSAS) object;
+                    target.addTree( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _treeList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _sequenceSetList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                VAMSAS target = (VAMSAS) object;
+                return target.getSequenceSet();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    VAMSAS target = (VAMSAS) object;
+                    target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.SequenceSet();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _sequenceSetList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.VAMSASDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.VAMSAS.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java
new file mode 100755
index 0000000..4617903
--- /dev/null
+++ b/src/jalview/schemabinding/version2/VamsasModel.java
@@ -0,0 +1,118 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class VamsasModel.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class VamsasModel extends VAMSAS 
+implements java.io.Serializable
+{
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public VamsasModel() {
+        super();
+    } //-- jalview.schemabinding.version2.VamsasModel()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.VamsasModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.VamsasModel.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/VamsasModelDescriptor.java
new file mode 100755
index 0000000..e40d9c8
--- /dev/null
+++ b/src/jalview/schemabinding/version2/VamsasModelDescriptor.java
@@ -0,0 +1,166 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class VamsasModelDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class VamsasModelDescriptor extends VAMSASDescriptor {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public VamsasModelDescriptor() {
+        super();
+        setExtendsWithoutFlatten(new VAMSASDescriptor());
+        nsURI = "www.jalview.org";
+        xmlName = "vamsasModel";
+    } //-- jalview.schemabinding.version2.VamsasModelDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return super.getExtends();
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        if (identity == null)
+            return super.getIdentity();
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.VamsasModel.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
new file mode 100755
index 0000000..557e454
--- /dev/null
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -0,0 +1,1600 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Viewport.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Viewport implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _conservationSelected
+     */
+    private boolean _conservationSelected;
+
+    /**
+     * keeps track of state for field: _conservationSelected
+     */
+    private boolean _has_conservationSelected;
+
+    /**
+     * Field _pidSelected
+     */
+    private boolean _pidSelected;
+
+    /**
+     * keeps track of state for field: _pidSelected
+     */
+    private boolean _has_pidSelected;
+
+    /**
+     * Field _bgColour
+     */
+    private java.lang.String _bgColour;
+
+    /**
+     * Field _consThreshold
+     */
+    private int _consThreshold;
+
+    /**
+     * keeps track of state for field: _consThreshold
+     */
+    private boolean _has_consThreshold;
+
+    /**
+     * Field _pidThreshold
+     */
+    private int _pidThreshold;
+
+    /**
+     * keeps track of state for field: _pidThreshold
+     */
+    private boolean _has_pidThreshold;
+
+    /**
+     * Field _title
+     */
+    private java.lang.String _title;
+
+    /**
+     * Field _showFullId
+     */
+    private boolean _showFullId;
+
+    /**
+     * keeps track of state for field: _showFullId
+     */
+    private boolean _has_showFullId;
+
+    /**
+     * Field _showText
+     */
+    private boolean _showText;
+
+    /**
+     * keeps track of state for field: _showText
+     */
+    private boolean _has_showText;
+
+    /**
+     * Field _showColourText
+     */
+    private boolean _showColourText;
+
+    /**
+     * keeps track of state for field: _showColourText
+     */
+    private boolean _has_showColourText;
+
+    /**
+     * Field _showBoxes
+     */
+    private boolean _showBoxes;
+
+    /**
+     * keeps track of state for field: _showBoxes
+     */
+    private boolean _has_showBoxes;
+
+    /**
+     * Field _wrapAlignment
+     */
+    private boolean _wrapAlignment;
+
+    /**
+     * keeps track of state for field: _wrapAlignment
+     */
+    private boolean _has_wrapAlignment;
+
+    /**
+     * Field _renderGaps
+     */
+    private boolean _renderGaps;
+
+    /**
+     * keeps track of state for field: _renderGaps
+     */
+    private boolean _has_renderGaps;
+
+    /**
+     * Field _showSequenceFeatures
+     */
+    private boolean _showSequenceFeatures;
+
+    /**
+     * keeps track of state for field: _showSequenceFeatures
+     */
+    private boolean _has_showSequenceFeatures;
+
+    /**
+     * Field _showAnnotation
+     */
+    private boolean _showAnnotation;
+
+    /**
+     * keeps track of state for field: _showAnnotation
+     */
+    private boolean _has_showAnnotation;
+
+    /**
+     * Field _showConservation
+     */
+    private boolean _showConservation;
+
+    /**
+     * keeps track of state for field: _showConservation
+     */
+    private boolean _has_showConservation;
+
+    /**
+     * Field _showQuality
+     */
+    private boolean _showQuality;
+
+    /**
+     * keeps track of state for field: _showQuality
+     */
+    private boolean _has_showQuality;
+
+    /**
+     * Field _showIdentity
+     */
+    private boolean _showIdentity;
+
+    /**
+     * keeps track of state for field: _showIdentity
+     */
+    private boolean _has_showIdentity;
+
+    /**
+     * Field _xpos
+     */
+    private int _xpos;
+
+    /**
+     * keeps track of state for field: _xpos
+     */
+    private boolean _has_xpos;
+
+    /**
+     * Field _ypos
+     */
+    private int _ypos;
+
+    /**
+     * keeps track of state for field: _ypos
+     */
+    private boolean _has_ypos;
+
+    /**
+     * Field _width
+     */
+    private int _width;
+
+    /**
+     * keeps track of state for field: _width
+     */
+    private boolean _has_width;
+
+    /**
+     * Field _height
+     */
+    private int _height;
+
+    /**
+     * keeps track of state for field: _height
+     */
+    private boolean _has_height;
+
+    /**
+     * Field _startRes
+     */
+    private int _startRes;
+
+    /**
+     * keeps track of state for field: _startRes
+     */
+    private boolean _has_startRes;
+
+    /**
+     * Field _startSeq
+     */
+    private int _startSeq;
+
+    /**
+     * keeps track of state for field: _startSeq
+     */
+    private boolean _has_startSeq;
+
+    /**
+     * Field _fontName
+     */
+    private java.lang.String _fontName;
+
+    /**
+     * Field _fontSize
+     */
+    private int _fontSize;
+
+    /**
+     * keeps track of state for field: _fontSize
+     */
+    private boolean _has_fontSize;
+
+    /**
+     * Field _fontStyle
+     */
+    private int _fontStyle;
+
+    /**
+     * keeps track of state for field: _fontStyle
+     */
+    private boolean _has_fontStyle;
+
+    /**
+     * Field _annotationColours
+     */
+    private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
+    /**
+     * Field _hiddenColumnsList
+     */
+    private java.util.Vector _hiddenColumnsList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Viewport() {
+        super();
+        _hiddenColumnsList = new Vector();
+    } //-- jalview.schemabinding.version2.Viewport()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addHiddenColumns
+     * 
+     * 
+     * 
+     * @param vHiddenColumns
+     */
+    public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _hiddenColumnsList.addElement(vHiddenColumns);
+    } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) 
+
+    /**
+     * Method addHiddenColumns
+     * 
+     * 
+     * 
+     * @param index
+     * @param vHiddenColumns
+     */
+    public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _hiddenColumnsList.insertElementAt(vHiddenColumns, index);
+    } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) 
+
+    /**
+     * Method deleteConsThreshold
+     * 
+     */
+    public void deleteConsThreshold()
+    {
+        this._has_consThreshold= false;
+    } //-- void deleteConsThreshold() 
+
+    /**
+     * Method deleteConservationSelected
+     * 
+     */
+    public void deleteConservationSelected()
+    {
+        this._has_conservationSelected= false;
+    } //-- void deleteConservationSelected() 
+
+    /**
+     * Method deleteFontSize
+     * 
+     */
+    public void deleteFontSize()
+    {
+        this._has_fontSize= false;
+    } //-- void deleteFontSize() 
+
+    /**
+     * Method deleteFontStyle
+     * 
+     */
+    public void deleteFontStyle()
+    {
+        this._has_fontStyle= false;
+    } //-- void deleteFontStyle() 
+
+    /**
+     * Method deleteHeight
+     * 
+     */
+    public void deleteHeight()
+    {
+        this._has_height= false;
+    } //-- void deleteHeight() 
+
+    /**
+     * Method deletePidSelected
+     * 
+     */
+    public void deletePidSelected()
+    {
+        this._has_pidSelected= false;
+    } //-- void deletePidSelected() 
+
+    /**
+     * Method deletePidThreshold
+     * 
+     */
+    public void deletePidThreshold()
+    {
+        this._has_pidThreshold= false;
+    } //-- void deletePidThreshold() 
+
+    /**
+     * Method deleteRenderGaps
+     * 
+     */
+    public void deleteRenderGaps()
+    {
+        this._has_renderGaps= false;
+    } //-- void deleteRenderGaps() 
+
+    /**
+     * Method deleteShowAnnotation
+     * 
+     */
+    public void deleteShowAnnotation()
+    {
+        this._has_showAnnotation= false;
+    } //-- void deleteShowAnnotation() 
+
+    /**
+     * Method deleteShowBoxes
+     * 
+     */
+    public void deleteShowBoxes()
+    {
+        this._has_showBoxes= false;
+    } //-- void deleteShowBoxes() 
+
+    /**
+     * Method deleteShowColourText
+     * 
+     */
+    public void deleteShowColourText()
+    {
+        this._has_showColourText= false;
+    } //-- void deleteShowColourText() 
+
+    /**
+     * Method deleteShowConservation
+     * 
+     */
+    public void deleteShowConservation()
+    {
+        this._has_showConservation= false;
+    } //-- void deleteShowConservation() 
+
+    /**
+     * Method deleteShowFullId
+     * 
+     */
+    public void deleteShowFullId()
+    {
+        this._has_showFullId= false;
+    } //-- void deleteShowFullId() 
+
+    /**
+     * Method deleteShowIdentity
+     * 
+     */
+    public void deleteShowIdentity()
+    {
+        this._has_showIdentity= false;
+    } //-- void deleteShowIdentity() 
+
+    /**
+     * Method deleteShowQuality
+     * 
+     */
+    public void deleteShowQuality()
+    {
+        this._has_showQuality= false;
+    } //-- void deleteShowQuality() 
+
+    /**
+     * Method deleteShowSequenceFeatures
+     * 
+     */
+    public void deleteShowSequenceFeatures()
+    {
+        this._has_showSequenceFeatures= false;
+    } //-- void deleteShowSequenceFeatures() 
+
+    /**
+     * Method deleteShowText
+     * 
+     */
+    public void deleteShowText()
+    {
+        this._has_showText= false;
+    } //-- void deleteShowText() 
+
+    /**
+     * Method deleteStartRes
+     * 
+     */
+    public void deleteStartRes()
+    {
+        this._has_startRes= false;
+    } //-- void deleteStartRes() 
+
+    /**
+     * Method deleteStartSeq
+     * 
+     */
+    public void deleteStartSeq()
+    {
+        this._has_startSeq= false;
+    } //-- void deleteStartSeq() 
+
+    /**
+     * Method deleteWidth
+     * 
+     */
+    public void deleteWidth()
+    {
+        this._has_width= false;
+    } //-- void deleteWidth() 
+
+    /**
+     * Method deleteWrapAlignment
+     * 
+     */
+    public void deleteWrapAlignment()
+    {
+        this._has_wrapAlignment= false;
+    } //-- void deleteWrapAlignment() 
+
+    /**
+     * Method deleteXpos
+     * 
+     */
+    public void deleteXpos()
+    {
+        this._has_xpos= false;
+    } //-- void deleteXpos() 
+
+    /**
+     * Method deleteYpos
+     * 
+     */
+    public void deleteYpos()
+    {
+        this._has_ypos= false;
+    } //-- void deleteYpos() 
+
+    /**
+     * Method enumerateHiddenColumns
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateHiddenColumns()
+    {
+        return _hiddenColumnsList.elements();
+    } //-- java.util.Enumeration enumerateHiddenColumns() 
+
+    /**
+     * Returns the value of field 'annotationColours'.
+     * 
+     * @return AnnotationColours
+     * @return the value of field 'annotationColours'.
+     */
+    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+    {
+        return this._annotationColours;
+    } //-- jalview.schemabinding.version2.AnnotationColours getAnnotationColours() 
+
+    /**
+     * Returns the value of field 'bgColour'.
+     * 
+     * @return String
+     * @return the value of field 'bgColour'.
+     */
+    public java.lang.String getBgColour()
+    {
+        return this._bgColour;
+    } //-- java.lang.String getBgColour() 
+
+    /**
+     * Returns the value of field 'consThreshold'.
+     * 
+     * @return int
+     * @return the value of field 'consThreshold'.
+     */
+    public int getConsThreshold()
+    {
+        return this._consThreshold;
+    } //-- int getConsThreshold() 
+
+    /**
+     * Returns the value of field 'conservationSelected'.
+     * 
+     * @return boolean
+     * @return the value of field 'conservationSelected'.
+     */
+    public boolean getConservationSelected()
+    {
+        return this._conservationSelected;
+    } //-- boolean getConservationSelected() 
+
+    /**
+     * Returns the value of field 'fontName'.
+     * 
+     * @return String
+     * @return the value of field 'fontName'.
+     */
+    public java.lang.String getFontName()
+    {
+        return this._fontName;
+    } //-- java.lang.String getFontName() 
+
+    /**
+     * Returns the value of field 'fontSize'.
+     * 
+     * @return int
+     * @return the value of field 'fontSize'.
+     */
+    public int getFontSize()
+    {
+        return this._fontSize;
+    } //-- int getFontSize() 
+
+    /**
+     * Returns the value of field 'fontStyle'.
+     * 
+     * @return int
+     * @return the value of field 'fontStyle'.
+     */
+    public int getFontStyle()
+    {
+        return this._fontStyle;
+    } //-- int getFontStyle() 
+
+    /**
+     * Returns the value of field 'height'.
+     * 
+     * @return int
+     * @return the value of field 'height'.
+     */
+    public int getHeight()
+    {
+        return this._height;
+    } //-- int getHeight() 
+
+    /**
+     * Method getHiddenColumns
+     * 
+     * 
+     * 
+     * @param index
+     * @return HiddenColumns
+     */
+    public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _hiddenColumnsList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);
+    } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) 
+
+    /**
+     * Method getHiddenColumns
+     * 
+     * 
+     * 
+     * @return HiddenColumns
+     */
+    public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()
+    {
+        int size = _hiddenColumnsList.size();
+        jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() 
+
+    /**
+     * Method getHiddenColumnsCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getHiddenColumnsCount()
+    {
+        return _hiddenColumnsList.size();
+    } //-- int getHiddenColumnsCount() 
+
+    /**
+     * Returns the value of field 'pidSelected'.
+     * 
+     * @return boolean
+     * @return the value of field 'pidSelected'.
+     */
+    public boolean getPidSelected()
+    {
+        return this._pidSelected;
+    } //-- boolean getPidSelected() 
+
+    /**
+     * Returns the value of field 'pidThreshold'.
+     * 
+     * @return int
+     * @return the value of field 'pidThreshold'.
+     */
+    public int getPidThreshold()
+    {
+        return this._pidThreshold;
+    } //-- int getPidThreshold() 
+
+    /**
+     * Returns the value of field 'renderGaps'.
+     * 
+     * @return boolean
+     * @return the value of field 'renderGaps'.
+     */
+    public boolean getRenderGaps()
+    {
+        return this._renderGaps;
+    } //-- boolean getRenderGaps() 
+
+    /**
+     * Returns the value of field 'showAnnotation'.
+     * 
+     * @return boolean
+     * @return the value of field 'showAnnotation'.
+     */
+    public boolean getShowAnnotation()
+    {
+        return this._showAnnotation;
+    } //-- boolean getShowAnnotation() 
+
+    /**
+     * Returns the value of field 'showBoxes'.
+     * 
+     * @return boolean
+     * @return the value of field 'showBoxes'.
+     */
+    public boolean getShowBoxes()
+    {
+        return this._showBoxes;
+    } //-- boolean getShowBoxes() 
+
+    /**
+     * Returns the value of field 'showColourText'.
+     * 
+     * @return boolean
+     * @return the value of field 'showColourText'.
+     */
+    public boolean getShowColourText()
+    {
+        return this._showColourText;
+    } //-- boolean getShowColourText() 
+
+    /**
+     * Returns the value of field 'showConservation'.
+     * 
+     * @return boolean
+     * @return the value of field 'showConservation'.
+     */
+    public boolean getShowConservation()
+    {
+        return this._showConservation;
+    } //-- boolean getShowConservation() 
+
+    /**
+     * Returns the value of field 'showFullId'.
+     * 
+     * @return boolean
+     * @return the value of field 'showFullId'.
+     */
+    public boolean getShowFullId()
+    {
+        return this._showFullId;
+    } //-- boolean getShowFullId() 
+
+    /**
+     * Returns the value of field 'showIdentity'.
+     * 
+     * @return boolean
+     * @return the value of field 'showIdentity'.
+     */
+    public boolean getShowIdentity()
+    {
+        return this._showIdentity;
+    } //-- boolean getShowIdentity() 
+
+    /**
+     * Returns the value of field 'showQuality'.
+     * 
+     * @return boolean
+     * @return the value of field 'showQuality'.
+     */
+    public boolean getShowQuality()
+    {
+        return this._showQuality;
+    } //-- boolean getShowQuality() 
+
+    /**
+     * Returns the value of field 'showSequenceFeatures'.
+     * 
+     * @return boolean
+     * @return the value of field 'showSequenceFeatures'.
+     */
+    public boolean getShowSequenceFeatures()
+    {
+        return this._showSequenceFeatures;
+    } //-- boolean getShowSequenceFeatures() 
+
+    /**
+     * Returns the value of field 'showText'.
+     * 
+     * @return boolean
+     * @return the value of field 'showText'.
+     */
+    public boolean getShowText()
+    {
+        return this._showText;
+    } //-- boolean getShowText() 
+
+    /**
+     * Returns the value of field 'startRes'.
