X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasDatastore.java;h=f1cba4f66ab24f373107e9a716c30c3d6e0f8084;hb=4484ac6bdcc92f0e0e430f64d3587f026fafb476;hp=6a117b2e5a5fb40e149043ab63973b96d43a9b53;hpb=8247c538f13da72c218ef52714ac9ca4acf564d3;p=jalview.git

diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java
index 6a117b2..f1cba4f 100755
--- a/src/jalview/io/VamsasDatastore.java
+++ b/src/jalview/io/VamsasDatastore.java
@@ -19,12 +19,6 @@
 
 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.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -32,16 +26,40 @@ import jalview.datamodel.AlignmentView;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.gui.*;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.TreePanel;
 
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Vector;
-import java.util.jar.*;
-import org.exolab.castor.xml.*;
-import org.exolab.castor.mapping.Mapping;
+
+import org.vamsas.client.Vobject;
+import org.vamsas.client.VorbaId;
+import org.vamsas.objects.core.Alignment;
+import org.vamsas.objects.core.AlignmentSequence;
+import org.vamsas.objects.core.AlignmentSequenceAnnotation;
+import org.vamsas.objects.core.AnnotationElement;
+import org.vamsas.objects.core.DataSet;
+import org.vamsas.objects.core.DataSetAnnotations;
+import org.vamsas.objects.core.DbRef;
+import org.vamsas.objects.core.Entry;
+import org.vamsas.objects.core.Glyph;
+import org.vamsas.objects.core.Input;
+import org.vamsas.objects.core.Link;
+import org.vamsas.objects.core.Newick;
+import org.vamsas.objects.core.Param;
+import org.vamsas.objects.core.Property;
+import org.vamsas.objects.core.Provenance;
+import org.vamsas.objects.core.RangeAnnotation;
+import org.vamsas.objects.core.RangeType;
+import org.vamsas.objects.core.Seg;
+import org.vamsas.objects.core.Sequence;
+import org.vamsas.objects.core.Tree;
+import org.vamsas.objects.core.VAMSAS;
+import org.vamsas.test.simpleclient.ClientDoc;
 
 /*
  *
@@ -51,7 +69,8 @@ import org.exolab.castor.mapping.Mapping;
  *
  */
 
-public class VamsasDatastore {
+public class VamsasDatastore
+{
   Entry provEntry = null;
 
   // AlignViewport av;
@@ -66,8 +85,9 @@ public class VamsasDatastore {
   IdentityHashMap jv2vobj;
 
   public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv,
-      IdentityHashMap jv2vobj, Entry provEntry) {
-      this.cdoc = cdoc;
+                         IdentityHashMap jv2vobj, Entry provEntry)
+  {
+    this.cdoc = cdoc;
     this.vobj2jv = vobj2jv;
     this.jv2vobj = jv2vobj;
     this.provEntry = provEntry;
@@ -92,9 +112,12 @@ public class VamsasDatastore {
   /**
    * @return the Vobject bound to Jalview datamodel object
    */
-  protected Vobject getjv2vObj(Object jvobj) {
+  protected Vobject getjv2vObj(Object jvobj)
+  {
     if (jv2vobj.containsKey(jvobj))
-      return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
+    {
+      return cdoc.getObject( (VorbaId) jv2vobj.get(jvobj));
+    }
     return null;
   }
 
@@ -103,38 +126,53 @@ public class VamsasDatastore {
    * @param vobj
    * @return Jalview datamodel object bound to the vamsas document object
    */
-  protected Object getvObj2jv(org.vamsas.client.Vobject vobj) {
+  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");
+          .debug("Registering new object and returning null for getvObj2jv");
       return null;
     }
     if (vobj2jv.containsKey(vobj.getVorbaId()))
+    {
       return vobj2jv.get(vobj.getVorbaId());
+    }
     return null;
   }
 
-  protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) {
+  protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj)
+  {
     VorbaId id = vobj.getVorbaId();
     if (id == null)
     {
       id = cdoc.registerObject(vobj);
-      if (id==null || vobj.getVorbaId()==null)
-        Cache.log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj);
+      if (id == null || vobj.getVorbaId() == null)
+      {
+        Cache.log.error("Failed to get id for " +
+                        (vobj.isRegisterable() ? "registerable" :
+                         "unregisterable") + " object " + vobj);
+      }
     }
 
-    if (vobj2jv.containsKey(vobj.getVorbaId()) && !((VorbaId)vobj2jv.get(vobj.getVorbaId())).equals(jvobj)) {
-      Cache.log.debug("Warning? Overwriting existing vamsas id binding for "+vobj.getVorbaId(), new Exception("Overwriting vamsas id binding."));
+    if (vobj2jv.containsKey(vobj.getVorbaId()) &&
+        ! ( (VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
+    {
+      Cache.log.debug("Warning? Overwriting existing vamsas id binding for " +
+                      vobj.getVorbaId(),
+                      new Exception("Overwriting vamsas id binding."));
     }
-    else if (jv2vobj.containsKey(jvobj) && !((VorbaId)jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
+    else if (jv2vobj.containsKey(jvobj) &&
+             ! ( (VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
     {
-      Cache.log.debug("Warning? Overwriting existing jalview object binding for "+jvobj, new Exception("Overwriting jalview object binding."));
+      Cache.log.debug(
+          "Warning? Overwriting existing jalview object binding for " + jvobj,
+          new Exception("Overwriting jalview object binding."));
     }
     /* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+" already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to bindjvvobj"));
-    }*/
+         }*/
     // we just update the hash's regardless!
     vobj2jv.put(vobj.getVorbaId(), jvobj);
     // JBPNote - better implementing a hybrid invertible hash.
@@ -147,7 +185,8 @@ public class VamsasDatastore {
    * @param av alignViewport to be stored
    * @param aFtitle title for alignment
    */
-  public void storeVAMSAS(AlignViewport av, String aFtitle) {
+  public void storeVAMSAS(AlignViewport av, String aFtitle)
+  {
     try
     {
       jalview.datamodel.AlignmentI jal = av.getAlignment();
@@ -182,7 +221,8 @@ public class VamsasDatastore {
       // flag.
       // this *will* break when alignment contains both nucleotide and amino
       // acid sequences.
-      String dict = jal.isNucleotide() ? org.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+      String dict = jal.isNucleotide() ?
+          org.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
           : org.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
       for (int i = 0; i < jal.getHeight(); i++)
       {
@@ -215,8 +255,9 @@ public class VamsasDatastore {
 
           for (int sf = 0; sf < sfSize; sf++)
           {
-            jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) sq
-            .getSequenceFeatures()[sf];
+            jalview.datamodel.SequenceFeature feature = (jalview.datamodel.
+                SequenceFeature) sq
+                .getSequenceFeatures()[sf];
 
             DataSetAnnotations dsa = (DataSetAnnotations) getjv2vObj(feature);
             if (dsa == null)
@@ -269,7 +310,7 @@ public class VamsasDatastore {
               // contain more residues than were originally referenced - we must
               // then make a number of dataset sequence entries
               System.out
-              .println("update dataset sequence database references.");
+                  .println("update dataset sequence database references.");
             }
           }
 
@@ -287,7 +328,9 @@ public class VamsasDatastore {
         alignment = new Alignment();
         bindjvvobj(av, alignment);
         if (alignment.getProvenance() == null)
+        {
           alignment.setProvenance(new Provenance());
+        }
         addProvenance(alignment.getProvenance(), "added"); // TODO: insert some
         // sensible source
         // here
@@ -324,30 +367,33 @@ public class VamsasDatastore {
         else
         {
           System.out
-          .println("update edited alignment to new alignment in document.");
+              .println("update edited alignment to new alignment in document.");
         }
       }
       // ////////////////////////////////////////////
       // SAVE Alignment Sequence Features
-      for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
+      for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize;
+           i++)
       {
         AlignmentSequence valseq;
         SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment
-            .getAlignmentSequence(i));
+                                                 .getAlignmentSequence(i));
         if (alseq != null && alseq.getSequenceFeatures() != null)
         {
           jalview.datamodel.SequenceFeature[] features = alseq
-          .getSequenceFeatures();
+              .getSequenceFeatures();
           for (int f = 0; f < features.length; f++)
           {
             if (features[f] != null)
             {
-              AlignmentSequenceAnnotation valseqf = (AlignmentSequenceAnnotation) getjv2vObj(features[i]);
+              AlignmentSequenceAnnotation valseqf = (
+                  AlignmentSequenceAnnotation) getjv2vObj(features[i]);
               if (valseqf == null)
               {
 
