From 141ad7e898f94594bacb1c77eabbcd837505409c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 24 Jan 2007 17:28:58 +0000
Subject: [PATCH] output now takes alignment, not just sequences

---
 src/jalview/appletgui/APopupMenu.java    |   18 +-
 src/jalview/appletgui/AlignFrame.java    |   38 +-
 src/jalview/appletgui/AlignViewport.java |    6 +-
 src/jalview/io/AppletFormatAdapter.java  |   16 +-
 src/jalview/io/FastaFile.java            |   11 +-
 src/jalview/io/VamsasDatastore.java      | 1502 ------------------------------
 6 files changed, 47 insertions(+), 1544 deletions(-)

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 0c0f562..8f1836c 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -326,22 +326,6 @@ public class APopupMenu
   void outputText(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
-    Vector vseqs = new Vector();
-
-      String [] selection = ap.av.getViewAsString(true);
-      SequenceI [] seqs = ap.av.getSelectionAsNewSequence();
-      if (selection != null)
-      {
-        for (int i = 0; i < selection.length; i++)
-        {
-          Sequence seq = new Sequence(
-              seqs[i].getName(),
-              selection[i],
-              seqs[i].getStart(), seqs[i].getEnd());
-          seq.setDescription(seqs[i].getDescription());
-          vseqs.addElement( seq );
-      }
-    }
 
     Frame frame = new Frame();
     frame.add(cap);
@@ -351,7 +335,7 @@ public class APopupMenu
 
     cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
         e.getActionCommand(),
-        vseqs,
+      new Alignment( ap.av.getSelectionAsNewSequence() ),
         ap.av.showJVSuffix));
 
   }
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 147e035..479d771 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -504,7 +504,7 @@ public void itemStateChanged(ItemEvent evt)
     else if (source == outputAnnotations)
       outputAnnotations();
     else if(source == outputFeatures)
-      outputFeatures();
+      outputFeatures(true, "Jalview");
     else if(source==closeMenuItem)
       closeMenuItem_actionPerformed();
     else if(source==copy)
@@ -655,7 +655,7 @@ public void itemStateChanged(ItemEvent evt)
                                      "Alignment output - " + e.getActionCommand(),
                                      600, 500);
     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
-                                              viewport.getAlignment().getSequences(),
+                                              viewport.getAlignment(),
                                                       viewport.showJVSuffix));
   }
 
@@ -682,18 +682,32 @@ public void itemStateChanged(ItemEvent evt)
       viewport.alignment.getAlignmentAnnotation() ) );
   }
 
-  public void outputFeatures()
+  public String outputFeatures(boolean displayTextbox, String format)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
-    Frame frame = new Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
-                                     "Features",
-                                     600, 500);
+    String features;
+    if (format.equalsIgnoreCase("Jalview"))
+      features = new FeaturesFile().printJalviewFormat(
+              viewport.alignment.getSequencesArray(),
+              viewport.featuresDisplayed);
+    else
+      features = new FeaturesFile().printGFFFormat(
+             viewport.alignment.getSequencesArray(),
+             viewport.featuresDisplayed);
+
+
+    if(displayTextbox)
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame,
+                                       "Features",
+                                       600, 500);
+
+      cap.setText(features);
+    }
 
-    cap.setText(new FeaturesFile().printJalviewFormat(
-                viewport.alignment.getSequencesArray(),
-                viewport.featuresDisplayed));
+    return features;
   }
 
   void launchFullApplication()
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 88a0b0f..7fc240f 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -204,6 +204,8 @@ public class AlignViewport
               11f,
               AlignmentAnnotation.BAR_GRAPH);
           conservation.hasText = true;
+          conservation.autoCalculated = true;
+
 
 
           if (showConservation)
@@ -220,6 +222,7 @@ public class AlignViewport
                                               11f,
                                               AlignmentAnnotation.BAR_GRAPH);
             quality.hasText = true;
+            quality.autoCalculated = true;
 
             alignment.addAnnotation(quality);
           }
@@ -229,6 +232,7 @@ public class AlignViewport
                                              new Annotation[1], 0f, 100f,
                                              AlignmentAnnotation.BAR_GRAPH);
         consensus.hasText = true;
+        consensus.autoCalculated = true;
 
          if (showConsensus)
          {
@@ -1303,7 +1307,7 @@ public class AlignViewport
 
     resetAllColourSchemes();
 