+     * 
+     * @return int
+     * @return the value of field 'startRes'.
+     */
+    public int getStartRes()
+    {
+        return this._startRes;
+    } //-- int getStartRes() 
+
+    /**
+     * Returns the value of field 'startSeq'.
+     * 
+     * @return int
+     * @return the value of field 'startSeq'.
+     */
+    public int getStartSeq()
+    {
+        return this._startSeq;
+    } //-- int getStartSeq() 
+
+    /**
+     * Returns the value of field 'title'.
+     * 
+     * @return String
+     * @return the value of field 'title'.
+     */
+    public java.lang.String getTitle()
+    {
+        return this._title;
+    } //-- java.lang.String getTitle() 
+
+    /**
+     * Returns the value of field 'width'.
+     * 
+     * @return int
+     * @return the value of field 'width'.
+     */
+    public int getWidth()
+    {
+        return this._width;
+    } //-- int getWidth() 
+
+    /**
+     * Returns the value of field 'wrapAlignment'.
+     * 
+     * @return boolean
+     * @return the value of field 'wrapAlignment'.
+     */
+    public boolean getWrapAlignment()
+    {
+        return this._wrapAlignment;
+    } //-- boolean getWrapAlignment() 
+
+    /**
+     * Returns the value of field 'xpos'.
+     * 
+     * @return int
+     * @return the value of field 'xpos'.
+     */
+    public int getXpos()
+    {
+        return this._xpos;
+    } //-- int getXpos() 
+
+    /**
+     * Returns the value of field 'ypos'.
+     * 
+     * @return int
+     * @return the value of field 'ypos'.
+     */
+    public int getYpos()
+    {
+        return this._ypos;
+    } //-- int getYpos() 
+
+    /**
+     * Method hasConsThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasConsThreshold()
+    {
+        return this._has_consThreshold;
+    } //-- boolean hasConsThreshold() 
+
+    /**
+     * Method hasConservationSelected
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasConservationSelected()
+    {
+        return this._has_conservationSelected;
+    } //-- boolean hasConservationSelected() 
+
+    /**
+     * Method hasFontSize
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasFontSize()
+    {
+        return this._has_fontSize;
+    } //-- boolean hasFontSize() 
+
+    /**
+     * Method hasFontStyle
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasFontStyle()
+    {
+        return this._has_fontStyle;
+    } //-- boolean hasFontStyle() 
+
+    /**
+     * Method hasHeight
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasHeight()
+    {
+        return this._has_height;
+    } //-- boolean hasHeight() 
+
+    /**
+     * Method hasPidSelected
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasPidSelected()
+    {
+        return this._has_pidSelected;
+    } //-- boolean hasPidSelected() 
+
+    /**
+     * Method hasPidThreshold
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasPidThreshold()
+    {
+        return this._has_pidThreshold;
+    } //-- boolean hasPidThreshold() 
+
+    /**
+     * Method hasRenderGaps
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasRenderGaps()
+    {
+        return this._has_renderGaps;
+    } //-- boolean hasRenderGaps() 
+
+    /**
+     * Method hasShowAnnotation
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowAnnotation()
+    {
+        return this._has_showAnnotation;
+    } //-- boolean hasShowAnnotation() 
+
+    /**
+     * Method hasShowBoxes
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowBoxes()
+    {
+        return this._has_showBoxes;
+    } //-- boolean hasShowBoxes() 
+
+    /**
+     * Method hasShowColourText
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowColourText()
+    {
+        return this._has_showColourText;
+    } //-- boolean hasShowColourText() 
+
+    /**
+     * Method hasShowConservation
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowConservation()
+    {
+        return this._has_showConservation;
+    } //-- boolean hasShowConservation() 
+
+    /**
+     * Method hasShowFullId
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowFullId()
+    {
+        return this._has_showFullId;
+    } //-- boolean hasShowFullId() 
+
+    /**
+     * Method hasShowIdentity
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowIdentity()
+    {
+        return this._has_showIdentity;
+    } //-- boolean hasShowIdentity() 
+
+    /**
+     * Method hasShowQuality
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowQuality()
+    {
+        return this._has_showQuality;
+    } //-- boolean hasShowQuality() 
+
+    /**
+     * Method hasShowSequenceFeatures
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowSequenceFeatures()
+    {
+        return this._has_showSequenceFeatures;
+    } //-- boolean hasShowSequenceFeatures() 
+
+    /**
+     * Method hasShowText
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasShowText()
+    {
+        return this._has_showText;
+    } //-- boolean hasShowText() 
+
+    /**
+     * Method hasStartRes
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasStartRes()
+    {
+        return this._has_startRes;
+    } //-- boolean hasStartRes() 
+
+    /**
+     * Method hasStartSeq
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasStartSeq()
+    {
+        return this._has_startSeq;
+    } //-- boolean hasStartSeq() 
+
+    /**
+     * Method hasWidth
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasWidth()
+    {
+        return this._has_width;
+    } //-- boolean hasWidth() 
+
+    /**
+     * Method hasWrapAlignment
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasWrapAlignment()
+    {
+        return this._has_wrapAlignment;
+    } //-- boolean hasWrapAlignment() 
+
+    /**
+     * Method hasXpos
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasXpos()
+    {
+        return this._has_xpos;
+    } //-- boolean hasXpos() 
+
+    /**
+     * Method hasYpos
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasYpos()
+    {
+        return this._has_ypos;
+    } //-- boolean hasYpos() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Method removeAllHiddenColumns
+     * 
+     */
+    public void removeAllHiddenColumns()
+    {
+        _hiddenColumnsList.removeAllElements();
+    } //-- void removeAllHiddenColumns() 
+
+    /**
+     * Method removeHiddenColumns
+     * 
+     * 
+     * 
+     * @param index
+     * @return HiddenColumns
+     */
+    public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)
+    {
+        java.lang.Object obj = _hiddenColumnsList.elementAt(index);
+        _hiddenColumnsList.removeElementAt(index);
+        return (jalview.schemabinding.version2.HiddenColumns) obj;
+    } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) 
+
+    /**
+     * Sets the value of field 'annotationColours'.
+     * 
+     * @param annotationColours the value of field
+     * 'annotationColours'.
+     */
+    public void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours annotationColours)
+    {
+        this._annotationColours = annotationColours;
+    } //-- void setAnnotationColours(jalview.schemabinding.version2.AnnotationColours) 
+
+    /**
+     * Sets the value of field 'bgColour'.
+     * 
+     * @param bgColour the value of field 'bgColour'.
+     */
+    public void setBgColour(java.lang.String bgColour)
+    {
+        this._bgColour = bgColour;
+    } //-- void setBgColour(java.lang.String) 
+
+    /**
+     * Sets the value of field 'consThreshold'.
+     * 
+     * @param consThreshold the value of field 'consThreshold'.
+     */
+    public void setConsThreshold(int consThreshold)
+    {
+        this._consThreshold = consThreshold;
+        this._has_consThreshold = true;
+    } //-- void setConsThreshold(int) 
+
+    /**
+     * Sets the value of field 'conservationSelected'.
+     * 
+     * @param conservationSelected the value of field
+     * 'conservationSelected'.
+     */
+    public void setConservationSelected(boolean conservationSelected)
+    {
+        this._conservationSelected = conservationSelected;
+        this._has_conservationSelected = true;
+    } //-- void setConservationSelected(boolean) 
+
+    /**
+     * Sets the value of field 'fontName'.
+     * 
+     * @param fontName the value of field 'fontName'.
+     */
+    public void setFontName(java.lang.String fontName)
+    {
+        this._fontName = fontName;
+    } //-- void setFontName(java.lang.String) 
+
+    /**
+     * Sets the value of field 'fontSize'.
+     * 
+     * @param fontSize the value of field 'fontSize'.
+     */
+    public void setFontSize(int fontSize)
+    {
+        this._fontSize = fontSize;
+        this._has_fontSize = true;
+    } //-- void setFontSize(int) 
+
+    /**
+     * Sets the value of field 'fontStyle'.
+     * 
+     * @param fontStyle the value of field 'fontStyle'.
+     */
+    public void setFontStyle(int fontStyle)
+    {
+        this._fontStyle = fontStyle;
+        this._has_fontStyle = true;
+    } //-- void setFontStyle(int) 
+
+    /**
+     * Sets the value of field 'height'.
+     * 
+     * @param height the value of field 'height'.
+     */
+    public void setHeight(int height)
+    {
+        this._height = height;
+        this._has_height = true;
+    } //-- void setHeight(int) 
+
+    /**
+     * Method setHiddenColumns
+     * 
+     * 
+     * 
+     * @param index
+     * @param vHiddenColumns
+     */
+    public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _hiddenColumnsList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _hiddenColumnsList.setElementAt(vHiddenColumns, index);
+    } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) 
+
+    /**
+     * Method setHiddenColumns
+     * 
+     * 
+     * 
+     * @param hiddenColumnsArray
+     */
+    public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)
+    {
+        //-- copy array
+        _hiddenColumnsList.removeAllElements();
+        for (int i = 0; i < hiddenColumnsArray.length; i++) {
+            _hiddenColumnsList.addElement(hiddenColumnsArray[i]);
+        }
+    } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) 
+
+    /**
+     * Sets the value of field 'pidSelected'.
+     * 
+     * @param pidSelected the value of field 'pidSelected'.
+     */
+    public void setPidSelected(boolean pidSelected)
+    {
+        this._pidSelected = pidSelected;
+        this._has_pidSelected = true;
+    } //-- void setPidSelected(boolean) 
+
+    /**
+     * Sets the value of field 'pidThreshold'.
+     * 
+     * @param pidThreshold the value of field 'pidThreshold'.
+     */
+    public void setPidThreshold(int pidThreshold)
+    {
+        this._pidThreshold = pidThreshold;
+        this._has_pidThreshold = true;
+    } //-- void setPidThreshold(int) 
+
+    /**
+     * Sets the value of field 'renderGaps'.
+     * 
+     * @param renderGaps the value of field 'renderGaps'.
+     */
+    public void setRenderGaps(boolean renderGaps)
+    {
+        this._renderGaps = renderGaps;
+        this._has_renderGaps = true;
+    } //-- void setRenderGaps(boolean) 
+
+    /**
+     * Sets the value of field 'showAnnotation'.
+     * 
+     * @param showAnnotation the value of field 'showAnnotation'.
+     */
+    public void setShowAnnotation(boolean showAnnotation)
+    {
+        this._showAnnotation = showAnnotation;
+        this._has_showAnnotation = true;
+    } //-- void setShowAnnotation(boolean) 
+
+    /**
+     * Sets the value of field 'showBoxes'.
+     * 
+     * @param showBoxes the value of field 'showBoxes'.
+     */
+    public void setShowBoxes(boolean showBoxes)
+    {
+        this._showBoxes = showBoxes;
+        this._has_showBoxes = true;
+    } //-- void setShowBoxes(boolean) 
+
+    /**
+     * Sets the value of field 'showColourText'.
+     * 
+     * @param showColourText the value of field 'showColourText'.
+     */
+    public void setShowColourText(boolean showColourText)
+    {
+        this._showColourText = showColourText;
+        this._has_showColourText = true;
+    } //-- void setShowColourText(boolean) 
+
+    /**
+     * Sets the value of field 'showConservation'.
+     * 
+     * @param showConservation the value of field 'showConservation'
+     */
+    public void setShowConservation(boolean showConservation)
+    {
+        this._showConservation = showConservation;
+        this._has_showConservation = true;
+    } //-- void setShowConservation(boolean) 
+
+    /**
+     * Sets the value of field 'showFullId'.
+     * 
+     * @param showFullId the value of field 'showFullId'.
+     */
+    public void setShowFullId(boolean showFullId)
+    {
+        this._showFullId = showFullId;
+        this._has_showFullId = true;
+    } //-- void setShowFullId(boolean) 
+
+    /**
+     * Sets the value of field 'showIdentity'.
+     * 
+     * @param showIdentity the value of field 'showIdentity'.
+     */
+    public void setShowIdentity(boolean showIdentity)
+    {
+        this._showIdentity = showIdentity;
+        this._has_showIdentity = true;
+    } //-- void setShowIdentity(boolean) 
+
+    /**
+     * Sets the value of field 'showQuality'.
+     * 
+     * @param showQuality the value of field 'showQuality'.
+     */
+    public void setShowQuality(boolean showQuality)
+    {
+        this._showQuality = showQuality;
+        this._has_showQuality = true;
+    } //-- void setShowQuality(boolean) 
+
+    /**
+     * Sets the value of field 'showSequenceFeatures'.
+     * 
+     * @param showSequenceFeatures the value of field
+     * 'showSequenceFeatures'.
+     */
+    public void setShowSequenceFeatures(boolean showSequenceFeatures)
+    {
+        this._showSequenceFeatures = showSequenceFeatures;
+        this._has_showSequenceFeatures = true;
+    } //-- void setShowSequenceFeatures(boolean) 
+
+    /**
+     * Sets the value of field 'showText'.
+     * 
+     * @param showText the value of field 'showText'.
+     */
+    public void setShowText(boolean showText)
+    {
+        this._showText = showText;
+        this._has_showText = true;
+    } //-- void setShowText(boolean) 
+
+    /**
+     * Sets the value of field 'startRes'.
+     * 
+     * @param startRes the value of field 'startRes'.
+     */
+    public void setStartRes(int startRes)
+    {
+        this._startRes = startRes;
+        this._has_startRes = true;
+    } //-- void setStartRes(int) 
+
+    /**
+     * Sets the value of field 'startSeq'.
+     * 
+     * @param startSeq the value of field 'startSeq'.
+     */
+    public void setStartSeq(int startSeq)
+    {
+        this._startSeq = startSeq;
+        this._has_startSeq = true;
+    } //-- void setStartSeq(int) 
+
+    /**
+     * Sets the value of field 'title'.
+     * 
+     * @param title the value of field 'title'.
+     */
+    public void setTitle(java.lang.String title)
+    {
+        this._title = title;
+    } //-- void setTitle(java.lang.String) 
+
+    /**
+     * Sets the value of field 'width'.
+     * 
+     * @param width the value of field 'width'.
+     */
+    public void setWidth(int width)
+    {
+        this._width = width;
+        this._has_width = true;
+    } //-- void setWidth(int) 
+
+    /**
+     * Sets the value of field 'wrapAlignment'.
+     * 
+     * @param wrapAlignment the value of field 'wrapAlignment'.
+     */
+    public void setWrapAlignment(boolean wrapAlignment)
+    {
+        this._wrapAlignment = wrapAlignment;
+        this._has_wrapAlignment = true;
+    } //-- void setWrapAlignment(boolean) 
+
+    /**
+     * Sets the value of field 'xpos'.
+     * 
+     * @param xpos the value of field 'xpos'.
+     */
+    public void setXpos(int xpos)
+    {
+        this._xpos = xpos;
+        this._has_xpos = true;
+    } //-- void setXpos(int) 
+
+    /**
+     * Sets the value of field 'ypos'.
+     * 
+     * @param ypos the value of field 'ypos'.