-                valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
-                    new AlignmentSequenceAnnotation(), features[i]);
+                valseqf = (AlignmentSequenceAnnotation)
+                    getDSAnnotationFromJalview(
+                        new AlignmentSequenceAnnotation(), features[i]);
                 if (valseqf.getProvenance() == null)
                 {
                   valseqf.setProvenance(new Provenance());
@@ -369,7 +415,7 @@ public class VamsasDatastore {
       if (jal.getAlignmentAnnotation() != null)
       {
         jalview.datamodel.AlignmentAnnotation[] aa = jal
-        .getAlignmentAnnotation();
+            .getAlignmentAnnotation();
         java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from
         // alignment columns to
         // sequence positions.
@@ -381,8 +427,11 @@ public class VamsasDatastore {
           }
           if (aa[i].sequenceRef != null)
           {
-            org.vamsas.objects.core.AlignmentSequence alsref = (org.vamsas.objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);
-            org.vamsas.objects.core.AlignmentSequenceAnnotation an = (org.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[i]);
+            org.vamsas.objects.core.AlignmentSequence alsref = (org.vamsas.
+                objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);
+            org.vamsas.objects.core.AlignmentSequenceAnnotation an = (org.
+                vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[
+                i]);
             int[] gapMap = null;
             if (AlSeqMaps.containsKey(aa[i].sequenceRef))
             {
@@ -394,7 +443,9 @@ public class VamsasDatastore {
               // map from alignment position to sequence position.
               int[] sgapMap = aa[i].sequenceRef.gapMap();
               for (int a = 0; a < sgapMap.length; a++)
+              {
                 gapMap[sgapMap[a]] = a;
+              }
             }
             if (an == null)
             {
@@ -404,17 +455,21 @@ public class VamsasDatastore {
               vSeg.setInclusive(true);
               vSeg.setEnd(gapMap.length);
               an.addSeg(vSeg);
-              an.setType("jalview:SecondaryStructurePrediction");// TODO: better fix this rough guess ;)
+              an.setType("jalview:SecondaryStructurePrediction"); // TODO: better fix this rough guess ;)
               alsref.addAlignmentSequenceAnnotation(an);
-              bindjvvobj(aa[i],an);
+              bindjvvobj(aa[i], an);
               // LATER: much of this is verbatim from the alignmentAnnotation
               // method below. suggests refactoring to make rangeAnnotation the
               // base class
               an.setDescription(aa[i].description);
               if (aa[i].graph > 0)
+              {
                 an.setGraph(true); // aa[i].graph);
+              }
               else
+              {
                 an.setGraph(false);
+              }
               an.setLabel(aa[i].label);
               an.setProvenance(dummyProvenance()); // get provenance as user
               // created, or jnet, or
@@ -439,25 +494,30 @@ public class VamsasDatastore {
                 ae.setDescription(aa[i].annotations[a].description);
                 ae.addGlyph(new Glyph());
                 ae.getGlyph(0)
-                .setContent(aa[i].annotations[a].displayCharacter); // assume
+                    .setContent(aa[i].annotations[a].displayCharacter); // assume
                 // jax-b
                 // takes
                 // care
                 // of
                 // utf8
                 // translation
-                if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+                if (aa[i].graph !=
+                    jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+                {
                   ae.addValue(aa[i].annotations[a].value);
-                ae.setPosition(gapMap[a]+1); // position w.r.t. AlignmentSequence
+                }
+                ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence
                 // symbols
                 if (aa[i].annotations[a].secondaryStructure != ' ')
                 {
                   // we only write an annotation where it really exists.
                   Glyph ss = new Glyph();
                   ss
-                  .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+                      .setDict(org.vamsas.objects.utils.GlyphDictionary.
+                               PROTEIN_SS_3STATE);
                   ss.setContent(String
-                      .valueOf(aa[i].annotations[a].secondaryStructure));
+                                .valueOf(aa[i].annotations[a].
+                                         secondaryStructure));
                   ae.addGlyph(ss);
                 }
                 an.addAnnotationElement(ae);
@@ -475,14 +535,16 @@ public class VamsasDatastore {
               {
                 // verify existing alignment sequence annotation is up to date
                 System.out
-                .println("make new alignment sequence annotation if modification has happened.");
+                    .println(
+                    "make new alignment sequence annotation if modification has happened.");
               }
             }
           }
           else
           {
             // add Alignment Annotation
-            org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
+            org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas.
+                objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
             if (an == null)
             {
               an = new org.vamsas.objects.core.AlignmentAnnotation();
@@ -495,27 +557,32 @@ public class VamsasDatastore {
               vSeg.setEnd(jal.getWidth());
               an.addSeg(vSeg);
               if (aa[i].graph > 0)
+              {
                 an.setGraph(true); // aa[i].graph);
+              }
               an.setLabel(aa[i].label);
               an.setProvenance(dummyProvenance());
-              if (aa[i].graph!=aa[i].NO_GRAPH) {
+              if (aa[i].graph != aa[i].NO_GRAPH)
+              {
                 an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -
                 // originally we
-              // were going to
-              // store
-              // graphGroup in
-              // the Jalview
-              // specific
-              // bits.
+                // were going to
+                // store
+                // graphGroup in
+                // the Jalview
+                // specific
+                // bits.
                 an.setGraph(true);
-              } else {
+              }
+              else
+              {
                 an.setGraph(false);
               }
               AnnotationElement ae;
 
               for (int a = 0; a < aa[i].annotations.length; a++)
               {
-                if ((aa[i] == null) || (aa[i].annotations[a] == null))
+                if ( (aa[i] == null) || (aa[i].annotations[a] == null))
                 {
                   continue;
                 }
@@ -524,7 +591,7 @@ public class VamsasDatastore {
                 ae.setDescription(aa[i].annotations[a].description);
                 ae.addGlyph(new Glyph());
                 ae.getGlyph(0)
-                .setContent(aa[i].annotations[a].displayCharacter); // assume
+                    .setContent(aa[i].annotations[a].displayCharacter); // assume
                 // jax-b
                 // takes
                 // care
@@ -532,27 +599,34 @@ public class VamsasDatastore {
                 // utf8
                 // translation
                 ae.addValue(aa[i].annotations[a].value);
-                ae.setPosition(a+1);
+                ae.setPosition(a + 1);
                 if (aa[i].annotations[a].secondaryStructure != ' ')
                 {
                   Glyph ss = new Glyph();
                   ss
-                  .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+                      .setDict(org.vamsas.objects.utils.GlyphDictionary.
+                               PROTEIN_SS_3STATE);
                   ss.setContent(String
-                      .valueOf(aa[i].annotations[a].secondaryStructure));
+                                .valueOf(aa[i].annotations[a].
+                                         secondaryStructure));
                   ae.addGlyph(ss);
                 }
                 an.addAnnotationElement(ae);
               }
-              if (aa[i].editable) {
+              if (aa[i].editable)
+              {
                 //an.addProperty(newProperty("jalview:editable", null, "true"));
                 an.setModifiable(true);
               }
-              if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH) {
+              if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+              {
                 an.setGraph(true);
                 an.setGroup(Integer.toString(aa[i].graphGroup));
-                an.addProperty(newProperty("jalview:graphType",null,
-                    ((aa[i].graph==jalview.datamodel.AlignmentAnnotation.BAR_GRAPH) ? "BAR_GRAPH" : "LINE_GRAPH")));
+                an.addProperty(newProperty("jalview:graphType", null,
+                                           ( (aa[i].graph ==
+                                              jalview.datamodel.AlignmentAnnotation.
+                                              BAR_GRAPH) ? "BAR_GRAPH" :
+                                            "LINE_GRAPH")));
 
