X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=b8466f0872e22923a9c7688fbf447c40add60d08;hb=61505ac1511435b067e647f5c7c9050e5c1eef41;hp=bfd97f03b7c0ec5235a91b091db2231dc6286780;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index bfd97f0..b8466f0 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -18,694 +18,1445 @@
  */
 package jalview.gui;
 
+
+import jalview.schemes.*;
+
+import jalview.gui.*;
+
 import java.io.*;
+
 import java.net.*;
+
 import java.util.*;
+
 import java.util.jar.*;
 
 import javax.swing.*;
 
-import jalview.binding.*;
-import jalview.io.*;
-import jalview.schemes.*;
+import org.exolab.castor.xml.*;
 
-public class Jalview2XML
-{
-  // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
-  public static void SaveState(File statefile)
-  {
-    long creation = System.currentTimeMillis();
-    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+import jalview.schemabinding.version2.*;
 
-    if (frames == null)
-    {
-      return;
-    }
 
-    try
-    {
-      FileOutputStream fos = new FileOutputStream(statefile);
-      JarOutputStream jout = new JarOutputStream(fos);
 
-      //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-      ////////////////////////////////////////////////////
-      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
-          "UTF-8"));
 
-      Vector shortNames = new Vector();
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview2XML
+{
+    // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
+    public void SaveState(File statefile)
+    {
+        long creation = System.currentTimeMillis();
+        JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
-      //REVERSE ORDER
-      for (int i = frames.length - 1; i > -1; i--)
-      {
-        if (frames[i] instanceof AlignFrame)
+        if (frames == null)
         {
-          AlignFrame af = (AlignFrame) frames[i];
+            return;
+        }
 
-          String shortName = af.getTitle();
+        try
+        {
+            FileOutputStream fos = new FileOutputStream(statefile);
+            JarOutputStream jout = new JarOutputStream(fos);
 
-          if (shortName.indexOf(File.separatorChar) > -1)
-          {
-            shortName = shortName.substring(shortName.lastIndexOf(
-                File.separatorChar) + 1);
-          }
+            //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+            ////////////////////////////////////////////////////
+            PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+                        "UTF-8"));
 
-          int count = 1;
+            Vector shortNames = new Vector();
 
-          while (shortNames.contains(shortName))
-          {
-            if (shortName.endsWith("_" + (count - 1)))
+            //REVERSE ORDER
+            for (int i = frames.length - 1; i > -1; i--)
             {
-              shortName = shortName.substring(0,
-                                              shortName.lastIndexOf("_"));
-            }
+                if (frames[i] instanceof AlignFrame)
+                {
+                    AlignFrame af = (AlignFrame) frames[i];
 
-            shortName = shortName.concat("_" + count);
-            count++;
-          }
+                    String shortName = af.getTitle();
 
-          shortNames.addElement(shortName);
+                    if (shortName.indexOf(File.separatorChar) > -1)
+                    {
+                        shortName = shortName.substring(shortName.lastIndexOf(
+                                    File.separatorChar) + 1);
+                    }
 
-          if (!shortName.endsWith(".xml"))
-          {
-            shortName = shortName + ".xml";
-          }
+                    int count = 1;
 
-          SaveState(af, creation, shortName, jout, out);
-        }
-      }
+                    while (shortNames.contains(shortName))
+                    {
+                        if (shortName.endsWith("_" + (count - 1)))
+                        {
+                            shortName = shortName.substring(0,
+                                    shortName.lastIndexOf("_"));
+                        }
 
-      out.close();
-      jout.close();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
+                        shortName = shortName.concat("_" + count);
+                        count++;
+                    }
 
-  // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-  public static void SaveState(AlignFrame af, String jarFile, String fileName)
-  {
-    try
-    {
-      FileOutputStream fos = new FileOutputStream(jarFile);
-      JarOutputStream jout = new JarOutputStream(fos);
+                    shortNames.addElement(shortName);
+
+                    if (!shortName.endsWith(".xml"))
+                    {
+                        shortName = shortName + ".xml";
+                    }
 
-      //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-      ////////////////////////////////////////////////////
-      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
-          "UTF-8"));
+                    SaveState(af, creation, shortName, jout, out);
+                }
+            }
 
-      SaveState(af, System.currentTimeMillis(), fileName, jout, out);
-      out.close();
-      jout.close();
+            out.close();
+            jout.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
     }
-    catch (Exception ex)
+
+    // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
+    public void SaveAlignment(AlignFrame af, String jarFile,
+        String fileName)
     {
-    }
-  }
+        try
+        {
+            FileOutputStream fos = new FileOutputStream(jarFile);
+            JarOutputStream jout = new JarOutputStream(fos);
 
-  public static void SaveState(AlignFrame af, long timeStamp,
-                               String fileName, JarOutputStream jout,
-                               PrintWriter out)
-  {
-    Vector seqids = new Vector();
-    Vector userColours = new Vector();
+            //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+            ////////////////////////////////////////////////////
+            PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+                        "UTF-8"));
 
-    AlignViewport av = af.viewport;
+            SaveState(af, System.currentTimeMillis(), fileName, jout, out);
+            out.close();
+            jout.close();
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+    }
 
-    JalviewModel object = new JalviewModel();
-    object.setVamsasModel(new VamsasModel());
+    /**
+     * DOCUMENT ME!
+     *
+     * @param af DOCUMENT ME!
+     * @param timeStamp DOCUMENT ME!
+     * @param fileName DOCUMENT ME!
+     * @param jout DOCUMENT ME!
+     * @param out DOCUMENT ME!
+     */
+    public void SaveState(AlignFrame af, long timeStamp,
+        String fileName, JarOutputStream jout, PrintWriter out)
+    {
+        Vector seqids = new Vector();
+        Vector userColours = new Vector();
 
