From: jprocter <Jim Procter>
Date: Mon, 27 Mar 2006 17:42:19 +0000 (+0000)
Subject: part finished (still finishing the updateJalview method of VamsasDatastore)
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=072fc418c393cbd2a40dfa1d3e46f90178b79572;p=jalview.git

part finished (still finishing the updateJalview method of VamsasDatastore)
---

diff --git a/src/jalview/gui/VamsasClient.java b/src/jalview/gui/VamsasClient.java
index 8d635a3..76e9599 100755
--- a/src/jalview/gui/VamsasClient.java
+++ b/src/jalview/gui/VamsasClient.java
@@ -8,6 +8,7 @@ import java.io.FileOutputStream;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.Hashtable;
+import java.util.IdentityHashMap;
 import java.util.Vector;
 import java.util.jar.JarOutputStream;
 
@@ -42,9 +43,33 @@ public class VamsasClient extends ArchiveClient {
 		Cache.log.info("Jalview loading the Vamsas Session.");
 		// load in the vamsas archive for the first time
 		ClientDoc cdoc = this.getUpdateable();
+		updateJalview(cdoc);
+		
+	}
+	/**
+	 * this will close all windows currently in Jalview.
+	 *
+	 */
+	protected void closeWindows() {
+		JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+        if (frames == null)
+        {
+            return;
+        }
+
+        try
+        {	
+            for (int i = frames.length - 1; i > -1; i--) {
+            	frames[i].dispose();	
+            }
+        } catch (Exception e) {
+        	Cache.log.error("Whilst closing windows",e);
+        }
 		
 	}
 	public void get_update(VamsasArchive doc) {
+		// Close windows - load update.
 		Cache.log.info("Jalview updating from Vamsas Session.");
 	}
 	public void push_update() {
@@ -56,10 +81,22 @@ public class VamsasClient extends ArchiveClient {
 		// stop any update/watcher thread.
 		Cache.log.info("Jalview disconnecting from the Vamsas Session.");
 	}
-	java.util.Hashtable jv2vobj = null;
+	public void updateJalview(ClientDoc cdoc) {
+		
+	}
+	protected void _updateAlignFrame(ClientDoc cdoc, AlignFrame av) {
+		
+	}
+	/**
+	 * jalview object binding to VorbaIds
+	 */
+	IdentityHashMap jv2vobj = null;
+	Hashtable vobj2jv = null;
 	public void updateVamsasDocument(ClientDoc doc) {
-		if (jv2vobj==null)
-			jv2vobj = new Hashtable();
+		if (jv2vobj==null) {
+			jv2vobj = new IdentityHashMap();
+			vobj2jv = new Hashtable();
+		}
 		// wander through frames 
 		JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
@@ -83,7 +120,9 @@ public class VamsasClient extends ArchiveClient {
                 if (frames[i] instanceof AlignFrame)
                 {
                 	AlignFrame af = (AlignFrame) frames[i];
+                	
                 	// check if this frame has an associated alignment object ?
+                	
                 	// update alignment and root from frame.
 
                 }
diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java
index 6b793c6..3915446 100755
--- a/src/jalview/io/VamsasDatastore.java
+++ b/src/jalview/io/VamsasDatastore.java
@@ -19,10 +19,20 @@
 
 package jalview.io;
 
+import org.vamsas.client.Vobject;
+import org.vamsas.client.VorbaId;
 import org.vamsas.objects.core.*;
+import org.vamsas.objects.utils.DocumentStuff;
+import org.vamsas.test.simpleclient.ClientDoc;
 
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceI;
 import jalview.gui.*;
 import java.io.*;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
 import java.util.jar.*;
 import org.exolab.castor.xml.*;
 import org.exolab.castor.mapping.Mapping;
@@ -34,25 +44,26 @@ import org.exolab.castor.mapping.Mapping;
  "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer");
  }
 
-*/
+ */
 
 public class VamsasDatastore
 {
+	Entry provEntry=null;
 	AlignViewport av;
-        org.exolab.castor.types.Date date
-              = new org.exolab.castor.types.Date(new java.util.Date());
-
-	public VamsasDatastore(AlignViewport av)
-	{
-		this.av = av;
+	org.exolab.castor.types.Date date
+	= new org.exolab.castor.types.Date(new java.util.Date());
+	ClientDoc cdoc;
+	Hashtable vobj2jv;
+	IdentityHashMap jv2vobj;
+	public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv, IdentityHashMap jv2vobj, Entry provEntry) {
+		
+		this.cdoc = cdoc;
+		this.vobj2jv = vobj2jv;
+		this.jv2vobj = jv2vobj;
+		this.provEntry = provEntry;
 	}
-
-        public void store(String file)
-        {
-          storeVAMSAS(file);
-        }
-
-        public void storeJalview(String file, AlignFrame af)
+	
+	/* public void storeJalview(String file, AlignFrame af)
         {
           try
           {
@@ -80,499 +91,569 @@ public class VamsasDatastore
         }
 
 
-
-        public VAMSAS storeVAMSAS(String file)
-        {
-          long time = System.currentTimeMillis();
-          VAMSAS vamsas = new VAMSAS();
-
-          try
-          {
-            FileOutputStream fos = new FileOutputStream(file);
-            JarOutputStream jout = new JarOutputStream(fos);
-
-
-            ////////////////////////////////////////////////////
-            //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-            PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
