X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=aab41cabccd92614870e97a0bff4796afaeb69c5;hb=6a91de2e48559da8034762a7d77a143435362029;hp=061dfca64f0fad12b5c43c11ed94ac15c90a21cb;hpb=266c4e2544701f88a8d21294b4a4f4cc42cf76cc;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 061dfca..aab41ca 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -26,12 +26,22 @@ import java.util.jar.*;
 import javax.swing.*;
 
 import org.exolab.castor.xml.*;
+
+import uk.ac.vamsas.objects.utils.MapList;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 import jalview.schemabinding.version2.*;
 import jalview.schemes.*;
 import jalview.structure.StructureSelectionManager;
 
 /**
- * DOCUMENT ME!
+ * Write out the current jalview desktop state
+ * as a Jalview XML stream.
+ * 
+ * Note: the vamsas objects referred to here are primitive
+ * versions of the VAMSAS project schema elements - they are
+ * not the same and most likely never will be :)
  *
  * @author $author$
  * @version $Revision$
@@ -39,7 +49,54 @@ import jalview.structure.StructureSelectionManager;
 public class Jalview2XML
 {
 
-  Hashtable seqRefIds;
+  Hashtable seqRefIds = null;
+
+  Vector frefedSequence = null;
+
+  public void resolveFrefedSequences()
+  {
+    if (frefedSequence.size() > 0)
+    {
+      int r = 0, rSize = frefedSequence.size();
+      while (r < rSize)
+      {
+        Object[] ref = (Object[]) frefedSequence.elementAt(r);
+        if (ref != null)
+        {
+          String sref = (String) ref[0];
+          if (seqRefIds.containsKey(sref))
+          {
+            if (ref[1] instanceof jalview.datamodel.Mapping)
+            {
+              SequenceI seq = (SequenceI) seqRefIds.get(sref);
+              while (seq.getDatasetSequence() != null)
+              {
+                seq = seq.getDatasetSequence();
+              }
+              ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
+            }
+            else
+            {
+              System.err
+                      .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
+                              + ref[1].getClass() + " type objects.");
+            }
+            frefedSequence.remove(r);
+            rSize--;
+          }
+          else
+          {
+            r++;
+          }
+        }
+        else
+        {
+          frefedSequence.remove(r);
+          rSize--;
+        }
+      }
+    }
+  }
 
   /**
    * This maintains a list of viewports, the key being the
@@ -51,6 +108,7 @@ public class Jalview2XML
   Hashtable annotationIds = new Hashtable();
 
   String uniqueSetSuffix = "";
+
   /**
    * List of pdbfiles added to Jar
    */
@@ -74,7 +132,7 @@ public class Jalview2XML
       //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
       ////////////////////////////////////////////////////
       PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
-          "UTF-8"));
+              "UTF-8"));
 
       Vector shortNames = new Vector();
 
@@ -89,8 +147,8 @@ public class Jalview2XML
 
           if (shortName.indexOf(File.separatorChar) > -1)
           {
-            shortName = shortName.substring(shortName.lastIndexOf(
-                File.separatorChar) + 1);
+            shortName = shortName.substring(shortName
+                    .lastIndexOf(File.separatorChar) + 1);
           }
 
           int count = 1;
@@ -99,8 +157,8 @@ public class Jalview2XML
           {
             if (shortName.endsWith("_" + (count - 1)))
             {
-              shortName = shortName.substring(0,
-                                              shortName.lastIndexOf("_"));
+              shortName = shortName
+                      .substring(0, shortName.lastIndexOf("_"));
             }
 
             shortName = shortName.concat("_" + count);
@@ -117,28 +175,27 @@ public class Jalview2XML
           int ap, apSize = af.alignPanels.size();
           for (ap = 0; ap < apSize; ap++)
           {
-            AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
-                elementAt(ap);
+            AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
+                    .elementAt(ap);
 
-            SaveState(apanel,
-                      apSize == 1 ? shortName : ap + shortName,
-                      jout, out);
+            SaveState(apanel, apSize == 1 ? shortName : ap + shortName,
+                    jout, out);
           }
         }
       }
 
       out.close();
       jout.close();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
+      //TODO: inform user of the problem - they need to know if their data was not saved !
       ex.printStackTrace();
     }
   }
 
   // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
   public boolean SaveAlignment(AlignFrame af, String jarFile,
-                               String fileName)
+          String fileName)
   {
     try
     {
@@ -146,21 +203,19 @@ public class Jalview2XML
       FileOutputStream fos = new FileOutputStream(jarFile);
       JarOutputStream jout = new JarOutputStream(fos);
       PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
-          "UTF-8"));
+              "UTF-8"));
       for (ap = 0; ap < apSize; ap++)
       {
-        AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap);
+        AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
+                .elementAt(ap);
 
-        SaveState(apanel,
-                  apSize == 1 ? fileName : fileName + ap,
-                  jout, out);
+        SaveState(apanel, apSize == 1 ? fileName : fileName + ap, jout, out);
       }
 
       out.close();
       jout.close();
       return true;
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
       return false;
@@ -176,10 +231,8 @@ public class Jalview2XML
    * @param jout DOCUMENT ME!
    * @param out DOCUMENT ME!
    */
-  public JalviewModel SaveState(AlignmentPanel ap,
-                                String fileName,
-                                JarOutputStream jout,
-                                PrintWriter out)
+  public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+          JarOutputStream jout, PrintWriter out)
   {
     if (seqRefIds == null)
     {
@@ -209,10 +262,15 @@ public class Jalview2XML
 
     vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
-    if(jal.getProperties()!=null)
+    if (jal.getDataset() != null)
+    {
+      // dataset id is the dataset's hashcode
+      vamsasSet.setDatasetId(jal.getDataset().hashCode() + "");
+    }
+    if (jal.getProperties() != null)
     {
       Enumeration en = jal.getProperties().keys();
-      while(en.hasMoreElements())
+      while (en.hasMoreElements())
       {
         String key = en.nextElement().toString();
         SequenceSetProperties ssp = new SequenceSetProperties();
@@ -238,27 +296,7 @@ public class Jalview2XML
       }
       else
       {
-        vamsasSeq = new Sequence();
-        vamsasSeq.setId(id + "");
-        vamsasSeq.setName(jds.getName());
-        vamsasSeq.setSequence(jds.getSequenceAsString());
-        vamsasSeq.setDescription(jds.getDescription());
-
-        if (jds.getDatasetSequence().getDBRef() != null)
-        {
-          jalview.datamodel.DBRefEntry[] dbrefs =
-              jds.getDatasetSequence().getDBRef();
-
-          for (int d = 0; d < dbrefs.length; d++)
-          {
-            DBRef dbref = new DBRef();
-            dbref.setSource(dbrefs[d].getSource());
-            dbref.setVersion(dbrefs[d].getVersion());
-            dbref.setAccessionId(dbrefs[d].getAccessionId());
-            vamsasSeq.addDBRef(dbref);
-          }
-        }
-
+        vamsasSeq = createVamsasSequence(id, jds);
         vamsasSet.addSequence(vamsasSeq);
         seqRefIds.put(id + "", jal.getSequenceAt(i));
       }
@@ -275,20 +313,16 @@ public class Jalview2XML
         jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 
         if (av.hiddenRepSequences != null
-            && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
+                && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
         {
-          jalview.datamodel.SequenceI[] reps =
-              ( (jalview.datamodel.SequenceGroup)
-               av.hiddenRepSequences.get(
-                   jal.getSequenceAt(i))).getSequencesInOrder(jal);
+          jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
+                  .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
 
           for (int h = 0; h < reps.length; h++)
           {
             if (reps[h] != jal.getSequenceAt(i))
             {
-              jseq.addHiddenSequences(
-                  jal.findIndex(reps[h])
-                  );
+              jseq.addHiddenSequences(jal.findIndex(reps[h]));
             }
           }
         }
@@ -296,8 +330,8 @@ public class Jalview2XML
 