-    object.setCreationDate(new java.util.Date(timeStamp));
+        AlignViewport av = af.viewport;
 
-    jalview.datamodel.AlignmentI jal = af.viewport.alignment;
+        JalviewModel object = new JalviewModel();
+        object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 
-    SequenceSet vamsasSet = new SequenceSet();
-    Sequence vamsasSeq;
-    JalviewModelSequence jms = new JalviewModelSequence();
+        object.setCreationDate(new java.util.Date(timeStamp));
+        object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 
-    vamsasSet.setGapChar(jal.getGapCharacter() + "");
+        jalview.datamodel.AlignmentI jal = af.viewport.alignment;
+        jalview.datamodel.AlignmentI jalhidden = null;
 
-    JSeq jseq;
+        if(av.hasHiddenRows)
+        {
+          jalhidden = jal;
+          jal = jal.getHiddenSequences().getFullAlignment();
+        }
 
-    //SAVE SEQUENCES
-    int id = 0;
 
-    for (int i = 0; i < jal.getHeight(); i++)
-    {
-      seqids.add(jal.getSequenceAt(i));
+        SequenceSet vamsasSet = new SequenceSet();
+        Sequence vamsasSeq;
+        JalviewModelSequence jms = new JalviewModelSequence();
 
-      vamsasSeq = new Sequence();
-      vamsasSeq.setId(id + "");
-      vamsasSeq.setName(jal.getSequenceAt(i).getName());
-      vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
+        vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
-      jseq = new JSeq();
-      jseq.setStart(jal.getSequenceAt(i).getStart());
-      jseq.setEnd(jal.getSequenceAt(i).getEnd());
+        JSeq jseq;
+        Vector pdbfiles = null;
 
-      jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
+        //SAVE SEQUENCES
+        int id = 0;
+        for (int i = 0; i < jal.getHeight(); i++)
+        {
+            seqids.add(jal.getSequenceAt(i));
+            vamsasSeq = new Sequence();
+            vamsasSeq.setId(id + "");
+            vamsasSeq.setName(jal.getSequenceAt(i).getName());
+            vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
+            vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
+
+            if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)
+            {
+              jalview.datamodel.DBRefEntry [] dbrefs =
+                  jal.getSequenceAt(i).getDatasetSequence().getDBRef();
+
+              for(int d=0; d<dbrefs.length; d++)
+              {
+                DBRef dbref = new DBRef();
+                dbref.setSource( dbrefs[d].getSource() );
+                dbref.setVersion( dbrefs[d].getVersion());
+                dbref.setAccessionId(dbrefs[d].getAccessionId());
+                vamsasSeq.addDBRef(dbref);
+              }
+            }
 
-      jseq.setId(id);
+            jseq = new JSeq();
+            jseq.setStart(jal.getSequenceAt(i).getStart());
+            jseq.setEnd(jal.getSequenceAt(i).getEnd());
+            jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
 
-      jms.addJSeq(jseq);
-      vamsasSet.addSequence(vamsasSeq);
-      id++;
-    }
+            jseq.setId(id);
 
-    //SAVE TREES
-    if (af.viewport.currentTree != null)
-    {
-      object.getVamsasModel().addTree(af.viewport.currentTree.toString());
-    }
+            if (av.hasHiddenRows)
+            {
+              jseq.setHidden(jalhidden.getHiddenSequences().isHidden(
+                  jal.getSequenceAt(i)));
+
+              if(jal.getSequenceAt(i).getHiddenSequences()!=null)
+              {
+                jalview.datamodel.SequenceI [] reps =
+                    jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
+
+                for(int h=0; h<reps.length; h++)
+                {
+                  jseq.addHiddenSequences(
+                      jal.findIndex(reps[h])
+                      );
+                }
+              }
+            }
 
-    //SAVE ANNOTATIONS
-    if (jal.getAlignmentAnnotation() != null)
-    {
-      jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 
-      for (int i = 0; i < aa.length; i++)
-      {
-        if (aa[i].label.equals("Quality") ||
-            aa[i].label.equals("Conservation") ||
-            aa[i].label.equals("Consensus"))
-        {
-          continue;
-        }
+            if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
+            {
+              jalview.datamodel.SequenceFeature[] sf
+                  = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+              int index = 0;
+              while(index < sf.length)
+              {
+                Features features = new Features();
+
+                features.setBegin(sf[index].getBegin());
+                features.setEnd(sf[index].getEnd());
+                features.setDescription(sf[index].getDescription());
+                features.setType(sf[index].getType());
+                features.setFeatureGroup(sf[index].getFeatureGroup());
+                features.setScore(sf[index].getScore());
+                if(sf[index].links!=null)
+                {
+                  for(int l=0; l<sf[index].links.size(); l++)
+                  {
+                    OtherData keyValue = new OtherData();
+                    keyValue.setKey("LINK_"+l);
+                    keyValue.setValue(sf[index].links.elementAt(l).toString());
+                    features.addOtherData(keyValue);
+                  }
+                }
+                if(sf[index].otherDetails!=null)
+                {
+                  String key;
+                  Enumeration keys = sf[index].otherDetails.keys();
+                  while(keys.hasMoreElements())
+                  {
+                    key = keys.nextElement().toString();
+                    OtherData keyValue = new OtherData();
+                    keyValue.setKey( key );
+                    keyValue.setValue(
+                        sf[index].otherDetails.get(key).toString());
+                    features.addOtherData(keyValue);
+                  }
+                }
+
+                jseq.addFeatures(features);
+                index ++;
+              }
+            }
 