-                "UTF-8"));
-
-            jalview.datamodel.AlignmentI jal = av.getAlignment();
-
-
-            ///////////////////////////////////////////
-            // SAVE THE DATASET
-            DataSet dataset = new DataSet();
-            vamsas.addDataSet(dataset);
-
-            Sequence sequence;
-            DbRef dbref;
-            for (int i = 0; i < jal.getHeight(); i++)
-            {
-              sequence = new Sequence();
-              sequence.setSequence(jal.getDataset().getSequenceAt(i).getSequence());
-              sequence.setName(jal.getDataset().getSequenceAt(i).getName());
-              sequence.setStart(jal.getDataset().getSequenceAt(i).getStart());
-              sequence.setEnd(jal.getDataset().getSequenceAt(i).getEnd());
-
-
-              if(jal.getDataset().getSequenceAt(i).getSequenceFeatures()!=null)
-              {
-                int sfSize = jal.getDataset().getSequenceAt(i).getSequenceFeatures().length;
-
-                for (int sf = 0; sf < sfSize; sf++)
-                {
-                  jalview.datamodel.SequenceFeature feature =
-                      (jalview.datamodel.SequenceFeature)
-                      jal.getDataset().getSequenceAt(i).getSequenceFeatures()[sf];
-
-                  DataSetAnnotations dsa = new DataSetAnnotations();
-                  dsa.setType(feature.getType());
-                  dsa.setBegin(feature.getBegin());
-                  dsa.setEnd(feature.getEnd());
-                  dsa.setDescription(feature.getDescription());
-                  dsa.setStatus(feature.getStatus());
-                  dsa.addProvenance(dummyProvenance());
-                  dsa.setSeqRef(sequence);
-                  dsa.setId("sf"+(time++));
-                  dataset.addDataSetAnnotations(dsa);
-                }
-              }
-
-              if(jal.getDataset().getSequenceAt(i).getDBRef()!=null)
-              {
-                java.util.Vector entries = jal.getDataset().getSequenceAt(i).getDBRef();
-                jalview.datamodel.DBRefEntry dbentry;
-                for(int db=0; db<entries.size(); db++)
-                {
-                  dbentry = (jalview.datamodel.DBRefEntry)entries.elementAt(db);
-                  dbref = new DbRef();
-                  dbref.setAccessionId( dbentry.getAccessionId() );
-                  dbref.setSource( dbentry.getSource() );
-                  dbref.setVersion( dbentry.getVersion() );
-                  dbref.setId("db"+(time++));
-                  sequence.addDbRef(dbref);
-                }
-
-              }
-
-
-              if(jal.getDataset().getSequenceAt(i).getVamsasId()==null)
-                sequence.setId("ds" + (time++));
-              else
-                sequence.setId(jal.getDataset().getSequenceAt(i).getVamsasId());
-
-              dataset.addSequence(sequence);
-            }
-            // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));
-            //////////////////////////////////////////////
-
-
-            //////////////////////////////////////////////
-            //Save the Alignments
-            Alignment alignment = new Alignment();
-            alignment.setGapChar(av.getGapCharacter() + "");
-            AlignmentSequence alseq = null;
-            for (int i = 0; i < jal.getHeight(); i++)
-            {
-              alseq = new AlignmentSequence();
-              alseq.setSequence(
-                  jal.getSequenceAt(i).getSequence()
-                  );
-              alseq.setName(jal.getSequenceAt(i).getName());
-              alseq.setStart(jal.getSequenceAt(i).getStart());
-              alseq.setEnd(jal.getSequenceAt(i).getEnd());
-              alseq.setRefid(dataset.getSequence(i));
-              alseq.setId("as" + (time++));
-              alignment.addAlignmentSequence(alseq);
-            }
-            // alignment.setProvenance(getVamsasProvenance(jal.getProvenance()));
-            dataset.addAlignment(alignment);
-            //////////////////////////////////////////////
-
-
-
-            //////////////////////////////////////////////
-            //SAVE ANNOTATIONS
-            if (jal.getAlignmentAnnotation() != null)
-            {
-                jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
-
-                for (int i = 0; i < aa.length; i++)
-                {
-                    if (aa[i].label.equals("Quality") ||
-                            aa[i].label.equals("Conservation") ||
-                            aa[i].label.equals("Consensus"))
-                    {
-                        continue;
-                    }
-
-                    AlignmentAnnotations an = new AlignmentAnnotations();
-
-                    an.setDescription(aa[i].description);
-                    // JBPNote - have to deal with the many lines for one graph thing
-                    if (aa[i].graph>0)
-                    	an.setGraph(true); //aa[i].graph);
-                    // JBPNote - store graphGroup in the Jalview specific bits.