+     */
+    public void setYpos(int ypos)
+    {
+        this._ypos = ypos;
+        this._has_ypos = true;
+    } //-- void setYpos(int) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Object
+     */
+    public static java.lang.Object unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.Viewport.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/jalview/schemabinding/version2/ViewportDescriptor.java b/src/jalview/schemabinding/version2/ViewportDescriptor.java
new file mode 100755
index 0000000..b98f97b
--- /dev/null
+++ b/src/jalview/schemabinding/version2/ViewportDescriptor.java
@@ -0,0 +1,1293 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class ViewportDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public ViewportDescriptor() {
+        super();
+        nsURI = "www.jalview.org";
+        xmlName = "Viewport";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _conservationSelected
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasConservationSelected())
+                    return null;
+                return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteConservationSelected();
+                        return;
+                    }
+                    target.setConservationSelected( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _conservationSelected
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _pidSelected
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasPidSelected())
+                    return null;
+                return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deletePidSelected();
+                        return;
+                    }
+                    target.setPidSelected( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _pidSelected
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _bgColour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                return target.getBgColour();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    target.setBgColour( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _bgColour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _consThreshold
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasConsThreshold())
+                    return null;
+                return new java.lang.Integer(target.getConsThreshold());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteConsThreshold();
+                        return;
+                    }
+                    target.setConsThreshold( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _consThreshold
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _pidThreshold
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasPidThreshold())
+                    return null;
+                return new java.lang.Integer(target.getPidThreshold());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deletePidThreshold();
+                        return;
+                    }
+                    target.setPidThreshold( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _pidThreshold
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _title
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                return target.getTitle();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    target.setTitle( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _title
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showFullId
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasShowFullId())
+                    return null;
+                return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowFullId();
+                        return;
+                    }
+                    target.setShowFullId( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showFullId
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showText
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasShowText())
+                    return null;
+                return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowText();
+                        return;
+                    }
+                    target.setShowText( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showText
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showColourText
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasShowColourText())
+                    return null;
+                return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowColourText();
+                        return;
+                    }
+                    target.setShowColourText( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showColourText
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showBoxes
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasShowBoxes())
+                    return null;
+                return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowBoxes();
+                        return;
+                    }
+                    target.setShowBoxes( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showBoxes
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _wrapAlignment
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasWrapAlignment())
+                    return null;
+                return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteWrapAlignment();
+                        return;
+                    }
+                    target.setWrapAlignment( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _wrapAlignment
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _renderGaps
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasRenderGaps())
+                    return null;
+                return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteRenderGaps();
+                        return;
+                    }
+                    target.setRenderGaps( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _renderGaps
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showSequenceFeatures
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasShowSequenceFeatures())
+                    return null;
+                return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowSequenceFeatures();
+                        return;
+                    }
+                    target.setShowSequenceFeatures( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showSequenceFeatures
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showAnnotation
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasShowAnnotation())
+                    return null;
+                return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowAnnotation();
+                        return;
+                    }
+                    target.setShowAnnotation( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showAnnotation
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showConservation
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConservation", "showConservation", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasShowConservation())
+                    return null;
+                return (target.getShowConservation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowConservation();
+                        return;
+                    }
+                    target.setShowConservation( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showConservation
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showQuality
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showQuality", "showQuality", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasShowQuality())
+                    return null;
+                return (target.getShowQuality() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowQuality();
+                        return;
+                    }
+                    target.setShowQuality( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showQuality
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _showIdentity
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showIdentity", "showIdentity", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasShowIdentity())
+                    return null;
+                return (target.getShowIdentity() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteShowIdentity();
+                        return;
+                    }
+                    target.setShowIdentity( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _showIdentity
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _xpos
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasXpos())
+                    return null;
+                return new java.lang.Integer(target.getXpos());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteXpos();
+                        return;
+                    }
+                    target.setXpos( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _xpos
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _ypos
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasYpos())
+                    return null;
+                return new java.lang.Integer(target.getYpos());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteYpos();
+                        return;
+                    }
+                    target.setYpos( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _ypos
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _width
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasWidth())
+                    return null;
+                return new java.lang.Integer(target.getWidth());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteWidth();
+                        return;
+                    }
+                    target.setWidth( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _width
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _height
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasHeight())
+                    return null;
+                return new java.lang.Integer(target.getHeight());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteHeight();
+                        return;
+                    }
+                    target.setHeight( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _height
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _startRes
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasStartRes())
+                    return null;
+                return new java.lang.Integer(target.getStartRes());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteStartRes();
+                        return;
+                    }
+                    target.setStartRes( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _startRes
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _startSeq
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasStartSeq())
+                    return null;
+                return new java.lang.Integer(target.getStartSeq());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteStartSeq();
+                        return;
+                    }
+                    target.setStartSeq( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _startSeq
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _fontName
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                return target.getFontName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    target.setFontName( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _fontName
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _fontSize
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasFontSize())
+                    return null;
+                return new java.lang.Integer(target.getFontSize());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteFontSize();
+                        return;
+                    }
+                    target.setFontSize( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _fontSize
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _fontStyle
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasFontStyle())
+                    return null;
+                return new java.lang.Integer(target.getFontStyle());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteFontStyle();
+                        return;
+                    }
+                    target.setFontStyle( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        } );
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _fontStyle
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _annotationColours
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                return target.getAnnotationColours();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.AnnotationColours();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _annotationColours
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _hiddenColumnsList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                return target.getHiddenColumns();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.HiddenColumns();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _hiddenColumnsList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- jalview.schemabinding.version2.ViewportDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return jalview.schemabinding.version2.Viewport.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
new file mode 100644
index 0000000..bcd8e7c
--- /dev/null
+++ b/src/jalview/util/ShiftList.java
@@ -0,0 +1,119 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.util;
+
+import jalview.datamodel.SequenceI;
+
+import java.util.*;
+
+/**
+ * ShiftList
+ * Simple way of mapping a linear series to a new linear range with new points introduced.
+ * Use at your own risk!
+ * Now growing to be used for interval ranges (position, offset) storing deletions/insertions
+ */
+public class ShiftList
+{
+    public Vector shifts;
+  public ShiftList()
+  {
+    shifts = new Vector();
+  }
+
+  /**
+   * addShift
+   * @param pos start position for shift (in original reference frame)
+   * @param shift length of shift
+   */
+  public void addShift(int pos, int shift)
+  {
+    int sidx = 0;
+    int[] rshift=null;
+    while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
+      sidx++;
+    if (sidx==shifts.size())
+      shifts.insertElementAt(new int[] { pos, shift}, sidx);
+    else
+      rshift[1]+=shift;
+  }
+
+  /**
+   * shift
+   *
+   * @param pos int
+   * @return int shifted position
+   */
+  public int shift(int pos)
+  {
+    if (shifts.size()==0)
+      return pos;
+    int shifted=pos;
+    int sidx=0;
+    int rshift[];
+    while (sidx<shifts.size()
+           &&
+           (rshift=((int[]) shifts.elementAt(sidx++)))[0]<=pos) {
+      shifted += rshift[1];
+    }
+    return shifted;
+  }
+
+  /**
+   * clear all shifts
+   */
+  public void clear()
+  {
+    shifts.removeAllElements();
+  }
+  /**
+   * invert the shifts
+   * @return ShiftList with inverse shift operations
+   */
+  public ShiftList getInverse() {
+    ShiftList inverse=new ShiftList();
+    if (shifts!=null) {
+      for (int i=0,j=shifts.size(); i<j; i++) {
+        int[] sh=(int[]) shifts.elementAt(i);
+        if (sh!=null)
+          inverse.shifts.addElement(new int[] {sh[0], -sh[1]});
+      }
+    }
+    return inverse;
+  }
+
+  /**
+   * parse a 1d map of position 1<i<n to L<pos[i]<N
+   * such as that returned from SequenceI.gapMap()
+   * @param gapMap
+   * @return shifts from map index to mapped position
+   */
+  public static ShiftList parseMap(int[] gapMap) {
+    ShiftList shiftList = null;
+    if (gapMap!=null && gapMap.length>0) {
+      shiftList=new ShiftList();
+      for (int i=0,p=0; i<gapMap.length; p++,i++) {
+        if (p!=gapMap[i]) {
+          shiftList.addShift(p, gapMap[i]-p);
+          p=gapMap[i];
+        }
+      }
+    }
+    return shiftList;
+  }
+}
diff --git a/src/jalview/util/TableSorter.java b/src/jalview/util/TableSorter.java
new file mode 100755
index 0000000..c03e804
--- /dev/null
+++ b/src/jalview/util/TableSorter.java
@@ -0,0 +1,501 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.util;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.*;
+import java.util.List;
+
+import javax.swing.*;
+import javax.swing.event.TableModelEvent;
+import javax.swing.event.TableModelListener;
+import javax.swing.table.*;
+
+/**
+ * TableSorter is a decorator for TableModels; adding sorting
+ * functionality to a supplied TableModel. TableSorter does
+ * not store or copy the data in its TableModel; instead it maintains
+ * a map from the row indexes of the view to the row indexes of the
+ * model. As requests are made of the sorter (like getValueAt(row, col))
+ * they are passed to the underlying model after the row numbers
+ * have been translated via the internal mapping array. This way,
+ * the TableSorter appears to hold another copy of the table
+ * with the rows in a different order.
+ * <p/>
+ * TableSorter registers itself as a listener to the underlying model,
+ * just as the JTable itself would. Events recieved from the model
+ * are examined, sometimes manipulated (typically widened), and then
+ * passed on to the TableSorter's listeners (typically the JTable).
+ * If a change to the model has invalidated the order of TableSorter's
+ * rows, a note of this is made and the sorter will resort the
+ * rows the next time a value is requested.
+ * <p/>
+ * When the tableHeader property is set, either by using the
+ * setTableHeader() method or the two argument constructor, the
+ * table header may be used as a complete UI for TableSorter.
+ * The default renderer of the tableHeader is decorated with a renderer
+ * that indicates the sorting status of each column. In addition,
+ * a mouse listener is installed with the following behavior:
+ * <ul>
+ * <li>
+ * Mouse-click: Clears the sorting status of all other columns
+ * and advances the sorting status of that column through three
+ * values: {NOT_SORTED, ASCENDING, DESCENDING} (then back to
+ * NOT_SORTED again).
+ * <li>
+ * SHIFT-mouse-click: Clears the sorting status of all other columns
+ * and cycles the sorting status of the column through the same
+ * three values, in the opposite order: {NOT_SORTED, DESCENDING, ASCENDING}.
+ * <li>
+ * CONTROL-mouse-click and CONTROL-SHIFT-mouse-click: as above except
+ * that the changes to the column do not cancel the statuses of columns
+ * that are already sorting - giving a way to initiate a compound
+ * sort.
+ * </ul>
+ * <p/>
+ * This is a long overdue rewrite of a class of the same name that
+ * first appeared in the swing table demos in 1997.
+ *
+ * @author Philip Milne
+ * @author Brendon McLean
+ * @author Dan van Enckevort
+ * @author Parwinder Sekhon
+ * @version 2.0 02/27/04
+ */
+
+public class TableSorter extends AbstractTableModel {
+    protected TableModel tableModel;
+
+    public static final int DESCENDING = -1;
+    public static final int NOT_SORTED = 0;
+    public static final int ASCENDING = 1;
+
+    private static Directive EMPTY_DIRECTIVE = new Directive(-1, NOT_SORTED);
+
+    public static final Comparator COMPARABLE_COMAPRATOR = new Comparator() {
+        public int compare(Object o1, Object o2) {
+            return ((Comparable) o1).compareTo(o2);
+        }
+    };
+    public static final Comparator LEXICAL_COMPARATOR = new Comparator() {
+        public int compare(Object o1, Object o2) {
+            return o1.toString().compareTo(o2.toString());
+        }
+    };
+
+    private Row[] viewToModel;
+    private int[] modelToView;
+
+    private JTableHeader tableHeader;
+    private MouseListener mouseListener;
+    private TableModelListener tableModelListener;
+    private Map columnComparators = new HashMap();
+    private List sortingColumns = new ArrayList();
+
+    public TableSorter() {
+        this.mouseListener = new MouseHandler();
+        this.tableModelListener = new TableModelHandler();
+    }
+
+    public TableSorter(TableModel tableModel) {
+        this();
+        setTableModel(tableModel);
+    }
+
+    public TableSorter(TableModel tableModel, JTableHeader tableHeader) {
+        this();
+        setTableHeader(tableHeader);
+        setTableModel(tableModel);
+    }
+
+    private void clearSortingState() {
+        viewToModel = null;
+        modelToView = null;
+    }
+
+    public TableModel getTableModel() {
+        return tableModel;
+    }
+
+    public void setTableModel(TableModel tableModel) {
+        if (this.tableModel != null) {
+            this.tableModel.removeTableModelListener(tableModelListener);
+        }
+
+        this.tableModel = tableModel;
+        if (this.tableModel != null) {
+            this.tableModel.addTableModelListener(tableModelListener);
+        }
+
+        clearSortingState();
+        fireTableStructureChanged();
+    }
+
+    public JTableHeader getTableHeader() {
+        return tableHeader;
+    }
+
+    public void setTableHeader(JTableHeader tableHeader) {
+        if (this.tableHeader != null) {
+            this.tableHeader.removeMouseListener(mouseListener);
+            TableCellRenderer defaultRenderer = this.tableHeader.getDefaultRenderer();
+            if (defaultRenderer instanceof SortableHeaderRenderer) {
+                this.tableHeader.setDefaultRenderer(((SortableHeaderRenderer) defaultRenderer).tableCellRenderer);
+            }
+        }
+        this.tableHeader = tableHeader;
+        if (this.tableHeader != null) {
+            this.tableHeader.addMouseListener(mouseListener);
+            this.tableHeader.setDefaultRenderer(
+                    new SortableHeaderRenderer(this.tableHeader.getDefaultRenderer()));
+        }
+    }
+
+    public boolean isSorting() {
+        return sortingColumns.size() != 0;
+    }
+
+    private Directive getDirective(int column) {
+        for (int i = 0; i < sortingColumns.size(); i++) {
+            Directive directive = (Directive)sortingColumns.get(i);
+            if (directive.column == column) {
+                return directive;
+            }
+        }
+        return EMPTY_DIRECTIVE;
+    }
+
+    public int getSortingStatus(int column) {
+        return getDirective(column).direction;
+    }
+
+    private void sortingStatusChanged() {
+        clearSortingState();
+        fireTableDataChanged();
+        if (tableHeader != null) {
+            tableHeader.repaint();
+        }
+    }
+
+    public void setSortingStatus(int column, int status) {
+        Directive directive = getDirective(column);
+        if (directive != EMPTY_DIRECTIVE) {
+            sortingColumns.remove(directive);
+        }
+        if (status != NOT_SORTED) {
+            sortingColumns.add(new Directive(column, status));
+        }
+        sortingStatusChanged();
+    }
+
+    protected Icon getHeaderRendererIcon(int column, int size) {
+        Directive directive = getDirective(column);
+        if (directive == EMPTY_DIRECTIVE) {
+            return null;
+        }
+        return new Arrow(directive.direction == DESCENDING, size, sortingColumns.indexOf(directive));
+    }
+
+    private void cancelSorting() {
+        sortingColumns.clear();
+        sortingStatusChanged();
+    }
+
+    public void setColumnComparator(Class type, Comparator comparator) {
+        if (comparator == null) {
+            columnComparators.remove(type);
+        } else {
+            columnComparators.put(type, comparator);
+        }
+    }
+
+    protected Comparator getComparator(int column) {
+        Class columnType = tableModel.getColumnClass(column);
+        Comparator comparator = (Comparator) columnComparators.get(columnType);
+        if (comparator != null) {
+            return comparator;
+        }
+        if (Comparable.class.isAssignableFrom(columnType)) {
+            return COMPARABLE_COMAPRATOR;
+        }
+        return LEXICAL_COMPARATOR;
+    }
+
+    private Row[] getViewToModel() {
+        if (viewToModel == null) {
+            int tableModelRowCount = tableModel.getRowCount();
+            viewToModel = new Row[tableModelRowCount];
+            for (int row = 0; row < tableModelRowCount; row++) {
+                viewToModel[row] = new Row(row);
+            }
+
+            if (isSorting()) {
+                Arrays.sort(viewToModel);
+            }
+        }
+        return viewToModel;
+    }
+
+    public int modelIndex(int viewIndex) {
+        return getViewToModel()[viewIndex].modelIndex;
+    }
+
+    private int[] getModelToView() {
+        if (modelToView == null) {
+            int n = getViewToModel().length;
+            modelToView = new int[n];
+            for (int i = 0; i < n; i++) {
+                modelToView[modelIndex(i)] = i;
+            }
+        }
+        return modelToView;
+    }
+
+    // TableModel interface methods
+
+    public int getRowCount() {
+        return (tableModel == null) ? 0 : tableModel.getRowCount();
+    }
+
+    public int getColumnCount() {
+        return (tableModel == null) ? 0 : tableModel.getColumnCount();
+    }
+
+    public String getColumnName(int column) {
+        return tableModel.getColumnName(column);
+    }
+
+    public Class getColumnClass(int column) {
+        return tableModel.getColumnClass(column);
+    }
+
+    public boolean isCellEditable(int row, int column) {
+        return tableModel.isCellEditable(modelIndex(row), column);
+    }
+
+    public Object getValueAt(int row, int column) {
+        return tableModel.getValueAt(modelIndex(row), column);
+    }
+
+    public void setValueAt(Object aValue, int row, int column) {
+        tableModel.setValueAt(aValue, modelIndex(row), column);
+    }
+
+    // Helper classes
+
+    private class Row implements Comparable {
+        private int modelIndex;
+
+        public Row(int index) {
+            this.modelIndex = index;
+        }
+
+        public int compareTo(Object o) {
+            int row1 = modelIndex;
+            int row2 = ((Row) o).modelIndex;
+
+            for (Iterator it = sortingColumns.iterator(); it.hasNext();) {
+                Directive directive = (Directive) it.next();
+                int column = directive.column;
+                Object o1 = tableModel.getValueAt(row1, column);
+                Object o2 = tableModel.getValueAt(row2, column);
+
+                int comparison = 0;
+                // Define null less than everything, except null.
+                if (o1 == null && o2 == null) {
+                    comparison = 0;
+                } else if (o1 == null) {
+                    comparison = -1;
+                } else if (o2 == null) {
+                    comparison = 1;
+                } else {
+                    comparison = getComparator(column).compare(o1, o2);
+                }
+                if (comparison != 0) {
+                    return directive.direction == DESCENDING ? -comparison : comparison;
+                }
+            }
+            return 0;
+        }
+    }
+
+    private class TableModelHandler implements TableModelListener {
+        public void tableChanged(TableModelEvent e) {
+            // If we're not sorting by anything, just pass the event along.
+            if (!isSorting()) {
+                clearSortingState();
+                fireTableChanged(e);
+                return;
+            }
+
+            // If the table structure has changed, cancel the sorting; the
+            // sorting columns may have been either moved or deleted from
+            // the model.
+            if (e.getFirstRow() == TableModelEvent.HEADER_ROW) {
+                cancelSorting();
+                fireTableChanged(e);
+                return;
+            }
+
+            // We can map a cell event through to the view without widening
+            // when the following conditions apply:
+            //
+            // a) all the changes are on one row (e.getFirstRow() == e.getLastRow()) and,
+            // b) all the changes are in one column (column != TableModelEvent.ALL_COLUMNS) and,
+            // c) we are not sorting on that column (getSortingStatus(column) == NOT_SORTED) and,
+            // d) a reverse lookup will not trigger a sort (modelToView != null)
+            //
+            // Note: INSERT and DELETE events fail this test as they have column == ALL_COLUMNS.
+            //
+            // The last check, for (modelToView != null) is to see if modelToView
+            // is already allocated. If we don't do this check; sorting can become
+            // a performance bottleneck for applications where cells
+            // change rapidly in different parts of the table. If cells
+            // change alternately in the sorting column and then outside of
+            // it this class can end up re-sorting on alternate cell updates -
+            // which can be a performance problem for large tables. The last
+            // clause avoids this problem.
+            int column = e.getColumn();
+            if (e.getFirstRow() == e.getLastRow()
+                    && column != TableModelEvent.ALL_COLUMNS
+                    && getSortingStatus(column) == NOT_SORTED
+                    && modelToView != null) {
+                int viewIndex = getModelToView()[e.getFirstRow()];
+                fireTableChanged(new TableModelEvent(TableSorter.this,
+                                                     viewIndex, viewIndex,
+                                                     column, e.getType()));
+                return;
+            }
+
+            // Something has happened to the data that may have invalidated the row order.