-    alignment.adjustSequenceAnnotations();
+  //AW  alignment.adjustSequenceAnnotations();
   }
 
   void resetAllColourSchemes()
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 232de57..85be22d 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -39,7 +39,7 @@
 
         public static final String [] WRITEABLE_FORMATS = new String[]
             {
-            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"
+            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"  //, "AMSA"
         };
 
 
@@ -175,14 +175,9 @@
          * @return DOCUMENT ME!
          */
         public String formatSequences(String format,
-                                      Vector seqs,
+                                      AlignmentI alignment,
                                       boolean jvsuffix)
         {
-            SequenceI[] s = new SequenceI[seqs.size()];
-
-            for (int i = 0; i < seqs.size(); i++)
-                s[i] = (SequenceI) seqs.elementAt(i);
-
             try
             {
                 AlignFile afile = null;
@@ -219,11 +214,14 @@
                 {
                   afile = new StockholmFile();
                 }
-
+                else if (format.equals("AMSA"))
+                {
+                  afile = new AMSAFile(alignment);
+                }
 
                 afile.addJVSuffix(jvsuffix);
 
-                afile.setSeqs(s);
+                afile.setSeqs( alignment.getSequencesArray() );
 
                 return afile.print();
             }
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 71d372e..fe5e02f 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -33,6 +33,13 @@ import java.util.*;
  */
 public class FastaFile extends AlignFile
 {
+  /**
+   * Length of a sequence line
+   */
+  int len = 72;
+
+  StringBuffer out;
+
     /**
      * Creates a new FastaFile object.
      */
@@ -159,7 +166,6 @@ public class FastaFile extends AlignFile
         }
     }
 
-
     /**
      * DOCUMENT ME!
      *
@@ -172,8 +178,7 @@ public class FastaFile extends AlignFile
      */
     public String print(SequenceI[] s)
     {
-        int len = 72;
-        StringBuffer out = new StringBuffer();
+        out = new StringBuffer();
         int i = 0;
 
         while ((i < s.length) && (s[i] != null))
diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java
index 6a117b2..6af457e 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;
@@ -52,1501 +46,5 @@ import org.exolab.castor.mapping.Mapping;
  */
 