-        Annotation an = new Annotation();
-        an.setDescription(aa[i].description);
-        an.setGraph(aa[i].isGraph);
-        an.setLabel(aa[i].label);
+            if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
+            {
+              Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
+              while(en.hasMoreElements())
+              {
+                Pdbids pdb = new Pdbids();
+                jalview.datamodel.PDBEntry entry
+                   = (jalview.datamodel.PDBEntry)en.nextElement();
+
+                pdb.setId(entry.getId());
+                pdb.setType(entry.getType());
+
+                if(entry.getFile()!=null)
+                {
+                  if(pdbfiles==null)
+                    pdbfiles = new Vector();
+
+
+                  if(!pdbfiles.contains(entry.getId()))
+                  {
+                    pdbfiles.addElement(entry.getId());
+                    try
+                    {
+                      File file = new File(entry.getFile());
+                      if(file.exists())
+                      {
+                        byte[] data = new byte[ (int) file.length()];
+                        jout.putNextEntry(new JarEntry(entry.getId()));
+                        DataInputStream dis = new DataInputStream(new
+                            FileInputStream(file));
+                        dis.readFully(data);
+
+                        DataOutputStream dout = new DataOutputStream(jout);
+                        dout.write(data, 0, data.length);
+                        jout.closeEntry();
+                      }
+                    }
+                    catch (Exception ex)
+                    {
+                      ex.printStackTrace();
+                    }
+                  }
+                }
+
+
+                if(entry.getProperty()!=null)
+                {
+                  PdbentryItem item = new PdbentryItem();
+                  Hashtable properties = entry.getProperty();
+                  Enumeration en2 = properties.keys();
+                  while(en2.hasMoreElements())
+                  {
+                    Property prop = new Property();
+                    String key = en2.nextElement().toString();
+                    prop.setName(key);
+                    prop.setValue( properties.get(key).toString() );
+                    item.addProperty(prop);
+                  }
+                  pdb.addPdbentryItem(item);
+                }
+
+                jseq.addPdbids(pdb);
+              }
+            }
 
-        AnnotationElement ae;
+            jms.addJSeq(jseq);
+            vamsasSet.addSequence(vamsasSeq);
+            id++;
+        }
 
-        for (int a = 0; a < aa[i].annotations.length; a++)
+        //SAVE TREES
+        ///////////////////////////////////
+        if (af.viewport.currentTree != null)
         {
-          if ( (aa[i] == null) || (aa[i].annotations[a] == null))
+          // FIND ANY ASSOCIATED TREES
+          // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
+          if (Desktop.desktop != null)
           {
-            continue;
+            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.treeCanvas.av.alignment == jal)
+                {
+                  Tree tree = new Tree();
+                  tree.setTitle(tp.getTitle());
+                  tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
+                  tree.setNewick(tp.getTree().toString());
+                  tree.setThreshold(tp.treeCanvas.threshold);
+
+                  tree.setFitToWindow(tp.fitToWindow.getState());
+                  tree.setFontName(tp.getTreeFont().getName());
+                  tree.setFontSize(tp.getTreeFont().getSize());
+                  tree.setFontStyle(tp.getTreeFont().getStyle());
+                  tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+
+                  tree.setShowBootstrap(tp.bootstrapMenu.getState());
+                  tree.setShowDistances(tp.distanceMenu.getState());
+
+                  tree.setHeight(tp.getHeight());
+                  tree.setWidth(tp.getWidth());
+                  tree.setXpos(tp.getX());
+                  tree.setYpos(tp.getY());
+
+                  jms.addTree(tree);
+                }
+              }
+            }
           }
+        }
+
+        //SAVE ANNOTATIONS
+        if (jal.getAlignmentAnnotation() != null)
+        {
+            jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 
-          ae = new AnnotationElement();
-          ae.setDescription(aa[i].annotations[a].description);
-          ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
-          ae.setValue(aa[i].annotations[a].value);
-          ae.setPosition(a);
-          ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
-                                   "");
-          an.addAnnotationElement(ae);
+            for (int i = 0; i < aa.length; i++)
+            {
+                Annotation an = new Annotation();
+
+                if (aa[i].label.equals("Quality") ||
+                        aa[i].label.equals("Conservation") ||
+                        aa[i].label.equals("Consensus"))
+                {
+                    an.setLabel(aa[i].label);
+                    an.setGraph(true);
+                    vamsasSet.addAnnotation(an);
+                    continue;
+                }
+
+
+                an.setDescription(aa[i].description);
+
+                if(aa[i].sequenceRef!=null)
+                 {
+                   an.setSequenceRef(aa[i].sequenceRef.getName());
+                 }
+
+                if(aa[i].graph>0)
+                {
+                  an.setGraph(true);
+                  an.setGraphType(aa[i].graph);
+                  an.setGraphGroup(aa[i].graphGroup);
+                  if(aa[i].getThreshold()!=null)
+                  {
+                    ThresholdLine line = new ThresholdLine();
+                    line.setLabel(aa[i].getThreshold().label);
+                    line.setValue(aa[i].getThreshold().value);
+                    line.setColour(aa[i].getThreshold().colour.getRGB());
+                    an.setThresholdLine(line);
+                  }
+                }
+                else
+                  an.setGraph(false);
+
+                an.setLabel(aa[i].label);
+
+                AnnotationElement ae;
+
+                for (int a = 0; a < aa[i].annotations.length; a++)
+                {
+                    if ((aa[i] == null) || (aa[i].annotations[a] == null))
+                    {
+                        continue;
+                    }
+
+                    ae = new AnnotationElement();
+                    ae.setDescription(aa[i].annotations[a].description);
+                    ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+                    ae.setValue(aa[i].annotations[a].value);
+                    ae.setPosition(a);
+                    ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
+                        "");
+
+                    if(aa[i].annotations[a].colour!=java.awt.Color.black)
+                      ae.setColour(aa[i].annotations[a].colour.getRGB());
+
+                    an.addAnnotationElement(ae);
+                }
+
+                vamsasSet.addAnnotation(an);
+            }
         }
 