+            clearSortingState();
+            fireTableDataChanged();
+            return;
+        }
+    }
+
+    private class MouseHandler extends MouseAdapter {
+        public void mouseClicked(MouseEvent e) {
+            JTableHeader h = (JTableHeader) e.getSource();
+            TableColumnModel columnModel = h.getColumnModel();
+            int viewColumn = columnModel.getColumnIndexAtX(e.getX());
+            int column = columnModel.getColumn(viewColumn).getModelIndex();
+            if (column != -1) {
+                int status = getSortingStatus(column);
+                if (!e.isControlDown()) {
+                    cancelSorting();
+                }
+                // Cycle the sorting states through {NOT_SORTED, ASCENDING, DESCENDING} or
+                // {NOT_SORTED, DESCENDING, ASCENDING} depending on whether shift is pressed.
+                status = status + (e.isShiftDown() ? -1 : 1);
+                status = (status + 4) % 3 - 1; // signed mod, returning {-1, 0, 1}
+                setSortingStatus(column, status);
+            }
+        }
+    }
+
+    private static class Arrow implements Icon {
+        private boolean descending;
+        private int size;
+        private int priority;
+
+        public Arrow(boolean descending, int size, int priority) {
+            this.descending = descending;
+            this.size = size;
+            this.priority = priority;
+        }
+
+        public void paintIcon(Component c, Graphics g, int x, int y) {
+            Color color = c == null ? Color.GRAY : c.getBackground();
+            // In a compound sort, make each succesive triangle 20%
+            // smaller than the previous one.
+            int dx = (int)(size/2*Math.pow(0.8, priority));
+            int dy = descending ? dx : -dx;
+            // Align icon (roughly) with font baseline.
+            y = y + 5*size/6 + (descending ? -dy : 0);
+            int shift = descending ? 1 : -1;
+            g.translate(x, y);
+
+            // Right diagonal.
+            g.setColor(color.darker());
+            g.drawLine(dx / 2, dy, 0, 0);
+            g.drawLine(dx / 2, dy + shift, 0, shift);
+
+            // Left diagonal.
+            g.setColor(color.brighter());
+            g.drawLine(dx / 2, dy, dx, 0);
+            g.drawLine(dx / 2, dy + shift, dx, shift);
+
+            // Horizontal line.
+            if (descending) {
+                g.setColor(color.darker().darker());
+            } else {
+                g.setColor(color.brighter().brighter());
+            }
+            g.drawLine(dx, 0, 0, 0);
+
+            g.setColor(color);
+            g.translate(-x, -y);
+        }
+
+        public int getIconWidth() {
+            return size;
+        }
+
+        public int getIconHeight() {
+            return size;
+        }
+    }
+
+    private class SortableHeaderRenderer implements TableCellRenderer {
+        private TableCellRenderer tableCellRenderer;
+
+        public SortableHeaderRenderer(TableCellRenderer tableCellRenderer) {
+            this.tableCellRenderer = tableCellRenderer;
+        }
+
+        public Component getTableCellRendererComponent(JTable table,
+                                                       Object value,
+                                                       boolean isSelected,
+                                                       boolean hasFocus,
+                                                       int row,
+                                                       int column) {
+            Component c = tableCellRenderer.getTableCellRendererComponent(table,
+                    value, isSelected, hasFocus, row, column);
+            if (c instanceof JLabel) {
+                JLabel l = (JLabel) c;
+                l.setHorizontalTextPosition(JLabel.LEFT);
+                int modelColumn = table.convertColumnIndexToModel(column);
+                l.setIcon(getHeaderRendererIcon(modelColumn, l.getFont().getSize()));
+            }
+            return c;
+        }
+    }
+
+    private static class Directive {
+        private int column;
+        private int direction;
+
+        public Directive(int column, int direction) {
+            this.column = column;
+            this.direction = direction;
+        }
+    }
+}
diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
new file mode 100644
index 0000000..fb82808
--- /dev/null
+++ b/src/jalview/ws/MsaWSThread.java
@@ -0,0 +1,695 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import java.util.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.gui.*;
+import vamsas.objects.simple.MsaResult;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ *
+ * <p>
+ * Description:
+ * </p>
+ *
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ *
+ * <p>
+ * Company: Dundee University
+ * </p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+class MsaWSThread
+    extends WSThread implements WSClientI
+{
+  boolean submitGaps = false; // pass sequences including gaps to alignment
+
+  // service
+
+  boolean preserveOrder = true; // and always store and recover sequence
+
+  // order
+
+  class MsaWSJob extends WSThread.WSJob
+  {
+    // hold special input for this
+    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
+        SequenceSet();
+
+    /**
+     * MsaWSJob
+     *
+     * @param jobNum
+     *            int
+     * @param jobId
+     *            String
+     */
+    public MsaWSJob(int jobNum, SequenceI[] inSeqs)
+    {
+      this.jobnum = jobNum;
+      if (!prepareInput(inSeqs, 2))
+      {
+        submitted = true;
+        subjobComplete = true;
+        result = new MsaResult();
+        result.setFinished(true);
+        result.setStatus("Job never ran - input returned to user.");
+      }
+
+    }
+
+    Hashtable SeqNames = new Hashtable();
+    Vector emptySeqs = new Vector();
+    /**
+     * prepare input sequences for MsaWS service
+     * @param seqs jalview sequences to be prepared
+     * @param minlen minimum number of residues required for this MsaWS service
+     * @return true if seqs contains sequences to be submitted to service.
+     */
+    private boolean prepareInput(SequenceI[] seqs, int minlen)
+    {
+      int nseqs = 0;
+      if (minlen < 0)
+      {
+        throw new Error("Implementation error: minlen must be zero or more.");
+      }
+      for (int i = 0; i < seqs.length; i++)
+      {
+        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          nseqs++;
+        }
+      }
+      boolean valid = nseqs > 1; // need at least two seqs
+      vamsas.objects.simple.Sequence[] seqarray =
+          (valid)
+          ? new vamsas.objects.simple.Sequence[nseqs]
+          : null;
+      for (int i = 0, n = 0; i < seqs.length; i++)
+      {
+
+        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+        // for
+        // any
+        // subjob
+        SeqNames.put(newname, jalview.analysis.SeqsetUtils
+                     .SeqCharacterHash(seqs[i]));
+        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          seqarray[n] = new vamsas.objects.simple.Sequence();
+          seqarray[n].setId(newname);
+          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequence()
+                               : AlignSeq.extractGaps(
+                                   jalview.util.Comparison.GapChars, seqs[i]
+                                   .getSequence()));
+        }
+        else
+        {
+          String empty = null;
+          if (seqs[i].getEnd() >= seqs[i].getStart())
+          {
+            empty = (submitGaps) ? seqs[i].getSequence()
+                : AlignSeq.extractGaps(
+                    jalview.util.Comparison.GapChars, seqs[i]
+                    .getSequence());
+          }
+          emptySeqs.add(new String[]
+                        {newname, empty});
+        }
+      }
+      this.seqs = new vamsas.objects.simple.SequenceSet();
+      this.seqs.setSeqs(seqarray);
+      return valid;
+    }
+
+    /**
+     *
+     * @return true if getAlignment will return a valid alignment result.
+     */
+    public boolean hasResults()
+    {
+      if (subjobComplete && result != null && result.isFinished()
+          && ((MsaResult) result).getMsa() != null && ((MsaResult) result).getMsa().getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+
+    public Object[] getAlignment()
+    {
+
+      if (result != null && result.isFinished())
+      {
+        SequenceI[] alseqs = null;
+        char alseq_gapchar = '-';
+        int alseq_l = 0;
+        if (((MsaResult) result).getMsa() != null)
+        {
+          alseqs = getVamsasAlignment(((MsaResult) result).getMsa());
+          alseq_gapchar = ((MsaResult) result).getMsa().getGapchar().charAt(0);
+          alseq_l = alseqs.length;
+        }
+        if (emptySeqs.size() > 0)
+        {
+          SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
+          // get width
+          int i, w = 0;
+          if (alseq_l > 0)
+          {
+            for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
+            {
+              if (w < alseqs[i].getLength())
+              {
+                w = alseqs[i].getLength();
+              }
+              t_alseqs[i] = alseqs[i];
+              alseqs[i] = null;
+            }
+          }
+          // check that aligned width is at least as wide as emptySeqs width.
+          int ow = w, nw = w;
+          for (i = 0, w = emptySeqs.size(); i < w; i++)
+          {
+            String[] es = (String[]) emptySeqs.get(i);
+            if (es != null && es[1] != null)
+            {
+              int sw = es[1].length();
+              if (nw < sw)
+              {
+                nw = sw;
+              }
+            }
+          }
+          // make a gapped string.
+          StringBuffer insbuff = new StringBuffer(w);
+          for (i = 0; i < nw; i++)
+          {
+            insbuff.append(alseq_gapchar);
+          }
+          if (ow < nw)
+          {
+            for (i = 0; i < alseq_l; i++)
+            {
+              int sw = t_alseqs[i].getLength();
+              if (nw > sw)
+              {
+                // pad at end
+                alseqs[i].setSequence(t_alseqs[i].getSequence() +
+                                      insbuff.substring(0, sw - nw));
+              }
+            }
+          }
+          for (i = 0, w = emptySeqs.size(); i < w; i++)
+          {
+            String[] es = (String[]) emptySeqs.get(i);
+            if (es[1] == null)
+            {
+              t_alseqs[i +
+                  alseq_l] = new jalview.datamodel.Sequence(es[0],
+                  insbuff.toString(), 1, 0);
+            }
+            else
+            {
+              if (es[1].length() < nw)
+              {
+                t_alseqs[i +
+                    alseq_l] = new jalview.datamodel.Sequence(es[0],
+                    es[1] + insbuff.substring(0, nw - es[1].length()), 1,
+                    1 + es[1].length());
+              }
+              else
+              {
+                t_alseqs[i +
+                    alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]);
+              }
+            }
+          }
+          alseqs = t_alseqs;
+        }
+        AlignmentOrder msaorder = new AlignmentOrder(alseqs);
+        // always recover the order - makes parseResult()'s life easier.
+        jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
+        // account for any missing sequences
+        jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
+        return new Object[]
+            {
+            alseqs, msaorder};
+      }
+      return null;
+    }
+    /**
+     * mark subjob as cancelled and set result object appropriatly
+     */
+    void cancel() {
+      cancelled=true;
+      subjobComplete = true;
+      result = null;
+    }
+    /**
+     *
+     * @return boolean true if job can be submitted.
+     */
+    boolean hasValidInput() {
+      if (seqs.getSeqs()!=null)
+        return true;
+      return false;
+    }
+  }
+
+
+  String alTitle; // name which will be used to form new alignment window.
+  Alignment dataset; // dataset to which the new alignment will be
+
+  // associated.
+
+  ext.vamsas.MuscleWS server = null;
+  /**
+   * set basic options for this (group) of Msa jobs
+   *
+   * @param subgaps
+   *            boolean
+   * @param presorder
+   *            boolean
+   */
+  MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
+              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+              AlignmentView alview,
+              String wsname, boolean subgaps, boolean presorder)
+  {
+    this.server = server;
+    this.WsUrl = wsUrl;
+    this.wsInfo = wsinfo;
+    this.WebServiceName = wsname;
+    this.input = alview;
+    this.submitGaps = subgaps;
+    this.preserveOrder = presorder;
+    this.alignFrame = alFrame;
+  }
+
+  /**
+   * create one or more Msa jobs to align visible seuqences in _msa
+   *
+   * @param title
+   *            String
+   * @param _msa
+   *            AlignmentView
+   * @param subgaps
+   *            boolean
+   * @param presorder
+   *            boolean
+   * @param seqset
+   *            Alignment
+   */
+  MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
+              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+              String wsname, String title, AlignmentView _msa, boolean subgaps,
+              boolean presorder, Alignment seqset)
+  {
+    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
+    OutputHeader = wsInfo.getProgressText();
+    alTitle = title;
+    dataset = seqset;
+    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
+    if (conmsa != null)
+    {
+      int njobs = conmsa.length;
+      jobs = new MsaWSJob[njobs];
+      for (int j = 0; j < njobs; j++)
+      {
+        if (j != 0)
+        {
+          jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
+        }
+        else
+        {
+          jobs[j] = new MsaWSJob(0, conmsa[j]);
+        }
+        if (njobs > 0)
+          wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
+        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
+      }
+    }
+  }
+  public boolean isCancellable()
+  {
+    return true;
+  }
+
+  public void cancelJob()
+  {
+    if (!jobComplete && jobs != null)
+    {
+      boolean cancelled = true;
+      for (int job = 0; job < jobs.length; job++)
+      {
+        if (jobs[job].submitted && !jobs[job].subjobComplete)
+        {
+          String cancelledMessage = "";
+          try
+          {
+            vamsas.objects.simple.WsJobId cancelledJob = server
+                .cancel(jobs[job].jobId);
+            if (cancelledJob.getStatus() == 2)
+            {
+              // CANCELLED_JOB
+              cancelledMessage = "Job cancelled.";
+              ((MsaWSJob) jobs[job]).cancel();
+              wsInfo.setStatus(jobs[job].jobnum,
+                               WebserviceInfo.STATE_CANCELLED_OK);
+            }
+            else if (cancelledJob.getStatus() == 3)
+            {
+              // VALID UNSTOPPABLE JOB
+              cancelledMessage +=
+                  "Server cannot cancel this job. just close the window.\n";
+              cancelled = false;
+              // wsInfo.setStatus(jobs[job].jobnum,
+              //                 WebserviceInfo.STATE_RUNNING);
+            }
+
+            if (cancelledJob.getJobId() != null)
+            {
+              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
+            }
+
+            cancelledMessage += "\n";
+          }
+          catch (Exception exc)
+          {
+            cancelledMessage +=
+                ("\nProblems cancelling the job : Exception received...\n"
+                 + exc + "\n");
+            Cache.log.warn("Exception whilst cancelling "+jobs[job].jobId,exc);
+          }
+          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
+                                 + cancelledMessage + "\n");
+        }
+      }
+      if (cancelled)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+        jobComplete = true;
+      }
+      this.interrupt(); // kick thread to update job states.
+    }
+    else
+    {
+      if (!jobComplete)
+      {
+        wsInfo
+            .setProgressText(OutputHeader
+                             + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+      }
+    }
+  }
+  void pollJob(WSJob job) throws Exception {
+    ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);
+  }
+  void StartJob(WSJob job)
+  {
+    if (!(job instanceof MsaWSJob)) {
+      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "+job.getClass());
+    }
+    MsaWSJob j = (MsaWSJob) job;
+    if (j.submitted)
+    {
+      if (Cache.log.isDebugEnabled())
+      {
+        Cache.log.debug("Tried to submit an already submitted job " + j.jobId);
+      }
+      return;
+    }
+    if (j.seqs.getSeqs() == null)
+    {
+      // special case - selection consisted entirely of empty sequences...
+      j.submitted = true;
+      j.result = new MsaResult();
+      j.result.setFinished(true);
+      j.result.setStatus("Empty Alignment Job");
+      ((MsaResult) j.result).setMsa(null);
+    }
+    try
+    {
+      vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);
+
+      if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
+      {
+        j.jobId = jobsubmit.getJobId();
+        j.submitted = true;
+        j.subjobComplete = false;
+        // System.out.println(WsURL + " Job Id '" + jobId + "'");
+      }
+      else
+      {
+        if (jobsubmit == null)
+        {
+          throw new Exception(
+              "Server at "
+              + WsUrl
+              +
+              " returned null object, it probably cannot be contacted. Try again later ?");
+        }
+
+        throw new Exception(jobsubmit.getJobId());
+      }
+    }
+    catch (Exception e)
+    {
+      // TODO: JBPNote catch timeout or other fault types explicitly
+      // For unexpected errors
+      System.err
+          .println(WebServiceName
+                   + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+                   + "When contacting Server:" + WsUrl + "\n"
+                   + e.toString() + "\n");
+      j.allowedServerExceptions = 0;
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo
+          .appendProgressText(
+              j.jobnum,
+              "Failed to submit sequences for alignment.\n"
+              + "It is most likely that there is a problem with the server.\n"
+              + "Just close the window\n");
+
+      // e.printStackTrace(); // TODO: JBPNote DEBUG
+    }
+  }
+
+  private jalview.datamodel.Sequence[] getVamsasAlignment(
+      vamsas.objects.simple.Alignment valign)
+  {
+    vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
+    jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.