 public class VamsasDatastore {
-  Entry provEntry = null;
-
-  // AlignViewport 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 storeJalview(String file, AlignFrame af) { try { // 1. Load the
-   * mapping information from the file Mapping map = new
-   * Mapping(getClass().getClassLoader()); java.net.URL url =
-   * getClass().getResource("/jalview_mapping.xml"); map.loadMapping(url); // 2.
-   * Unmarshal the data // Unmarshaller unmar = new Unmarshaller();
-   * //unmar.setIgnoreExtraElements(true); //unmar.setMapping(map); // uni =
-   * (UniprotFile) unmar.unmarshal(new FileReader(file)); // 3. marshal the data
-   * with the total price back and print the XML in the console Marshaller
-   * marshaller = new Marshaller( new FileWriter(file) );
-   *
-   * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) {
-   * e.printStackTrace(); } }
-   *
-   *
-   */
-  /**
-   * @return the Vobject bound to Jalview datamodel object
-   */
-  protected Vobject getjv2vObj(Object jvobj) {
-    if (jv2vobj.containsKey(jvobj))
-      return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
-    return null;
-  }
-
-  /**
-   *
-   * @param vobj
-   * @return Jalview datamodel object bound to the vamsas document object
-   */
-  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(vobj.getVorbaId());
-    return null;
-  }
-
-  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 (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()))
-    {
-      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.
-    jv2vobj.put(jvobj, vobj.getVorbaId());
-  }
-
-  /**
-   * put the alignment viewed by AlignViewport into cdoc.
-   *
-   * @param av alignViewport to be stored
-   * @param aFtitle title for alignment
-   */
-  public void storeVAMSAS(AlignViewport av, String aFtitle) {
-    try
-    {
-      jalview.datamodel.AlignmentI jal = av.getAlignment();
-      boolean nw = false;
-      VAMSAS root = null; // will be resolved based on Dataset Parent.
-      // /////////////////////////////////////////
-      // SAVE THE DATASET
-      if (jal.getDataset() == null)
-      {
-        Cache.log.warn("Creating new dataset for an alignment.");
-        jal.setDataset(null);
-      }
-      DataSet dataset = (DataSet) getjv2vObj(jal.getDataset());
-      if (dataset == null)
-      {
-        root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
-        dataset = new DataSet();
-        root.addDataSet(dataset);
-        bindjvvobj(jal.getDataset(), dataset);
-        dataset.setProvenance(dummyProvenance());
-        dataset.getProvenance().addEntry(provEntry);
-        nw = true;
-      }
-      else
-      {
-        root = (VAMSAS) dataset.getV_parent();
-      }
-      // update dataset
-      Sequence sequence;
-      DbRef dbref;
-      // set new dataset and alignment sequences based on alignment Nucleotide
-      // flag.
-      // this *will* break when alignment contains both nucleotide and amino
-      // acid sequences.
-      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++)
-      {
-        SequenceI sq = jal.getSequenceAt(i).getDatasetSequence(); // only insert
-        // referenced
-        // sequences
-        // to dataset.
-        sequence = (Sequence) getjv2vObj(sq);
-        if (sequence == null)
-        {
-          sequence = new Sequence();
-          bindjvvobj(sq, sequence);
-          sq.setVamsasId(sequence.getVorbaId().getId());
-          sequence.setSequence(sq.getSequenceAsString());
-          sequence.setDictionary(dict);
-          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. and update any new
-          // features/references.
-          System.out.println("update dataset sequence object.");
-        }
-        if (sq.getSequenceFeatures() != null)
-        {
-          int sfSize = sq.getSequenceFeatures().length;
-
-          for (int sf = 0; sf < sfSize; sf++)
-          {
-            jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) sq
-            .getSequenceFeatures()[sf];
-
-            DataSetAnnotations dsa = (DataSetAnnotations) getjv2vObj(feature);
-            if (dsa == null)
-            {
-              dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
-                  new DataSetAnnotations(), feature);
-              if (dsa.getProvenance() == null)
-              {
-                dsa.setProvenance(new Provenance());
-              }
-              addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
-              // to update
-              dsa.setSeqRef(sequence);
-              bindjvvobj(feature, dsa);
-              dataset.addDataSetAnnotations(dsa);
-            }
-            else
-            {
-              // todo: verify and update dataset annotations for sequence
-              System.out.println("update dataset sequence annotations.");
-            }
-          }
-        }
-
-        if (sq.getDBRef() != null)
-        {
-          DBRefEntry[] entries = sq.getDBRef();
-          jalview.datamodel.DBRefEntry dbentry;
-          for (int db = 0; db < entries.length; db++)
-          {
-            dbentry = entries[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());
-              /*
-               * TODO: Maps are not yet supported by Jalview. Map vMap = new
-               * Map(); vMap.set dbref.addMap(vMap);
-               */
-              sequence.addDbRef(dbref);
-            }
-            else
-            {
-              // TODO: verify and update dbrefs in vamsas document
-              // there will be trouble when a dataset sequence is modified to