                 /** and on and on..
                  vProperty=new Property();
@@ -567,7 +641,8 @@ public class VamsasDatastore {
               if (an.getModifiable())
               {
                 // verify annotation - update (perhaps)
-                Cache.log.info("update alignment sequence annotation. not yet implemented.");
+                Cache.log.info(
+                    "update alignment sequence annotation. not yet implemented.");
               }
               else
               {
@@ -621,7 +696,7 @@ public class VamsasDatastore {
                 else
                 {
                   System.out
-                  .println("Add modified tree as new tree in document.");
+                      .println("Add modified tree as new tree in document.");
                 }
               }
             }
@@ -639,13 +714,18 @@ public class VamsasDatastore {
 
   }
 
-  private Property newProperty(String name, String type, String content) {
-    Property vProperty=new Property();
+  private Property newProperty(String name, String type, String content)
+  {
+    Property vProperty = new Property();
     vProperty.setName(name);
-    if (type!=null)
+    if (type != null)
+    {
       vProperty.setType(type);
+    }
     else
+    {
       vProperty.setType("String");
+    }
     vProperty.setContent(content);
     return vProperty;
   }
@@ -660,7 +740,8 @@ public class VamsasDatastore {
    * @return
    */
   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
-      SequenceFeature feature) {
+      SequenceFeature feature)
+  {
     dsa.setType(feature.getType());
     Seg vSeg = new Seg();
     vSeg.setStart(feature.getBegin());
@@ -679,9 +760,13 @@ public class VamsasDatastore {
         {
           Link vLink = new Link();
           if (sep > 0)
+          {
             vLink.setContent(link.substring(0, sep - 1));
+          }
           else
+          {
             vLink.setContent("");
+          }
           vLink.setHref(link.substring(sep + 1)); // TODO: validate href.
           dsa.addLink(vLink);
         }
@@ -699,10 +784,11 @@ public class VamsasDatastore {
    * @param tp
    * @return
    */
-  private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) {
+  private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
+  {
     Provenance prov = new Provenance();
     prov.addEntry(new Entry());
-    prov.getEntry(0).setAction("imported "+tp.getTitle());
+    prov.getEntry(0).setAction("imported " + tp.getTitle());
     prov.getEntry(0).setUser(provEntry.getUser());
     prov.getEntry(0).setApp(provEntry.getApp());
     prov.getEntry(0).setDate(provEntry.getDate());
@@ -714,7 +800,7 @@ public class VamsasDatastore {
       // the document.
       // vInput.setObjRef(getjv2vObj(jal));
       vInput.setObjRef(getjv2vObj(tp.getViewPort()));
-      prov.getEntry(0).setAction("created "+tp.getTitle());
+      prov.getEntry(0).setAction("created " + tp.getTitle());
       prov.getEntry(0).addInput(vInput);
       vInput.setName("jalview:seqdist");
       prov.getEntry(0).addParam(new Param());
@@ -724,12 +810,12 @@ public class VamsasDatastore {
 
       int ranges[] = tp.getTree().seqData.getVisibleContigs();
       // VisibleContigs are with respect to alignment coordinates. Still need offsets
-      int start= tp.getTree().seqData.getAlignmentOrigin();
+      int start = tp.getTree().seqData.getAlignmentOrigin();
       for (int r = 0; r < ranges.length; r += 2)
       {
         Seg visSeg = new Seg();
-        visSeg.setStart(1+start+ranges[r]);
-        visSeg.setEnd(start+ranges[r + 1]);
+        visSeg.setStart(1 + start + ranges[r]);
+        visSeg.setEnd(start + ranges[r + 1]);
         visSeg.setInclusive(true);
         vInput.addSeg(visSeg);
       }
@@ -743,47 +829,56 @@ public class VamsasDatastore {
    * @return Object[] { AlignmentView, AlignmentI - reference alignment for
    *         input }
    */
-  private Object[] recoverInputData(Provenance tp) {
+  private Object[] recoverInputData(Provenance tp)
+  {
     for (int pe = 0; pe < tp.getEntryCount(); pe++)
     {
       if (tp.getEntry(pe).getInputCount() > 0)
       {
         if (tp.getEntry(pe).getInputCount() > 1)
+        {
           Cache.log.warn("Ignoring additional input spec in provenance entry "
-              + tp.getEntry(pe).toString());
+                         + tp.getEntry(pe).toString());
+        }
         // LATER: deal sensibly with multiple inputs.
         Input vInput = tp.getEntry(pe).getInput(0);
         if (vInput.getObjRef() instanceof org.vamsas.objects.core.Alignment)
         {
           // recover an AlignmentView for the input data
-          AlignViewport javport = (AlignViewport) getvObj2jv((org.vamsas.client.Vobject) vInput
+          AlignViewport javport = (AlignViewport) getvObj2jv( (org.vamsas.
+              client.Vobject) vInput
               .getObjRef());
           jalview.datamodel.AlignmentI jal = javport.getAlignment();
-          jalview.datamodel.CigarArray view = javport.getAlignment().getCompactAlignment();
+          jalview.datamodel.CigarArray view = javport.getAlignment().
+              getCompactAlignment();
           int from = 1, to = jal.getWidth();
-          int offset=0; // deleteRange modifies its frame of reference
+          int offset = 0; // deleteRange modifies its frame of reference
           for (int r = 0, s = vInput.getSegCount(); r < s; r++)
           {
             Seg visSeg = vInput.getSeg(r);
-            int se[] = getSegRange(visSeg,true); // jalview doesn't do bidirection alignments yet.
+            int se[] = getSegRange(visSeg, true); // jalview doesn't do bidirection alignments yet.
             if (to < se[1])
+            {
               Cache.log.warn("Ignoring invalid segment in InputData spec.");
+            }
             else
             {
               if (se[0] > from)
               {
-                view.deleteRange(offset+from-1, offset+se[0] - 2);
-                offset-=se[0]-from;
+                view.deleteRange(offset + from - 1, offset + se[0] - 2);
+                offset -= se[0] - from;
               }
               from = se[1] + 1;
             }
           }
           if (from < to)
           {
-            view.deleteRange(offset+from-1, offset+to-1); // final deletion - TODO: check off by
+            view.deleteRange(offset + from - 1, offset + to - 1); // final deletion - TODO: check off by
             // one for to
           }
-          return new Object[] { new AlignmentView(view), jal };
+          return new Object[]
+              {
+              new AlignmentView(view), jal};
         }
       }
     }
@@ -799,21 +894,24 @@ public class VamsasDatastore {
    * @param ensureDirection when true - always ensure start is less than end.
    * @return int[] { start, end, direction} where direction==1 for range running from end to start.
    */
-  private int[] getSegRange(Seg visSeg, boolean ensureDirection) {
+  private int[] getSegRange(Seg visSeg, boolean ensureDirection)
+  {
     boolean incl = visSeg.getInclusive();
     // adjust for inclusive flag.
     int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
     // region.
     int start = visSeg.getStart() + (incl ? 0 : pol);
     int end = visSeg.getEnd() + (incl ? 0 : -pol);
-    if (ensureDirection && pol==-1)
+    if (ensureDirection && pol == -1)
     {
       // jalview doesn't deal with inverted ranges, yet.
       int t = end;
       end = start;
       start = t;
     }
-    return new int[] { start, end, pol<0 ? 1 : 0 };
+    return new int[]
+        {
+        start, end, pol < 0 ? 1 : 0};
   }
 
   /**
@@ -821,11 +919,13 @@ public class VamsasDatastore {
    * @param annotation
    * @return true if annotation is not to be stored in document
    */
-  private boolean isJalviewOnly(AlignmentAnnotation annotation) {
+  private boolean isJalviewOnly(AlignmentAnnotation annotation)
+  {
     return annotation.label.equals("Quality")
-    || annotation.label.equals("Conservation")
-    || annotation.label.equals("Consensus");
+        || annotation.label.equals("Conservation")
+        || annotation.label.equals("Consensus");
   }
+
   /**
    * This will return the first AlignFrame viewing AlignViewport av.
    * It will break if there are more than one AlignFrames viewing a particular av.
@@ -833,89 +933,112 @@ public class VamsasDatastore {
    * @param av
    * @return alignFrame for av
    */
-  public AlignFrame getAlignFrameFor(AlignViewport av) {
+  public AlignFrame getAlignFrameFor(AlignViewport av)
+  {
     if (Desktop.desktop != null)
     {
       javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
       for (int t = 0; t < frames.length; t++)
       {
-        if (frames[t] instanceof AlignFrame) {
-          if (((AlignFrame) frames[t]).getViewport()==av)
+        if (frames[t] instanceof AlignFrame)
+        {
+          if ( ( (AlignFrame) frames[t]).getViewport() == av)
+          {
             return (AlignFrame) frames[t];
+          }
         }
       }
     }
     return null;
   }
-  public void updateToJalview() {
+
+  public void updateToJalview()
+  {
     VAMSAS _roots[] = cdoc.getVamsasRoots();
 