+        length];
+
+    for (int i = 0, j = seqs.length; i < j; i++)
+    {
+      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
+                                              .getSeq());
+    }
+
+    return msa;
+  }
+
+  void parseResult()
+  {
+    int results = 0; // number of result sets received
+    JobStateSummary finalState = new JobStateSummary();
+    try
+    {
+      for (int j = 0; j < jobs.length; j++)
+      {
+        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+        if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
+        {
+          results++;
+          vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result).getMsa();
+          if (valign != null)
+          {
+            wsInfo.appendProgressText(jobs[j].jobnum,
+                                      "\nAlignment Object Method Notes\n");
+            String[] lines = valign.getMethod();
+            for (int line = 0; line < lines.length; line++)
+            {
+              wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");
+            }
+            // JBPNote The returned files from a webservice could be
+            //  hidden behind icons in the monitor window that,
+            // when clicked, pop up their corresponding data
+          }
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+
+      Cache.log.error("Unexpected exception when processing results for " +
+                      alTitle, ex);
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+    }
+    if (results > 0)
+    {
+      wsInfo.showResultsNewFrame
+          .addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(
+            java.awt.event.ActionEvent evt)
+        {
+          displayResults(true);
+        }
+      });
+      wsInfo.mergeResults
+          .addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(
+            java.awt.event.ActionEvent evt)
+        {
+          displayResults(false);
+        }
+      });
+      wsInfo.setResultsReady();
+    } else
+      wsInfo.setFinishedNoResults();
+  }
+
+  void displayResults(boolean newFrame)
+  {
+    // view input or result data for each block
+    Vector alorders = new Vector();
+    SequenceI[][] results=new SequenceI[jobs.length][];
+    AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
+    SequenceI[] first=null;
+    for (int j=0; j<jobs.length; j++) {
+      if (jobs[j].hasResults()) {
+        Object[] res = ( (MsaWSJob) jobs[j]).getAlignment();
+        alorders.add(res[1]);
+        results[j] = (SequenceI[]) res[0];
+        orders[j] = (AlignmentOrder) res[1];
+//    SequenceI[] alignment = input.getUpdated
+      } else {
+        results[j]=null;
+      }
+    }
+    Object[] newview = input.getUpdatedView(results, orders, '-');
+    // trash references to original result data
+    for (int j=0; j<jobs.length; j++) {
+      results[j] = null;
+      orders[j] = null;
+    }
+    SequenceI[] alignment = (SequenceI[]) newview[0];
+    ColumnSelection columnselection = (ColumnSelection) newview[1];
+    Alignment al = new Alignment(alignment);
+    if (dataset != null)
+    {
+      al.setDataset(dataset);
+    }
+
+    // JBNote- TODO: warn user if a block is input rather than aligned data ?
+
+    if (newFrame)
+    {
+      AlignFrame af = new AlignFrame(al, columnselection);
+
+      // >>>This is a fix for the moment, until a better solution is
+      // found!!<<<
+      af.getFeatureRenderer().transferSettings(
+          alignFrame.getFeatureRenderer());
+      // update orders
+      if (alorders.size() > 0)
+      {
+        if (alorders.size() == 1)
+        {
+          af.addSortByOrderMenuItem(WebServiceName + " Ordering",
+                                    (AlignmentOrder) alorders.get(0));
+        }
+        else
+        {
+          // construct a non-redundant ordering set
+          Vector names = new Vector();
+          for (int i = 0, l = alorders.size(); i < l; i++)
+          {
+            String orderName = new String(" Region " + i);
+            int j = i + 1;
+            int r = l;
+            while (j < l)
+            {
+              if ( ( (AlignmentOrder) alorders.get(i)).equals( ( (
+                  AlignmentOrder) alorders.get(j))))
+              {
+                alorders.remove(j);
+                l--;
+                orderName += "," + j;
+              }
+              else
+              {
+                j++;
+              }
+            }
+
+            if (i == 0 && j == 1)
+            {
+              names.add(new String(""));
+            }
+            else
+            {
+              names.add(orderName);
+            }
+          }
+          for (int i = 0, l = alorders.size(); i < l; i++)
+          {
+            af.addSortByOrderMenuItem(WebServiceName
+                                      +( (String) names.get(i)) +
+                                      " Ordering",
+                                      (AlignmentOrder) alorders.get(i));
+          }
+        }
+      }
+
+      Desktop.addInternalFrame(af, alTitle,
+                               AlignFrame.NEW_WINDOW_WIDTH,
+                               AlignFrame.NEW_WINDOW_HEIGHT);
+
+    }
+    else
+    {
+      System.out.println("MERGE WITH OLD FRAME");
+
+    }
+  }
+
+  public boolean canMergeResults()
+  {
+    return false;
+  }
+}
diff --git a/src/jalview/ws/WSThread.java b/src/jalview/ws/WSThread.java
new file mode 100644
index 0000000..86ee49a
--- /dev/null
+++ b/src/jalview/ws/WSThread.java
@@ -0,0 +1,269 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+ package jalview.ws;
+
+import jalview.gui.AlignFrame;
+import jalview.gui.WebserviceInfo;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.Desktop;
+import javax.swing.JOptionPane;
+import jalview.bin.Cache;
+
+public abstract class WSThread extends Thread
+{
+    /**
+     * Generic properties for Web Service Client threads.
+     */
+    AlignFrame alignFrame=null;
+  WebserviceInfo wsInfo = null;
+  AlignmentView input=null;
+  boolean jobComplete = false;
+  abstract class WSJob {
+      /**
+       * Generic properties for an individual job within a Web Service Client thread
+       */
+    int jobnum = 0; // WebServiceInfo pane for this job
+    String jobId; // ws job ticket
+    boolean cancelled = false;
+    int allowedServerExceptions = 3; // job dies if too many exceptions.
+    boolean submitted = false;
+    boolean subjobComplete = false;
+    /**
+     *
+     * @return true if job has completed and valid results are available
+     */
+    abstract boolean hasResults();
+    /**
+     *
+     * @return boolean true if job can be submitted.
+     */
+    abstract boolean hasValidInput();
+    vamsas.objects.simple.Result result;
+  }
+  class JobStateSummary {
+    int running = 0;
+    int queuing = 0;
+    int finished = 0;
+    int error = 0;
+    int serror = 0;
+    int cancelled = 0;
+    int results = 0;
+    void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
+                             WSJob j)
+    {
+      if (j.result != null)
+      {
+        String progheader = "";
+        // Parse state of job[j]
+        if (j.result.isRunning())
+        {
+          running++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
+        }
+        else if (j.result.isQueued())
+        {
+          queuing++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
+        }
+        else if (j.result.isFinished())
+        {
+          finished++;
+          j.subjobComplete = true;
+          if (j.hasResults())
+            results++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else if (j.result.isFailed())
+        {
+          progheader += "Job failed.\n";
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+          error++;
+        }
+        else if (j.result.isServerError())
+        {
+          serror++;
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum,
+                           WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        }
+        else if (j.result.isBroken() || j.result.isFailed())
+        {
+          error++;
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+        }
+        // and pass on any sub-job messages to the user
+        wsInfo.setProgressText(j.jobnum, OutputHeader);
+        wsInfo.appendProgressText(j.jobnum, progheader);
+        if (j.result.getStatus() != null)
+        {
+          wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
+        }
+      }
+      else
+      {
+        if (j.submitted && j.subjobComplete)
+        {
+          if (j.allowedServerExceptions == 0)
+          {
+            serror++;
+          }
+          else if (j.result == null)
+          {
+            error++;
+          }
+        }
+      }
+    }
+  }
+
+  WSJob jobs[] = null;
+  String WebServiceName = null;
+  String OutputHeader;
+  String WsUrl = null;
+  abstract void pollJob(WSJob job) throws Exception;
+  public void run()
+  {
+  JobStateSummary jstate=null;
+  if (jobs==null)
+    jobComplete=true;
+  while (!jobComplete)
+  {
+    jstate = new JobStateSummary();
+    for (int j = 0; j < jobs.length; j++)
+    {
+
+      if (!jobs[j].submitted && jobs[j].hasValidInput())
+      {
+        StartJob(jobs[j]);
+      }
+
+      if (jobs[j].submitted && !jobs[j].subjobComplete)
+      {
+        try
+        {
+          pollJob(jobs[j]);
+          if (jobs[j].result == null)
+          {
+            throw (new Exception(
+                "Timed out when communicating with server\nTry again later.\n"));
+          }
+          jalview.bin.Cache.log.debug("Job " + j + " Result state " +
+                                      jobs[j].result.getState()
+                                      + "(ServerError=" +
+                                      jobs[j].result.isServerError() + ")");
+        }
+        catch (Exception ex)
+        {
+          // Deal with Transaction exceptions
+          wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
+                                    + " Server exception!\n" + ex.getMessage());
+          Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+                         + ") Server exception: " + ex.getMessage());
+
+          if (jobs[j].allowedServerExceptions > 0)
+          {
+            jobs[j].allowedServerExceptions--;
+            Cache.log.debug("Sleeping after a server exception.");
+            try
+            {
+              Thread.sleep(5000);
+            }
+            catch (InterruptedException ex1)
+            {
+            }
+          }
+          else
+          {
+            Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+            jobs[j].subjobComplete = true;
+            wsInfo.setStatus(jobs[j].jobnum,
+                             WebserviceInfo.STATE_STOPPED_SERVERERROR);
+          }
+        }
+        catch (OutOfMemoryError er)
+        {
+          jobComplete = true;
+          jobs[j].subjobComplete = true;
+          jobs[j].result = null; // may contain out of date result object
+          wsInfo.setStatus(jobs[j].jobnum,
+                           WebserviceInfo.STATE_STOPPED_ERROR);
+          JOptionPane
+              .showInternalMessageDialog(
+                  Desktop.desktop,
+                  "Out of memory handling result for job !!"
+                  +
+              "\nSee help files for increasing Java Virtual Machine memory.",
+                  "Out of memory", JOptionPane.WARNING_MESSAGE);
+          Cache.log.error("Out of memory when retrieving Job " + j + " id:" +
+                          WsUrl + "/" + jobs[j].jobId, er);
+          System.gc();
+        }
+      }
+      jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+    }
+    // Decide on overall state based on collected jobs[] states
+    if (jstate.running > 0)
+    {
+      wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+    }
+    else if (jstate.queuing > 0)
+    {
+      wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+    }
+    else
+    {
+      jobComplete = true;
+      if (jstate.finished > 0)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+      }
+      else if (jstate.error > 0)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+      }
+      else if (jstate.serror > 0)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      }
+    }
+    if (!jobComplete)
+    {
+      try
+      {
+        Thread.sleep(5000);
+      }
+      catch (InterruptedException e)
+      {
+        Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
+      }
+      // System.out.println("I'm alive "+alTitle);
+    }
+  }
+  if (jobComplete && jobs!=null)
+  {
+    parseResult(); // tidy up and make results available to user
+  } else {
+    Cache.log.debug("WebServiceJob poll loop finished with no jobs created.");
+  }
+}
+abstract void StartJob(WSJob job);
+abstract void parseResult();
+}
diff --git a/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java b/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
new file mode 100755
index 0000000..b65a847
--- /dev/null
+++ b/src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
@@ -0,0 +1,235 @@
+/**
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on 19.03.2004
+ * @author Andreas Prlic
+ *
+ */
+package org.biojava.dasobert.das;
+
+
+import java.net.URL                         ;
+import java.io.InputStream                  ;
+import org.xml.sax.InputSource              ;
+import org.xml.sax.XMLReader                ;
+import javax.xml.parsers.*                  ;
+import org.xml.sax.*                        ;
+import java.util.ArrayList                  ;
+import java.util.List;
+import java.util.logging.*                  ;
+import java.net.HttpURLConnection           ;
+import java.io.IOException;
+import java.net.ConnectException;
+import java.lang.reflect.Method;
+
+
+
+
+/**
+ * A class to perform a DAS features request
+ *
+ * @author Andreas Prlic
+ *
+ */
+public class DAS_FeatureRetrieve {
+
+    List features ;
+    Logger logger     ;
+    int comeBackLater;
+    URL url;
+    /**
+     * @param url the URL the features should be downloaded from
+     *
+     */
+    public DAS_FeatureRetrieve(URL url) {
+        super();
+
+        logger = Logger.getLogger("org.biojava.spice");
+        features = new ArrayList() ;
+        comeBackLater = -1;
+        this.url=url;
+        reload();
+    }
+
+
+    /** contact the DAS-feature server again. Usually
+     * it is not necessary to call this again, because the constructor already does, but
+     * if comeBackLater > -1 this should be called again.
+     *
+     */
+    public void reload(){
+
+        try {
+
+            InputStream dasInStream = null;
+            try {
+                dasInStream	= open(url);
+            } catch (Exception e ){
+                comeBackLater = -1;
+                logger.log(Level.FINE,"could not open connection to " + url,e);
+                return ;
+            }
+
+
+            SAXParserFactory spfactory =
+                SAXParserFactory.newInstance();
+
+            spfactory.setValidating(false);
+
+            SAXParser saxParser = null ;
+
+            try{
+                saxParser =
+                    spfactory.newSAXParser();
+            } catch (ParserConfigurationException e) {
+                e.printStackTrace();
+            }
+
+
+
+            String vali = System.getProperty("XMLVALIDATION");
+
+            boolean validation = false ;
+            if ( vali != null )
+                if ( vali.equals("true") )
+                    validation = true ;
+
+
+            XMLReader xmlreader = saxParser.getXMLReader();
+
+            //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
+            try {
+                xmlreader.setFeature("http://xml.org/sax/features/validation", validation);
+            } catch (SAXException e) {
+                logger.log(Level.FINE,"Cannot set validation " + validation);
+            }
+
+            try {
+                xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validation);
+            } catch (SAXNotRecognizedException e){
+                e.printStackTrace();
+                logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
+
+            }
+
+            DAS_Feature_Handler cont_handle = new DAS_Feature_Handler() ;
+            cont_handle.setDASCommand(url.toString());
+            xmlreader.setContentHandler(cont_handle);
+            xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
+            InputSource insource = new InputSource() ;
+            insource.setByteStream(dasInStream);
+
+            try {
+                xmlreader.parse(insource);
+                features = cont_handle.get_features();
+                comeBackLater = cont_handle.getComBackLater();
+            }
+            catch ( Exception e){
+                e.printStackTrace();
+                logger.log(Level.FINE,"error while parsing response from "+ url);
+                comeBackLater = -1;
+                features = new ArrayList();
+            }
+        }
+        catch (Exception ex) {
+            ex.printStackTrace();
+            comeBackLater = -1;
+        }
+    }
+
+
+    /** open HttpURLConnection. Recommended way to open
+     * HttpURLConnections, since this take care of setting timeouts
+     * properly for java 1.4 and 1.5*/
+    public static HttpURLConnection openHttpURLConnection(URL url)
+    throws IOException, ConnectException {
+    HttpURLConnection huc = null;
+    huc = (HttpURLConnection) url.openConnection();
+
+    String os_name    = java.lang.System.getProperty("os.name");
+    String os_version = java.lang.System.getProperty("os.version");
+    String os_arch    = java.lang.System.getProperty("os.arch");
+    String VERSION = "1.0";
+
+    String userAgent = "Jalview " + VERSION + "("+os_name+"; "+os_arch + " ; "+ os_version+")";
+    //e.g. "Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.7.2) Gecko/20040803"
+     huc.addRequestProperty("User-Agent", userAgent);
+    //logger.finest("opening "+url);
+
+
+    // use reflection to determine if get and set timeout methods for urlconnection are available
+        // seems java 1.5 does not watch the System properties any longer...
+        // and java 1.4 did not provide these...
+    // for 1.4 see setSystemProperties
+    int timeout = 15000;
+    try {
+        // try to use reflection to set timeout property
+        Class urlconnectionClass = Class.forName("java.net.HttpURLConnection");
+
+            Method setconnecttimeout = urlconnectionClass.getMethod (
+                                     "setConnectTimeout", new Class [] {int.class}
+                                     );
+        setconnecttimeout.invoke(huc,new Object[] {new Integer(timeout)});
+
+        Method setreadtimeout = urlconnectionClass.getMethod (
+                                  "setReadTimeout", new Class[] {int.class}
+                                  );
+        setreadtimeout.invoke(huc,new Object[] {new Integer(timeout)});
+        //System.out.println("successfully set java 1.5 timeout");
+    } catch (Exception e) {
+        //e.printStackTrace();
+        // most likely it was a NoSuchMEthodException and we are running java 1.4.
+    }
+    return huc;
+    }
+
+
+    private InputStream open(URL url)
+    throws java.io.IOException, java.net.ConnectException
+    {
+        InputStream inStream = null;
+
+
+        HttpURLConnection huc = openHttpURLConnection(url);
+
+        inStream = huc.getInputStream();
+
+        return inStream;
+
+    }
+
+    /** returns a List of Features
+     * @return a List of Maps containing the features*/
+    public List get_features() {
+
+        return features;
+    }
+
+    /** returns the comeBackLater value - if a server returned suchh -
+     *
+     * @return comeBackLater in seconds, or -1 if not provided by server
+     */
+    public int getComeBackLater(){
+
+        return comeBackLater;
+
+    }
+
+
+}
diff --git a/src/org/biojava/dasobert/das/DAS_Feature_Handler.java b/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
new file mode 100755
index 0000000..105388e
--- /dev/null
+++ b/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
@@ -0,0 +1,190 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on 19.03.2004
+ * @author Andreas Prlic
+ *
+ */
+package org.biojava.dasobert.das;
+
+import org.xml.sax.helpers.DefaultHandler;
+import org.xml.sax.Attributes;
+
+import java.util.ArrayList ;
+import java.util.HashMap ;
+import java.util.List;
+
+/**
+ * a class to parse the response of a DAS - Feature request
+ * @author Andreas Prlic
+ *
+ */
+public class DAS_Feature_Handler  extends DefaultHandler{
+    
+    /**
+     * 
+     */
+    List features ;
+    boolean first_flag ;
+    HashMap feature ;
+    String featurefield ;
+    String characterdata ;
+    String dasCommand ;
+    
+    int comeBackLater ;
+
+    int maxFeatures ;
+
+    public DAS_Feature_Handler() {
+        super();
+        
+        features= new ArrayList() ;
+        first_flag = true ;
+        featurefield = "" ;
+        characterdata = "";
+        dasCommand = "" ;
+        comeBackLater = -1; 
+	maxFeatures = -1;
+    }
+
+    /** specifies a maximum number of features to be downloaded. if a
+	server returns more, they will be ignored.  default is to load
+	all features 
+    @param max the maximium number of features to be downloaded
+    */
+
+    public void setMaxFeatures(int max) {
+	maxFeatures = max;
+    }
+
+    public int getMaxFeatures() {
+	return maxFeatures;
+    }
+    
+    public void setDASCommand(String cmd) { dasCommand = cmd ;}
+    public String getDASCommand() { return dasCommand; }
+    
+    public List get_features() {
+        return features ;
+    }
+    
+    public int getComBackLater(){
+        return comeBackLater;
+    }
+    
+    void start_feature(String uri, String name, String qName, Attributes atts) {
+
+	if (( maxFeatures > 0 ) && ( features.size() > maxFeatures ) ) {
+	    characterdata = "";
+	    return;
+	}
+        feature = new HashMap() ;
+        String id 	= atts.getValue("id");
+        feature.put("id",id);
+        feature.put("dassource",dasCommand);
+        characterdata = "";
+    }
+    
+    void add_featuredata(String uri, String name, String qName) {
+        //System.out.println("featurefield "+featurefield+ " data "+characterdata);
+        // NOTE can have multiple lines ..