-              // 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.");
-            }
-          }
-
-        }
-      }
-      // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));
-      // ////////////////////////////////////////////
-
-      // ////////////////////////////////////////////
-      // Save the Alignments
-
-      Alignment alignment = (Alignment) getjv2vObj(av); // this is so we can get the alignviewport back
-      if (alignment == null)
-      {
-        alignment = new Alignment();
-        bindjvvobj(av, alignment);
-        if (alignment.getProvenance() == null)
-          alignment.setProvenance(new Provenance());
-        addProvenance(alignment.getProvenance(), "added"); // TODO: insert some
-        // sensible source
-        // here
-        dataset.addAlignment(alignment);
-        {
-          Property title = new Property();
-          title.setName("jalview:AlTitle");
-          title.setType("string");
-          title.setContent(aFtitle);
-          alignment.addProperty(title);
-        }
-        alignment.setGapChar(String.valueOf(av.getGapCharacter()));
-        AlignmentSequence alseq = null;
-        for (int i = 0; i < jal.getHeight(); i++)
-        {
-          alseq = new AlignmentSequence();
-          // TODO: VAMSAS: translate lowercase symbols to annotation ?
-          alseq.setSequence(jal.getSequenceAt(i).getSequenceAsString());
-          alseq.setName(jal.getSequenceAt(i).getName());
-          alseq.setStart(jal.getSequenceAt(i).getStart());
-          alseq.setEnd(jal.getSequenceAt(i).getEnd());
-          alseq.setRefid(getjv2vObj(jal.getSequenceAt(i).getDatasetSequence()));
-          alignment.addAlignmentSequence(alseq);
-          bindjvvobj(jal.getSequenceAt(i), alseq);
-        }
-      }
-      else
-      {
-        // todo: verify and update mutable alignment props.
-        if (alignment.getModifiable())
-        {
-          System.out.println("update alignment in document.");
-        }
-        else
-        {
-          System.out
-          .println("update edited alignment to new alignment in document.");
-        }
-      }
-      // ////////////////////////////////////////////
-      // SAVE Alignment Sequence Features
-      for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
-      {
-        AlignmentSequence valseq;
-        SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment
-            .getAlignmentSequence(i));
-        if (alseq != null && alseq.getSequenceFeatures() != null)
-        {
-          jalview.datamodel.SequenceFeature[] features = alseq
-          .getSequenceFeatures();
-          for (int f = 0; f < features.length; f++)
-          {
-            if (features[f] != null)
-            {
-              AlignmentSequenceAnnotation valseqf = (AlignmentSequenceAnnotation) getjv2vObj(features[i]);
-              if (valseqf == null)
-              {
-
-                valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
-                    new AlignmentSequenceAnnotation(), features[i]);
-                if (valseqf.getProvenance() == null)
-                {
-                  valseqf.setProvenance(new Provenance());
-                }
-                addProvenance(valseqf.getProvenance(), "created"); // JBPNote -
-                // need to
-                // update
-                bindjvvobj(features[i], valseqf);
-                valseq.addAlignmentSequenceAnnotation(valseqf);
-              }
-            }
-
-          }
-        }
-      }
-
-      // ////////////////////////////////////////////
-      // SAVE ANNOTATIONS
-      if (jal.getAlignmentAnnotation() != null)
-      {
-        jalview.datamodel.AlignmentAnnotation[] aa = jal
-        .getAlignmentAnnotation();
-        java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from
-        // alignment columns to
-        // sequence positions.
-        for (int i = 0; i < aa.length; i++)
-        {
-          if (aa[i] == null || isJalviewOnly(aa[i]))
-          {
-            continue;
-          }
-          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]);
-            int[] gapMap = null;
-            if (AlSeqMaps.containsKey(aa[i].sequenceRef))
-            {
-              gapMap = (int[]) AlSeqMaps.get(aa[i].sequenceRef);
-            }
-            else
-            {
-              gapMap = new int[aa[i].sequenceRef.getLength()];
-              // 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)
-            {
-              an = new org.vamsas.objects.core.AlignmentSequenceAnnotation();
-              Seg vSeg = new Seg();
-              vSeg.setStart(1);
-              vSeg.setInclusive(true);
-              vSeg.setEnd(gapMap.length);
-              an.addSeg(vSeg);
-              an.setType("jalview:SecondaryStructurePrediction");// TODO: better fix this rough guess ;)
-              alsref.addAlignmentSequenceAnnotation(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
-              // something else.
-              an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -
-              // originally we
-              // were going to
-              // store
-              // graphGroup in
-              // the Jalview
-              // specific
-              // bits.
-              AnnotationElement ae;
-              for (int a = 0; a < aa[i].annotations.length; a++)
-              {
-                if (aa[i].annotations[a] == null)
-                {
-                  continue;
-                }
-
-                ae = new AnnotationElement();
-                ae.setDescription(aa[i].annotations[a].description);