-    for (int _root = 0; _root<_roots.length; _root++) {
+    for (int _root = 0; _root < _roots.length; _root++)
+    {
       VAMSAS root = _roots[_root];
-      boolean newds=false;
-      for (int _ds=0,_nds=root.getDataSetCount(); _ds<_nds; _ds++) {
+      boolean newds = false;
+      for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
+      {
         // ///////////////////////////////////
         // ///LOAD DATASET
         DataSet dataset = root.getDataSet(_ds);
         int i, iSize = dataset.getSequenceCount();
         Vector dsseqs;
-        jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
-        int jremain=0;
-        if (jdataset==null) {
+        jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment)
+            getvObj2jv(dataset);
+        int jremain = 0;
+        if (jdataset == null)
+        {
           Cache.log.debug("Initialising new jalview dataset fields");
-          newds=true;
-          dsseqs=new Vector();
-        } else {
+          newds = true;
+          dsseqs = new Vector();
+        }
+        else
+        {
           Cache.log.debug("Update jalview dataset from vamsas.");
-          jremain=jdataset.getHeight();
-          dsseqs=jdataset.getSequences();
+          jremain = jdataset.getHeight();
+          dsseqs = jdataset.getSequences();
         }
 
         // TODO: test sequence merging - we preserve existing non vamsas
         // sequences but add in any new vamsas ones, and don't yet update any
         // sequence attributes
-        for (i = 0; i < iSize ; i++)
+        for (i = 0; i < iSize; i++)
         {
           Sequence vdseq = dataset.getSequence(i);
           jalview.datamodel.SequenceI dsseq = (SequenceI) getvObj2jv(vdseq);
-          if (dsseq!=null) {
+          if (dsseq != null)
+          {
             if (!dsseq.getSequence().equals(vdseq.getSequence()))
-              throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
+            {
+              throw new Error(
+                  "Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
+            }
             jremain--;
-          } else {
+          }
+          else
+          {
             dsseq = new jalview.datamodel.Sequence(
                 dataset.getSequence(i).getName(),
                 dataset.getSequence(i).getSequence(),
                 dataset.getSequence(i).getStart(),
-                dataset.getSequence(i).getEnd()  );
+                dataset.getSequence(i).getEnd());
             dsseq.setDescription(dataset.getSequence(i).getDescription());
             bindjvvobj(dsseq, dataset.getSequence(i));
             dsseq.setVamsasId(dataset.getSequence(i).getVorbaId().getId());
             dsseqs.add(dsseq);
           }
-          if (vdseq.getDbRefCount()>0) {
-            DbRef [] dbref = vdseq.getDbRef();
-            for(int db=0; db<dbref.length; db++)
+          if (vdseq.getDbRefCount() > 0)
+          {
+            DbRef[] dbref = vdseq.getDbRef();
+            for (int db = 0; db < dbref.length; db++)
             {
-              jalview.datamodel.DBRefEntry dbr=(jalview.datamodel.DBRefEntry) getvObj2jv(dbref[db]);
-              if (dbr==null) {
+              jalview.datamodel.DBRefEntry dbr = (jalview.datamodel.DBRefEntry)
+                  getvObj2jv(dbref[db]);
+              if (dbr == null)
+              {
                 // add new dbref
-                dsseq.addDBRef(dbr= new jalview.datamodel.DBRefEntry
-                    (
-                        dbref[db].getSource().toString(),
-                        dbref[db].getVersion().toString(),
-                        dbref[db].getAccessionId().toString()));
+                dsseq.addDBRef(dbr = new jalview.datamodel.DBRefEntry
+                               (
+                                   dbref[db].getSource().toString(),
+                                   dbref[db].getVersion().toString(),
+                                   dbref[db].getAccessionId().toString()));
                 bindjvvobj(dbr, dbref[db]);
               }
             }
           }
         }
 
-        if (newds) {
+        if (newds)
+        {
           SequenceI[] seqs = new SequenceI[dsseqs.size()];
-          for (i=0,iSize=dsseqs.size(); i<iSize; i++) {
-            seqs[i]=(SequenceI) dsseqs.elementAt(i);
+          for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
+          {
+            seqs[i] = (SequenceI) dsseqs.elementAt(i);
             dsseqs.setElementAt(null, i);
           }
           jdataset = new jalview.datamodel.Alignment(seqs);
@@ -924,20 +1047,33 @@ public class VamsasDatastore {
         }
         // ////////
         // add any new dataset sequence feature annotations
-        if (dataset.getDataSetAnnotations() != null) {
-          for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++) {
-            DataSetAnnotations dseta=dataset.getDataSetAnnotations(dsa);
-            SequenceI dsSeq=(SequenceI) getvObj2jv((Vobject) dseta.getSeqRef());
-            if (dsSeq==null) {
-              jalview.bin.Cache.log.warn("Couldn't resolve jalview sequenceI for dataset object reference "+((Vobject)dataset.getDataSetAnnotations(dsa).getSeqRef()).getVorbaId().getId());
-            } else {
-              if (dseta.getAnnotationElementCount()==0) {
-                jalview.datamodel.SequenceFeature sf=(jalview.datamodel.SequenceFeature) getvObj2jv(dseta);
-                if (sf==null) {
-                  dsSeq.addSequenceFeature(sf=getJalviewSeqFeature(dseta));
+        if (dataset.getDataSetAnnotations() != null)
+        {
+          for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)
+          {
+            DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa);
+            SequenceI dsSeq = (SequenceI) getvObj2jv( (Vobject) dseta.getSeqRef());
+            if (dsSeq == null)
+            {
+              jalview.bin.Cache.log.warn(
+                  "Couldn't resolve jalview sequenceI for dataset object reference " +
+                  ( (Vobject) dataset.getDataSetAnnotations(dsa).getSeqRef()).
+                  getVorbaId().getId());
+            }
+            else
+            {
+              if (dseta.getAnnotationElementCount() == 0)
+              {
+                jalview.datamodel.SequenceFeature sf = (jalview.datamodel.
+                    SequenceFeature) getvObj2jv(dseta);
+                if (sf == null)
+                {
+                  dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dseta));
                   bindjvvobj(sf, dseta);
                 }
-              } else {
+              }
+              else
+              {
                 // TODO: deal with alignmentAnnotation style annotation
                 // appearing on dataset sequences.
                 // JBPNote: we could just add them to all alignments but
@@ -949,71 +1085,100 @@ public class VamsasDatastore {
           }
         }
 
-        if (dataset.getAlignmentCount()>0) {
+        if (dataset.getAlignmentCount() > 0)
+        {
           // LOAD ALIGNMENTS from DATASET
 