-                    an.setLabel(aa[i].label);
-                    an.setProvenance(dummyProvenance());
-
-                    AnnotationElement ae;
-
-                    for (int a = 0; a < aa[i].annotations.length; a++)
-                    {
-                        if ((aa[i] == null) || (aa[i].annotations[a] == null))
-                        {
-                            continue;
-                        }
-
-                        ae = new AnnotationElement();
-                        ae.setDescription(aa[i].annotations[a].description);
-                        ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
-                        ae.setValue(aa[i].annotations[a].value);
-                        ae.setPosition(a);
-                        ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
-                            "");
-                        an.addAnnotationElement(ae);
-                    }
-
-                    alignment.addAlignmentAnnotations(an);
-                }
-            }
-            ///////////////////////////////////////////////////////
-
-
-          ////////////////////////////////////////////////
-          ///SAVE THE TREES
-          ///////////////////////////////////
-          // FIND ANY ASSOCIATED TREES
-          if (Desktop.desktop != null)
-          {
-            javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
-            for (int t = 0; t < frames.length; t++)
-            {
-              if (frames[t] instanceof TreePanel)
-              {
-                TreePanel tp = (TreePanel) frames[t];
-
-                if (tp.getAlignment() == jal)
-                {
-                  Tree tree = new Tree();
-                  tree.setTitle(tp.getTitle());
-                  Newick newick = new Newick();
-                  newick.setContent( tp.getTree().toString() );
-                  newick.setTitle( tp.getTitle() );
-                  newick.setId("t"+(time++));
-                  tree.addNewick( newick );
-                  tree.setProvenance(dummyProvenance());
-                  alignment.addTree(tree);
-                }
-              }
-            }
-          }
-
-
-            JarEntry entry = new JarEntry("vamsas.xml");
-            jout.putNextEntry(entry);
-
-            vamsas.marshal(out);
-
-            out.close();
-            jout.close();
-
-
-          }
-          catch (Exception ex)
-          {
-            ex.printStackTrace();
-          }
-
-          return vamsas;
+	 */
+	
+	protected Vobject getjv2vObj(Object jvobj) {
+		if (jv2vobj.containsKey(jvobj))
+			return cdoc.getObject(((VorbaId)jv2vobj.get(jvobj)));
+		return null;
 	}
-
-        Tree jalview2VamsasTree()
-        {
-          Tree tree = new Tree();
-
-          return tree;
-        }
-
-
-	public void load(String file)
+	
+	protected Object getvObj2jv(org.vamsas.client.Vobject vobj) {
+		VorbaId id = vobj.getVorbaId();
+		if (id==null) {
+			id = cdoc.registerObject(vobj);
+			Cache.log.debug("Registering new object and returning null for getvObj2jv");
+			return null;
+		}
+		if (vobj2jv.containsKey(vobj.getVorbaId()))
+			return vobj2jv.get(id);
+		return null;
+	}
+	protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) {
+		VorbaId id = vobj.getVorbaId();
+		if (id==null) {
+			id = cdoc.registerObject(vobj);
+		}
+		if (vobj2jv.containsKey(vobj.getVorbaId())||jv2vobj.containsKey(jvobj)) {
+			Cache.log.error("Duplicate object binding!");
+		} else {
+			vobj2jv.put(vobj.getVorbaId(),jvobj);// JBPNote - better implementing a hybrid invertible hash.
+			jv2vobj.put(jvobj,vobj.getVorbaId());				
+		}
+	}
+	
+	public void storeVAMSAS(AlignViewport av) 
 	{
-          VAMSAS vamsas = new VAMSAS() ;
-
-          try
-          {
-            FileInputStream fis = new FileInputStream(file);
-            JarInputStream jin = new JarInputStream(fis);
-
-
-            ////////////////////////////////////////////////////
-            //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-            InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-            JarEntry jarentry = jin.getNextJarEntry();
-            System.out.println("reading: "+jarentry.getName());
-            vamsas = (VAMSAS) vamsas.unmarshal(in);
-
-
-            /////////////////////////////////////
-            /////LOAD DATASET
-            DataSet dataset = vamsas.getDataSet(0);
-
-            int i, iSize = dataset.getSequenceCount();
-            jalview.datamodel.Sequence [] seqs = new jalview.datamodel.Sequence[iSize];
-            DbRef [] dbref;
-
-            for (i = 0; i < iSize ; i++)
-            {
-              seqs[i] = new jalview.datamodel.Sequence(
-                  dataset.getSequence(i).getName(),
-                  dataset.getSequence(i).getSequence(),
-                   dataset.getSequence(i).getStart(),
-                     dataset.getSequence(i).getEnd()  );
-              seqs[i].setVamsasId(dataset.getSequence(i).getId());
-
-              if (dataset.getDataSetAnnotations() != null)
-              {
-                for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)
-                {
-                  if (dataset.getDataSetAnnotations(dsa).getSeqRef() ==
-                      dataset.getSequence(i))
-                  {
-                    seqs[i].addSequenceFeature(new jalview.datamodel.