+        
+	if (( maxFeatures > 0 ) && ( features.size() > maxFeatures ) ) {
+	    return;
+	}
+
+
+        String data = (String)feature.get(featurefield);
+        if (data != null){
+            characterdata = data + " " + characterdata;
+        }
+        
+        feature.put(featurefield,characterdata);
+        featurefield = "";
+        characterdata = "";
+    }
+    
+    private void addLink(String uri, String name, String qName, Attributes atts) {
+        String href = atts.getValue("href");
+        feature.put("LINK",href);
+        characterdata="";
+        featurefield = "LINK-TEXT";
+                
+    }
+    
+    public void startElement (String uri, String name, String qName, Attributes atts){
+        //System.out.println("new element "+qName);
+        
+        if (qName.equals("FEATURE")) 
+            start_feature(uri,  name,  qName,  atts);
+        else if ( qName.equals("LINK"))
+            addLink(uri,name,qName, atts);
+        else if ( qName.equals("METHOD") || 
+                qName.equals("TYPE") ||
+                qName.equals("START") ||
+                qName.equals("END") ||
+                qName.equals("NOTE") ||                
+                qName.equals("SCORE")
+        ){
+            characterdata ="";
+            featurefield = qName ;
+        }
+        
+    }
+    
+    public void startDocument() {
+    }
+    
+    public void endDocument ()	{        
+    }
+    public void endElement(String uri, String name, String qName) {
+
+        if ( qName.equals("METHOD") || 
+                qName.equals("TYPE") ||
+                qName.equals("START") ||
+                qName.equals("END") ||
+                qName.equals("NOTE") || 
+                qName.equals("LINK") || 
+                qName.equals("SCORE")
+        ) {
+            add_featuredata(uri,name,qName);
+        }
+        else if ( qName.equals("FEATURE")) {
+
+	    if ( maxFeatures > 0 ) {
+		if ( features.size() < maxFeatures ) {
+		     features.add(feature);
+		} 
+	    } else {
+		// no restriction
+		features.add(feature);
+	    }
+        }
+    }
+    
+    public void characters (char ch[], int start, int length){
+
+        for (int i = start; i < start + length; i++) {
+            
+            characterdata += ch[i];
+        }
+        
+    }
+    
+}
diff --git a/src/org/biojava/dasobert/das/FeatureThread.java b/src/org/biojava/dasobert/das/FeatureThread.java
new file mode 100755
index 0000000..8c8923e
--- /dev/null
+++ b/src/org/biojava/dasobert/das/FeatureThread.java
@@ -0,0 +1,180 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on 21.09.2004
+ * @author Andreas Prlic
+ *
+ */
+
+package org.biojava.dasobert.das ;
+
+import java.util.*;
+import java.net.*;
+import java.util.logging.* ;
+import org.biojava.dasobert.eventmodel.FeatureListener;
+import org.biojava.dasobert.eventmodel.FeatureEvent;
+import org.biojava.dasobert.dasregistry.Das1Source;
+
+/** a thread that connects to a DAS - Feature service and gets the features
+ * 
+ * @author Andreas Prlic
+ */
+
+
+
+public class FeatureThread
+    implements Runnable 
+{
+    
+    /** number of times the client tries to reconnect to the server if a "come back later" is returned.
+     * the server should provide a reasonable estimation how long it will take him to create results.
+     * if this number of requests is still not successfull, give up.
+     */
+    public static int MAX_COME_BACK_ITERATIONS = 5;
+
+    public static int MAX_NR_FEATURES = 300;
+
+    static Logger logger = Logger.getLogger("org.biojava.spice");
+
+    Das1Source dasSource;
+    String ac ;
+    List featureListeners;
+    Thread thread;
+    
+    public FeatureThread (String accessionCode, Das1Source dasSource) {
+	this.dasSource = dasSource;
+	this.ac = accessionCode;
+	featureListeners = new ArrayList();
+    }
+
+    public void addFeatureListener(FeatureListener li) {
+	featureListeners.add(li);
+    }
+    
+    public void clearFeatureListeners() {
+	featureListeners.clear();
+    }
+
+    public synchronized void stop(){
+	thread = null;
+	notify();
+    }
+
+    
+
+
+    public void run() {
+	Thread me = Thread.currentThread();
+	while ( thread == me) {
+	    String url = dasSource.getUrl();
+	    String queryString = url + "features?segment="+ ac ;
+	    URL cmd = null ;
+	    try {
+		cmd = new URL(queryString);
+	    } catch (MalformedURLException e ) {
+		logger.warning("got MalformedURL from das source " +dasSource);
+		e.printStackTrace();
+		
+	    }
+
+	    logger.info("requesting features from " + cmd);
+	    DAS_FeatureRetrieve ftmp = new DAS_FeatureRetrieve(cmd);
+        
+	    
+	    int comeBackLater = ftmp.getComeBackLater();
+	    int securityCounter = 0;
+	    while ( (thread == me) && ( comeBackLater > 0 )) {
+		securityCounter++;
+		if ( securityCounter >= MAX_COME_BACK_ITERATIONS){
+		    comeBackLater = -1; 
+		    break;
+                
+		}
+		notifyComeBackLater(comeBackLater);
+		// server is still calculating - asks us to come back later
+		try {
+		    wait (comeBackLater);
+		} catch (InterruptedException e){
+		    comeBackLater = -1;
+		    break;
+		}
+                
+		ftmp.reload();
+		comeBackLater = ftmp.getComeBackLater(); 
+	    }
+
+	    if ( ! (thread == me ) ) {
+		break;
+	    }
+
+	    List features = ftmp.get_features();
+        
+	    // a fallback mechanism to prevent DAS sources from bringing down spice
+	    if ( features.size() > MAX_NR_FEATURES){
+		logger.warning("DAS source returned more than " + MAX_NR_FEATURES + "features. " +
+			       " throwing away excess features at " +cmd);
+		features = features.subList(0,MAX_NR_FEATURES);
+	    }
+      
+              
+	    // notify FeatureListeners
+	    Map[] feats = (Map[])features.toArray(new Map[features.size()]);
+	    notifyFeatureListeners(feats);
+
+	    break;
+
+
+	}
+	thread = null;
+
+    }
+
+    public void start() {
+	thread = new Thread(this);
+	thread.start();
+    }
+
+    private void notifyFeatureListeners(Map[] feats){
+        logger.finest("FeatureThread found " + feats.length + " features");
+        FeatureEvent fevent = new FeatureEvent(feats,dasSource);
+        Iterator fiter = featureListeners.iterator();
+        while (fiter.hasNext()){
+            FeatureListener fi = (FeatureListener)fiter.next();
+            fi.newFeatures(fevent);
+        }
+    }
+    
+ /** the Annotation server requested to be queried again in a while
+     * 
+     * @param comeBackLater
+     */
+    private void notifyComeBackLater(int comeBackLater){
+        FeatureEvent event = new FeatureEvent(new HashMap[0],dasSource);
+        event.setComeBackLater(comeBackLater);
+        Iterator fiter = featureListeners.iterator();
+        while (fiter.hasNext()){
+            FeatureListener fi = (FeatureListener)fiter.next();
+            fi.comeBackLater(event);
+        }
+        
+    }
+
+
+}
+
diff --git a/src/org/biojava/dasobert/das2/Das2Capability.java b/src/org/biojava/dasobert/das2/Das2Capability.java
new file mode 100755
index 0000000..5b5c17c
--- /dev/null
+++ b/src/org/biojava/dasobert/das2/Das2Capability.java
@@ -0,0 +1,45 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Feb 9, 2006
+ *
+ */
+package org.biojava.dasobert.das2;
+
+public interface Das2Capability {
+
+    public boolean equals(Das2Capability other);
+    public int hashCode();
+    
+    public void setCapability(String type);
+    public String getCapability();
+    
+    public void setQueryUri(String id);
+    public String getQueryUri();
+    
+    public void setFormats(String[] formats);
+    public String[] getFormats();
+    
+    /** checks if this capability is actually of das1 style
+     * 
+     * @return boolean true if the capability is in DAS1 style
+     */
+    public boolean isDas1Style();
+    
+}
diff --git a/src/org/biojava/dasobert/das2/Das2CapabilityImpl.java b/src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
new file mode 100755
index 0000000..273defa
--- /dev/null
+++ b/src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
@@ -0,0 +1,109 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Feb 9, 2006
+ *
+ */
+package org.biojava.dasobert.das2;
+
+public class Das2CapabilityImpl 
+implements Das2Capability{
+
+    String capability;
+    String[] formats;
+    String queryId;
+    
+    public static String DAS1_CAPABILITY_PREFIX = "das1:";
+    
+    public Das2CapabilityImpl() {
+        super();
+        capability = "undef";
+        queryId = "";
+        formats = new String[0];
+
+    }
+    
+    public boolean isDas1Style(){
+        
+        if ( capability == null)
+            return false;
+        if ( capability.length() < DAS1_CAPABILITY_PREFIX.length())
+            return false;
+        if ( capability.substring(0,DAS1_CAPABILITY_PREFIX.length()).equals(DAS1_CAPABILITY_PREFIX))
+            return true;
+        return false;
+    
+    }
+    
+    public boolean equals(Das2Capability other){
+        
+        boolean status = true;
+        
+        if (!  capability.equals(other.getCapability()))
+            status = false;
+        if ( ! queryId.equals(other.getQueryUri()))
+            status = false;
+        
+        return status;
+    }
+    
+    public int hashCode(){
+        int h = 7;
+        h = 31 * h + ( null == capability ? 0 : capability.hashCode()) ;
+        h = 31 * h + ( null == queryId    ? 0 : queryId.hashCode()) ;
+        
+        return h;
+    }
+    
+    public String toString(){
+        String txt ="capability " + capability + " queryId " + queryId;
+        return txt;
+    }
+
+    public String getCapability() {
+        
+        return capability;
+    }
+
+    public String[] getFormats() {      
+        return formats;
+    }
+
+    public String getQueryUri() {      
+        return queryId;
+    }
+
+    public void setCapability(String type) {
+       capability = type;
+        
+    }
+
+    public void setFormats(String[] formats) {
+       
+        this.formats = formats; 
+    }
+
+    public void setQueryUri(String id) {
+       queryId = id;
+        
+    }
+    
+    
+
+}
diff --git a/src/org/biojava/dasobert/das2/Das2Source.java b/src/org/biojava/dasobert/das2/Das2Source.java
new file mode 100755
index 0000000..21a008a
--- /dev/null
+++ b/src/org/biojava/dasobert/das2/Das2Source.java
@@ -0,0 +1,40 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Feb 9, 2006
+ *
+ */
+package org.biojava.dasobert.das2;
+
+import org.biojava.dasobert.dasregistry.DasSource;
+
+public interface Das2Source
+extends DasSource {
+
+   public Das2Capability[] getDas2Capabilities();
+   public void setDas2Capabilities(Das2Capability[] capabilities);
+   
+   /** test if this is a DAS1 source represented as a DAS2 source
+    *  if true - this source can be converted into a DAS1 source by using
+    *  DasSourceConverter.toDas1(Das2Source);
+    *
+    * @return true if the DasSource has DAS1 capabilties
+    */
+   public boolean hasDas1Capabilities();
+}
diff --git a/src/org/biojava/dasobert/das2/Das2SourceImpl.java b/src/org/biojava/dasobert/das2/Das2SourceImpl.java
new file mode 100755
index 0000000..aca49b2
--- /dev/null
+++ b/src/org/biojava/dasobert/das2/Das2SourceImpl.java
@@ -0,0 +1,144 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Feb 9, 2006
+ *
+ */
+package org.biojava.dasobert.das2;
+
+import org.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.DasSource;
+
+public class Das2SourceImpl 
+extends Das1Source
+implements Das2Source 
+
+{
+
+    Das2Capability[] capabilities;
+    
+    public Das2SourceImpl() {
+        super();
+
+        capabilities = new Das2Capability[0];
+    }
+    
+    
+    /**  compare if two DasSources are identical
+     * 
+     */
+    public boolean equals(DasSource other){
+        
+        if ( this == other)
+            return true;
+        
+        if ( ( other == null) || (other.getClass() != this.getClass()))    
+            return false;
+       
+        // to compare if two Das2Sources are identical we do the following:
+        //  we check the capabilities
+        
+        Das2SourceImpl d2o = (Das2SourceImpl)other;
+        
+        if ( nickname.equals(d2o.getNickname()))
+            return true;
+        
+        Das2Capability[] othercaps = d2o.getDas2Capabilities();
+        
+        if ( ! (capabilities.length == othercaps.length))
+            return false;
+        
+        for ( int x=0;x<capabilities.length;x++){
+            Das2Capability tmpcap = capabilities[x];
+            boolean foundCap = false;
+            for (int y=0; y< othercaps.length;y++){
+                Das2Capability tmpcapo = othercaps[y];
+                if ( tmpcap.equals(tmpcapo))
+                    foundCap = true;
+            }
+            if ( ! foundCap)
+                return false;
+        }
+        
+        
+        //TODO?
+        // should we add a check for coordinate systems?
+        // but we already check for the endpoints, that should be enough...
+        
+        return true;
+        
+    }
+    
+    public int hashCode(){
+        int h = 7 ;
+        
+        h = 31 * h + (null == nickname ? 0 :  nickname.hashCode());
+        
+        for ( int x=0;x<capabilities.length;x++){
+            Das2Capability cap = capabilities[x];
+            h = 31 * h + cap.hashCode();
+        }
+        
+        return h;
+    }
+    
+    
+    public boolean hasDas1Capabilities(){
+        
+        // test if any of the capabilities is a das1 capabilitiy
+        
+        for (int i = 0 ; i < capabilities.length; i++) {
+            Das2Capability cap = capabilities[i];
+            if ( cap.isDas1Style())
+                return true;            
+        }
+        return false;
+        
+        
+    }
+    
+    public String[] getCapabilities() {
+        //todo mark as not needed / not appropriate ...
+        return super.getCapabilities();
+    }
+
+
+
+    public void setCapabilities(String[] u) {
+        // TODO Auto-generated method stub
+        super.setCapabilities(u);
+    }
+
+
+
+    public Das2Capability[] getDas2Capabilities() {
+        // TODO Auto-generated method stub
+        return capabilities;
+    }
+
+    public void setDas2Capabilities(Das2Capability[] capabilities) {
+        // TODO Auto-generated method stub
+        this.capabilities = capabilities;
+        
+    }
+    
+    
+    
+
+}
diff --git a/src/org/biojava/dasobert/das2/DasSourceConverter.java b/src/org/biojava/dasobert/das2/DasSourceConverter.java
new file mode 100755
index 0000000..513ba3f
--- /dev/null
+++ b/src/org/biojava/dasobert/das2/DasSourceConverter.java
@@ -0,0 +1,82 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on Mar 23, 2006
+ *
+ */
+package org.biojava.dasobert.das2;
+
+//import org.biojava.bio.program.das.dasalignment.DASException;
+import org.biojava.dasobert.dasregistry.Das1Source;
+
+public class DasSourceConverter {
+
+    public DasSourceConverter() {
+        super();
+
+    }
+
+
+    /** convert a das2 source to a das 1 source.