-          for (int al=0,nal=dataset.getAlignmentCount(); al<nal; al++) {
-            org.vamsas.objects.core.Alignment alignment = dataset.getAlignment(al);
+          for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++)
+          {
+            org.vamsas.objects.core.Alignment alignment = dataset.getAlignment(
+                al);
             AlignViewport av = (AlignViewport) getvObj2jv(alignment);
-            jalview.datamodel.AlignmentI jal=null;
-            if (av!=null)
+            jalview.datamodel.AlignmentI jal = null;
+            if (av != null)
+            {
               jal = av.getAlignment();
+            }
             iSize = alignment.getAlignmentSequenceCount();
-            boolean newal=(jal==null) ? true : false;
-            Vector newasAnnots=new Vector();
-            char gapChar=' '; // default for new alignments read in from the document
-            if (jal!=null) {
-              dsseqs=jal.getSequences(); // for merge/update
-              gapChar=jal.getGapCharacter();
-            } else {
-              dsseqs=new Vector();
+            boolean newal = (jal == null) ? true : false;
+            Vector newasAnnots = new Vector();
+            char gapChar = ' '; // default for new alignments read in from the document
+            if (jal != null)
+            {
+              dsseqs = jal.getSequences(); // for merge/update
+              gapChar = jal.getGapCharacter();
             }
-            char valGapchar=alignment.getGapChar().charAt(0);
+            else
+            {
+              dsseqs = new Vector();
+            }
+            char valGapchar = alignment.getGapChar().charAt(0);
             for (i = 0; i < iSize; i++)
             {
               AlignmentSequence valseq = alignment.getAlignmentSequence(i);
               jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
-              if (alseq!=null) {
+              if (alseq != null)
+              {
                 //TODO: upperCase/LowerCase situation here ? do we allow it ?
                 //if (!alseq.getSequence().equals(valseq.getSequence())) {
                 // throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
                 if (Cache.log.isDebugEnabled())
-                  Cache.log.debug("Updating apparently edited sequence "+alseq.getName());
+                {
+                  Cache.log.debug("Updating apparently edited sequence " +
+                                  alseq.getName());
+                }
                 // this might go *horribly* wrong
-                alseq.setSequence(new String(valseq.getSequence()).replace(valGapchar, gapChar));
+                alseq.setSequence(new String(valseq.getSequence()).replace(
+                    valGapchar, gapChar));
                 jremain--;
-              } else {
+              }
+              else
+              {
                 alseq = new jalview.datamodel.Sequence(
                     valseq.getName(),
                     valseq.getSequence().replace(valGapchar, gapChar),
                     valseq.getStart(),
-                    valseq.getEnd()  );
+                    valseq.getEnd());
 
-                Vobject datsetseq = (Vobject)valseq.getRefid();
-                if (datsetseq!=null) {
-                  alseq.setDatasetSequence((SequenceI)getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI
-                } else {
-                  Cache.log.error("Invalid dataset sequence id (null) for alignment sequence "+valseq.getVorbaId());
+                Vobject datsetseq = (Vobject) valseq.getRefid();
+                if (datsetseq != null)
+                {
+                  alseq.setDatasetSequence( (SequenceI) getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI
+                }
+                else
+                {
+                  Cache.log.error(
+                      "Invalid dataset sequence id (null) for alignment sequence " +
+                      valseq.getVorbaId());
                 }
                 bindjvvobj(alseq, valseq);
                 alseq.setVamsasId(valseq.getVorbaId().getId());
                 dsseqs.add(alseq);
               }
-              if (valseq.getAlignmentSequenceAnnotationCount()>0) {
-                AlignmentSequenceAnnotation[] vasannot=valseq.getAlignmentSequenceAnnotation();
-                for (int a=0; a<vasannot.length; a++) {
-                  jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: 1:many jalview alignment sequence annotations
-                  if (asa==null) {
+              if (valseq.getAlignmentSequenceAnnotationCount() > 0)
+              {
+                AlignmentSequenceAnnotation[] vasannot = valseq.
+                    getAlignmentSequenceAnnotation();
+                for (int a = 0; a < vasannot.length; a++)
+                {
+                  jalview.datamodel.AlignmentAnnotation asa = (jalview.
+                      datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: 1:many jalview alignment sequence annotations
+                  if (asa == null)
+                  {
                     int se[] = getBounds(vasannot[a]);
                     asa = getjAlignmentAnnotation(jal, vasannot[a]);
-                    asa.sequenceRef=alseq;
-                    asa.createSequenceMapping(alseq, alseq.getStart()+se[0], false); // TODO: verify that positions in alseqAnnotation correspond to ungapped residue positions.
+                    asa.sequenceRef = alseq;
+                    asa.createSequenceMapping(alseq, alseq.getStart() + se[0], false); // TODO: verify that positions in alseqAnnotation correspond to ungapped residue positions.
                     bindjvvobj(asa, vasannot[a]);
                     newasAnnots.add(asa);
-                  } else {
+                  }
+                  else
+                  {
                     // update existing annotation - can do this in place
-                    if (vasannot[a].getModifiable()) {
-                      Cache.log.info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
+                    if (vasannot[a].getModifiable())
+                    {
+                      Cache.log.info(
+                          "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
                       // TODO: should at least replace with new one - otherwise things will break
                       // basically do this:
                       // int se[] = getBounds(vasannot[a]);
@@ -1025,49 +1190,62 @@ public class VamsasDatastore {
                 }
               }
             }
-            if (jal==null) {
+            if (jal == null)
+            {
               SequenceI[] seqs = new SequenceI[dsseqs.size()];
-              for (i=0,iSize=dsseqs.size(); i<iSize; i++) {
-                seqs[i]=(SequenceI) dsseqs.elementAt(i);
+              for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
+              {
+                seqs[i] = (SequenceI) dsseqs.elementAt(i);
                 dsseqs.setElementAt(null, i);
               }
               jal = new jalview.datamodel.Alignment(seqs);
-              Cache.log.debug("New vamsas alignment imported into jalview "+alignment.getVorbaId().getId());
+              Cache.log.debug("New vamsas alignment imported into jalview " +
+                              alignment.getVorbaId().getId());
               jal.setDataset(jdataset);
             }
-            if (newasAnnots!=null && newasAnnots.size()>0) {
+            if (newasAnnots != null && newasAnnots.size() > 0)
+            {
               // Add the new sequence annotations in to the alignment.
-              for (int an=0,anSize=newasAnnots.size(); an<anSize; an++) {
-                jal.addAnnotation((AlignmentAnnotation) newasAnnots.elementAt(an));
+              for (int an = 0, anSize = newasAnnots.size(); an < anSize; an++)
+              {
+                jal.addAnnotation( (AlignmentAnnotation) newasAnnots.elementAt(
+                    an));
                 // TODO: check if anything has to be done - like calling adjustForAlignment or something.
                 newasAnnots.setElementAt(null, an);
               }
-              newasAnnots=null;
+              newasAnnots = null;
             }
             // //////////////////////////////////////////
             // //LOAD ANNOTATIONS FOR THE ALIGNMENT
             // ////////////////////////////////////
-            if (alignment.getAlignmentAnnotationCount()>0)
+            if (alignment.getAlignmentAnnotationCount() > 0)
             {
-              org.vamsas.objects.core.AlignmentAnnotation[] an = alignment.getAlignmentAnnotation();
+              org.vamsas.objects.core.AlignmentAnnotation[] an = alignment.
+                  getAlignmentAnnotation();
 
               for (int j = 0; j < an.length; j++)
               {
-                jalview.datamodel.AlignmentAnnotation jan=(jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);
-                if (jan!=null) {
+                jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.
+                    AlignmentAnnotation) getvObj2jv(an[j]);
+                if (jan != null)
+                {
                   // update or stay the same.
                   // TODO: should at least replace with a new one - otherwise things will break
                   // basically do this:
                   // jan.update(getjAlignmentAnnotation(jal, an[a])); //  update from another annotation object in place.
 