-                ae.addGlyph(new Glyph());
-                ae.getGlyph(0)
-                .setContent(aa[i].annotations[a].displayCharacter); // assume
-                // jax-b
-                // takes
-                // care
-                // of
-                // utf8
-                // translation
-                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
-                // 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);
-                  ss.setContent(String
-                      .valueOf(aa[i].annotations[a].secondaryStructure));
-                  ae.addGlyph(ss);
-                }
-                an.addAnnotationElement(ae);
-              }
-            }
-            else
-            {
-              // update reference sequence Annotation
-              if (an.getModifiable())
-              {
-                // verify existing alignment sequence annotation is up to date
-                System.out.println("update alignment sequence annotation.");
-              }
-              else
-              {
-                // verify existing alignment sequence annotation is up to date
-                System.out
-                .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]);
-            if (an == null)
-            {
-              an = new org.vamsas.objects.core.AlignmentAnnotation();
-              an.setType("jalview:AnnotationRow");
-              an.setDescription(aa[i].description);
-              alignment.addAlignmentAnnotation(an);
-              Seg vSeg = new Seg();
-              vSeg.setStart(1);
-              vSeg.setInclusive(true);
-              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) {
-                an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -
-                // originally we
-              // were going to
-              // store
-              // graphGroup in
-              // the Jalview
-              // specific
-              // bits.
-                an.setGraph(true);
-              } 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))
-                {
-                  continue;
-                }
-
-                ae = new AnnotationElement();
-                ae.setDescription(aa[i].annotations[a].description);
-                ae.addGlyph(new Glyph());
-                ae.getGlyph(0)
-                .setContent(aa[i].annotations[a].displayCharacter); // assume
-                // jax-b
-                // takes
-                // care
-                // of
-                // utf8
-                // translation
-                ae.addValue(aa[i].annotations[a].value);
-                ae.setPosition(a+1);
-                if (aa[i].annotations[a].secondaryStructure != ' ')
-                {
-                  Glyph ss = new Glyph();
-                  ss
-                  .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
-                  ss.setContent(String
-                      .valueOf(aa[i].annotations[a].secondaryStructure));
-                  ae.addGlyph(ss);
-                }
-                an.addAnnotationElement(ae);
-              }
-              if (aa[i].editable) {
-                //an.addProperty(newProperty("jalview:editable", null, "true"));
-                an.setModifiable(true);
-              }
-              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")));
-
-                /** and on and on..
-                 vProperty=new Property();
-                  vProperty.setName("jalview:graphThreshhold");
-                  vProperty.setContent(aa[i].threshold);
-                 */
-
-              }
-            }
-            else
-            {
-              if (an.getModifiable())
-              {
-                // verify annotation - update (perhaps)
-                Cache.log.info("update alignment sequence annotation. not yet implemented.");
-              }
-              else
-              {
-                // verify annotation - update (perhaps)
-                Cache.log.info("updated alignment sequence annotation added.");
-              }
-            }
-          }
-        }
-      }
-      // /////////////////////////////////////////////////////
-
-      // //////////////////////////////////////////////
-      // /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 = (Tree) getjv2vObj(tp);
-              if (tree == null)
-              {
-                tree = new Tree();
-                bindjvvobj(tp, tree);
-                tree.setTitle(tp.getTitle());
-                Newick newick = new Newick();
-                // TODO: translate sequenceI to leaf mappings to vamsas
-                // references - see tree specification in schema.
-                newick.setContent(tp.getTree().toString());
-                newick.setTitle(tp.getTitle());
-                tree.addNewick(newick);
-                tree.setProvenance(makeTreeProvenance(jal, tp));
-                alignment.addTree(tree);
-              }
-              else
-              {
-                if (tree.getModifiable())
-                {
-                  // verify any changes.
-                  System.out.println("Update tree in document.");
-                }
-                else
-                {
-                  System.out
-                  .println("Add modified tree as new tree in document.");
-                }
-              }
-            }
-          }
-        }
-      }
-      // Store Jalview specific stuff in the Jalview appData
-      // not implemented in the SimpleDoc interface.
-    }
-
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-