       if (jds.getDatasetSequence().getSequenceFeatures() != null)
       {
-        jalview.datamodel.SequenceFeature[] sf
-            = jds.getDatasetSequence().getSequenceFeatures();
+        jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
+                .getSequenceFeatures();
         int index = 0;
         while (index < sf.length)
         {
@@ -328,8 +362,7 @@ public class Jalview2XML
               key = keys.nextElement().toString();
               OtherData keyValue = new OtherData();
               keyValue.setKey(key);
-              keyValue.setValue(
-                  sf[index].otherDetails.get(key).toString());
+              keyValue.setValue(sf[index].otherDetails.get(key).toString());
               features.addOtherData(keyValue);
             }
           }
@@ -345,8 +378,8 @@ public class Jalview2XML
         while (en.hasMoreElements())
         {
           Pdbids pdb = new Pdbids();
-          jalview.datamodel.PDBEntry entry
-              = (jalview.datamodel.PDBEntry) en.nextElement();
+          jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
+                  .nextElement();
 
           pdb.setId(entry.getId());
           pdb.setType(entry.getType());
@@ -362,7 +395,6 @@ public class Jalview2XML
               if (!jmol.pdbentry.getId().equals(entry.getId()))
                 continue;
 
-
               StructureState state = new StructureState();
               state.setVisible(true);
               state.setXpos(jmol.getX());
@@ -371,7 +403,7 @@ public class Jalview2XML
               state.setHeight(jmol.getHeight());
 
               String statestring = jmol.viewer.getStateInfo();
-              if(state!=null)
+              if (state != null)
               {
                 state.setContent(statestring.replaceAll("\n", ""));
               }
@@ -385,7 +417,6 @@ public class Jalview2XML
             }
           }
 
-
           if (entry.getFile() != null)
           {
             pdb.setFile(entry.getFile());
@@ -402,20 +433,19 @@ public class Jalview2XML
                 File file = new File(entry.getFile());
                 if (file.exists() && jout != null)
                 {
-                  byte[] data = new byte[ (int) file.length()];
+                  byte[] data = new byte[(int) file.length()];
                   jout.putNextEntry(new JarEntry(entry.getId()));
-                  DataInputStream dis = new DataInputStream(new
-                      FileInputStream(file));
+                  DataInputStream dis = new DataInputStream(
+                          new FileInputStream(file));
                   dis.readFully(data);
 
                   DataOutputStream dout = new DataOutputStream(jout);
                   dout.write(data, 0, data.length);
                   jout.closeEntry();
                 }
-              }
-              catch (Exception ex)
+              } catch (Exception ex)
               {
-                  ex.printStackTrace();
+                ex.printStackTrace();
               }
 
             }
@@ -448,6 +478,38 @@ public class Jalview2XML
     {
       jal = av.alignment;
     }
+    // SAVE MAPPINGS
+    if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
+    {
+      jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
+      for (int i = 0; i < jac.length; i++)
+      {
+        AlcodonFrame alc = new AlcodonFrame();
+        vamsasSet.addAlcodonFrame(alc);
+        for (int p = 0; p < jac[i].aaWidth; i++)
+        {
+          Alcodon cmap = new Alcodon();
+          cmap.setPos1(jac[i].codons[p][0]);
+          cmap.setPos2(jac[i].codons[p][1]);
+          cmap.setPos3(jac[i].codons[p][2]);
+          alc.addAlcodon(cmap);
+        }
+        if (jac[i].getProtMappings() != null
+                && jac[i].getProtMappings().length > 0)
+        {
+          SequenceI[] dnas = jac[i].getdnaSeqs();
+          jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
+          for (int m = 0; m < pmaps.length; m++)
+          {
+            AlcodMap alcmap = new AlcodMap();
+            alcmap.setDnasq("" + dnas[m].hashCode());
+            alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
+                    false));
+            alc.addAlcodMap(alcmap);
+          }
+        }
+      }
+    }
 
     //SAVE TREES
     ///////////////////////////////////
@@ -469,7 +531,7 @@ public class Jalview2XML
             {
               Tree tree = new Tree();
               tree.setTitle(tp.getTitle());
-              tree.setCurrentTree( (av.currentTree == tp.getTree()));
+              tree.setCurrentTree((av.currentTree == tp.getTree()));
               tree.setNewick(tp.getTree().toString());
               tree.setThreshold(tp.treeCanvas.threshold);
 
@@ -497,7 +559,8 @@ public class Jalview2XML
     //SAVE ANNOTATIONS
     if (jal.getAlignmentAnnotation() != null)
     {
-      jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
+      jalview.datamodel.AlignmentAnnotation[] aa = jal
+              .getAlignmentAnnotation();
 
       for (int i = 0; i < aa.length; i++)
       {
@@ -510,9 +573,8 @@ public class Jalview2XML
 
         an.setId(aa[i].annotationId);
 
-        if (aa[i] == av.quality ||
-            aa[i] == av.conservation ||
-            aa[i] == av.consensus)
+        if (aa[i] == av.quality || aa[i] == av.conservation
+                || aa[i] == av.consensus)
         {
           an.setLabel(aa[i].label);
           an.setGraph(true);
@@ -554,7 +616,7 @@ public class Jalview2XML
           an.setScore(aa[i].getScore());
         }
         AnnotationElement ae;
-        if (aa[i].annotations!=null)
+        if (aa[i].annotations != null)
         {
           an.setScoreOnly(false);
           for (int a = 0; a < aa[i].annotations.length; a++)
@@ -567,7 +629,7 @@ public class Jalview2XML
             ae = new AnnotationElement();
             if (aa[i].annotations[a].description != null)
               ae.setDescription(aa[i].annotations[a].description);
-            if(aa[i].annotations[a].displayCharacter!=null)
+            if (aa[i].annotations[a].displayCharacter != null)
               ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 
             if (!Float.isNaN(aa[i].annotations[a].value))
@@ -575,19 +637,22 @@ public class Jalview2XML
 
             ae.setPosition(a);
             if (aa[i].annotations[a].secondaryStructure != ' '
-                && aa[i].annotations[a].secondaryStructure != '\0')
-              ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
-                                       + "");
+                    && aa[i].annotations[a].secondaryStructure != '\0')
+              ae
+                      .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+                              + "");
 
-            if (aa[i].annotations[a].colour!=null
-                && aa[i].annotations[a].colour != java.awt.Color.black)
+            if (aa[i].annotations[a].colour != null
+                    && aa[i].annotations[a].colour != java.awt.Color.black)
             {
               ae.setColour(aa[i].annotations[a].colour.getRGB());
             }
 
             an.addAnnotationElement(ae);
           }
-        } else {
+        }
+        else
+        {
           an.setScoreOnly(true);
         }
         vamsasSet.addAnnotation(an);
@@ -603,9 +668,8 @@ public class Jalview2XML
       {
         groups[i] = new JGroup();
 