                   Cache.log.debug("update from vamsas alignment annotation to existing jalview alignment annotation.");
-                  if (an[j].getModifiable()) {
+                  if (an[j].getModifiable())
+                  {
                     // TODO: user defined annotation is totally mutable... - so load it up or throw away if locally edited.
-                    Cache.log.info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
+                    Cache.log.info(
+                        "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
                   }
                   // TODO: compare annotation element rows
                   // TODO: compare props.
-                } else {
+                }
+                else
+                {
                   jan = getjAlignmentAnnotation(jal, an[j]);
                   jal.addAnnotation(jan);
                   bindjvvobj(jan, an[j]);
@@ -1075,29 +1253,40 @@ public class VamsasDatastore {
               }
             }
             AlignFrame alignFrame;
-            if (av==null) {
-              Cache.log.debug("New alignframe for alignment "+alignment.getVorbaId());
+            if (av == null)
+            {
+              Cache.log.debug("New alignframe for alignment " +
+                              alignment.getVorbaId());
               // ///////////////////////////////
               // construct alignment view
-              alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-              av=alignFrame.getViewport();
-              String title = alignment.getProvenance().getEntry(alignment.getProvenance().getEntryCount()-1).getAction();
-              if (alignment.getPropertyCount()>0) {
-                for (int p=0,pe=alignment.getPropertyCount(); p<pe; p++) {
-                  if (alignment.getProperty(p).getName().equals("jalview:AlTitle")) {
+              alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH,
+                                          AlignFrame.DEFAULT_HEIGHT);
+              av = alignFrame.getViewport();
+              String title = alignment.getProvenance().getEntry(alignment.
+                  getProvenance().getEntryCount() - 1).getAction();
+              if (alignment.getPropertyCount() > 0)
+              {
+                for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++)
+                {
+                  if (alignment.getProperty(p).getName().equals(
+                      "jalview:AlTitle"))
+                  {
                     title = alignment.getProperty(p).getContent();
                   }
                 }
               }
               // TODO: automatically create meaningful title for a vamsas alignment using its provenance.
-              jalview.gui.Desktop.addInternalFrame(alignFrame, title + "("+alignment.getVorbaId()+")",
+              jalview.gui.Desktop.addInternalFrame(alignFrame,
+                  title + "(" + alignment.getVorbaId() + ")",
                   AlignFrame.DEFAULT_WIDTH,
                   AlignFrame.DEFAULT_HEIGHT);
               bindjvvobj(av, alignment);
-            } else {
+            }
+            else
+            {
               // find the alignFrame for jal.
               // TODO: fix this so we retrieve the alignFrame handing av *directly*
-              alignFrame=getAlignFrameFor(av);
+              alignFrame = getAlignFrameFor(av);
             }
             // LOAD TREES
             // /////////////////////////////////////
@@ -1107,24 +1296,35 @@ public class VamsasDatastore {
               for (int t = 0; t < alignment.getTreeCount(); t++)
               {
                 Tree tree = alignment.getTree(t);
-                TreePanel tp=(TreePanel) getvObj2jv(tree);
-                if (tp!=null) {
-                  Cache.log.info("Update from vamsas document to alignment associated tree not implemented yet.");
-                } else {
+                TreePanel tp = (TreePanel) getvObj2jv(tree);
+                if (tp != null)
+                {
+                  Cache.log.info(
+                      "Update from vamsas document to alignment associated tree not implemented yet.");
+                }
+                else
+                {
                   // make a new tree
                   Object[] idata = this.recoverInputData(tree.getProvenance());
-                  try {
-                    AlignmentView inputData=null;
-                    if (idata!=null && idata[0]!=null)
+                  try
+                  {
+                    AlignmentView inputData = null;
+                    if (idata != null && idata[0] != null)
+                    {
                       inputData = (AlignmentView) idata[0];
+                    }
                     tp = alignFrame.ShowNewickTree(
                         new jalview.io.NewickFile(tree.getNewick(0).getContent()),
-                        tree.getNewick(0).getTitle()+" ("+tree.getVorbaId()+")",inputData,
+                        tree.getNewick(0).getTitle() + " (" + tree.getVorbaId() +
+                        ")", inputData,
                         600, 500,
                         t * 20 + 50, t * 20 + 50);
                     bindjvvobj(tp, tree);
-                  } catch (Exception e) {
-                    Cache.log.warn("Problems parsing treefile '"+tree.getNewick(0).getContent()+"'",e);
+                  }
+                  catch (Exception e)
+                  {
+                    Cache.log.warn("Problems parsing treefile '" +
+                                   tree.getNewick(0).getContent() + "'", e);
                   }
                 }
               }
@@ -1135,219 +1335,334 @@ public class VamsasDatastore {
       }
     }
   }
+
   // bitfields - should be a template in j1.5
-  private static int HASSECSTR=0;
-  private static int HASVALS=1;
-  private static int HASHPHOB=2;
-  private static int HASDC=3;
-  private static int HASDESCSTR=4;
-  private static int HASTWOSTATE=5; // not used yet.
+  private static int HASSECSTR = 0;
+  private static int HASVALS = 1;
+  private static int HASHPHOB = 2;
+  private static int HASDC = 3;
+  private static int HASDESCSTR = 4;
+  private static int HASTWOSTATE = 5; // not used yet.
   /**
    * parses the AnnotationElements - if they exist - into jalview.datamodel.Annotation[] rows
    * Two annotation rows are made if there are distinct annotation for both at 'pos' and 'after pos' at any particular site.
    * @param annotation
    * @return { boolean[static int constants ], int[ae.length] - map to annotated object frame, jalview.datamodel.Annotation[], jalview.datamodel.Annotation[] (after)}
    */
-  private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation annotation) {
+  private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation
+                                        annotation)
+  {
     // set these attributes by looking in the annotation to decide what kind of alignment annotation rows will be made
     // TODO: potentially we might make several annotation rows from one vamsas alignment annotation. the jv2Vobj binding mechanism
     // may not quite cope with this (without binding an array of annotations to a vamsas alignment annotation)
     // summary flags saying what we found over the set of annotation rows.
-    boolean[] AeContent = new boolean[] { false, false, false, false, false};
+    boolean[] AeContent = new boolean[]
+        {
+        false, false, false, false, false};
     int[] rangeMap = getMapping(annotation);
-    jalview.datamodel.Annotation[][] anot=new jalview.datamodel.Annotation[][] {
+    jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
+        {
         new jalview.datamodel.Annotation[rangeMap.length],
         new jalview.datamodel.Annotation[rangeMap.length]
     };
-    boolean mergeable=true; //false  if 'after positions cant be placed on same annotation row as positions.
+    boolean mergeable = true; //false  if 'after positions cant be placed on same annotation row as positions.
 
-    if (annotation.getAnnotationElementCount()>0) {
+    if (annotation.getAnnotationElementCount() > 0)
+    {
       AnnotationElement ae[] = annotation.getAnnotationElement();
       for (int aa = 0; aa < ae.length; aa++)
       {
-        int pos = ae[aa].getPosition()-1;// pos counts from 1 to (|seg.start-seg.end|+1)
-        if (pos>=0 && pos<rangeMap.length) {
-          int row=ae[aa].getAfter()?1:0;
-          if (anot[row][pos]!=null) {
+        int pos = ae[aa].getPosition() - 1; // pos counts from 1 to (|seg.start-seg.end|+1)
+        if (pos >= 0 && pos < rangeMap.length)
+        {
+          int row = ae[aa].getAfter() ? 1 : 0;
+          if (anot[row][pos] != null)
+          {
             // only time this should happen is if the After flag is set.
-            Cache.log.debug("Ignoring duplicate annotation site at "+pos);
+            Cache.log.debug("Ignoring duplicate annotation site at " + pos);
             continue;
           }
-          if (anot[1-row][pos]!=null)
-            mergeable=false;
+          if (anot[1 - row][pos] != null)
+          {
+            mergeable = false;
+          }
           String desc = "";
-          if (ae[aa].getDescription()!=null) {
+          if (ae[aa].getDescription() != null)
+          {
             desc = ae[aa].getDescription();
-            if (desc.length()>0) {
+            if (desc.length() > 0)
+            {
               // have imported valid description string
-              AeContent[HASDESCSTR]=true;
+              AeContent[HASDESCSTR] = true;
             }
           }
-          String dc = null;//ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();
-          String ss = null;//ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();
+          String dc = null; //ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();
+          String ss = null; //ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();
           java.awt.Color colour = null;
-          if (ae[aa].getGlyphCount()>0) {
+          if (ae[aa].getGlyphCount() > 0)
+          {
             Glyph[] glyphs = ae[aa].getGlyph();
-            for (int g=0; g<glyphs.length; g++) {
-              if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) {
-                ss=glyphs[g].getContent();
-                AeContent[HASSECSTR]=true;
-              } else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) {
+            for (int g = 0; g < glyphs.length; g++)
+            {
+              if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+                                             GlyphDictionary.PROTEIN_SS_3STATE))
+              {
+                ss = glyphs[g].getContent();
+                AeContent[HASSECSTR] = true;
+              }
+              else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+                                                  GlyphDictionary.
+                                                  PROTEIN_HD_HYDRO))
+              {
                 Cache.log.debug("ignoring hydrophobicity glyph marker.");
-                AeContent[HASHPHOB]=true;
-                char c=(dc=glyphs[g].getContent()).charAt(0);
+                AeContent[HASHPHOB] = true;
+                char c = (dc = glyphs[g].getContent()).charAt(0);
                 // dc may get overwritten - but we still set the colour.
-                colour = new java.awt.Color(c=='+'?255:0,c=='.'?255:0,c=='-'?255:0);
+                colour = new java.awt.Color(c == '+' ? 255 : 0,
+                                            c == '.' ? 255 : 0,
+                                            c == '-' ? 255 : 0);
 