-  }
-
-  private Property newProperty(String name, String type, String content) {
-    Property vProperty=new Property();
-    vProperty.setName(name);
-    if (type!=null)
-      vProperty.setType(type);
-    else
-      vProperty.setType("String");
-    vProperty.setContent(content);
-    return vProperty;
-  }
-
-  /**
-   * correctly create a RangeAnnotation from a jalview sequence feature
-   *
-   * @param dsa
-   *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)
-   * @param feature
-   *          (the feature to be mapped from)
-   * @return
-   */
-  private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
-      SequenceFeature feature) {
-    dsa.setType(feature.getType());
-    Seg vSeg = new Seg();
-    vSeg.setStart(feature.getBegin());
-    vSeg.setEnd(feature.getEnd());
-    vSeg.setInclusive(true);
-    dsa.addSeg(vSeg);
-    dsa.setDescription(feature.getDescription());
-    dsa.setStatus(feature.getStatus());
-    if (feature.links != null && feature.links.size() > 0)
-    {
-      for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
-      {
-        String link = (String) feature.links.elementAt(i);
-        int sep = link.indexOf('|');
-        if (sep > -1)
-        {
-          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);
-        }
-      }
-    }
-    dsa.setGroup(feature.getFeatureGroup());
-    return dsa;
-  }
-
-  /**
-   * correctly creates provenance for trees calculated on an alignment by
-   * jalview.
-   *
-   * @param jal
-   * @param tp
-   * @return
-   */
-  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).setUser(provEntry.getUser());
-    prov.getEntry(0).setApp(provEntry.getApp());
-    prov.getEntry(0).setDate(provEntry.getDate());
-    if (tp.getTree().hasOriginalSequenceData())
-    {
-      Input vInput = new Input();
-      // LATER: check to see if tree input data is contained in this alignment -
-      // or just correctly resolve the tree's seqData to the correct alignment in
-      // the document.
-      // vInput.setObjRef(getjv2vObj(jal));
-      vInput.setObjRef(getjv2vObj(tp.getViewPort()));
-      prov.getEntry(0).setAction("created "+tp.getTitle());
-      prov.getEntry(0).addInput(vInput);
-      vInput.setName("jalview:seqdist");
-      prov.getEntry(0).addParam(new Param());
-      prov.getEntry(0).getParam(0).setName("treeType");
-      prov.getEntry(0).getParam(0).setType("utf8");
-      prov.getEntry(0).getParam(0).setContent("NJ");
-
-      int ranges[] = tp.getTree().seqData.getVisibleContigs();
-      // VisibleContigs are with respect to alignment coordinates. Still need offsets
-      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.setInclusive(true);
-        vInput.addSeg(visSeg);
-      }
-    }
-    return prov;
-  }
-
-  /**
-   *
-   * @param tp
-   * @return Object[] { AlignmentView, AlignmentI - reference alignment for
-   *         input }
-   */
-  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());
-        // 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
-              .getObjRef());
-          jalview.datamodel.AlignmentI jal = javport.getAlignment();
-          jalview.datamodel.CigarArray view = javport.getAlignment().getCompactAlignment();
-          int from = 1, to = jal.getWidth();
-          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.
-            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;
-              }
-              from = se[1] + 1;
-            }
-          }
-          if (from < to)
-          {
-            view.deleteRange(offset+from-1, offset+to-1); // final deletion - TODO: check off by
-            // one for to
-          }
-          return new Object[] { new AlignmentView(view), jal };
-        }
-      }
-    }
-    Cache.log.debug("Returning null for input data recovery from provenance.");
-    return null;
-  }
-
-  /**
-   * get start<end range of segment, adjusting for inclusivity flag and
-   * polarity.
-   *
-   * @param visSeg
-   * @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) {
-    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)
-    {
-      // jalview doesn't deal with inverted ranges, yet.
-      int t = end;
-      end = start;
-      start = t;
-    }
-    return new int[] { start, end, pol<0 ? 1 : 0 };
-  }
-
-  /**
-   *
-   * @param annotation
-   * @return true if annotation is not to be stored in document
-   */
-  private boolean isJalviewOnly(AlignmentAnnotation annotation) {
-    return annotation.label.equals("Quality")
-    || 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.
-   * This also shouldn't be in the io package.
-   * @param av
-   * @return alignFrame for 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)
-            return (AlignFrame) frames[t];
-        }
-      }
-    }
-    return null;
-  }
-  public void updateToJalview() {
-    VAMSAS _roots[] = cdoc.getVamsasRoots();
-
-    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++) {
-        // ///////////////////////////////////
-        // ///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) {
-          Cache.log.debug("Initialising new jalview dataset fields");
-          newds=true;
-          dsseqs=new Vector();
-        } else {
-          Cache.log.debug("Update jalview dataset from vamsas.");
-          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++)
-        {
-          Sequence vdseq = dataset.getSequence(i);
-          jalview.datamodel.SequenceI dsseq = (SequenceI) getvObj2jv(vdseq);
-          if (dsseq!=null) {
-            if (!dsseq.getSequence().equals(vdseq.getSequence()))