-        jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
-            jal.getGroups()
-            .elementAt(i);
+        jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
+                .getGroups().elementAt(i);
         groups[i].setStart(sg.getStartRes());
         groups[i].setEnd(sg.getEndRes());
         groups[i].setName(sg.getName());
@@ -617,32 +681,30 @@ public class Jalview2XML
 
             if (sg.cs instanceof jalview.schemes.UserColourScheme)
             {
-              groups[i].setColour(SetUserColourScheme(sg.cs,
-                  userColours,
-                  jms));
+              groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+                      jms));
             }
             else
             {
-              groups[i].setColour(ColourSchemeProperty.getColourName(sg.
-                  cs));
+              groups[i]
+                      .setColour(ColourSchemeProperty.getColourName(sg.cs));
             }
           }
           else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
           {
-            groups[i].setColour(
-                ColourSchemeProperty.getColourName(
-                    ( (jalview.schemes.AnnotationColourGradient) sg.cs).
-                    getBaseColour()));
+            groups[i]
+                    .setColour(ColourSchemeProperty
+                            .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
+                                    .getBaseColour()));
           }
           else if (sg.cs instanceof jalview.schemes.UserColourScheme)
           {
-            groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
-                jms));
+            groups[i]
+                    .setColour(SetUserColourScheme(sg.cs, userColours, jms));
           }
           else
           {
-            groups[i].setColour(ColourSchemeProperty.getColourName(
-                sg.cs));
+            groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
           }
 
           groups[i].setPidThreshold(sg.cs.getThreshold());
@@ -658,8 +720,8 @@ public class Jalview2XML
 
         for (int s = 0; s < sg.getSize(); s++)
         {
-          jalview.datamodel.Sequence seq =
-              (jalview.datamodel.Sequence) sg.getSequenceAt(s);
+          jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
+                  .getSequenceAt(s);
           groups[i].addSeq(seq.hashCode());
         }
       }
@@ -674,8 +736,6 @@ public class Jalview2XML
     view.setViewName(av.viewName);
     view.setGatheredViews(av.gatherViewsHere);
 
-
-
     if (ap.av.explodedPosition != null)
     {
       view.setXpos(av.explodedPosition.x);
@@ -697,13 +757,12 @@ public class Jalview2XML
     if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
     {
       view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
-                                           userColours, jms));
+              userColours, jms));
     }
-    else if (av.getGlobalColourScheme() instanceof jalview.schemes.
-             AnnotationColourGradient)
+    else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
     {
-      jalview.schemes.AnnotationColourGradient acg
-          = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme();
+      jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
+              .getGlobalColourScheme();
 
       AnnotationColours ac = new AnnotationColours();
       ac.setAboveThreshold(acg.getAboveThreshold());
@@ -712,11 +771,12 @@ public class Jalview2XML
       if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
       {
         ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
-                                               userColours, jms));
+                userColours, jms));
       }
       else
       {
-        ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
+        ac.setColourScheme(ColourSchemeProperty.getColourName(acg
+                .getBaseColour()));
       }
 
       ac.setMaxColour(acg.getMaxColour().getRGB());
@@ -726,8 +786,8 @@ public class Jalview2XML
     }
     else
     {
-      view.setBgColour(ColourSchemeProperty.getColourName(
-          av.getGlobalColourScheme()));
+      view.setBgColour(ColourSchemeProperty.getColourName(av
+              .getGlobalColourScheme()));
     }
 
     ColourSchemeI cs = av.getGlobalColourScheme();
@@ -769,27 +829,24 @@ public class Jalview2XML
 
     if (av.featuresDisplayed != null)
     {
-      jalview.schemabinding.version2.FeatureSettings fs
-          = new jalview.schemabinding.version2.FeatureSettings();
+      jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
 
-      String[] renderOrder =
-          ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+      String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 
       Vector settingsAdded = new Vector();
       for (int ro = 0; ro < renderOrder.length; ro++)
       {
         Setting setting = new Setting();
         setting.setType(renderOrder[ro]);
-        setting.setColour(
-            ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).
-            getRGB()
-            );
-
-        setting.setDisplay(
-            av.featuresDisplayed.containsKey(renderOrder[ro])
-            );
-        float rorder=ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(renderOrder[ro]);
-        if (rorder>-1) {
+        setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+                .getColour(renderOrder[ro]).getRGB());
+
+        setting.setDisplay(av.featuresDisplayed
+                .containsKey(renderOrder[ro]));
+        float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
+                renderOrder[ro]);
+        if (rorder > -1)
+        {
           setting.setOrder(rorder);
         }
         fs.addSetting(setting);
@@ -797,8 +854,8 @@ public class Jalview2XML
       }
 
       //Make sure we save none displayed feature settings
-      Enumeration en =
-          ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+      Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+              .keys();
       while (en.hasMoreElements())
       {
         String key = en.nextElement().toString();
@@ -809,13 +866,13 @@ public class Jalview2XML
 
         Setting setting = new Setting();
         setting.setType(key);
-        setting.setColour(
-            ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
-            );
+        setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+                .getColour(key).getRGB());
 
         setting.setDisplay(false);
-        float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(key);
-        if (rorder>-1)
+        float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
+                key);
+        if (rorder > -1)
         {
           setting.setOrder(rorder);
         }
@@ -823,7 +880,7 @@ public class Jalview2XML
         settingsAdded.addElement(key);
       }
       en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
-      Vector groupsAdded=new Vector();
+      Vector groupsAdded = new Vector();
       while (en.hasMoreElements())
       {
         String grp = en.nextElement().toString();
@@ -833,7 +890,10 @@ public class Jalview2XML
         }
         Group g = new Group();
         g.setName(grp);
-        g.setDisplay(((Boolean)ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.get(grp)).booleanValue());
+        g
+                .setDisplay(((Boolean) ap.seqPanel.seqCanvas
+                        .getFeatureRenderer().featureGroups.get(grp))
+                        .booleanValue());
         fs.addGroup(g);
         groupsAdded.addElement(grp);
       }
@@ -845,8 +905,8 @@ public class Jalview2XML
     {
       for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
       {
-        int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
-            elementAt(c);
+        int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+                .elementAt(c);
         HiddenColumns hc = new HiddenColumns();
         hc.setStart(region[0]);
         hc.setEnd(region[1]);
@@ -875,8 +935,7 @@ public class Jalview2XML
         jout.putNextEntry(entry);
 
         object.marshal(out);
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -884,27 +943,138 @@ public class Jalview2XML
     return object;
   }
 
+  private Sequence createVamsasSequence(int id, SequenceI jds)
+  {
+    return createVamsasSequence(true, id, jds, null);
+  }
+
+  private Sequence createVamsasSequence(boolean recurse, int id,
+          SequenceI jds, SequenceI parentseq)
+  {
+    Sequence vamsasSeq = new Sequence();
+    vamsasSeq.setId(id + "");
+    vamsasSeq.setName(jds.getName());
+    vamsasSeq.setSequence(jds.getSequenceAsString());
+    vamsasSeq.setDescription(jds.getDescription());
+    jalview.datamodel.DBRefEntry[] dbrefs = null;
+    if (jds.getDatasetSequence() != null)
+    {
+      vamsasSeq.setDsseqid(jds.getDatasetSequence().hashCode() + "");
+      if (jds.getDatasetSequence().getDBRef() != null)
+      {
+        dbrefs = jds.getDatasetSequence().getDBRef();
+      }
+    }
+    else
+    {
+      vamsasSeq.setDsseqid(id + ""); // so we can tell which sequences really are dataset sequences only
+      dbrefs = jds.getDBRef();
+    }
+    if (dbrefs != null)
+    {
+      for (int d = 0; d < dbrefs.length; d++)
+      {
+        DBRef dbref = new DBRef();
+        dbref.setSource(dbrefs[d].getSource());
+        dbref.setVersion(dbrefs[d].getVersion());
+        dbref.setAccessionId(dbrefs[d].getAccessionId());
+        if (dbrefs[d].hasMap())
+        {
+          Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+                  jds, recurse);
+          dbref.setMapping(mp);
+        }
+        vamsasSeq.addDBRef(dbref);
+      }
+    }
+    return vamsasSeq;
+  }
+
+  private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
+          SequenceI parentseq, SequenceI jds, boolean recurse)
+  {
+    Mapping mp = null;
+    if (jmp.getMap() != null)
+    {
+      mp = new Mapping();
+
+      jalview.util.MapList mlst = jmp.getMap();
+      int r[] = mlst.getFromRanges();
+      for (int s = 0; s < r.length; s += 2)
+      {
+        MapListFrom mfrom = new MapListFrom();
+        mfrom.setStart(r[s]);
+        mfrom.setEnd(r[s + 1]);
+        mp.addMapListFrom(mfrom);
+      }
+      r = mlst.getToRanges();
+      for (int s = 0; s < r.length; s += 2)
+      {
+        MapListTo mto = new MapListTo();
+        mto.setStart(r[s]);
+        mto.setEnd(r[s + 1]);
+        mp.addMapListTo(mto);
+      }
+      mp.setMapFromUnit(mlst.getFromRatio());
+      mp.setMapToUnit(mlst.getToRatio());
+      if (jmp.getTo() != null)
+      {
+        MappingChoice mpc = new MappingChoice();
+        if (recurse
+                && (parentseq != jmp.getTo() || parentseq
+                        .getDatasetSequence() != jmp.getTo()))
+        {
+          mpc.setSequence(createVamsasSequence(false, jmp.getTo()
+                  .hashCode(), jmp.getTo(), jds));
+        }
+        else
+        {
+          long jmpid = 0;
+          SequenceI ps = null;
+          if (parentseq != jmp.getTo()
+                  && parentseq.getDatasetSequence() != jmp.getTo())
+          {
+            // chaining dbref rather than a handshaking one
+            jmpid = (ps = jmp.getTo()).hashCode();
+          }
+          else
+          {
+            jmpid = (ps = parentseq).hashCode();
+          }
+          mpc.setDseqFor("" + jmpid);
+          if (!seqRefIds.containsKey(mpc.getDseqFor()))
+          {
+            jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+            seqRefIds.put(mpc.getDseqFor(), ps);
+          }
+          else
+          {
+            jalview.bin.Cache.log.debug("reusing DseqFor ID");
+          }
+        }
+        mp.setMappingChoice(mpc);
+      }
+    }
+    return mp;
+  }
+
   String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
-                             Vector userColours, JalviewModelSequence jms)
+          Vector userColours, JalviewModelSequence jms)
   {
     String id = null;
-    jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
-        cs;
+    jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 
     if (!userColours.contains(ucs))
     {
       userColours.add(ucs);
 