-              } else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.DEFAULT)) {
+              }
+              else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+                                                  GlyphDictionary.DEFAULT))
+              {
                 dc = glyphs[g].getContent();
-                AeContent[HASDC]=true;
-              } else {
-                Cache.log.debug("Ignoring unknown glyph type "+glyphs[g].getDict());
+                AeContent[HASDC] = true;
+              }
+              else
+              {
+                Cache.log.debug("Ignoring unknown glyph type " +
+                                glyphs[g].getDict());
               }
             }
           }
-          float val=0;
-          if (ae[aa].getValueCount()>0) {
-            AeContent[HASVALS]=true;
-            if (ae[aa].getValueCount()>1) {
-              Cache.log.warn("ignoring additional "+(ae[aa].getValueCount()-1)+"values in annotation element.");
+          float val = 0;
+          if (ae[aa].getValueCount() > 0)
+          {
+            AeContent[HASVALS] = true;
+            if (ae[aa].getValueCount() > 1)
+            {
+              Cache.log.warn("ignoring additional " +
+                             (ae[aa].getValueCount() - 1) +
+                             "values in annotation element.");
             }
             val = ae[aa].getValue(0);
           }
-          if (colour==null) {
-            anot[row][pos]=new jalview.datamodel.Annotation((dc!=null) ? dc : "", desc, (ss!=null)?ss.charAt(0):' ', val);
-          } else {
-            anot[row][pos]=new jalview.datamodel.Annotation((dc!=null) ? dc : "", desc, (ss!=null)?ss.charAt(0):' ', val, colour);
+          if (colour == null)
+          {
+            anot[row][pos] = new jalview.datamodel.Annotation( (dc != null) ?
+                dc : "", desc, (ss != null) ? ss.charAt(0) : ' ', val);
+          }
+          else
+          {
+            anot[row][pos] = new jalview.datamodel.Annotation( (dc != null) ?
+                dc : "", desc, (ss != null) ? ss.charAt(0) : ' ', val, colour);
           }
-        } else {
-          Cache.log.warn("Ignoring out of bound annotation element "+aa+" in "+annotation.getVorbaId().getId());
+        }
+        else
+        {
+          Cache.log.warn("Ignoring out of bound annotation element " + aa +
+                         " in " + annotation.getVorbaId().getId());
         }
       }
       // decide on how many annotation rows are needed.
-      if (mergeable) {
-        for (int i=0; i<anot[0].length;i++) {
-          if (anot[1][i]!=null) {
+      if (mergeable)
+      {
+        for (int i = 0; i < anot[0].length; i++)
+        {
+          if (anot[1][i] != null)
+          {
             anot[0][i] = anot[1][i];
-            anot[0][i].description = anot[0][i].description+" (after)";
-            AeContent[HASDESCSTR]=true; // we have valid description string data
+            anot[0][i].description = anot[0][i].description + " (after)";
+            AeContent[HASDESCSTR] = true; // we have valid description string data
             anot[1][i] = null;
           }
         }
         anot[1] = null;
-      } else {
-        for (int i=0; i<anot[0].length;i++) {
-          anot[1][i].description = anot[1][i].description+" (after)";
+      }
+      else
+      {
+        for (int i = 0; i < anot[0].length; i++)
+        {
+          anot[1][i].description = anot[1][i].description + " (after)";
         }
       }
-      return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
-    } else {
+      return new Object[]
+          {
+          AeContent, rangeMap, anot[0], anot[1]};
+    }
+    else
+    {
       // no annotations to parse. Just return an empty annotationElement[] array.
-      return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
+      return new Object[]
+          {
+          AeContent, rangeMap, anot[0], anot[1]};
     }
     // return null;
   }
+
   /**
    * @param jal the jalview alignment to which the annotation will be attached (ideally - freshly updated from corresponding vamsas alignment)
    * @param annotation
    * @return unbound jalview alignment annotation object.
    */
-  private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview.datamodel.AlignmentI jal, org.vamsas.objects.core.RangeAnnotation annotation) {
-    jalview.datamodel.AlignmentAnnotation jan =null;
-    if (annotation==null)
+  private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview.
+      datamodel.AlignmentI jal,
+      org.vamsas.objects.core.RangeAnnotation annotation)
+  {
+    jalview.datamodel.AlignmentAnnotation jan = null;
+    if (annotation == null)
+    {
       return null;
+    }
     // boolean hasSequenceRef=annotation.getClass().equals(org.vamsas.objects.core.AlignmentSequenceAnnotation.class);
     //boolean hasProvenance=hasSequenceRef || (annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class));
     /*int se[] = getBounds(annotation);
-    if (se==null)
+         if (se==null)
       se=new int[] {0,jal.getWidth()-1};
      */
     Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation);
-    String a_label=annotation.getLabel();
-    String a_descr=annotation.getDescription();
-    if (a_label==null || a_label.length()==0) {
+    String a_label = annotation.getLabel();
+    String a_descr = annotation.getDescription();
+    if (a_label == null || a_label.length() == 0)
+    {
       a_label = annotation.getType();
-      if (a_label.length()==0)
+      if (a_label.length() == 0)
+      {
         a_label = "Unamed annotation";
+      }
     }
-    if (a_descr==null || a_descr.length()==0) {
-      a_descr = "Annotation of type '"+annotation.getType()+"'";
+    if (a_descr == null || a_descr.length() == 0)
+    {
+      a_descr = "Annotation of type '" + annotation.getType() + "'";
     }
-    if (parsedRangeAnnotation==null) {
-      Cache.log.debug("Inserting empty annotation row elements for a whole-alignment annotation.");
-
+    if (parsedRangeAnnotation == null)
+    {
+      Cache.log.debug(
+          "Inserting empty annotation row elements for a whole-alignment annotation.");
 
-    } else {
-      if (parsedRangeAnnotation[3]!=null) {
-        Cache.log.warn("Ignoring 'After' annotation row in "+annotation.getVorbaId());
+    }
+    else
+    {
+      if (parsedRangeAnnotation[3] != null)
+      {
+        Cache.log.warn("Ignoring 'After' annotation row in " +
+                       annotation.getVorbaId());
       }
-      jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
-      boolean[] has=(boolean[])parsedRangeAnnotation[0];
+      jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[])
+          parsedRangeAnnotation[2];
+      boolean[] has = (boolean[]) parsedRangeAnnotation[0];
       // VAMSAS: getGraph is only on derived annotation for alignments - in this way its 'odd' - there is already an existing TODO about removing this flag as being redundant
       /*if ((annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class) && ((org.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
           || (hasSequenceRef=true && ((org.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {
-      */
-      if (has[HASVALS]) {
+       */
+      if (has[HASVALS])
+      {
         // make bounds and automatic description strings for jalview user's benefit (these shouldn't be written back to vamsas document)
-        boolean first=true;
-        float min=0,max=1;
-        int lastval=0;
-        for (int i=0;i<arow.length; i++) {
-          if (arow[i]!=null) {
-            if (i-lastval>1) {
+        boolean first = true;
+        float min = 0, max = 1;
+        int lastval = 0;
+        for (int i = 0; i < arow.length; i++)
+        {
+          if (arow[i] != null)
+          {
+            if (i - lastval > 1)
+            {
               // do some interpolation *between* points
-              if (arow[lastval]!=null) {
-                float interval = arow[i].value-arow[lastval].value;
-                interval/=i-lastval;
+              if (arow[lastval] != null)
+              {
+                float interval = arow[i].value - arow[lastval].value;
+                interval /= i - lastval;
                 float base = arow[lastval].value;
-                for (int ip=lastval+1,np=0; ip<i; np++,ip++) {
-                  arow[ip] = new jalview.datamodel.Annotation("","",' ', interval*np+base);
+                for (int ip = lastval + 1, np = 0; ip < i; np++, ip++)
+                {
+                  arow[ip] = new jalview.datamodel.Annotation("", "", ' ',
+                      interval * np + base);
                   // NB - Interpolated points don't get a tooltip and description.
                 }
               }
             }
-            lastval=i;
+            lastval = i;
             // check range - shouldn't we have a min and max property in the annotation object ?
-            if (first) { min=max=arow[i].value; first=false;}
-            else { if (arow[i].value<min) { min=arow[i].value; }
-            else if (arow[i].value>max) { max=arow[i].value; }
+            if (first)
+            {
+              min = max = arow[i].value;
+              first = false;
+            }
+            else
+            {
+              if (arow[i].value < min)
+              {
+                min = arow[i].value;
+              }
+              else if (arow[i].value > max)
+              {
+                max = arow[i].value;
+              }
             }
             // make tooltip and display char value
-            if (!has[HASDESCSTR]) arow[i].description = arow[i].value + "";
-            if (!has[HASDC]) arow[i].displayCharacter=arow[i].value+"";
+            if (!has[HASDESCSTR])
+            {
+              arow[i].description = arow[i].value + "";
+            }
+            if (!has[HASDC])
+            {
+              arow[i].displayCharacter = arow[i].value + "";
+            }
           }
         }
-        int type=jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;
-        if (has[HASHPHOB]) {
+        int type = jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;
+        if (has[HASHPHOB])
+        {
           type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
         }
-        jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow, min, max, type);
-      } else {
+        jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow,
+            min, max, type);
+      }
+      else
+      {
         jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow);
         jan.setThreshold(null);
       }
-      if (annotation.getLinkCount()>0) {
-        Cache.log.warn("Ignoring "+annotation.getLinkCount()+"links added to AlignmentAnnotation.");
+      if (annotation.getLinkCount() > 0)
+      {
+        Cache.log.warn("Ignoring " + annotation.getLinkCount() +
+                       "links added to AlignmentAnnotation.");
       }
-      if (annotation.getModifiable()) {
-        jan.editable=true;
+      if (annotation.getModifiable())
+      {
+        jan.editable = true;
       }
 