-        vamsasSet.addAnnotation(an);
-      }
-    }
+        //SAVE GROUPS
+        if (jal.getGroups() != null)
+        {
+            JGroup[] groups = new JGroup[jal.getGroups().size()];
 
-    //SAVE GROUPS
-    if (jal.getGroups() != null)
-    {
-      JGroup[] groups = new JGroup[jal.getGroups().size()];
+            for (int i = 0; i < groups.length; i++)
+            {
+                groups[i] = new JGroup();
+
+                jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
+                                                                                          .elementAt(i);
+                groups[i].setStart(sg.getStartRes());
+                groups[i].setEnd(sg.getEndRes());
+                groups[i].setName(sg.getName());
+                if(sg.cs!=null)
+                {
+                  if (sg.cs.conservationApplied())
+                  {
+                    groups[i].setConsThreshold(sg.cs.getConservationInc());
+
+                    if (sg.cs instanceof jalview.schemes.UserColourScheme)
+                    {
+                      groups[i].setColour(SetUserColourScheme(sg.cs,
+                          userColours,
+                          jms));
+                    }
+                    else
+                    {
+                      groups[i].setColour(ColourSchemeProperty.getColourName(sg.
+                          cs));
+                    }
+                  }
+                  else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
+                  {
+                    groups[i].setColour(
+                        ColourSchemeProperty.getColourName(
+                      ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
+                  }
+                  else if (sg.cs instanceof jalview.schemes.UserColourScheme)
+                  {
+                    groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+                        jms));
+                  }
+                  else
+                  {
+                    groups[i].setColour(ColourSchemeProperty.getColourName(
+                        sg.cs));
+                  }
+
+                  groups[i].setPidThreshold(sg.cs.getThreshold());
+                }
+
+                groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
+                groups[i].setDisplayBoxes(sg.getDisplayBoxes());
+                groups[i].setDisplayText(sg.getDisplayText());
+                groups[i].setColourText(sg.getColourText());
+
+                for (int s = 0; s < sg.getSize(false); s++)
+                {
+                    jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
+                    int index = seqids.indexOf(seq);
+                    groups[i].addSeq(index);
+                }
+            }
+
+            jms.setJGroup(groups);
+        }
 
-      for (int i = 0; i < groups.length; i++)
-      {
-        groups[i] = new JGroup();
 
-        jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
-            jal.getGroups()
-            .elementAt(i);
-        groups[i].setStart(sg.getStartRes());
-        groups[i].setEnd(sg.getEndRes());
-        groups[i].setName(sg.getName());
+        ///////////SAVE VIEWPORT
+        Viewport view = new Viewport();
+        view.setTitle(af.getTitle());
+        view.setXpos(af.getX());
+        view.setYpos(af.getY());
+        view.setWidth(af.getWidth());
+        view.setHeight(af.getHeight());
+        view.setStartRes(av.startRes);
+        view.setStartSeq(av.startSeq);
 
-        if (sg.cs instanceof ConservationColourScheme)
+        if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
         {
-          groups[i].setConsThreshold( ( (ConservationColourScheme) sg.cs).inc);
+            view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
+                    userColours, jms));
         }
-
-        if (sg.cs instanceof ResidueColourScheme)
+        else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
         {
-          groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).
-                                    getThreshold());
+           jalview.schemes.AnnotationColourGradient acg
+              = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
+
+            AnnotationColours ac = new AnnotationColours();
+            ac.setAboveThreshold(acg.getAboveThreshold());
+            ac.setThreshold(acg.getAnnotationThreshold());
+            ac.setAnnotation(acg.getAnnotation());
+            if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+              ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+                    userColours, jms));
+            else
+              ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
+
+            ac.setMaxColour(acg.getMaxColour().getRGB());
+            ac.setMinColour(acg.getMinColour().getRGB());
+            view.setAnnotationColours(ac);
+            view.setBgColour("AnnotationColourGradient");
         }
-        else if (sg.cs instanceof ScoreColourScheme)
+        else
         {
-          groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());
+            view.setBgColour(ColourSchemeProperty.getColourName(
+                    av.getGlobalColourScheme()));
         }
 