       java.awt.Color[] colours = ucs.getColours();
-      jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.
-          version2.UserColours();
-      jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.
-          schemabinding.version2.UserColourScheme();
+      jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
+      jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 
       for (int i = 0; i < colours.length; i++)
       {
-        jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
-            version2.Colour();
+        jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
         col.setName(ResidueProperties.aa[i]);
         col.setRGB(jalview.util.Format.getHexString(colours[i]));
         jbucs.addColour(col);
@@ -914,8 +1084,7 @@ public class Jalview2XML
         colours = ucs.getLowerCaseColours();
         for (int i = 0; i < colours.length; i++)
         {
-          jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
-              version2.Colour();
+          jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
           col.setName(ResidueProperties.aa[i].toLowerCase());
           col.setRGB(jalview.util.Format.getHexString(colours[i]));
           jbucs.addColour(col);
@@ -932,7 +1101,7 @@ public class Jalview2XML
   }
 
   jalview.schemes.UserColourScheme GetUserColourScheme(
-      JalviewModelSequence jms, String id)
+          JalviewModelSequence jms, String id)
   {
     UserColours[] uc = jms.getUserColours();
     UserColours colours = null;
@@ -951,20 +1120,20 @@ public class Jalview2XML
 
     for (int i = 0; i < 24; i++)
     {
-      newColours[i] = new java.awt.Color(Integer.parseInt(
-          colours.getUserColourScheme().getColour(i).getRGB(), 16));
+      newColours[i] = new java.awt.Color(Integer.parseInt(colours
+              .getUserColourScheme().getColour(i).getRGB(), 16));
     }
 
-    jalview.schemes.UserColourScheme ucs =
-        new jalview.schemes.UserColourScheme(newColours);
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+            newColours);
 
     if (colours.getUserColourScheme().getColourCount() > 24)
     {
       newColours = new java.awt.Color[23];
       for (int i = 0; i < 23; i++)
       {
-        newColours[i] = new java.awt.Color(Integer.parseInt(
-            colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
+        newColours[i] = new java.awt.Color(Integer.parseInt(colours
+                .getUserColourScheme().getColour(i + 24).getRGB(), 16));
       }
       ucs.setLowerCaseColours(newColours);
     }
@@ -985,7 +1154,7 @@ public class Jalview2XML
 
     seqRefIds = new Hashtable();
     viewportsAdded = new Hashtable();
-
+    frefedSequence = new Vector();
     Hashtable gatherToThisFrame = new Hashtable();
 
     String errorMessage = null;
@@ -1041,24 +1210,21 @@ public class Jalview2XML
           //Some other file here.
           entryCount++;
         }
-      }
-      while (jarentry != null);
-    }
-    catch(java.io.FileNotFoundException ex)
+      } while (jarentry != null);
+      resolveFrefedSequences();
+    } catch (java.io.FileNotFoundException ex)
     {
       ex.printStackTrace();
-      errorMessage = "Couldn't locate Jalview XML file : "+file;
-      System.err.println("Exception whilst loading jalview XML file : " +
-                         ex + "\n");
-    }
-    catch (java.net.UnknownHostException ex)
+      errorMessage = "Couldn't locate Jalview XML file : " + file;
+      System.err.println("Exception whilst loading jalview XML file : "
+              + ex + "\n");
+    } catch (java.net.UnknownHostException ex)
     {
       ex.printStackTrace();
-      errorMessage = "Couldn't locate Jalview XML file : " +file;
-      System.err.println("Exception whilst loading jalview XML file : " +
-                         ex + "\n");
-    }
-    catch (Exception ex)
+      errorMessage = "Couldn't locate Jalview XML file : " + file;
+      System.err.println("Exception whilst loading jalview XML file : "
+              + ex + "\n");
+    } catch (Exception ex)
     {
       //Is Version 1 Jar file?
       af = new Jalview2XML_V1().LoadJalviewAlign(file);
@@ -1070,8 +1236,8 @@ public class Jalview2XML
       }
       ex.printStackTrace();
 
-      System.err.println("Exception whilst loading jalview XML file : " +
-                         ex + "\n");
+      System.err.println("Exception whilst loading jalview XML file : "
+              + ex + "\n");
     }
 
     if (Desktop.instance != null)
@@ -1080,13 +1246,12 @@ public class Jalview2XML
     }
 
     Enumeration en = gatherToThisFrame.elements();
-    while(en.hasMoreElements())
+    while (en.hasMoreElements())
     {
-      Desktop.instance.gatherViews(
-          (AlignFrame) en.nextElement());
+      Desktop.instance.gatherViews((AlignFrame) en.nextElement());
     }
 
-    if(errorMessage!=null)
+    if (errorMessage != null)
     {
       final String finalErrorMessage = errorMessage;
       javax.swing.SwingUtilities.invokeLater(new Runnable()
@@ -1094,9 +1259,8 @@ public class Jalview2XML
         public void run()
         {
           JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                                finalErrorMessage,
-                                                "Error loading Jalview file",
-                                                JOptionPane.WARNING_MESSAGE);
+                  finalErrorMessage, "Error loading Jalview file",
+                  JOptionPane.WARNING_MESSAGE);
         }
       });
     }
@@ -1105,6 +1269,7 @@ public class Jalview2XML
   }
 
   Hashtable alreadyLoadedPDB;
+
   String loadPDBFile(String file, String pdbId)
   {
     if (alreadyLoadedPDB == null)
@@ -1130,8 +1295,7 @@ public class Jalview2XML
       do
       {
         entry = jin.getNextJarEntry();
-      }
-      while (!entry.getName().equals(pdbId));
+      } while (!entry.getName().equals(pdbId));
 
       BufferedReader in = new BufferedReader(new InputStreamReader(jin));
       File outFile = File.createTempFile("jalview_pdb", ".txt");
@@ -1139,7 +1303,7 @@ public class Jalview2XML
       PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
       String data;
 