-                                               SequenceFeature(
-                        dataset.getDataSetAnnotations(dsa).getType(),
-                        dataset.getDataSetAnnotations(dsa).getDescription(),
-                        dataset.getDataSetAnnotations(dsa).getStatus(),
-                        dataset.getDataSetAnnotations(dsa).getBegin(),
-                        dataset.getDataSetAnnotations(dsa).getEnd(),
-                        "vamsas"));
-                  }
-                }
-              }
-              dbref = dataset.getSequence(i).getDbRef();
-
-              if(dbref.length>0)
-              {
-                for(int db=0; db<dbref.length; db++)
-                {
-                  seqs[i].addDBRef( new jalview.datamodel.DBRefEntry
-                      (
-                           dbref[db].getSource().toString(),
-                           dbref[db].getVersion().toString(),
-                           dbref[db].getAccessionId().toString()));
-                }
-              }
-            }
-            jalview.datamodel.Alignment jdataset = new jalview.datamodel.Alignment(seqs);
-            ////////////////////////////////////////////////
-
-
-            //////////////////////////////////////
-            ////LOAD ALIGNMENT
-            Alignment alignment = dataset.getAlignment(0);
-            iSize = alignment.getAlignmentSequenceCount();
-            seqs = new jalview.datamodel.Sequence[iSize];
-            String id;
-            int j, jSize = jdataset.getHeight();
-            for (i = 0; i < iSize; i++)
-            {
-              seqs[i] = new jalview.datamodel.Sequence(
-                  alignment.getAlignmentSequence(i).getName(),
-                  alignment.getAlignmentSequence(i).getSequence(),
-                  alignment.getAlignmentSequence(i).getStart(),
-                  alignment.getAlignmentSequence(i).getEnd());
-
-              id = ( (Sequence) alignment.getAlignmentSequence(i).getRefid()).getId();
-
-             for(j=0; j<jSize; j++)
-             {
-               if(jdataset.getSequenceAt(j).getVamsasId().equals(id))
-               {
-                 seqs[i].setDatasetSequence( jdataset.getSequenceAt(j) );
-                 break;
-               }
-             }
-            }
-            jalview.datamodel.Alignment jal = new jalview.datamodel.Alignment(seqs);
-            jal.setDataset(jdataset);
-            /*jal.getDataset().setProvenance(
-                getJalviewProvenance(dataset.getProvenance()));
-            jal.setProvenance(
-                getJalviewProvenance(alignment.getProvenance()));
-            */
-             //////////////////////////////////////////////
-
-
-            ////////////////////////////////////////////
-            ////LOAD ANNOTATIONS
-            ////////////////////
-            if (alignment.getAlignmentAnnotationsCount()>0)
-            {
-              AlignmentAnnotations[] an = alignment.getAlignmentAnnotations();
-
-              for (j = 0; j < an.length; j++)
-              {
-                boolean topaliBreakpoint = false;
-
-                AnnotationElement[] ae = an[j].getAnnotationElement();
-                jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[jal.
-                    getWidth()];
-
-                try{
-
-                  for (int aa = 0; aa < ae.length; aa++)
-                  {
-                    String dc = ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();
-                    String desc = ae[aa].getDescription()==null ? "desc" : ae[aa].getDescription();
-                    String ss = ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();
-                    float value = ae[aa].getValue();
-
-                    if(an[j].getGraph())
-                    {
-                      dc = value+"";
-                      desc = value + "";
-                    }
-                    anot[ae[aa].getPosition()-1] = new jalview.datamodel.
-                        Annotation(dc,desc,ss.charAt(0),value);
-
-                    if(desc.equals("TOPALi Partition Breakpoint"))
-                      topaliBreakpoint = true;
-
-                  }
-                }catch(Exception ex)
-                {
-                  ex.printStackTrace();
-                  System.out.println("problem parsing annotations\n"+ex);}
-
-                jalview.datamodel.AlignmentAnnotation jaa = null;
-
-                if (an[j].getGraph())
-                {
-                  jaa = new jalview.datamodel.AlignmentAnnotation(an[j].getLabel(),
-                      an[j].getDescription(), anot, 0, 0, 1);
-                }
-                else
-                {
-                  String label = an[j].getLabel();
-                  if(topaliBreakpoint)
-                    label = "TOPALi Partition Breakpoint";
-                  jaa = new jalview.datamodel.AlignmentAnnotation(label,
-                      an[j].getDescription(), anot);
-                }
-
-                jal.addAnnotation(jaa);
-              }
-            }
-            /////////////////////////////////
-
-            AlignFrame alignFrame = new AlignFrame(jal);
-            jalview.gui.Desktop.addInternalFrame(alignFrame, "VAMSAS LOAD",
-                                                 AlignFrame.NEW_WINDOW_WIDTH,
-                                                 AlignFrame.NEW_WINDOW_HEIGHT);
-
-            //LOAD TREES
-            ///////////////////////////////////////
-            if (alignment.getTreeCount() > 0)
-            {
-                for (int t = 0; t < alignment.getTreeCount(); t++)
-                {
-                  Tree tree = alignment.getTree(t);
-
-                  alignFrame.ShowNewickTree(
-                      new jalview.io.NewickFile(tree.getNewick(0).getContent()),
-                      tree.getNewick(0).getTitle(),
-                      600, 500,
-                      t * 20 + 50, t * 20 + 50);
-                }
-            }
-
-
-            in.close();
-            jin.close();
-          }
-          catch (Exception ex)
-          {
-            ex.printStackTrace();
-          }
-
-
+		long time = System.currentTimeMillis();
+		
+		try
+		{
+			
+			jalview.datamodel.AlignmentI jal = av.getAlignment();
+			
+			
+			///////////////////////////////////////////
+			// SAVE THE DATASET
+			VAMSAS root = cdoc.getVamsasRoots()[0];
+			if (jal.getDataset()==null) {
+				Cache.log.warn("Creating new dataset for an alignment.");
+				jal.setDataset(null); // 
+			}
+			boolean nw=false;
+			DataSet dataset = (DataSet) getjv2vObj(jal.getDataset());
+			if (dataset==null) {
+				dataset = new DataSet();
+				root.addDataSet(dataset);
+				bindjvvobj(jal.getDataset(),dataset);
+				nw=true;
+			} //else {
+			// should really check root corresponds to dataset.