-        if (sg.cs instanceof jalview.schemes.UserColourScheme)
+        ColourSchemeI cs = av.getGlobalColourScheme();
+
+        if(cs!=null)
         {
-          groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
-                                                  jms));
+          if (cs.conservationApplied())
+          {
+            view.setConsThreshold(cs.getConservationInc());
+            if (cs instanceof jalview.schemes.UserColourScheme)
+              view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+          }
+
+          if (cs instanceof ResidueColourScheme)
+          {
+            view.setPidThreshold(cs.getThreshold());
+          }
         }
-        else
+
+        view.setConservationSelected(av.getConservationSelected());
+        view.setPidSelected(av.getAbovePIDThreshold());
+        view.setFontName(av.font.getName());
+        view.setFontSize(av.font.getSize());
+        view.setFontStyle(av.font.getStyle());
+        view.setRenderGaps(av.renderGaps);
+        view.setShowAnnotation(av.getShowAnnotation());
+        view.setShowBoxes(av.getShowBoxes());
+        view.setShowColourText(av.getColourText());
+        view.setShowConservation(av.showConservation);
+        view.setShowFullId(av.getShowJVSuffix());
+        view.setShowIdentity(av.showIdentity);
+        view.setShowQuality(av.showQuality);
+        view.setShowSequenceFeatures(av.showSequenceFeatures);
+        view.setShowText(av.getShowText());
+        view.setWrapAlignment(av.getWrapAlignment());
+
+        if(av.featuresDisplayed!=null)
         {
-          groups[i].setColour(ColourSchemeProperty.getColourName(
-              sg.cs));
-        }
+          jalview.schemabinding.version2.FeatureSettings fs
+              = new jalview.schemabinding.version2.FeatureSettings();
+
+          String [] renderOrder =
+              af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+
+          Vector settingsAdded = new Vector();
+          for(int ro=0; ro<renderOrder.length; ro++)
+          {
+            Setting setting = new Setting();
+            setting.setType(renderOrder[ro]);
+            setting.setColour(
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
+                );
+
+            setting.setDisplay(
+                av.featuresDisplayed.containsKey(renderOrder[ro])
+                );
+
+            fs.addSetting(setting);
+            settingsAdded.addElement(renderOrder[ro]);
+          }
+
+          //Make sure we save none displayed feature settings
+          Enumeration en =
+              af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+          while(en.hasMoreElements())
+          {
+            String key = en.nextElement().toString();
+            if(settingsAdded.contains(key))
+              continue;
 
-        groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
-        groups[i].setDisplayBoxes(sg.getDisplayBoxes());
-        groups[i].setDisplayText(sg.getDisplayText());
-        groups[i].setColourText(sg.getColourText());
+            Setting setting = new Setting();
+            setting.setType(key);
+            setting.setColour(
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
+                );
 
-        for (int s = 0; s < sg.getSize(); s++)
+            setting.setDisplay(false);
+
+            fs.addSetting(setting);
+            settingsAdded.addElement(key);
+          }
+
+          jms.setFeatureSettings(fs);
+
+        }
+
+        if(av.hasHiddenColumns)
         {
-          jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.
-              getSequenceAt(s);
-          int index = seqids.indexOf(seq);
-          groups[i].addSeq(index);
+          for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
+          {
+            int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
+            HiddenColumns hc = new HiddenColumns();
+            hc.setStart(region[0]);
+            hc.setEnd(region[1]);
+            view.addHiddenColumns(hc);
+          }
         }
-      }
 
-      jms.setJGroup(groups);
-    }
+        jms.addViewport(view);
 
-    ///////////SAVE VIEWPORT
-    Viewport view = new Viewport();
-    view.setTitle(af.getTitle());
-    view.setXpos(af.getX());
-    view.setYpos(af.getY());
-    view.setWidth(af.getWidth());
-    view.setHeight(af.getHeight());
-    view.setStartRes(av.startRes);
-    view.setStartSeq(av.startSeq);
-
-    if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
-    {
-      view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
-                                           userColours, jms));
-    }
-    else
-    {
-      view.setBgColour(ColourSchemeProperty.getColourName(
-          av.getGlobalColourScheme()));
-    }
 
-    ColourSchemeI cs = av.getGlobalColourScheme();
+        object.setJalviewModelSequence(jms);
+        object.getVamsasModel().addSequenceSet(vamsasSet);
 
-    if (cs instanceof ConservationColourScheme)
-    {
-      view.setConsThreshold( ( (ConservationColourScheme) cs).inc);
-    }
+        try
+        {
+            if (!fileName.endsWith(".xml"))
+            {
+                fileName = fileName + ".xml";
+            }
 
-    if (cs instanceof ResidueColourScheme)
-    {
-      view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());
-    }
-    else if (cs instanceof ScoreColourScheme)
-    {
-      view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());
+            JarEntry entry = new JarEntry(fileName);
+            jout.putNextEntry(entry);
+
+            object.marshal(out);
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
     }
 
-    view.setConservationSelected(av.getConservationSelected());
-    view.setPidSelected(av.getAbovePIDThreshold());
-    view.setFontName(av.font.getFontName());
-    view.setFontSize(av.font.getSize());
-    view.setFontStyle(av.font.getStyle());
-    view.setRenderGaps(av.renderGaps);
-    view.setShowAnnotation(av.getShowAnnotation());
-    view.setShowBoxes(av.getShowBoxes());
-    view.setShowColourText(av.getColourText());
-    view.setShowConservation(av.showConservation);
-    view.setShowFullId(av.getShowFullId());
-    view.setShowIdentity(av.showIdentity);
-    view.setShowQuality(av.showQuality);
-    view.setShowSequenceFeatures(av.showSequenceFeatures);
-    view.setShowText(av.getShowText());
-    view.setWrapAlignment(av.getWrapAlignment());
-
-    jms.addViewport(view);
-
-    object.setJalviewModelSequence(jms);
-    object.getVamsasModel().addSequenceSet(vamsasSet);
-
-    try
+    String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+        Vector userColours, JalviewModelSequence jms)
     {
-      if (!fileName.endsWith(".xml"))
-      {
-        fileName = fileName + ".xml";
-      }
+        String id = null;
+        jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 
-      JarEntry entry = new JarEntry(fileName);
-      jout.putNextEntry(entry);
+        if (!userColours.contains(ucs))
+        {
+            userColours.add(ucs);
+
+            java.awt.Color[] colours = ucs.getColours();
+            jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
+            jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
+
+            for (int i = 0; i < colours.length; i++)
+            {
+                jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
+                col.setRGB(jalview.util.Format.getHexString(colours[i]));
+                jbucs.addColour(col);
+            }
 