-      if (annotation.getPropertyCount()>0) {
+      if (annotation.getPropertyCount() > 0)
+      {
         // look for special jalview properties
-        org.vamsas.objects.core.Property[] props=annotation.getProperty();
-        for (int p=0;p<props.length; p++) {
-          if (props[p].getName().equalsIgnoreCase("jalview:graphType")) {
-            try {
+        org.vamsas.objects.core.Property[] props = annotation.getProperty();
+        for (int p = 0; p < props.length; p++)
+        {
+          if (props[p].getName().equalsIgnoreCase("jalview:graphType"))
+          {
+            try
+            {
               // probably a jalview annotation graph so recover the visualization hints.
-              jan.graph = jalview.datamodel.AlignmentAnnotation.getGraphValueFromString(props[p].getContent());
-            } catch (Exception e) {
-              Cache.log.debug("Invalid graph type value in jalview:graphType property.");
+              jan.graph = jalview.datamodel.AlignmentAnnotation.
+                  getGraphValueFromString(props[p].getContent());
+            }
+            catch (Exception e)
+            {
+              Cache.log.debug(
+                  "Invalid graph type value in jalview:graphType property.");
             }
-            try {
-              if (annotation.getGroup()!=null && annotation.getGroup().length()>0)
+            try
+            {
+              if (annotation.getGroup() != null &&
+                  annotation.getGroup().length() > 0)
+              {
                 jan.graphGroup = Integer.parseInt(annotation.getGroup());
-            } catch (Exception e) {
+              }
+            }
+            catch (Exception e)
+            {
               Cache.log.info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
             }
           }
@@ -1361,7 +1676,8 @@ public class VamsasDatastore {
     return null;
   }
 
-  private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta) {
+  private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
+  {
     int[] se = getBounds(dseta);
     SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta.getType(),
         dseta.getDescription(), dseta.getStatus(), se[0], se[1], dseta
@@ -1384,61 +1700,79 @@ public class VamsasDatastore {
    * @param dseta
    * @return int[] { start, end}
    */
-  private int[] getBounds(RangeType dseta) {
+  private int[] getBounds(RangeType dseta)
+  {
     if (dseta != null)
     {
       int[] se = null;
-      if (dseta.getSegCount()>0 && dseta.getPosCount()>0)
+      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
+      {
         throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+      }
       if (dseta.getSegCount() > 0)
       {
-        se = getSegRange(dseta.getSeg(0),true);
+        se = getSegRange(dseta.getSeg(0), true);
         for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
         {
           int nse[] = getSegRange(dseta.getSeg(s), true);
           if (se[0] > nse[0])
+          {
             se[0] = nse[0];
+          }
           if (se[1] < nse[1])
+          {
             se[1] = nse[1];
+          }
         }
       }
       if (dseta.getPosCount() > 0)
       {
         // could do a polarity for pos range too. and pass back indication of discontinuities.
         int pos = dseta.getPos(0).getI();
-        se = new int[] { pos, pos };
+        se = new int[]
+            {
+            pos, pos};
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
           if (se[0] > pos)
+          {
             se[0] = pos;
+          }
           if (se[1] < pos)
+          {
             se[1] = pos;
+          }
         }
       }
       return se;
     }
     return null;
   }
+
   /**
    * map from a rangeType's internal frame to the referenced object's coordinate frame.
    * @param dseta
    * @return int [] { ref(pos)...} for all pos in rangeType's frame.
    */
-  private int[] getMapping(RangeType dseta) {
-    Vector posList=new Vector();
+  private int[] getMapping(RangeType dseta)
+  {
+    Vector posList = new Vector();
     if (dseta != null)
     {
       int[] se = null;
-      if (dseta.getSegCount()>0 && dseta.getPosCount()>0)
+      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
+      {
         throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+      }
       if (dseta.getSegCount() > 0)
       {
         for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
         {
           se = getSegRange(dseta.getSeg(s), false);
-          int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1);
-          for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) {
+          int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
+          for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
+          {
             posList.add(new Integer(p));
           }
         }
@@ -1454,15 +1788,19 @@ public class VamsasDatastore {
         }
       }
     }
-    if (posList!=null && posList.size()>0) {
-      int[] range=new int[posList.size()];
-      for (int i=0; i<range.length; i++)
-        range[i] = ((Integer)posList.elementAt(i)).intValue();
+    if (posList != null && posList.size() > 0)
+    {
+      int[] range = new int[posList.size()];
+      for (int i = 0; i < range.length; i++)
+      {
+        range[i] = ( (Integer) posList.elementAt(i)).intValue();
+      }
       posList.clear();
       return range;
     }
     return null;
   }
+
   /* not needed now.
    * Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov) {
     jalview.datamodel.ProvenanceEntry[] entries = null;
@@ -1504,15 +1842,17 @@ public class VamsasDatastore {
     }
 
     return prov;
-  }
+     }
    */
-  jalview.datamodel.Provenance getJalviewProvenance(Provenance prov) {
+  jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
+  {
     // TODO: fix App and Action entries and check use of provenance in jalview.
     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());
+                     prov.getEntry(i).getDate().toDate(),
+                     prov.getEntry(i).getId());
     }
 
     return jprov;
@@ -1523,29 +1863,37 @@ public class VamsasDatastore {
    * @return default initial provenance list for a Jalview created vamsas
    *         object.
    */
-  Provenance dummyProvenance() {
+  Provenance dummyProvenance()
+  {
     return dummyProvenance(null);
   }
 
-  Entry dummyPEntry(String action) {
+  Entry dummyPEntry(String action)
+  {
     Entry entry = new Entry();
     entry.setApp(this.provEntry.getApp());
     if (action != null)
+    {
       entry.setAction(action);
+    }
     else
+    {
       entry.setAction("created.");
+    }
     entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
     entry.setUser(this.provEntry.getUser());
     return entry;
   }
 
-  Provenance dummyProvenance(String action) {
+  Provenance dummyProvenance(String action)
+  {
     Provenance prov = new Provenance();
     prov.addEntry(dummyPEntry(action));
     return prov;
   }
 
-  void addProvenance(Provenance p, String action) {
+  void addProvenance(Provenance p, String action)
+  {
     p.addEntry(dummyPEntry(action));
   }