+			// }
+			// update dataset
+			Sequence sequence;
+			DbRef dbref;
+			for (int i = 0; i < jal.getHeight(); i++)
+			{
+				SequenceI sq = jal.getDataset().getSequenceAt(i);
+				sequence = (Sequence) getjv2vObj(sq);
+				if (sequence==null) {
+					sequence=new Sequence();
+					bindjvvobj(sq, sequence);
+					sq.setVamsasId(sequence.getVorbaId().getId());
+					sequence.setSequence(sq.getSequence());
+					sequence.setName(jal.getDataset().getSequenceAt(i).getName());
+					sequence.setStart(jal.getDataset().getSequenceAt(i).getStart());
+					sequence.setEnd(jal.getDataset().getSequenceAt(i).getEnd());
+					dataset.addSequence(sequence);
+				} else {
+					// verify principal attributes.
+					
+				}
+				
+				if(jal.getDataset().getSequenceAt(i).getSequenceFeatures()!=null)
+				{
+					int sfSize = jal.getDataset().getSequenceAt(i).getSequenceFeatures().length;
+					
+					for (int sf = 0; sf < sfSize; sf++)
+					{
+						jalview.datamodel.SequenceFeature feature =
+							(jalview.datamodel.SequenceFeature)
+							jal.getDataset().getSequenceAt(i).getSequenceFeatures()[sf];
+						
+						DataSetAnnotations dsa = (DataSetAnnotations) getjv2vObj(feature); 
+						if (dsa==null) {
+							dsa = new DataSetAnnotations();
+							bindjvvobj(feature, dsa);
+							dsa.setType(feature.getType());
+							dsa.setBegin(feature.getBegin());
+							dsa.setEnd(feature.getEnd());
+							dsa.setDescription(feature.getDescription());
+							dsa.setStatus(feature.getStatus());
+							if (dsa.getProvenance()==null) {
+								dsa.setProvenance(new Provenance());
+							}
+							
+							dsa.getProvenance().addEntry(provEntry); // JBPNote - need to update jalview datamodel.
+							dsa.setSeqRef(sequence);
+							dataset.addDataSetAnnotations(dsa);
+						} else {
+							// todo: verify
+						}
+					}
+				}
+				
+				if(jal.getDataset().getSequenceAt(i).getDBRef()!=null)
+				{
+					java.util.Vector entries = jal.getDataset().getSequenceAt(i).getDBRef();
+					jalview.datamodel.DBRefEntry dbentry;
+					for(int db=0; db<entries.size(); db++)
+					{
+						dbentry = (jalview.datamodel.DBRefEntry)entries.elementAt(db);
+						dbref = (DbRef) getjv2vObj(dbentry);
+						if (dbref==null) {
+							dbref = new DbRef();
+							bindjvvobj(dbentry, dbref);
+							dbref.setAccessionId( dbentry.getAccessionId() );
+							dbref.setSource( dbentry.getSource() );
+							dbref.setVersion( dbentry.getVersion() );
+							dbref.setId("db"+(time++));
+							sequence.addDbRef(dbref);
+						} else {
+							// todo: verify
+						}
+					}
+					
+				}
+				
+				/* not needed any more.
+				if(jal.getDataset().getSequenceAt(i).getVamsasId()==null)
+					sequence.setId("ds" + (time++));
+				else
+					sequence.setId(jal.getDataset().getSequenceAt(i).getVamsasId());
+				 */
+			}
+			// dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));
+			//////////////////////////////////////////////
+			
+			
+			//////////////////////////////////////////////
+			//Save the Alignments
+			
+			Alignment alignment = (Alignment) getjv2vObj(jal);
+			if (alignment==null) {
+				alignment=new Alignment();
+				bindjvvobj(jal, alignment);
+				if (alignment.getProvenance()==null)
+					alignment.setProvenance(new Provenance());
+				alignment.getProvenance().addEntry(provEntry);
+				dataset.addAlignment(alignment);
+				alignment.setGapChar(av.getGapCharacter() + "");
+				AlignmentSequence alseq = null;
+				for (int i = 0; i < jal.getHeight(); i++)
+				{
+					alseq = new AlignmentSequence();
+					alseq.setSequence(
+							jal.getSequenceAt(i).getSequence()
+					);
+					alseq.setName(jal.getSequenceAt(i).getName());
+					alseq.setStart(jal.getSequenceAt(i).getStart());
+					alseq.setEnd(jal.getSequenceAt(i).getEnd());
+					// how is this going to work ? find alseq in DataSet by..