-      object.marshal(out);
+            id = "ucs" + userColours.indexOf(ucs);
+            uc.setId(id);
+            uc.setUserColourScheme(jbucs);
+            jms.addUserColours(uc);
+        }
+
+        return id;
     }
-    catch (Exception ex)
+
+   jalview.schemes.UserColourScheme GetUserColourScheme(
+        JalviewModelSequence jms, String id)
     {
-      ex.printStackTrace();
-    }
-  }
+        UserColours[] uc = jms.getUserColours();
+        UserColours colours = null;
 
-  static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
-                                    Vector userColours,
-                                    JalviewModelSequence jms)
-  {
-    String id = null;
-    jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
-        cs;
+        for (int i = 0; i < uc.length; i++)
+        {
+            if (uc[i].getId().equals(id))
+            {
+                colours = uc[i];
 
-    if (!userColours.contains(ucs))
-    {
-      userColours.add(ucs);
+                break;
+            }
+        }
 
-      java.awt.Color[] colours = ucs.getColours();
-      jalview.binding.UserColours uc = new jalview.binding.UserColours();
-      jalview.binding.UserColourScheme jbucs = new jalview.binding.
-          UserColourScheme();
+        int csize = colours.getUserColourScheme().getColourCount();
+        java.awt.Color[] newColours = new java.awt.Color[csize];
 
-      for (int i = 0; i < colours.length; i++)
-      {
-        jalview.binding.Colour col = new jalview.binding.Colour();
-        col.setRGB(jalview.util.Format.getHexString(colours[i]));
-        jbucs.addColour(col);
-      }
+        for (int i = 0; i < csize; i++)
+        {
+            newColours[i] = new java.awt.Color(Integer.parseInt(
+                        colours.getUserColourScheme().getColour(i).getRGB(), 16));
+        }
 
-      id = "ucs" + userColours.indexOf(ucs);
-      uc.setId(id);
-      uc.setUserColourScheme(jbucs);
-      jms.addUserColours(uc);
+        return new jalview.schemes.UserColourScheme(newColours);
     }
 
-    return id;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     */
+    public AlignFrame LoadJalviewAlign(final String file)
+    {
+        jalview.gui.AlignFrame af = null;
+        try
+        {
+            //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+            URL url = null;
 
-  static jalview.schemes.UserColourScheme GetUserColourScheme(
-      JalviewModelSequence jms, String id)
-  {
-    UserColours[] uc = jms.getUserColours();
-    UserColours colours = null;
+            if (file.startsWith("http://"))
+            {
+                url = new URL(file);
+            }
 
-    for (int i = 0; i < uc.length; i++)
-    {
-      if (uc[i].getId().equals(id))
-      {
-        colours = uc[i];
+            JarInputStream jin = null;
+            JarEntry jarentry = null;
+            int entryCount = 1;
 
-        break;
-      }
-    }
+            do
+            {
+                if (url != null)
+                {
+                    jin = new JarInputStream(url.openStream());
+                }
+                else
+                {
+                    jin = new JarInputStream(new FileInputStream(file));
+                }
+
+                for (int i = 0; i < entryCount; i++)
+                {
+                    jarentry = jin.getNextJarEntry();
+                }
+
+                if (jarentry != null && jarentry.getName().endsWith(".xml"))
+                {
+                    InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+                    JalviewModel object = new JalviewModel();
+
+                    Unmarshaller unmar = new Unmarshaller(object);
+                    unmar.setValidation(false);
+                    object = (JalviewModel) unmar.unmarshal( in );
+
+                    af = LoadFromObject(object, file);
+                    entryCount++;
+                }
+                else if (jarentry != null)
+                {
+                  //Some other file here.
+                  entryCount++;
+                }
+            }
+            while (jarentry != null);
+        }
+        catch(java.net.UnknownHostException ex)
+        {
+          ex.printStackTrace();
+          System.err.println("Couldn't locate Jalview XML file : " +
+              ex + "\n");
 
-    int csize = colours.getUserColourScheme().getColourCount();
-    java.awt.Color[] newColours = new java.awt.Color[csize];
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
+              JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  "Couldn't locate " + file,
+                  "URL not found",
+                  JOptionPane.WARNING_MESSAGE);
+            }
+          });
+        }
+        catch (Exception ex)
+        {
 
-    for (int i = 0; i < csize; i++)
-    {
-      newColours[i] = new java.awt.Color(Integer.parseInt(
-          colours.getUserColourScheme().getColour(i).getRGB(), 16));
-    }
+          //Is Version 1 Jar file?
+          af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 
-    return new jalview.schemes.UserColourScheme(newColours);
-  }
+          if(af!=null)
+          {
+            System.out.println("Successfully loaded archive file");
+            return af;
+          }
+          ex.printStackTrace();
+            System.err.println("Exception whilst loading jalview XML file : " +
+                ex + "\n");
+            javax.swing.SwingUtilities.invokeLater(new Runnable()
+            {
+              public void run()
+              {
+
+                JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    "Error loading  " + file,
+                    "Error loading Jalview file",
+                    JOptionPane.WARNING_MESSAGE);
+              }});
+        }
 