+     * This only will work if is passes the Das2Source.isDas1Source() test
+     * i.e. this is really a das1 server there
+     *
+     * @param das2source a DAS2Source to be converted
+     * @return a Das1Source
+     * @throws DASException
+     */
+    public static Das1Source toDas1Source (Das2Source das2source) throws Exception{
+        if ( ! das2source.hasDas1Capabilities())
+            throw new Exception("this das source does not have das1 capabilitites");
+
+        Das1Source ds = new Das1Source();
+        ds.setAdminemail(das2source.getAdminemail());
+        ds.setDescription(das2source.getDescription());
+        ds.setHelperurl(das2source.getHelperurl());
+        ds.setRegisterDate(das2source.getRegisterDate());
+        ds.setLeaseDate(das2source.getLeaseDate());
+        ds.setLabels(das2source.getLabels());
+        ds.setCoordinateSystem(das2source.getCoordinateSystem());
+        ds.setNickname(das2source.getNickname());
+        ds.setId(das2source.getId());
+        ds.setLabels(das2source.getLabels());
+
+        // convert the capabilitites to das1 capabiltities and get the url
+        Das2Capability[] caps = das2source.getDas2Capabilities();
+        String[] das1capabilitites = new String[caps.length];
+        int DASPREFIXLENGTH = Das2CapabilityImpl.DAS1_CAPABILITY_PREFIX.length();
+
+        for ( int i = 0 ; i< caps.length;i++){
+            Das2Capability cap = caps[i];
+
+            String c = cap.getCapability();
+
+            das1capabilitites[i] = c.substring(DASPREFIXLENGTH,c.length());
+
+            String query_uri = cap.getQueryUri();
+
+            String url = query_uri.substring(0,(query_uri.length() - c.length() + DASPREFIXLENGTH));
+            ds.setUrl(url);
+        }
+        ds.setCapabilities(das1capabilitites);
+
+        return ds ;
+    }
+
+}
diff --git a/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java b/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
new file mode 100755
index 0000000..caf6798
--- /dev/null
+++ b/src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
@@ -0,0 +1,181 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Mar 15, 2006
+ *
+ */
+package org.biojava.dasobert.das2.io;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.biojava.dasobert.das2.Das2Capability;
+import org.biojava.dasobert.das2.Das2CapabilityImpl;
+import org.biojava.dasobert.das2.Das2Source;
+import org.biojava.dasobert.das2.Das2SourceImpl;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import org.biojava.dasobert.dasregistry.DasSource;
+import org.xml.sax.Attributes;
+import org.xml.sax.helpers.DefaultHandler;
+
+/** a parser for the DAS2 sources response
+ * 
+ * @author Andreas Prlic
+ * @since 6:53:45 PM
+ * @version %I% %G%
+ */
+public class DAS2SourceHandler extends DefaultHandler{
+
+    List sources;
+    Das2Source currentSource;
+    List coordinates;
+    List capabilities;
+    List labels;
+
+    public static final String LABELPROPERTY = "label";
+
+    public DAS2SourceHandler() {
+        super();
+        
+        sources       = new ArrayList();
+        currentSource = new Das2SourceImpl();
+        coordinates   = new ArrayList();
+        capabilities  = new ArrayList();
+	labels        = new ArrayList();
+    }
+    
+    private void startSource (String uri, String name, String qName, Attributes atts){
+        
+        String id = atts.getValue("uri");
+        String title = atts.getValue("title");
+        String doc_ref = atts.getValue("doc_href");
+        String description = atts.getValue("description");
+
+           
+        currentSource.setId(id);
+        currentSource.setNickname(title);
+        currentSource.setHelperurl(doc_ref);
+        currentSource.setDescription(description);
+        
+    }
+    
+    private DasCoordinateSystem getCoordinateSystem(String uri, String name, String qname, Attributes atts){
+        // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6" 
+        // source="Protein Sequence" authority="UniProt" test_range="P06213" />
+        DasCoordinateSystem dcs = new DasCoordinateSystem();
+        String id = atts.getValue("uri");
+        dcs.setUniqueId(id);
+        
+        String source = atts.getValue("source");
+        dcs.setCategory(source);
+        
+        String authority = atts.getValue("authority");
+        dcs.setName(authority);
+        
+        String test_range = atts.getValue("test_range");
+        dcs.setTestCode(test_range);
+        
+        try {
+            String taxidstr = atts.getValue("taxid");
+            int taxid = Integer.parseInt(taxidstr);
+            dcs.setNCBITaxId(taxid);
+        } catch (Exception e){}
+        
+        String version = atts.getValue("version");
+        if ( version != null)
+            dcs.setVersion(version);
+        
+        return dcs;
+    }
+    
+    public void startElement (String uri, String name, String qName, Attributes atts){
+        //System.out.println("new element "+qName);
+        
+        if (qName.equals("SOURCE")) {
+            //System.out.println("new Source " + atts.getValue(uri));
+            currentSource = new Das2SourceImpl();
+            coordinates = new ArrayList();
+            capabilities = new ArrayList();
+            
+            startSource(uri,name, qName, atts);
+            
+        } else if ( qName.equals("MAINTAINER")){
+            String email = atts.getValue("email");
+            currentSource.setAdminemail(email);
+        } else if ( qName.equals("COORDINATES")){
+            DasCoordinateSystem dcs = getCoordinateSystem(uri,name,qName,atts);
+            coordinates.add(dcs);
+            
+        } else if ( qName.equals("CAPABILITY")){
+            Das2Capability cap = getCapability(uri,name,qName,atts);
+            capabilities.add(cap);
+        } else if (qName.equals("PROPERTY")) {
+	    addProperty(uri,name,qName,atts);
+	}                
+    }
+    
+    private Das2Capability getCapability(String uri, String name, String qName, Attributes atts){
+        // e.g <CAPABILITY type="features" query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
+        Das2Capability cap = new Das2CapabilityImpl();
+        
+        String type = atts.getValue("type");
+        cap.setCapability(type);
+        String query_uri = atts.getValue("query_uri");
+        cap.setQueryUri(query_uri);
+        return cap;
+        
+    }
+    
+    private void addProperty(String uri, String name, String qName, Attributes atts){
+	String pname = atts.getValue("name");
+	String label = atts.getValue("value");
+	if ( pname.equals(LABELPROPERTY) )
+	    labels.add(label);
+    }
+    
+    public void startDocument(){
+        sources = new ArrayList();
+        coordinates = new ArrayList();
+        capabilities = new ArrayList();
+    }
+    
+    public void endElement(String uri, String name, String qName) {
+        if ( qName.equals("SOURCE")) {
+            currentSource.setDas2Capabilities((Das2Capability[])capabilities.toArray(new Das2Capability[capabilities.size()]));
+            //System.out.println("got coordinates " + coordinates.size());
+            currentSource.setCoordinateSystem((DasCoordinateSystem[])coordinates.toArray(new DasCoordinateSystem[coordinates.size()]));
+
+	    currentSource.setLabels((String[])labels.toArray(new String[labels.size()]));
+	    labels.clear();
+
+            //System.out.println("Das2SourceHandler endElement name " + name + " uri " + uri + " qName " + qName);
+            //System.out.println("Das2SourceHandler adding to source: " + currentSource.getId());    
+            sources.add(currentSource);   
+            currentSource = new Das2SourceImpl();
+        } 		
+    }
+    
+    public DasSource[] getSources(){    
+        //System.out.println("Das2SourceHandler: source size: " + sources.size());
+        return (DasSource[])sources.toArray(new DasSource[sources.size()]);
+    }
+    
+    
+
+}
diff --git a/src/org/biojava/dasobert/das2/io/DasSourceReader.java b/src/org/biojava/dasobert/das2/io/DasSourceReader.java
new file mode 100755
index 0000000..0b05df8
--- /dev/null
+++ b/src/org/biojava/dasobert/das2/io/DasSourceReader.java
@@ -0,0 +1,32 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Feb 24, 2006
+ *
+ */
+package org.biojava.dasobert.das2.io;
+
+import java.io.InputStream;
+
+import org.biojava.dasobert.dasregistry.DasSource;
+
+public interface DasSourceReader {
+
+    public DasSource[] readDasSource(InputStream stream);
+}
diff --git a/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java b/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
new file mode 100755
index 0000000..3f0a07a
--- /dev/null
+++ b/src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
@@ -0,0 +1,173 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on Feb 24, 2006
+ *
+ */
+package org.biojava.dasobert.das2.io;
+
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.URL;
+
+
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+
+//import org.biojava.dasobert.das.AlignmentThread;
+import org.biojava.dasobert.das.DAS_FeatureRetrieve;
+import org.biojava.dasobert.dasregistry.DasSource;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.SAXNotRecognizedException;
+import org.xml.sax.XMLReader;
+
+public class DasSourceReaderImpl implements DasSourceReader {
+
+    Exception loggedException;
+
+    public DasSourceReaderImpl() {
+        super();
+        loggedException = null;
+
+        // open the stream to a server and then parse the result ...
+    }
+
+    private InputStream open(URL url)
+    throws java.io.IOException, java.net.ConnectException
+    {
+        InputStream inStream = null;
+
+
+        HttpURLConnection huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
+
+        inStream = huc.getInputStream();
+
+        return inStream;
+
+    }
+
+
+    public DasSource[] readDasSource(URL url){
+        DasSource[] sources = new DasSource[0];
+
+        try {
+            InputStream stream = open(url);
+
+            sources = readDasSource(stream);
+        } catch (Exception e){
+            e.printStackTrace();
+            loggedException = e;
+        }
+        return sources;
+    }
+
+    /** read a DAS2 sources response and return a list of DAS sources.
+     *
+     */
+    public DasSource[] readDasSource(InputStream stream)  {
+
+        DasSource[] sources = new DasSource[0];
+
+        try {
+        SAXParserFactory spfactory =
+            SAXParserFactory.newInstance();
+
+        spfactory.setValidating(false);
+
+        SAXParser saxParser = null ;
+
+        try{
+            saxParser =
+                spfactory.newSAXParser();
+        } catch (ParserConfigurationException e) {
+            e.printStackTrace();
+            loggedException = e;
+        }
+
+        String vali = System.getProperty("XMLVALIDATION");
+
+        boolean validation = false ;
+        if ( vali != null )
+            if ( vali.equals("true") )
+                validation = true ;
+
+
+        XMLReader xmlreader = saxParser.getXMLReader();
+
+        //XMLReader xmlreader = XMLReaderFactory.createXMLReader();
+        try {
+            xmlreader.setFeature("http://xml.org/sax/features/validation", validation);
+        } catch (SAXException e) {
+            //logger.log(Level.FINE,"Cannot set validation " + validation);
+        }
+
+        try {
+            xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validation);
+        } catch (SAXNotRecognizedException e){
+            e.printStackTrace();
+            //logger.log(Level.FINE,"Cannot set load-external-dtd "+validation);
+
+        }
+
+        DAS2SourceHandler cont_handle = new DAS2SourceHandler() ;
+
+        xmlreader.setContentHandler(cont_handle);
+        xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
+        InputSource insource = new InputSource() ;
+        insource.setByteStream(stream);
+
+
+        xmlreader.parse(insource);
+        sources = cont_handle.getSources();
+
+
+
+        } catch (Exception e) {
+            e.printStackTrace();
+            loggedException = e;
+        }
+        return sources;
+    }
+
+    public Exception getLoggedException(){
+        return loggedException;
+    }
+
+    public static void main (String[] args){
+        String url = "http://www.spice-3d.org/dasregistry/das2/sources/";
+        DasSourceReaderImpl reader = new DasSourceReaderImpl();
+        try {
+            URL u = new URL(url);
+            DasSource[] sources = reader.readDasSource(u);
+            for (int i=0; i< sources.length;i++){
+                DasSource ds = sources[i];
+                System.out.println(ds.toString());
+            }
+
+        } catch (Exception e){
+            e.printStackTrace();
+        }
+
+    }
+
+
+
+}
diff --git a/src/org/biojava/dasobert/dasregistry/Das1Source.java b/src/org/biojava/dasobert/dasregistry/Das1Source.java
new file mode 100755
index 0000000..de007d6
--- /dev/null
+++ b/src/org/biojava/dasobert/dasregistry/Das1Source.java
@@ -0,0 +1,206 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on 15.04.2004
+ * @author Andreas Prlic
+ *
+ */
+package org.biojava.dasobert.dasregistry;
+
+import java.util.Date ;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+
+
+//import org.biojava.dasobert.das2.io.DasSourceWriter;
+//import org.biojava.dasobert.das2.io.DasSourceWriterImpl;
+//import org.biojava.utils.xml.PrettyXMLWriter;
+
+
+/** a simple Bean class to be returned via SOAP
+ * @author Andreas Prlic
+ */
+
+public class Das1Source implements DasSource {
+    String url                ;
+    protected String nickname           ;
+    String adminemail         ;
+    String description        ;
+    DasCoordinateSystem[] coordinateSystem ;
+    String[] capabilities     ;
+    String[] labels           ;
+    String helperurl          ;
+    Date   registerDate       ;
+    Date   leaseDate          ;
+    String id                 ;
+    boolean local;
+
+    boolean alertAdmin;
+
+    public static String EMPTY_ID = "UNK:-1" ;
+
+    public Das1Source () {
+        id               = EMPTY_ID;
+        url              = "";
+        adminemail       = "" ;
+        description      = "" ;
+        //String empty     = "" ;
+        nickname         = "" ;
+        coordinateSystem = new DasCoordinateSystem[0];
+        //coordinateSystem[0] = new DasCoordinateSystem();
+        capabilities     =  new String[0];
+        labels 	         = new String[0];
+        //capabilities[0]  = empty ;
+        registerDate     = new Date() ;
+        leaseDate        = new Date() ;
+        helperurl        = "";
+        local=true;
+    }
+
+
+    public boolean equals(DasSource other){
+        System.out.println("Das1Source equals, comparing with other DasSource");
+        if (! (other instanceof Das1Source))
+            return false;
+
+        Das1Source ods = (Das1Source) other;
+
+        if ( ods.getUrl().equals(url))
+            return true;
+        if ( ods.getNickname().equals(nickname))
+            return true;
+        return false;
+    }
+
+    public int hashCode() {
+        int h = 7;
+
+        h = 31 * h + ( null == nickname ? 0 : nickname.hashCode());
+        h = 31 * h + ( null == url ? 0 : url.hashCode());
+
+        return h;
+    }
+
+    /** the DAS2 string representation of this DAS source
+     *
+    public String toString() {
+
+        StringWriter writer = new StringWriter();
+
+        PrintWriter pw = new PrintWriter(writer);
+        PrettyXMLWriter xw = new PrettyXMLWriter(pw);
+
+        DasSourceWriter dswriter = new DasSourceWriterImpl();
+        try {
+            dswriter.writeDasSource(xw,this);
+        } catch (IOException e){
+            e.printStackTrace();
+        }
+
+        return writer.toString();
+
+    }
+    */
+    public void setLocal(boolean flag){ local = flag;}
+    public boolean isLocal(){return local;}
+
+    public void setId(String i) { id = i; }
+
+    /** get a the Id of the DasSource. The Id is a unique db
+     * identifier. The public DAS-Registry has Auto_Ids that look like
+     * DASSOURCE:12345; public look like XYZ:12345, where the XYZ
+     * prefix can be configured in the config file.
+     */
+    public String getId() { return id;}
+
+    public void setNickname(String name) {
+        nickname = name ;
+    }
+    public String getNickname(){
+        return nickname;
+    }
+    public void setUrl(String u) {
+        char lastChar = u.charAt(u.length()-1);
+        if ( lastChar  != '/')
+            u += "/";
+
+        url = u ;
+    }
+
+    public void setAdminemail (String u) {
+        adminemail = u ;
+    }
+
+    public void setDescription (String u) {
+        description = u;
+    }
+
+    public void setCoordinateSystem (DasCoordinateSystem[] u){
+        coordinateSystem=u ;
+    }
+
+    public void setCapabilities (String[] u){
+        capabilities = u ;
+    }
+
+    public String getUrl(){return url;}
+    public String getAdminemail(){return adminemail;}
+    public String getDescription(){return description;}
+    public String[] getCapabilities(){return capabilities;}
+    public DasCoordinateSystem[] getCoordinateSystem(){return coordinateSystem;}
+
+    public void setRegisterDate(Date d) {
+        registerDate = d;
+    }
+    public Date getRegisterDate() {
+        return registerDate ;
+    }
+    public void setLeaseDate(Date d) {
+        leaseDate =d ;
+    }
+    public Date getLeaseDate() {
+        return leaseDate ;
+    }
+
+    public void setLabels(String[] ls) {
+        labels = ls ;
+    }
+
+    public String[] getLabels() {
+        return labels;
+    }
+
+    public void setHelperurl(String url) {
+        helperurl = url;
+    }
+
+    public String getHelperurl() {
+        return helperurl;
+    }
+
+    public void setAlertAdmin(boolean flag) {
+        alertAdmin = flag;
+    }
+
+    public boolean getAlertAdmin() {
+        return alertAdmin;
+    }
+
+}
diff --git a/src/org/biojava/dasobert/dasregistry/Das2Validator.java b/src/org/biojava/dasobert/dasregistry/Das2Validator.java
new file mode 100755
index 0000000..a7fd293
--- /dev/null
+++ b/src/org/biojava/dasobert/dasregistry/Das2Validator.java
@@ -0,0 +1,43 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Mar 20, 2006
+ *
+ */
+package org.biojava.dasobert.dasregistry;
+
+import org.biojava.dasobert.das2.Das2Source;
+
+public class Das2Validator {
+
+    public Das2Validator() {
+        super();
+
+    }
+    
+    public boolean validate(Das2Source ds){
+        
+        // TODO this bit still needs to be implemented!