-      while ( (data = in.readLine()) != null)
+      while ((data = in.readLine()) != null)
       {
         out.println(data);
       }
@@ -1148,8 +1312,7 @@ public class Jalview2XML
       alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
       return outFile.getAbsolutePath();
 
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -1157,9 +1320,8 @@ public class Jalview2XML
     return null;
   }
 
-  AlignFrame LoadFromObject(JalviewModel object,
-                            String file,
-                            boolean loadTreesAndStructures)
+  AlignFrame LoadFromObject(JalviewModel object, String file,
+          boolean loadTreesAndStructures)
   {
     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
     Sequence[] vamsasSeq = vamsasSet.getSequence();
@@ -1185,16 +1347,17 @@ public class Jalview2XML
 
       if (seqRefIds.get(seqId) != null)
       {
-        tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+        tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
         multipleView = true;
       }
       else
       {
         jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
-                                              vamsasSeq[i].getSequence());
+                vamsasSeq[i].getSequence());
         jseq.setDescription(vamsasSeq[i].getDescription());
         jseq.setStart(JSEQ[i].getStart());
         jseq.setEnd(JSEQ[i].getEnd());
+        jseq.setVamsasId(uniqueSetSuffix + seqId);
         seqRefIds.put(vamsasSeq[i].getId(), jseq);
         tmpseqs.add(jseq);
       }
@@ -1206,38 +1369,46 @@ public class Jalview2XML
           hiddenSeqs = new Vector();
         }
 
-        hiddenSeqs.addElement(
-            (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+        hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
+                .get(seqId));
       }
 
     }
 
-    ///SequenceFeatures are added to the DatasetSequence,
-    // so we must create the dataset before loading features
+    ///
+    // Create the alignment object from the sequence set
     /////////////////////////////////
-
-
-    jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
-        tmpseqs.size()];
+    jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
+            .size()];
 
     tmpseqs.toArray(orderedSeqs);
 
-    jalview.datamodel.Alignment al =
-        new jalview.datamodel.Alignment(orderedSeqs);
+    jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
+            orderedSeqs);
 
-    for(int i=0; i<vamsasSet.getSequenceSetPropertiesCount(); i++ )
+    /// Add the alignment properties
+    for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
     {
       SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
       al.setProperty(ssp.getKey(), ssp.getValue());
     }
 
-
-    al.setDataset(null);
+    ///
+    // SequenceFeatures are added to the DatasetSequence,
+    // so we must create or recover the dataset before loading features
+    /////////////////////////////////
+    if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
+    {
+      // older jalview projects do not have a dataset id.
+      al.setDataset(null);
+    }
+    else
+    {
+      recoverDatasetFor(vamsasSet, al);
+    }
     /////////////////////////////////
-
 
     Hashtable pdbloaded = new Hashtable();
-
     if (!multipleView)
     {
       for (int i = 0; i < vamsasSeq.length; i++)
@@ -1247,11 +1418,10 @@ public class Jalview2XML
           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(),
-                features[f].getFeatureGroup());
+            jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
+                    features[f].getType(), features[f].getDescription(),
+                    features[f].getStatus(), features[f].getBegin(),
+                    features[f].getEnd(), features[f].getFeatureGroup());
 
             sf.setScore(features[f].getScore());
             for (int od = 0; od < features[f].getOtherDataCount(); od++)
@@ -1271,14 +1441,16 @@ public class Jalview2XML
             al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
           }
         }
-
+        if (vamsasSeq[i].getDBRefCount() > 0)
+        {
+          addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
+        }
         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();
+            jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
             entry.setId(ids[p].getId());
             entry.setType(ids[p].getType());
             if (ids[p].getFile() != null)
@@ -1296,29 +1468,57 @@ public class Jalview2XML
             al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
           }
         }
-        if (vamsasSeq[i].getDBRefCount() > 0)
+      }
+    }
+
+    /////////////////////////////////
+    // LOAD SEQUENCE MAPPINGS
+    if (vamsasSet.getAlcodonFrameCount() > 0)
+    {
+      AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
+      for (int i = 0; i < alc.length; i++)
+      {
+        jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
+                alc[i].getAlcodonCount());
+        if (alc[i].getAlcodonCount() > 0)
         {
-          for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
+          Alcodon[] alcods = alc[i].getAlcodon();
+          for (int p = 0; p < cf.codons.length; p++)
           {
-            jalview.datamodel.DBRefEntry entry =
-                new jalview.datamodel.DBRefEntry(
-                    vamsasSeq[i].getDBRef(d).getSource(),
-                    vamsasSeq[i].getDBRef(d).getVersion(),
-                    vamsasSeq[i].getDBRef(d).getAccessionId()
-                );
-            al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
+            cf.codons[p] = new int[3];
+            cf.codons[p][0] = (int) alcods[p].getPos1();
+            cf.codons[p][1] = (int) alcods[p].getPos2();
+            cf.codons[p][2] = (int) alcods[p].getPos3();
+          }
+        }
+        if (alc[i].getAlcodMapCount() > 0)
+        {
+          AlcodMap[] maps = alc[i].getAlcodMap();
+          for (int m = 0; m < maps.length; m++)
+          {
+            SequenceI dnaseq = (SequenceI) seqRefIds
+                    .get(maps[m].getDnasq());
+            // Load Mapping
+            // attach to dna sequence reference.
+            if (dnaseq != null)
+            {
+              if (maps[m].getMapping() != null)
+              {
+                jalview.datamodel.Mapping mapping = addMapping(maps[m]
+                        .getMapping());
+                cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+              }
+            }
           }
-
         }
+        al.addCodonFrame(cf);
       }
+
     }
 
-    /////////////////////////////////
     //////////////////////////////////
     //LOAD ANNOTATIONS
-    boolean hideQuality = true,
-        hideConservation = true,
-        hideConsensus = true;
+    boolean hideQuality = true, hideConservation = true, hideConsensus = true;
 
     if (vamsasSet.getAnnotationCount() > 0)
     {
@@ -1343,11 +1543,10 @@ public class Jalview2XML
         }
 
         if (an[i].getId() != null
-            && annotationIds.containsKey(an[i].getId()))
+                && annotationIds.containsKey(an[i].getId()))
         {
-          jalview.datamodel.AlignmentAnnotation jda =
-              (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
-              getId());
+          jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
+                  .get(an[i].getId());
           if (an[i].hasVisible())
             jda.visible = an[i].getVisible();
 
@@ -1361,27 +1560,24 @@ public class Jalview2XML
 
         if (!an[i].getScoreOnly())
         {
-          anot = new jalview.datamodel.Annotation[
-                    al.getWidth()];
+          anot = new jalview.datamodel.Annotation[al.getWidth()];
 
           for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
           {
-            if(ae[aa].getPosition()>=anot.length)
+            if (ae[aa].getPosition() >= anot.length)
               continue;
 
             anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 
-                    ae[aa].getDisplayCharacter(),
-                    ae[aa].getDescription(),
-                    (ae[aa].getSecondaryStructure()==null || ae[aa].getSecondaryStructure().length() == 0) ? ' ' :
-                      ae[aa].getSecondaryStructure().charAt(0),
-                      ae[aa].getValue()
-
-                            );
+            ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
+                    .getSecondaryStructure() == null || ae[aa]
+                    .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
+                    .getSecondaryStructure().charAt(0), ae[aa].getValue()
 
+            );
 
-              anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
-                  getColour());
+            anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
+                    .getColour());
           }
         }
         jalview.datamodel.AlignmentAnnotation jaa = null;
@@ -1389,18 +1585,16 @@ public class Jalview2XML
         if (an[i].getGraph())
         {
           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-              an[i].getDescription(), anot, 0, 0,
-              an[i].getGraphType());
+                  an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
 
           jaa.graphGroup = an[i].getGraphGroup();
 
           if (an[i].getThresholdLine() != null)
           {
-            jaa.setThreshold(new jalview.datamodel.GraphLine(
-                an[i].getThresholdLine().getValue(),
-                an[i].getThresholdLine().getLabel(),
-                new java.awt.Color(an[i].getThresholdLine().getColour()))
-                );
+            jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
+                    .getThresholdLine().getValue(), an[i]
+                    .getThresholdLine().getLabel(), new java.awt.Color(
+                    an[i].getThresholdLine().getColour())));
 