+					if (nw) {
+						// order is conserved because we just created a new dataset.
+						alseq.setRefid(dataset.getSequence(i));
+					}
+					alignment.addAlignmentSequence(alseq);
+				}
+			} else {
+				// todo: verify and update mutable alignment props.
+			}
+			//////////////////////////////////////////////
+			
+			
+			
+			//////////////////////////////////////////////
+			//SAVE ANNOTATIONS
+			if (jal.getAlignmentAnnotation() != null)
+			{
+				jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
+				
+				for (int i = 0; i < aa.length; i++)
+				{
+					if (aa[i].label.equals("Quality") ||
+							aa[i].label.equals("Conservation") ||
+							aa[i].label.equals("Consensus"))
+					{
+						continue;
+					}
+					AlignmentAnnotations an = (AlignmentAnnotations) getjv2vObj(aa[i]);
+					if (an==null) {
+						an = new AlignmentAnnotations();
+						an.setDescription(aa[i].description);
+						// JBPNote - have to deal with the many lines for one graph thing
+						if (aa[i].graph>0)
+							an.setGraph(true); //aa[i].graph);
+						// JBPNote - store graphGroup in the Jalview specific bits.
+						an.setLabel(aa[i].label);
+						an.setProvenance(dummyProvenance());
+						
+						AnnotationElement ae;
+						
+						for (int a = 0; a < aa[i].annotations.length; a++)
+						{
+							if ((aa[i] == null) || (aa[i].annotations[a] == null))
+							{
+								continue;
+							}
+							
+							ae = new AnnotationElement();
+							ae.setDescription(aa[i].annotations[a].description);
+							ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+							ae.setValue(aa[i].annotations[a].value);
+							ae.setPosition(a);
+							ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
+							"");
+							an.addAnnotationElement(ae);
+						}
+						
+						alignment.addAlignmentAnnotations(an);
+					} else {
+						// verify annotation - update (perhaps)
+					}
+				}
+			}
+			///////////////////////////////////////////////////////
+			
+			////////////////////////////////////////////////
+			///SAVE THE TREES
+			///////////////////////////////////
+			// FIND ANY ASSOCIATED TREES
+			if (Desktop.desktop != null)
+			{
+				javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+				
+				for (int t = 0; t < frames.length; t++)
+				{
+					if (frames[t] instanceof TreePanel)
+					{
+						TreePanel tp = (TreePanel) frames[t];
+						
+						if (tp.getAlignment() == jal)
+						{
+							// JBPNote - can recover alignment and Vamsas Alignment for an associated tree using the getjv2vObj()
+							
+							Tree tree = (Tree) getjv2vObj(tp);
+							if (tree==null) {
+								tree = new Tree();
+								bindjvvobj(tp,tree);
+								tree.setTitle(tp.getTitle());
+								Newick newick = new Newick();
+								newick.setContent( tp.getTree().toString() );
+								newick.setTitle( tp.getTitle() );
+								tree.addNewick( newick );
+								tree.setProvenance(dummyProvenance());
+								alignment.addTree(tree);
+							} else {
+								// verify any changes.
+							}
+						}
+					}
+				}
+			}
+		}
+		
+		catch (Exception ex)
+		{
+			ex.printStackTrace();
+		}
+		
 	}
-
-
-
-        Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov)
-        {
-          jalview.datamodel.ProvenanceEntry [] entries = null;
-
-
-          Provenance prov = new Provenance();
-          org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(
-      new java.util.Date());
-          Entry provEntry;
-
-          if(jprov!=null)
-          {
-            entries = jprov.getEntries();
-            for (int i = 0; i < entries.length; i++)
-            {
-              provEntry = new Entry();
-              try
-              {
-                date = new org.exolab.castor.types.Date(entries[i].getDate());
-              }
-              catch (Exception ex)
-              {
-                ex.printStackTrace();
-
-                date = new org.exolab.castor.types.Date(entries[i].getDate());
-              }
-              provEntry.setDate(date);
-              provEntry.setUser(entries[i].getUser());
-              provEntry.setAction(entries[i].getAction());
-              prov.addEntry(provEntry);
-            }
-          }
-          else
-          {
-            provEntry = new Entry();
-            provEntry.setDate(date);
-            provEntry.setUser(System.getProperty("user.name"));
-            provEntry.setAction("Jalview");
-            prov.addEntry(provEntry);
-          }
-
-          return prov;
-        }
-
-        jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
-        {
-
-          jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
-          for (int i = 0; i < prov.getEntryCount(); i++)
-          {
-            jprov.addEntry(
-                prov.getEntry(i).getUser(),
-                prov.getEntry(i).getAction(),
-                prov.getEntry(i).getDate().toDate(),
-                prov.getEntry(i).getId()
-                );
-          }
-
-          return jprov;
-        }
-