-  public static void LoadJalviewAlign(String file)
-  {
-    JalviewModel object = new JalviewModel();
+        return af;
+    }
 
-    try
+    String loadPDBFile(String file, String pdbId)
     {
-      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
-      URL url = null;
-
-      if (file.startsWith("http://"))
+      System.out.println("load file "+file);
+      try
       {
-        url = new URL(file);
-      }
-
-      JarInputStream jin = null;
-      JarEntry jarentry = null;
-      int entryCount = 1;
+        JarInputStream jin = null;
 
-      do
-      {
-        if (url != null)
+        if (file.startsWith("http://"))
         {
-          jin = new JarInputStream(url.openStream());
+          jin = new JarInputStream(new URL(file).openStream());
         }
         else
         {
           jin = new JarInputStream(new FileInputStream(file));
         }
 
-        for (int i = 0; i < entryCount; i++)
+        JarEntry entry = null;
+        do
         {
-          jarentry = jin.getNextJarEntry();
+          entry = jin.getNextJarEntry();
         }
+        while (!entry.getName().equals(pdbId));
+
+        BufferedReader in = new BufferedReader(new InputStreamReader(jin));
+        File outFile = File.createTempFile("jalview_pdb", ".txt");
+        outFile.deleteOnExit();
+        PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+        String data;
 
-        if (jarentry != null)
+        while ( (data = in.readLine()) != null)
         {
-          InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-          object = (JalviewModel) object.unmarshal(in);
-          LoadFromObject(object);
-          entryCount++;
+          out.println(data);
         }
+        out.close();
+        return outFile.getAbsolutePath();
+
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
       }
-      while (jarentry != null);
-    }
-    catch (Exception ex)
-    {
-      System.err.println("Exception whilst loading jalview XML file : " +
-                         ex + "\n");
-      ex.printStackTrace();
 
-      return;
+      return null;
     }
-  }
 
-  static void LoadFromObject(JalviewModel object)
-  {
-    Vector seqids = new Vector();
-    SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
-    Sequence[] vamsasSeq = vamsasSet.getSequence();
 
-    JalviewModelSequence jms = object.getJalviewModelSequence();
-
-    //////////////////////////////////
-    //LOAD SEQUENCES
-    jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[
-        vamsasSeq.length];
-    JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
-
-    for (int i = 0; i < vamsasSeq.length; i++)
+    AlignFrame LoadFromObject(JalviewModel object, String file)
     {
-      jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
-                                                vamsasSeq[i].getSequence());
-
-      jseqs[i].setStart(JSEQ[i].getStart());
-      jseqs[i].setEnd(JSEQ[i].getEnd());
-      jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
-      seqids.add(jseqs[i]);
-    }
+        Vector seqids = new Vector();
+        SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+        Sequence[] vamsasSeq = vamsasSet.getSequence();
+
+        JalviewModelSequence jms = object.getJalviewModelSequence();
+
+        //////////////////////////////////
+        //LOAD SEQUENCES
+        Vector hiddenSeqs = null;
+        jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
+        JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+        for (int i = 0; i < vamsasSeq.length; i++)
+        {
+            jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
+                    vamsasSeq[i].getSequence());
+            jseqs[i].setDescription( vamsasSeq[i].getDescription() );
 
-    /////////////////////////////////
-    jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
+            if(JSEQ[i].getHidden())
+            {
+              if(hiddenSeqs == null)
+                hiddenSeqs = new Vector();
+              hiddenSeqs.addElement(jseqs[i]);
+            }
+            jseqs[i].setStart(JSEQ[i].getStart());
+            jseqs[i].setEnd(JSEQ[i].getEnd());
+            jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
+            seqids.add(jseqs[i]);
+        }
 
-    /////////////////////////////////
-    //////////////////////////////////
-    //LOAD ANNOTATIONS
-    if (vamsasSet.getAnnotation() != null)
-    {
-      Annotation[] an = vamsasSet.getAnnotation();
+        ///SequenceFeatures are added to the DatasetSequence,
+        // so we must create the dataset before loading features
+        /////////////////////////////////
+        jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
+        al.setDataset(null);
+        /////////////////////////////////
 
-      for (int i = 0; i < an.length; i++)
-      {
-        AnnotationElement[] ae = an[i].getAnnotationElement();
-        jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
-            al.getWidth()];
 