           }
 
@@ -1408,7 +1602,7 @@ public class Jalview2XML
         else
         {
           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-              an[i].getDescription(), anot);
+                  an[i].getDescription(), anot);
         }
 
         if (an[i].getId() != null)
@@ -1421,9 +1615,8 @@ public class Jalview2XML
         {
           if (al.findName(an[i].getSequenceRef()) != null)
           {
-            jaa.createSequenceMapping(
-                al.findName(an[i].getSequenceRef()), 1, true
-                );
+            jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
+                    1, true);
             al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
           }
         }
@@ -1432,8 +1625,8 @@ public class Jalview2XML
           jaa.setScore(an[i].getScore());
         }
 
-        if(an[i].hasVisible())
-          jaa.visible =  an[i].getVisible();
+        if (an[i].hasVisible())
+          jaa.visible = an[i].getVisible();
 
         al.addAnnotation(jaa);
       }
@@ -1457,8 +1650,7 @@ public class Jalview2XML
           }
           else
           {
-            cs = ColourSchemeProperty.getColour(al,
-                                                groups[i].getColour());
+            cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
           }
 
           if (cs != null)
@@ -1472,8 +1664,8 @@ public class Jalview2XML
         for (int s = 0; s < groups[i].getSeqCount(); s++)
         {
           String seqId = groups[i].getSeq(s) + "";
-          jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
-              seqRefIds.get(seqId);
+          jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
+                  .get(seqId);
 
           if (ts != null)
           {
@@ -1486,14 +1678,14 @@ public class Jalview2XML
           continue;
         }
 
-        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());
+        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()));
+        sg
+                .setOutlineColour(new java.awt.Color(groups[i]
+                        .getOutlineColour()));
 
         sg.textColour = new java.awt.Color(groups[i].getTextCol1());
         sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
@@ -1502,9 +1694,8 @@ public class Jalview2XML
         if (groups[i].getConsThreshold() != 0)
         {
           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
-              "All",
-              ResidueProperties.propHash, 3, sg.getSequences(null), 0,
-              sg.getWidth() - 1);
+                  "All", ResidueProperties.propHash, 3, sg
+                          .getSequences(null), 0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);
@@ -1517,18 +1708,14 @@ public class Jalview2XML
     /////////////////////////////////
     // LOAD VIEWPORT
 
-    AlignFrame af = new AlignFrame(al,
-                                   view.getWidth(),
-                                   view.getHeight());
+    AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 
     af.setFileName(file, "Jalview");
 
     for (int i = 0; i < JSEQ.length; i++)
     {
-      af.viewport.setSequenceColour(
-          af.viewport.alignment.getSequenceAt(i),
-          new java.awt.Color(
-              JSEQ[i].getColour()));
+      af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
+              new java.awt.Color(JSEQ[i].getColour()));
     }
 
     //If we just load in the same jar file again, the sequenceSetId
@@ -1541,9 +1728,8 @@ public class Jalview2XML
 
     if (view.getSequenceSetId() != null)
     {
-      jalview.gui.AlignViewport av =
-          (jalview.gui.AlignViewport)
-          viewportsAdded.get(uniqueSeqSetId);
+      jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
+              .get(uniqueSeqSetId);
 
       af.viewport.sequenceSetID = uniqueSeqSetId;
       if (av != null)
@@ -1563,21 +1749,18 @@ public class Jalview2XML
     {
       for (int s = 0; s < JSEQ.length; s++)
       {
-        jalview.datamodel.SequenceGroup hidden =
-            new jalview.datamodel.SequenceGroup();
+        jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
 
         for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
         {
-          hidden.addSequence(
-              al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
-              , false
-              );
+          hidden.addSequence(al
+                  .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
         }
         af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
       }
 
-      jalview.datamodel.SequenceI[] hseqs = new
-          jalview.datamodel.SequenceI[hiddenSeqs.size()];
+      jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs
+              .size()];
 
       for (int s = 0; s < hiddenSeqs.size(); s++)
       {
@@ -1588,21 +1771,18 @@ public class Jalview2XML
 
     }
 
-    if ( (hideConsensus || hideQuality || hideConservation)
-        && al.getAlignmentAnnotation() != null)
+    if ((hideConsensus || hideQuality || hideConservation)
+            && al.getAlignmentAnnotation() != null)
     {
       int hSize = al.getAlignmentAnnotation().length;
       for (int h = 0; h < hSize; h++)
       {
-        if (
-            (hideConsensus &&
-             al.getAlignmentAnnotation()[h].label.equals("Consensus"))
-            ||
-            (hideQuality &&
-             al.getAlignmentAnnotation()[h].label.equals("Quality"))
-            ||
-            (hideConservation &&
-             al.getAlignmentAnnotation()[h].label.equals("Conservation")))
+        if ((hideConsensus && al.getAlignmentAnnotation()[h].label
+                .equals("Consensus"))
+                || (hideQuality && al.getAlignmentAnnotation()[h].label
+                        .equals("Quality"))
+                || (hideConservation && al.getAlignmentAnnotation()[h].label
+                        .equals("Conservation")))
         {
           al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
           hSize--;
@@ -1617,8 +1797,8 @@ public class Jalview2XML
       af.viewport.viewName = view.getViewName();
       af.setInitialTabVisible();
     }
-    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
-                 view.getHeight());
+    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
+            .getHeight());
 
     af.viewport.setShowAnnotation(view.getShowAnnotation());
     af.viewport.setAbovePIDThreshold(view.getPidSelected());
@@ -1628,8 +1808,8 @@ public class Jalview2XML
     af.viewport.setConservationSelected(view.getConservationSelected());
     af.viewport.setShowJVSuffix(view.getShowFullId());
     af.viewport.rightAlignIds = view.getRightAlignIds();
-    af.viewport.setFont(new java.awt.Font(view.getFontName(),
-                                          view.getFontStyle(), view.getFontSize()));
+    af.viewport.setFont(new java.awt.Font(view.getFontName(), view
+            .getFontStyle(), view.getFontSize()));
     af.alignPanel.fontChanged();
     af.viewport.setRenderGaps(view.getRenderGaps());
     af.viewport.setWrapAlignment(view.getWrapAlignment());
@@ -1659,54 +1839,47 @@ public class Jalview2XML
       else if (view.getBgColour().startsWith("Annotation"))
       {
         //int find annotation
-        for (int i = 0;
-             i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+        for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
         {
-          if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
-              equals(view.getAnnotationColours().getAnnotation()))
+          if (af.viewport.alignment.getAlignmentAnnotation()[i].label
+                  .equals(view.getAnnotationColours().getAnnotation()))
           {
-            if (af.viewport.alignment.getAlignmentAnnotation()[i].
-                getThreshold() == null)
+            if (af.viewport.alignment.getAlignmentAnnotation()[i]
+                    .getThreshold() == null)
             {
-              af.viewport.alignment.getAlignmentAnnotation()[i].
-                  setThreshold(
-                      new jalview.datamodel.GraphLine(
-                          view.getAnnotationColours().getThreshold(),
-                          "Threshold", java.awt.Color.black)
+              af.viewport.alignment.getAlignmentAnnotation()[i]
+                      .setThreshold(new jalview.datamodel.GraphLine(view
+                              .getAnnotationColours().getThreshold(),
+                              "Threshold", java.awt.Color.black)
 