-        Provenance dummyProvenance()
-        {
-          Provenance prov = new Provenance();
-          Entry entry = new Entry();
-          entry.setAction("Jalview");
-          entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
-          entry.setUser(System.getProperty("user.name"));
-          prov.addEntry(entry);
-          return prov;
-        }
-
-}
+	
+	
+	
+	public void updateJalview()
+	{
+		VAMSAS root = cdoc.getVamsasRoots()[0];
+		try
+		{
+			boolean newds=false;
+			for (int _ds=0,_nds=root.getDataSetCount(); _ds<_nds; _ds++) {
+				/////////////////////////////////////
+				/////LOAD DATASET
+				DataSet dataset = vamsas.getDataSet(_ds);
+				int i, iSize = dataset.getSequenceCount();
+				jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) vobj2jv(dataset);
+				if (jdataset!=null) {
+					// recover
+				} else {
+					newds=true;
+					// construct new dataset
+					jalview.datamodel.Sequence [] seqs = new jalview.datamodel.Sequence[iSize];
+					DbRef [] dbref;
+					for (i = 0; i < iSize ; i++)
+					{
+						seqs[i] = new jalview.datamodel.Sequence(
+								dataset.getSequence(i).getName(),
+								dataset.getSequence(i).getSequence(),
+								dataset.getSequence(i).getStart(),
+								dataset.getSequence(i).getEnd()  );
+						bindjvvobj(seqs[i], dataset.getSequence(i));
+						seqs[i].setVamsasId(dataset.getSequence(i).getVorbaId().getId());
+						
+						if (dataset.getDataSetAnnotations() != null)
+						{
+							for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)
+							{
+								// could be optimised
+								if (dataset.getDataSetAnnotations(dsa).getSeqRef() ==
+									dataset.getSequence(i))
+								{
+									jalview.datamodel.SequenceFeature sf;
+									seqs[i].addSequenceFeature(sf=new jalview.datamodel.
+											SequenceFeature(
+													dataset.getDataSetAnnotations(dsa).getType(),
+													dataset.getDataSetAnnotations(dsa).getDescription(),
+													dataset.getDataSetAnnotations(dsa).getStatus(),
+													dataset.getDataSetAnnotations(dsa).getBegin(),
+													dataset.getDataSetAnnotations(dsa).getEnd(),
+											"vamsas"));
+									bindjvvobj(sf, dataset.getDataSetAnnotations(dsa));
+								}
+							}
+						}
+						dbref = dataset.getSequence(i).getDbRef();
+						
+						if(dbref.length>0)
+						{
+							for(int db=0; db<dbref.length; db++)
+							{
+								jalview.datamodel.DBRefEntry dbr;
+								seqs[i].addDBRef(dbr= new jalview.datamodel.DBRefEntry
+										(
+												dbref[db].getSource().toString(),
+												dbref[db].getVersion().toString(),
+												dbref[db].getAccessionId().toString()));
+								bindjvvobj(dbr, dvref[db]);
+							}
+						}
+					}
+					jdataset = jalview.datamodel.Alignment(seqs); // complete construction
+					bindjvvobj(jdataset, dataset);
+				}
+				////////////////////////////////////////////////
+			}
+			for (int _al=0,_nal=dataset.getAlignmentCount(); _al<_nal; _al++) {
+				//////////////////////////////////////
+				////LOAD ALIGNMENT
+				Alignment alignment = dataset.getAlignment(_al);
+				iSize = alignment.getAlignmentSequenceCount();
+				jalview.datamodel.Alignment jal = getvObj2jv(alignment); 
+				if (jal!=null) {
+					// merge/update
+				} else {
+					seqs = new jalview.datamodel.Sequence[iSize];
+					String id;
+					int j, jSize = jdataset.getHeight();
+					for (i = 0; i < iSize; i++)
+					{
+						seqs[i] = new jalview.datamodel.Sequence(
+								alignment.getAlignmentSequence(i).getName(),
+								alignment.getAlignmentSequence(i).getSequence(),
+								alignment.getAlignmentSequence(i).getStart(),
+								alignment.getAlignmentSequence(i).getEnd());
+						bindjvvobj(seqs[i], alignment.getAlignmentSequence(i));
+						id = ( (Sequence) alignment.getAlignmentSequence(i).getRefid()).getVorbaId().getId();
+						
+						for(j=0; j<jSize; j++)
+						{
+							if(jdataset.getSequenceAt(j).getVamsasId().equals(id))
+							{
+								seqs[i].setDatasetSequence( jdataset.getSequenceAt(j) );
+								break;
+							}
+						}
+					}
+					jalview.datamodel.Alignment jal = new jalview.datamodel.Alignment(seqs);
+					bindjvvobj(jal, alignment);
+					jal.setDataset(jdataset);
+					/*jal.getDataset().setProvenance(
+                	getJalviewProvenance(dataset.getProvenance()));
+            		jal.setProvenance(
+                	getJalviewProvenance(alignment.getProvenance()));
+					 */
+					//////////////////////////////////////////////
+					
+					
+					////////////////////////////////////////////
+					////LOAD ANNOTATIONS
+					////////////////////
+					if (alignment.getAlignmentAnnotationsCount()>0)
+					{
+						AlignmentAnnotations[] an = alignment.getAlignmentAnnotations();
+						
+						for (j = 0; j < an.length; j++)
+						{
+							boolean topaliBreakpoint = false;
+							
+							AnnotationElement[] ae = an[j].getAnnotationElement();
+							jalview.datamodel.Annotation[] anot = getvObj2jv(ae);
+							if (anot!=null) {
+								// update or stay the same.