-              throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
-            jremain--;
-          } else {
-            dsseq = new jalview.datamodel.Sequence(
-                dataset.getSequence(i).getName(),
-                dataset.getSequence(i).getSequence(),
-                dataset.getSequence(i).getStart(),
-                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++)
-            {
-              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()));
-                bindjvvobj(dbr, dbref[db]);
-              }
-            }
-          }
-        }
-
-        if (newds) {
-          SequenceI[] seqs = new SequenceI[dsseqs.size()];
-          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);
-          Cache.log.debug("New vamsas dataset imported into jalview.");
-          bindjvvobj(jdataset, dataset);
-        }
-        // ////////
-        // 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));
-                  bindjvvobj(sf, dseta);
-                }
-              } else {
-                // TODO: deal with alignmentAnnotation style annotation
-                // appearing on dataset sequences.
-                // JBPNote: we could just add them to all alignments but
-                // that may complicate cross references in the jalview
-                // datamodel
-                Cache.log.warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
-              }
-            }
-          }
-        }
-
-        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);
-            AlignViewport av = (AlignViewport) getvObj2jv(alignment);
-            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();
-            }
-            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) {
-                //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());
-                // this might go *horribly* wrong
-                alseq.setSequence(new String(valseq.getSequence()).replace(valGapchar, gapChar));
-                jremain--;
-              } else {
-                alseq = new jalview.datamodel.Sequence(
-                    valseq.getName(),
-                    valseq.getSequence().replace(valGapchar, gapChar),
-                    valseq.getStart(),
-                    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());
-                }
-                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) {
-                    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.
-                    bindjvvobj(asa, vasannot[a]);
-                    newasAnnots.add(asa);
-                  } else {
-                    // update existing annotation - can do this in place
-                    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]);
-                      // asa.update(getjAlignmentAnnotation(jal, vasannot[a])); //  update from another annotation object in place.
-                      // asa.createSequenceMapping(alseq, se[0], false);
-
-                    }
-                  }
-                }
-              }
-            }
-            if (jal==null) {
-              SequenceI[] seqs = new SequenceI[dsseqs.size()];
-              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());
-              jal.setDataset(jdataset);
-            }
-            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));
-                // TODO: check if anything has to be done - like calling adjustForAlignment or something.
-                newasAnnots.setElementAt(null, an);
-              }
-              newasAnnots=null;
-            }
-            // //////////////////////////////////////////
-            // //LOAD ANNOTATIONS FOR THE ALIGNMENT
-            // ////////////////////////////////////
-            if (alignment.getAlignmentAnnotationCount()>0)
-            {
-              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) {
-                  // 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()) {
-                    // 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...");
-                  }
-                  // TODO: compare annotation element rows
-                  // TODO: compare props.
-                } else {
-                  jan = getjAlignmentAnnotation(jal, an[j]);
-                  jal.addAnnotation(jan);
-                  bindjvvobj(jan, an[j]);
-                }
-              }
-            }
-            AlignFrame alignFrame;
-            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")) {
-                    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()+")",
-                  AlignFrame.DEFAULT_WIDTH,
-                  AlignFrame.DEFAULT_HEIGHT);
-              bindjvvobj(av, alignment);
-            } else {
-              // find the alignFrame for jal.
-              // TODO: fix this so we retrieve the alignFrame handing av *directly*
-              alignFrame=getAlignFrameFor(av);
-            }
-            // LOAD TREES
-            // /////////////////////////////////////
-            if (alignment.getTreeCount() > 0)
-            {
-
-              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 {
-                  // make a new tree
-                  Object[] idata = this.recoverInputData(tree.getProvenance());
-                  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,
-                        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);
-                  }
-                }
-              }
-            }
-
-          }
-        }
-      }
-    }
-  }
-  // 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.