-                  );
+                      );
             }
 
-            if (view.getAnnotationColours().getColourScheme().equals(
-                "None"))
+            if (view.getAnnotationColours().getColourScheme()
+                    .equals("None"))
             {
-              cs = new AnnotationColourGradient(
-                  af.viewport.alignment.getAlignmentAnnotation()[i],
-                  new java.awt.Color(view.getAnnotationColours().
-                                     getMinColour()),
-                  new java.awt.Color(view.getAnnotationColours().
-                                     getMaxColour()),
-                  view.getAnnotationColours().getAboveThreshold());
+              cs = new AnnotationColourGradient(af.viewport.alignment
+                      .getAlignmentAnnotation()[i], new java.awt.Color(view
+                      .getAnnotationColours().getMinColour()),
+                      new java.awt.Color(view.getAnnotationColours()
+                              .getMaxColour()), view.getAnnotationColours()
+                              .getAboveThreshold());
             }
-            else if (view.getAnnotationColours().getColourScheme().
-                     startsWith("ucs"))
+            else if (view.getAnnotationColours().getColourScheme()
+                    .startsWith("ucs"))
             {
-              cs = new AnnotationColourGradient(
-                  af.viewport.alignment.getAlignmentAnnotation()[i],
-                  GetUserColourScheme(jms, view.getAnnotationColours().
-                                      getColourScheme()),
-                  view.getAnnotationColours().getAboveThreshold()
-                  );
+              cs = new AnnotationColourGradient(af.viewport.alignment
+                      .getAlignmentAnnotation()[i], GetUserColourScheme(
+                      jms, view.getAnnotationColours().getColourScheme()),
+                      view.getAnnotationColours().getAboveThreshold());
             }
             else
             {
-              cs = new AnnotationColourGradient(
-                  af.viewport.alignment.getAlignmentAnnotation()[i],
-                  ColourSchemeProperty.getColour(al,
-                                                 view.getAnnotationColours().
-                                                 getColourScheme()),
-                  view.getAnnotationColours().getAboveThreshold()
-                  );
+              cs = new AnnotationColourGradient(af.viewport.alignment
+                      .getAlignmentAnnotation()[i], ColourSchemeProperty
+                      .getColour(al, view.getAnnotationColours()
+                              .getColourScheme()), view
+                      .getAnnotationColours().getAboveThreshold());
             }
 
             // Also use these settings for all the groups
@@ -1714,9 +1887,8 @@ public class Jalview2XML
             {
               for (int g = 0; g < al.getGroups().size(); g++)
               {
-                jalview.datamodel.SequenceGroup sg
-                    = (jalview.datamodel.SequenceGroup) al.getGroups().
-                    elementAt(g);
+                jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
+                        .getGroups().elementAt(g);
 
                 if (sg.cs == null)
                 {
@@ -1736,10 +1908,9 @@ public class Jalview2XML
                     else*/
                 {
                   sg.cs = new AnnotationColourGradient(
-                      af.viewport.alignment.getAlignmentAnnotation()[i],
-                      sg.cs,
-                      view.getAnnotationColours().getAboveThreshold()
-                      );
+                          af.viewport.alignment.getAlignmentAnnotation()[i],
+                          sg.cs, view.getAnnotationColours()
+                                  .getAboveThreshold());
                 }
 
               }
@@ -1782,31 +1953,32 @@ public class Jalview2XML
     if (jms.getFeatureSettings() != null)
     {
       af.viewport.featuresDisplayed = new Hashtable();
-      String[] renderOrder = new String[jms.getFeatureSettings().
-          getSettingCount()];
+      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()));
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+                setting.getType(), new java.awt.Color(setting.getColour()));
         renderOrder[fs] = setting.getType();
         if (setting.hasOrder())
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), setting.getOrder());
+          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+                  setting.getType(), setting.getOrder());
         else
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), fs/jms.getFeatureSettings().getSettingCount());
+          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+                  setting.getType(),
+                  fs / jms.getFeatureSettings().getSettingCount());
         if (setting.getDisplay())
         {
-          af.viewport.featuresDisplayed.put(
-              setting.getType(), new Integer(setting.getColour()));
+          af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+                  setting.getColour()));
         }
       }
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
-          renderOrder;
+      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
       Hashtable fgtable;
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable=new Hashtable();
-      for (int gs=0;gs<jms.getFeatureSettings().getGroupCount(); gs++)
+      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+      for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
       {
         Group grp = jms.getFeatureSettings().getGroup(gs);
         fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
@@ -1817,17 +1989,16 @@ public class Jalview2XML
     {
       for (int c = 0; c < view.getHiddenColumnsCount(); c++)
       {
-        af.viewport.hideColumns(
-            view.getHiddenColumns(c).getStart(),
-            view.getHiddenColumns(c).getEnd() //+1
-            );
+        af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
+                .getHiddenColumns(c).getEnd() //+1
+                );
       }
     }
 
     af.setMenusFromViewport(af.viewport);
 
-    Desktop.addInternalFrame(af, view.getTitle(),
-                             view.getWidth(), view.getHeight());
+    Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
+            .getHeight());
 
     //LOAD TREES
     ///////////////////////////////////////
@@ -1840,25 +2011,22 @@ public class Jalview2XML
 
           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());
+          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()));
+            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.setTreeFont(new java.awt.Font(view.getFontName(), view
+                    .getFontStyle(), tree.getFontSize()));
           }
 
           tp.showPlaceholders(tree.getMarkUnlinked());
@@ -1873,15 +2041,14 @@ public class Jalview2XML
           }
         }
 
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
     }
 
     ////LOAD STRUCTURES
-    if(loadTreesAndStructures)
+    if (loadTreesAndStructures)
     {
       for (int i = 0; i < JSEQ.length; i++)
       {
@@ -1904,14 +2071,14 @@ public class Jalview2XML
 
               java.awt.Component comp = null;
 
-              JInternalFrame [] frames = Desktop.desktop.getAllFrames();
-              for(int f=0; f<frames.length; f++)
+              JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+              for (int f = 0; f < frames.length; f++)
               {
-                if(frames[f] instanceof AppJmol)
+                if (frames[f] instanceof AppJmol)
                 {
                   if (frames[f].getX() == x && frames[f].getY() == y
-                      && frames[f].getHeight() == height
-                      && frames[f].getWidth() == width)
+                          && frames[f].getHeight() == height
+                          && frames[f].getWidth() == width)
                   {
                     comp = frames[f];
                     break;
@@ -1919,44 +2086,37 @@ public class Jalview2XML
                 }
               }
 
-
               Desktop.desktop.getComponentAt(x, y);
 
               String pdbFile = loadPDBFile(file, ids[p].getId());
 
-              jalview.datamodel.SequenceI[] seq = new jalview.datamodel.
-                  SequenceI[]
-                  {
-                   (jalview.datamodel.SequenceI)
-                  seqRefIds.get(JSEQ[i].getId()+"")};
-
+              jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
+              { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
+                      + "") };
 
               if (comp == null)
               {
                 String state = ids[p].getStructureState(s).getContent();
 
-                StringBuffer newFileLoc = new StringBuffer(state.substring(0,
-                    state.indexOf("\"", state.indexOf("load")) + 1));
+                StringBuffer newFileLoc = new StringBuffer(state.substring(
+                        0, state.indexOf("\"", state.indexOf("load")) + 1));
 
                 newFileLoc.append(jpdb.getFile());
-                newFileLoc.append(state.substring(
-                    state.indexOf("\"", state.indexOf("load \"") + 6)));
+                newFileLoc.append(state.substring(state.indexOf("\"", state
+                        .indexOf("load \"") + 6)));
 
-                new AppJmol(pdbFile,
-                            ids[p].getId(),
-                            seq,
-                            af.alignPanel,
-                            newFileLoc.toString(),
-                            new java.awt.Rectangle(x, y, width, height));
+                new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
+                        newFileLoc.toString(), new java.awt.Rectangle(x, y,
+                                width, height));
 