+							} else {
+								// new one
+								anot=new jalview.datamodel.Annotation[jal.
+                                                                 getWidth()];
+								bindjvvobj(anot, ae);
+                                try{
+                                	for (int aa = 0; aa < ae.length; aa++)
+                                	{
+                                		String dc = ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();
+                                		String desc = ae[aa].getDescription()==null ? "desc" : ae[aa].getDescription();
+                                		String ss = ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();
+                                		float value = ae[aa].getValue();
+                                		if(an[j].getGraph())
+                                		{
+                                			dc = value+"";
+                                			desc = value + "";
+                                		}
+                                		anot[ae[aa].getPosition()-1] = new jalview.datamodel.
+                                		Annotation(dc,desc,ss.charAt(0),value);
+									
+                                		if(desc.equals("TOPALi Partition Breakpoint"))
+										topaliBreakpoint = true;
+									
+                                	}
+                                }catch(Exception ex)
+                                {
+                                	ex.printStackTrace();
+                                	System.out.println("problem parsing annotations\n"+ex);}
+                                }
+							jalview.datamodel.AlignmentAnnotation jaa = null;
+							if (an[j].getGraph())
+							{
+								jaa = new jalview.datamodel.AlignmentAnnotation(an[j].getLabel(),
+										an[j].getDescription(), anot, 0, 0, 1);
+							}
+							else
+							{
+								String label = an[j].getLabel();
+								if(topaliBreakpoint)
+									label = "TOPALi Partition Breakpoint";
+								jaa = new jalview.datamodel.AlignmentAnnotation(label,
+										an[j].getDescription(), anot);
+							}
+							
+							jal.addAnnotation(jaa);
+						}
+					}
+					/////////////////////////////////
+					
+					AlignFrame alignFrame = new AlignFrame(jal);
+					jalview.gui.Desktop.addInternalFrame(alignFrame, "VAMSAS LOAD",
+							AlignFrame.NEW_WINDOW_WIDTH,
+							AlignFrame.NEW_WINDOW_HEIGHT);
+					
+					//LOAD TREES
+					///////////////////////////////////////
+					if (alignment.getTreeCount() > 0)
+					{
+						for (int t = 0; t < alignment.getTreeCount(); t++)
+						{
+							Tree tree = alignment.getTree(t);
+							
+							alignFrame.ShowNewickTree(
+									new jalview.io.NewickFile(tree.getNewick(0).getContent()),
+									tree.getNewick(0).getTitle(),
+									600, 500,
+									t * 20 + 50, t * 20 + 50);
+						}
+					}
+					
+					
+					in.close();
+					jin.close();
+				}
+				catch (Exception ex)
+				{
+					ex.printStackTrace();
+				}
+				
+				
+			}
+			
+			
+			
+			Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov)
+			{
+				jalview.datamodel.ProvenanceEntry [] entries = null;
+				
+				
+				Provenance prov = new Provenance();
+				org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(
+						new java.util.Date());
+				Entry provEntry;
+				
+				if(jprov!=null)
+				{
+					entries = jprov.getEntries();
+					for (int i = 0; i < entries.length; i++)
+					{
+						provEntry = new Entry();
+						try
+						{
+							date = new org.exolab.castor.types.Date(entries[i].getDate());
+						}
+						catch (Exception ex)
+						{
+							ex.printStackTrace();
+							
+							date = new org.exolab.castor.types.Date(entries[i].getDate());
+						}
+						provEntry.setDate(date);
+						provEntry.setUser(entries[i].getUser());
+						provEntry.setAction(entries[i].getAction());
+						prov.addEntry(provEntry);
+					}
+				}
+				else
+				{
+					provEntry = new Entry();
+					provEntry.setDate(date);
+					provEntry.setUser(System.getProperty("user.name"));
+					provEntry.setAction("Jalview");
+					prov.addEntry(provEntry);
+				}
+				
+				return prov;
+			}
+			
+			jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
+			{
+				
+				jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
+				for (int i = 0; i < prov.getEntryCount(); i++)
+				{
+					jprov.addEntry(
+							prov.getEntry(i).getUser(),
+							prov.getEntry(i).getAction(),
+							prov.getEntry(i).getDate().toDate(),
+							prov.getEntry(i).getId()
+					);
+				}
+				
+				return jprov;
+			}
+			
+			Provenance dummyProvenance()
+			{
+				Provenance prov = new Provenance();
+				Entry entry = new Entry();
+				entry.setAction("Jalview");
+				entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
+				entry.setUser(System.getProperty("user.name"));
+				prov.addEntry(entry);
+				return prov;
+			}
+			
+		}