+        
+        return true;
+    }
+
+    
+    
+}
diff --git a/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java b/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
new file mode 100755
index 0000000..8715446
--- /dev/null
+++ b/src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
@@ -0,0 +1,116 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on 15.04.2004
+ * @author Andreas Prlic
+ *
+ */
+
+
+package org.biojava.dasobert.dasregistry ;
+
+import java.util.Comparator ;
+import java.util.Map ;
+import java.util.HashMap ;
+
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+
+/** a comparator to sort DasSources 
+ * @author Andreas Prlic 
+ */
+
+
+public abstract class DasCoordSysComparator
+    implements Comparator
+{ 
+
+    private final String name ;
+    private static final Map COMPS_BY_NAME;
+
+
+    public DasCoordSysComparator(String str) {
+	//System.out.println("new dasSourceComparator " + str);
+	name = str ;
+    }
+   
+    public static final Comparator BY_NAME = new DasCoordSysComparator("name") {
+        protected Comparable getField(DasCoordinateSystem ds) {
+            return ds.getName();
+        }
+    };    
+
+    public static final Comparator BY_ID = new DasCoordSysComparator("id") {
+        protected Comparable getField(DasCoordinateSystem ds) {
+            return ds.getUniqueId();
+        }
+    };    
+    public static final Comparator BY_CATEGORY = new DasCoordSysComparator("category") {
+        protected Comparable getField(DasCoordinateSystem ds) {
+            return ds.getCategory();
+        }
+    };
+    public static final Comparator BY_ORGANISM = new DasCoordSysComparator("organism") {
+        protected Comparable getField(DasCoordinateSystem ds) {
+            return ds.getOrganismName();
+        }
+    };
+    public static final Comparator BY_TAXID = new DasCoordSysComparator("taxid") {
+        protected Comparable getField(DasCoordinateSystem ds) {
+            return ds.getNCBITaxId()+"";
+        }
+    };
+   
+    
+
+    static {
+        COMPS_BY_NAME = new HashMap();
+        COMPS_BY_NAME.put(BY_ID.toString(),           BY_ID);
+	COMPS_BY_NAME.put(BY_NAME.toString(),         BY_NAME);
+        COMPS_BY_NAME.put(BY_CATEGORY.toString(),     BY_CATEGORY);
+        COMPS_BY_NAME.put(BY_ORGANISM.toString(),     BY_ORGANISM);
+        COMPS_BY_NAME.put(BY_TAXID.toString(),        BY_TAXID);
+    }
+
+   
+
+    public static Comparator fromString(String name) {
+        if (COMPS_BY_NAME.containsKey(name)) {
+            return (Comparator) COMPS_BY_NAME.get(name);
+        } else {
+            throw new IllegalArgumentException("Can't compare by key " + name);
+        }
+    }
+
+    protected abstract Comparable getField(DasCoordinateSystem ds);
+
+    /** compare two DasCoordSys objects */
+    public int compare( Object a, Object b) {
+        DasCoordinateSystem x = (DasCoordinateSystem) a ;
+        DasCoordinateSystem y = (DasCoordinateSystem) b ;
+        return getField(x).compareTo(getField(y));
+    }
+
+    public String toString() {
+        return name;
+    }
+
+
+}
+
+
diff --git a/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java b/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
new file mode 100755
index 0000000..31caaf5
--- /dev/null
+++ b/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
@@ -0,0 +1,159 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on 15.04.2004
+ * @author Andreas Prlic
+ *
+ */
+package org.biojava.dasobert.dasregistry;
+
+
+/** a Bean to be returned via SOAP. It takes care of the DAS -  coordinate Systems 
+ * @author Andreas Prlic
+ */
+public class DasCoordinateSystem {
+
+    String name;
+    String category;
+    String organism_name;
+    int ncbi_tax_id ;
+    String uniqueId ;
+    String version;
+    String testCode;
+    
+    public DasCoordinateSystem () {
+        uniqueId = "";
+        name = "";
+        category ="";
+        organism_name = "";
+        ncbi_tax_id = 0;
+        version = "";
+        testCode = "";
+    }
+
+    public boolean equals(DasCoordinateSystem other){
+        boolean match = true;
+        System.out.println("comparing " + this.toString() + " to " + other.toString());
+        // URI has piority 
+        if ( (! uniqueId.equals("")) && ( uniqueId.equals( other.getUniqueId())))
+            return true;
+        
+        if ( ncbi_tax_id != other.getNCBITaxId()) {
+            System.out.println("mismatch in ncbi tax id " + ncbi_tax_id + " != " + other.getNCBITaxId());
+            match = false;
+        }
+        if ( ! version.equals(other.getVersion() )){
+            System.out.println("mismatch in version");
+            match = false;
+        }
+        if ( ! category.equals(other.getCategory())  ) {
+            System.out.println("mismatch in category");
+            match = false;
+        }
+        if ( ! name.equals(other.getName())) {
+            System.out.println("mismatch in name");   
+            match = false;
+        }
+        System.out.println(" match: " + match);
+        
+        return match;
+    }
+    
+    public Object clone() {
+        DasCoordinateSystem d = new DasCoordinateSystem();
+        d.setTestCode(testCode);
+        d.setCategory(category);
+        d.setName(name);
+        d.setNCBITaxId(ncbi_tax_id);
+        d.setUniqueId(getUniqueId());
+        d.setOrganismName(getOrganismName());
+        d.setVersion(getVersion());
+        return d;
+    }
+    
+    public String getTestCode() {
+        return testCode;
+    }
+
+
+
+    public void setTestCode(String testCode) {
+        if ( testCode == null)
+            testCode = "";
+        this.testCode = testCode;
+    }
+
+
+
+    public void setUniqueId(String id) { uniqueId = id ;   }
+    public String getUniqueId() { return uniqueId;         }
+
+    public void setName(String n) { name = n; }
+    public String getName() { return name; }
+    
+    public void setCategory(String c) { category = c;}
+    public String getCategory() { return category;}
+
+    public void setOrganismName(String t) { organism_name  =t;} 
+    public String getOrganismName() { return organism_name;}
+
+    public void setNCBITaxId(int id) { ncbi_tax_id = id;}
+    public int getNCBITaxId(){ return ncbi_tax_id ;}
+    
+    
+    
+
+    public String getVersion() {
+        return version;
+    }
+
+    public void setVersion(String version) {
+        if ( version == null)
+            version = "";
+        this.version = version;
+    }
+
+    public String toString() {
+        String nam = name;
+        if ( ! version.equals(""))
+            nam += "_" + version;
+        
+	if ( organism_name.equals("") ) 
+	    return nam+","+category ;
+	else 
+	    return nam+","+category+"," + organism_name ;
+    }
+
+    public static DasCoordinateSystem fromString(String rawString) {
+	String[] spl = rawString.split(",");
+	DasCoordinateSystem dcs = new DasCoordinateSystem();
+	if ( spl.length == 2 ) {
+	    dcs.setName(spl[0]);	   
+	    dcs.setCategory(spl[1]);
+	} 
+	if ( spl.length == 3 ) {
+	    dcs.setName(spl[0]);
+	    dcs.setCategory(spl[1]);
+	    dcs.setOrganismName(spl[2]);
+	}
+	return dcs;
+    }
+
+
+}
diff --git a/src/org/biojava/dasobert/dasregistry/DasSource.java b/src/org/biojava/dasobert/dasregistry/DasSource.java
new file mode 100755
index 0000000..a2112b6
--- /dev/null
+++ b/src/org/biojava/dasobert/dasregistry/DasSource.java
@@ -0,0 +1,105 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Feb 8, 2006
+ *
+ */
+package org.biojava.dasobert.dasregistry;
+
+import java.util.Date;
+
+public interface DasSource {
+
+    public  void setLocal(boolean flag);
+
+    public  boolean isLocal();
+
+    /** compare if two das sources are equal
+     * 
+     * @param ds
+     * @return returns true if two DAS sources are equivalent
+     */
+    public boolean equals(DasSource ds);
+    
+    /** classes that implement equals, should also implement hashKey
+     * 
+     * @return the hash code of a das source
+     */
+    public int hashCode();
+    
+    
+    public  void setId(String i);
+
+    /** get a the Id of the DasSource. The Id is a unique db
+     * identifier. The public DAS-Registry has Auto_Ids that look like
+     * DASSOURCE:12345; public look like XYZ:12345, where the XYZ
+     * prefix can be configured in the config file.
+     * @return String the ID of a Das Source
+     */
+    public  String getId();
+
+    public  void setNickname(String name);
+
+    public  String getNickname();
+
+    public  void setUrl(String u);
+
+    public  void setAdminemail(String u);
+
+    public  void setDescription(String u);
+
+    public  void setCoordinateSystem(DasCoordinateSystem[] u);
+
+    public  void setCapabilities(String[] u);
+
+    public  String getUrl();
+
+    public  String getAdminemail();
+
+    public  String getDescription();
+
+    public  String[] getCapabilities();
+
+    public  DasCoordinateSystem[] getCoordinateSystem();
+
+    public  void setRegisterDate(Date d);
+
+    public  Date getRegisterDate();
+
+    public  void setLeaseDate(Date d);
+
+    public  Date getLeaseDate();
+
+    public  void setLabels(String[] ls);
+
+    public  String[] getLabels();
+
+    public  void setHelperurl(String url);
+
+    public  String getHelperurl();
+
+    // TestCode is now part of the coordinate system!
+    //public  void setTestCode(String code);
+    //public  String getTestCode();
+
+    public  void setAlertAdmin(boolean flag);
+
+    public  boolean getAlertAdmin();
+
+}
\ No newline at end of file
diff --git a/src/org/biojava/dasobert/dasregistry/DasSourceComparator.java b/src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
new file mode 100755
index 0000000..c07b32d
--- /dev/null
+++ b/src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
@@ -0,0 +1,140 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on 15.04.2004
+ * @author Andreas Prlic
+ *
+ */
+
+
+package org.biojava.dasobert.dasregistry ;
+
+import java.util.Comparator ;
+import java.util.Map ;
+import java.util.HashMap ;
+
+
+/** a comparator to sort DasSources 
+ * @author Andreas Prlic, Thomas Down
+ */
+
+
+public abstract class DasSourceComparator
+    implements Comparator
+{ 
+
+    private final String name ;
+    private static final Map COMPS_BY_NAME;
+
+
+    public DasSourceComparator(String str) {
+	//System.out.println("new dasSourceComparator " + str);
+	name = str ;
+    }
+   
+    public static final Comparator BY_ID = new DasSourceComparator("id") {
+        protected Comparable getField(DasSource ds) {
+            return ds.getId();
+        }
+    };    
+
+    public static final Comparator BY_NICKNAME = new DasSourceComparator("nickname") {
+        protected Comparable getField(DasSource ds) {
+            return ds.getNickname();
+        }
+    };    
+    public static final Comparator BY_REGISTER_DATE = new DasSourceComparator("registerdate") {
+        protected Comparable getField(DasSource ds) {
+            return ds.getRegisterDate();
+        }
+    };
+    public static final Comparator BY_LEASE_DATE = new DasSourceComparator("leasedate") {
+        protected Comparable getField(DasSource ds) {
+            return ds.getLeaseDate();
+        }
+    };
+    public static final Comparator BY_URL = new DasSourceComparator("url") {
+        protected Comparable getField(DasSource ds) {
+            return ds.getUrl();
+        }
+    };
+    public static final Comparator BY_ADMIN_EMAIL = new DasSourceComparator("adminemail") {
+        protected Comparable getField(DasSource ds) {
+            return ds.getAdminemail();
+        }
+    };
+    public static final Comparator BY_DESCRIPTION = new DasSourceComparator("description") {
+        protected Comparable getField(DasSource ds) {
+            return ds.getDescription();
+        }
+    };
+    public static final Comparator BY_CAPABILITIES = new DasSourceComparator("capabilities") {
+        protected Comparable getField(DasSource ds) {
+            String[] caps = ds.getCapabilities();
+            return caps.length == 0 ? "" : caps[0];
+        }
+    };
+    public static final Comparator BY_COORDINATE_SYSTEM = new DasSourceComparator("coordinateSystem") {
+        protected Comparable getField(DasSource ds) {
+            DasCoordinateSystem[] dcss = ds.getCoordinateSystem();
+            return dcss.length == 0 ? "" : dcss[0].toString();
+        }
+    };
+
+    static {
+        COMPS_BY_NAME = new HashMap();
+        COMPS_BY_NAME.put(BY_ID.toString(),                BY_ID);
+        COMPS_BY_NAME.put(BY_NICKNAME.toString(),          BY_NICKNAME);
+        COMPS_BY_NAME.put(BY_REGISTER_DATE.toString(),     BY_REGISTER_DATE);
+        COMPS_BY_NAME.put(BY_LEASE_DATE.toString(),        BY_LEASE_DATE);
+        COMPS_BY_NAME.put(BY_URL.toString(),               BY_URL);
+        COMPS_BY_NAME.put(BY_ADMIN_EMAIL.toString(),       BY_ADMIN_EMAIL);
+        COMPS_BY_NAME.put(BY_DESCRIPTION.toString(),       BY_DESCRIPTION);
+        COMPS_BY_NAME.put(BY_CAPABILITIES.toString(),      BY_CAPABILITIES);
+        COMPS_BY_NAME.put(BY_COORDINATE_SYSTEM.toString(), BY_COORDINATE_SYSTEM);
+    }
+
+   
+
+    public static Comparator fromString(String name) {
+        if (COMPS_BY_NAME.containsKey(name)) {
+            return (Comparator) COMPS_BY_NAME.get(name);
+        } else {
+            throw new IllegalArgumentException("Can't compare by key " + name);
+        }
+    }
+
+    protected abstract Comparable getField(DasSource ds);
+
+    /** compare two DasSource objects */
+    public int compare( Object a, Object b) {
+        
+        DasSource x = (DasSource) a ;
+        DasSource y = (DasSource) b ;
+        return getField(x).compareTo(getField(y));
+    }
+
+    public String toString() {
+        return name;
+    }
+
+
+}
+
+
diff --git a/src/org/biojava/dasobert/eventmodel/FeatureEvent.java b/src/org/biojava/dasobert/eventmodel/FeatureEvent.java
new file mode 100755
index 0000000..4c9ac37
--- /dev/null
+++ b/src/org/biojava/dasobert/eventmodel/FeatureEvent.java
@@ -0,0 +1,72 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Oct 28, 2005
+ *
+ */
+package org.biojava.dasobert.eventmodel;
+
+import java.util.Map;
+
+import org.biojava.dasobert.dasregistry.Das1Source;
+public class FeatureEvent {
+    
+    Map[] features;
+    Das1Source dasSource;
+    int comeBackLater;
+    
+    public FeatureEvent(Map[] features,Das1Source dasSource) {
+        super();
+        this.features =features;
+        this.dasSource = dasSource;
+        comeBackLater = -1;
+    }
+    
+    public int getComeBackLater(){
+        return comeBackLater;
+    }
+    
+    public void setComeBackLater(int comeBackLater){
+        this.comeBackLater = comeBackLater;
+    }
+    
+    
+    /** get the features that have been found.
+     * 
+     * do something like
+     * Map[] features = event.getFeatures();
+     * <pre>
+     * for (int i = 0 ; i< features;i++) {            
+     *      Map f = features[i];
+     *      String type = (String) f.get("TYPE") ;
+     *      System.out.println(type);
+     * }      
+     * </pre>
+     * @return a Map containng the features
+     */
+    public Map[] getFeatures(){
+        return features;
+    }
+    
+    public Das1Source getDasSource(){
+        return dasSource;
+    }
+    
+}
+
diff --git a/src/org/biojava/dasobert/eventmodel/FeatureListener.java b/src/org/biojava/dasobert/eventmodel/FeatureListener.java
new file mode 100755
index 0000000..0091ef1
--- /dev/null
+++ b/src/org/biojava/dasobert/eventmodel/FeatureListener.java
@@ -0,0 +1,49 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Oct 28, 2005
+ *
+ */
+package org.biojava.dasobert.eventmodel;
+
+//import org.biojava.spice.multipanel.eventmodel.FeatureEvent;
+
+/**  a feature listener that returns the raw features as returned by a DAS source.
+ * 
+ */  
+public interface FeatureListener {
+    
+    /** new features have been returned from the Annotation server 
+     * 
+     * @param e
+     */
+    public void newFeatures(FeatureEvent e);
+    
+    /** the server says that he is busy and we should try again in x seconds
+     * 
+     * @param e
+     */
+    public void comeBackLater(FeatureEvent e);
+    
+}
+
+    
+    
+    
+
diff --git a/src/org/biojava/dasobert/eventmodel/ObjectListener.java b/src/org/biojava/dasobert/eventmodel/ObjectListener.java
new file mode 100755
index 0000000..7b136a4
--- /dev/null
+++ b/src/org/biojava/dasobert/eventmodel/ObjectListener.java
@@ -0,0 +1,47 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Nov 1, 2005
+ *
+ */
+package org.biojava.dasobert.eventmodel;
+
+/** an interface for the listeners of new PDB code requested / new Uniprot code requested
+ * 
+ * @author Andreas Prlic
+ *
+ */
+public interface ObjectListener {
+    
+    /** a new object has been requested 
+     * 
+     * @param accessionCode
+     */
+    public void newObjectRequested(String accessionCode);
+    
+    /** no object with that accessionCode has been found
+     * 
+     * @param accessionCode
+     */
+    public void noObjectFound(String accessionCode);
+    
+    
+   // public void exceptionOccured(Exception e);
+   
+}
diff --git a/src/org/biojava/dasobert/eventmodel/SequenceEvent.java b/src/org/biojava/dasobert/eventmodel/SequenceEvent.java
new file mode 100755
index 0000000..c3123ff
--- /dev/null
+++ b/src/org/biojava/dasobert/eventmodel/SequenceEvent.java
@@ -0,0 +1,44 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Nov 20, 2005
+ *
+ */
+package org.biojava.dasobert.eventmodel;
+
+
+public class SequenceEvent {
+
+    String sequence;
+    String accessionCode;
+    public SequenceEvent(String accessionCode, String seq) {
+        super();
+        sequence = seq;
+        this.accessionCode = accessionCode;
+    }
+    
+    public String getAccessionCode(){
+        return accessionCode;
+    }
+    
+    public String getSequence(){
+        return sequence;
+    }
+
+}
diff --git a/src/org/biojava/dasobert/eventmodel/SequenceListener.java b/src/org/biojava/dasobert/eventmodel/SequenceListener.java
new file mode 100755
index 0000000..58cbdb3
--- /dev/null
+++ b/src/org/biojava/dasobert/eventmodel/SequenceListener.java
@@ -0,0 +1,55 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Jun 10, 2005
+ *
+ */
+package org.biojava.dasobert.eventmodel;
+
+/** An interface fore events related to selections of sequence
+ * position, sequence range and locking of the selection.
+ *
+ * @author Andreas Prlic
+ *
+ */
+public interface SequenceListener 
+extends ObjectListener{
+    
+    /* select a certain sequence position */
+    public void selectedSeqPosition(int position);
+    
+    /** select a certain range of a sequence 
+     * @param start the start
+     * @param end the end of the range
+     * */
+    public void selectedSeqRange(int start, int end);
+    
+    /** the current selecetion is locked and can not be changed 
+     * @param flag true if selection should be locked
+     * */
+    public void selectionLocked(boolean flag);
+    
+    public void newSequence(SequenceEvent e);
+    
+    /** clear what has been selected
+     * 
+     *
+     */
+    public void clearSelection();
+}