-  /**
-   * 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) {
-    // 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};
-    int[] rangeMap = getMapping(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.
-
-    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) {
-            // only time this should happen is if the After flag is set.
-            Cache.log.debug("Ignoring duplicate annotation site at "+pos);
-            continue;
-          }
-          if (anot[1-row][pos]!=null)
-            mergeable=false;
-          String desc = "";
-          if (ae[aa].getDescription()!=null) {
-            desc = ae[aa].getDescription();
-            if (desc.length()>0) {
-              // have imported valid description string
-              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();
-          java.awt.Color colour = null;
-          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)) {
-                Cache.log.debug("ignoring hydrophobicity glyph marker.");
-                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);
-
-              } 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());
-              }
-            }
-          }
-          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);
-          }
-        } 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) {
-            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[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)";
-        }
-      }
-      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 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)
-      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)
-      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) {
-      a_label = annotation.getType();
-      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 (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());
-      }
-      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]) {
-        // 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) {
-              // do some interpolation *between* points
-              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);
-                  // NB - Interpolated points don't get a tooltip and description.
-                }
-              }
-            }
-            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; }
-            }
-            // make tooltip and display char 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]) {
-          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);
-        jan.setThreshold(null);
-      }
-      if (annotation.getLinkCount()>0) {
-        Cache.log.warn("Ignoring "+annotation.getLinkCount()+"links added to AlignmentAnnotation.");
-      }
-      if (annotation.getModifiable()) {
-        jan.editable=true;
-      }
-
-      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 {
-              // 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.");
-            }
-            try {
-              if (annotation.getGroup()!=null && annotation.getGroup().length()>0)
-                jan.graphGroup = Integer.parseInt(annotation.getGroup());
-            } catch (Exception e) {
-              Cache.log.info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
-            }
-          }
-        }
-      }
-
-      return jan;
-
-    }
-
-    return null;
-  }
-
-  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
-        .getGroup());
-    if (dseta.getLinkCount() > 0)
-    {
-      Link[] links = dseta.getLink();
-      for (int i = 0; i < links.length; i++)
-      {
-        sf.addLink(links[i].getContent() + "|" + links[i].getHref());
-      }
-    }
-    return sf;
-  }
-
-  /**
-   * get real bounds of a RangeType's specification. start and end are an
-   * inclusive range within which all segments and positions lie.
-   * TODO: refactor to vamsas utils
-   * @param dseta
-   * @return int[] { start, end}
-   */
-  private int[] getBounds(RangeType dseta) {
-    if (dseta != null)
-    {
-      int[] se = null;
-      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);
-        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 };
-        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();
-    if (dseta != null)
-    {
-      int[] se = null;
-      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 ) {
-            posList.add(new Integer(p));
-          }
-        }
-      }
-      else if (dseta.getPosCount() > 0)
-      {
-        int pos = dseta.getPos(0).getI();
-
-        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
-        {
-          pos = dseta.getPos(p).getI();
-          posList.add(new Integer(pos));
-        }
-      }
-    }
-    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;
-    // TODO: fix App and Action here.
-    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")); // TODO: ext string
-      provEntry.setApp("JVAPP"); // TODO: ext string
-      provEntry.setAction(action);
-      prov.addEntry(provEntry);
-    }
-
-    return 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());
-    }
-
-    return jprov;
-  }
-
-  /**
-   *
-   * @return default initial provenance list for a Jalview created vamsas
-   *         object.
-   */
-  Provenance dummyProvenance() {
-    return dummyProvenance(null);
-  }
-
-  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 prov = new Provenance();
-    prov.addEntry(dummyPEntry(action));
-    return prov;
-  }
-
-  void addProvenance(Provenance p, String action) {
-    p.addEntry(dummyPEntry(action));
-  }
 
 }
-- 
1.7.10.2