               }
-              else if(comp!=null)
+              else if (comp != null)
               {
                 StructureSelectionManager.getStructureSelectionManager()
-                    .setMapping(seq, null, pdbFile,
+                        .setMapping(seq, null, pdbFile,
                                 jalview.io.AppletFormatAdapter.FILE);
 
-                ( (AppJmol) comp).addSequence(seq);
+                ((AppJmol) comp).addSequence(seq);
               }
             }
           }
@@ -1967,11 +2127,255 @@ public class Jalview2XML
     return af;
   }
 
+  private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
+  {
+    jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
+    Vector dseqs = null;
+    if (ds == null)
+    {
+      // create a list of new dataset sequences
+      dseqs = new Vector();
+    }
+    for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
+    {
+      Sequence vamsasSeq = vamsasSet.getSequence(i);
+      ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
+    }
+    // create a new dataset
+    if (ds == null)
+    {
+      SequenceI[] dsseqs = new SequenceI[dseqs.size()];
+      dseqs.copyInto(dsseqs);
+      ds = new jalview.datamodel.Alignment(dsseqs);
+      addDatasetRef(vamsasSet.getDatasetId(), ds);
+    }
+    // set the dataset for the newly imported alignment.
+    if (al.getDataset() == null)
+    {
+      al.setDataset(ds);
+    }
+  }
+  
+
+  /**
+   * 
+   * @param vamsasSeq sequence definition to create/merge dataset sequence for
+   * @param ds dataset alignment 
+   * @param dseqs vector to add new dataset sequence to
+   */
+  private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs)
+  {
+    jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId());
+    jalview.datamodel.SequenceI dsq = null;
+    if (sq!=null && sq.getDatasetSequence()!=null)
+    {
+      dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
+    }
+    
+    String sqid = vamsasSeq.getDsseqid();
+    if (dsq==null)
+    {
+      // need to create or add a new dataset sequence reference to this sequence
+      if (sqid != null)
+      {
+        dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
+      }
+      // check again
+      if (dsq == null)
+      {
+        // make a new dataset sequence
+        dsq = sq.createDatasetSequence();
+        if (sqid == null)
+        {
+          // make up a new dataset reference for this sequence
+          sqid = "" + dsq.hashCode();
+        }
+        dsq.setVamsasId(uniqueSetSuffix + sqid);
+        seqRefIds.put(sqid, dsq);
+        if (ds == null)
+        {
+          if (dseqs!=null)
+          {
+            dseqs.addElement(dsq);
+          }
+        }
+        else
+        {
+          ds.addSequence(dsq);
+        }
+      } else {
+        if (sq!=dsq)
+        {  // make this dataset sequence sq's dataset sequence
+          sq.setDatasetSequence(dsq);
+        }
+      }
+    }
+    // TODO: refactor this as a merge dataset sequence function
+    // now check that sq (the dataset sequence) sequence really is the union of all references to it
+    //boolean pre = sq.getStart() < dsq.getStart();
+    //boolean post = sq.getEnd() > dsq.getEnd();
+    //if (pre || post)
+    if (sq!=dsq)
+    {
+      StringBuffer sb = new StringBuffer();
+      String newres = jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, sq.getSequenceAsString());
+      if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length()>dsq.getLength())
+      {
+        // Update with the longer sequence.
+        synchronized (dsq)
+        {
+        /*if (pre)
+        {
+          sb.insert(0, newres
+                  .substring(0, dsq.getStart() - sq.getStart()));
+          dsq.setStart(sq.getStart());
+        }
+        if (post)
+        {
+          sb.append(newres.substring(newres.length() - sq.getEnd()
+                  - dsq.getEnd()));
+          dsq.setEnd(sq.getEnd());
+        }
+        */
+        dsq.setSequence(sb.toString());
+        }
+        //TODO: merges will never happen if we 'know' we have the real dataset sequence - this should be detected when id==dssid
+        System.err
+              .println("DEBUG Notice:  Merged dataset sequence"); // ("
+                      // + (pre ? "prepended" : "") + " "
+                      //+ (post ? "appended" : ""));
+      }
+    }
+  }
+
+  java.util.Hashtable datasetIds = null;
+
+  private Alignment getDatasetFor(String datasetId)
+  {
+    if (datasetIds == null)
+    {
+      datasetIds = new Hashtable();
+      return null;
+    }
+    if (datasetIds.containsKey(datasetId))
+    {
+      return (Alignment) datasetIds.get(datasetId);
+    }
+    return null;
+  }
+
+  private void addDatasetRef(String datasetId, Alignment dataset)
+  {
+    if (datasetIds == null)
+    {
+      datasetIds = new Hashtable();
+    }
+    datasetIds.put(datasetId, dataset);
+  }
+
+  private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
+  {
+    for (int d = 0; d < sequence.getDBRefCount(); d++)
+    {
+      DBRef dr = sequence.getDBRef(d);
+      jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
+              sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
+                      .getVersion(), sequence.getDBRef(d).getAccessionId());
+      if (dr.getMapping() != null)
+      {
+        entry.setMap(addMapping(dr.getMapping()));
+      }
+      datasetSequence.addDBRef(entry);
+    }
+  }
+
+  private jalview.datamodel.Mapping addMapping(Mapping m)
+  {
+    SequenceI dsto = null;
+    // Mapping m = dr.getMapping();
+    int fr[] = new int[m.getMapListFromCount() * 2];
+    Enumeration f = m.enumerateMapListFrom();
+    for (int _i = 0; f.hasMoreElements(); _i += 2)
+    {
+      MapListFrom mf = (MapListFrom) f.nextElement();
+      fr[_i] = mf.getStart();
+      fr[_i + 1] = mf.getEnd();
+    }
+    int fto[] = new int[m.getMapListToCount() * 2];
+    f = m.enumerateMapListTo();
+    for (int _i = 0; f.hasMoreElements(); _i += 2)
+    {
+      MapListTo mf = (MapListTo) f.nextElement();
+      fto[_i] = mf.getStart();
+      fto[_i + 1] = mf.getEnd();
+    }
+    jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
+            fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
+    if (m.getMappingChoice() != null)
+    {
+      MappingChoice mc = m.getMappingChoice();
+      if (mc.getDseqFor() != null)
+      {
+        if (seqRefIds.containsKey(mc.getDseqFor()))
+        {
+          /**
+           * recover from hash
+           */
+          jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor()));
+        }
+        else
+        {
+          frefedSequence.add(new Object[]
+          { mc.getDseqFor(), jmap });
+        }
+      }
+      else
+      {
+        /**
+         * local sequence definition
+         */
+        Sequence ms = mc.getSequence();
+        jalview.datamodel.Sequence djs=null;
+        String sqid = ms.getDsseqid();
+        if (sqid!=null && sqid.length()>0)
+        {
+          /*
+           * recover dataset sequence
+           */
+          djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
+        } else {
+          System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference");
+          sqid = ""+ms.hashCode(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen)
+        }
+        
+        if (djs==null) {
+          /**
+           * make a new dataset sequence and add it to refIds hash
+           */
+          djs = new jalview.datamodel.Sequence(ms
+                .getName(), ms.getSequence());
+          djs.setStart(jmap.getMap().getToLowest());
+          djs.setEnd(jmap.getMap().getToHighest());
+          djs.setVamsasId(uniqueSetSuffix + sqid);
+          jmap.setTo(djs);
+          seqRefIds.put(sqid, djs);
+          
+        }
+        jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+        addDBRefs(djs, ms);
+        
+      }
+    }
+    return (jmap);
+
+  }
+
   public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
-      boolean keepSeqRefs)
+          boolean keepSeqRefs)
   {
-    jalview.schemabinding.version2.JalviewModel jm
-        = SaveState(ap, null, null, null);
+    jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
+            null, null);
 
     if (!keepSeqRefs)
     {