-        for (int aa = 0; aa < ae.length; aa++)
+        Hashtable pdbloaded = new Hashtable();
+        for (int i = 0; i < vamsasSeq.length; i++)
         {
-          anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
-              getDisplayCharacter(),
-              ae[aa].getDescription(),
-              ae[aa].getSecondaryStructure().charAt(0),
-              ae[aa].getValue());
+          if (JSEQ[i].getFeaturesCount() > 0)
+          {
+            Features[] features = JSEQ[i].getFeatures();
+            for (int f = 0; f < features.length; f++)
+            {
+              jalview.datamodel.SequenceFeature sf
+                  = new jalview.datamodel.SequenceFeature(features[f].getType(),
+                  features[f].getDescription(), features[f].getStatus(),
+                  features[f].getBegin(), features[f].getEnd(),
+                  features[f].getFeatureGroup());
+
+              sf.setScore(features[f].getScore());
+              for(int od=0; od<features[f].getOtherDataCount(); od++)
+              {
+                OtherData keyValue = features[f].getOtherData(od);
+                if(keyValue.getKey().startsWith("LINK"))
+                  sf.addLink(keyValue.getValue());
+                else
+                  sf.setValue(keyValue.getKey(), keyValue.getValue());
+
+              }
+
+              al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+            }
+          }
+          if (JSEQ[i].getPdbidsCount() > 0)
+          {
+            Pdbids[] ids = JSEQ[i].getPdbids();
+            for (int p = 0; p < ids.length; p++)
+            {
+              jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
+              entry.setId(ids[p].getId());
+              entry.setType(ids[p].getType());
+              if (ids[p].getFile() != null)
+              {
+                if (!pdbloaded.containsKey(ids[p].getFile()))
+                {
+                  String tmppdb = loadPDBFile(file, ids[p].getId());
+                  entry.setFile(tmppdb);
+                  pdbloaded.put(ids[p].getId(), tmppdb);
+                }
+                else
+                  entry.setFile(pdbloaded.get(ids[p].getId()).toString());
+              }
+
+              al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+            }
+          }
+          if(vamsasSeq[i].getDBRefCount()>0)
+          {
+            for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)
+            {
+              jalview.datamodel.DBRefEntry entry =
+                  new jalview.datamodel.DBRefEntry(
+                      vamsasSeq[i].getDBRef(d).getSource(),
+                      vamsasSeq[i].getDBRef(d).getVersion(),
+                      vamsasSeq[i].getDBRef(d).getAccessionId()
+                      );
+              al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
+            }
+
+          }
         }
 
-        jalview.datamodel.AlignmentAnnotation jaa = null;
 
-        if (an[i].getGraph())
+
+         /////////////////////////////////
+        //////////////////////////////////
+        //LOAD ANNOTATIONS
+        boolean hideQuality = true,
+            hideConservation = true,
+            hideConsensus = true;
+
+        if (vamsasSet.getAnnotation() != null)
         {
-          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-              an[i].getDescription(), anot, 0, 0, 1);
+            Annotation[] an = vamsasSet.getAnnotation();
+
+            for (int i = 0; i < an.length; i++)
+            {
+               if (an[i].getLabel().equals("Quality"))
+                {
+                 hideQuality = false;
+                 continue;
+                }
+               else if(an[i].getLabel().equals("Conservation"))
+               {
+                 hideConservation = false;
+                 continue;
+               }
+               else if(an[i].getLabel().equals("Consensus"))
+               {
+                 hideConsensus = false;
+                 continue;
+               }
+
+                AnnotationElement[] ae = an[i].getAnnotationElement();
+                jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
+
+                for (int aa = 0; aa < ae.length; aa++)
+                {
+                    anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
+                            ae[aa].getDescription(),
+                            ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
+                            ae[aa].getValue());
+                    anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
+                }
+
+                jalview.datamodel.AlignmentAnnotation jaa = null;
+
+                if (an[i].getGraph())
+                {
+                  jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+                      an[i].getDescription(), anot, 0, 0,
+                      an[i].getGraphType());
+
+                  jaa.graphGroup = an[i].getGraphGroup();
+
+                  if (an[i].getThresholdLine() != null)
+                  {
+                    jaa.setThreshold(new jalview.datamodel.GraphLine(
+                                  an[i].getThresholdLine().getValue(),
+                                  an[i].getThresholdLine().getLabel(),
+                                new java.awt.Color(an[i].getThresholdLine().getColour()))
+                             );
+
+                  }
+
+                }
+                else
+                {
+                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+                            an[i].getDescription(), anot);
+                }
+
+                if(an[i].getSequenceRef()!=null)
+                {
+                  jaa.createSequenceMapping(
+                      al.findName(an[i].getSequenceRef()), 1
+                      );
+                  al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+                }
+
+                al.addAnnotation(jaa);
+            }
         }
-        else
+
+
+        //  af.changeColour() );
+        /////////////////////////
+        //LOAD GROUPS
+        if (jms.getJGroupCount() > 0)
         {
-          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-              an[i].getDescription(), anot);
+            JGroup[] groups = jms.getJGroup();
+
+            for (int i = 0; i < groups.length; i++)
+            {
+                ColourSchemeI cs = null;
+
+                if (groups[i].getColour() != null)
+                {
+                    if (groups[i].getColour().startsWith("ucs"))
+                    {
+                        cs = GetUserColourScheme(jms, groups[i].getColour());
+                    }
+                    else
+                    {
+                        cs = ColourSchemeProperty.getColour(al,
+                                groups[i].getColour());
+                    }
+
+                    if(cs!=null)
+                      cs.setThreshold(groups[i].getPidThreshold(), true);
+                }
+
+                Vector seqs = new Vector();
+                int[] ids = groups[i].getSeq();
+
+                for (int s = 0; s < ids.length; s++)
+                {
+                    seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
+                            ids[s]));
+                }
+
+                jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
+                        groups[i].getName(), cs, groups[i].getDisplayBoxes(),
+                        groups[i].getDisplayText(), groups[i].getColourText(),
+                        groups[i].getStart(), groups[i].getEnd());
+
+                sg.setOutlineColour(new java.awt.Color(
+                        groups[i].getOutlineColour()));
+
+                if (groups[i].getConsThreshold() != 0)
+                {
+                    jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
+                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,
+                            sg.getWidth() - 1);
+                    c.calculate();
+                    c.verdict(false, 25);
+                    sg.cs.setConservation(c);
+                }
+
+                al.addGroup(sg);
+            }
         }
 
-        al.addAnnotation(jaa);
-      }
-    }
 
-    /////////////////////////////////
-    // LOAD VIEWPORT
-    Viewport[] views = jms.getViewport();
-    Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+        /////////////////////////////////
+        // LOAD VIEWPORT
+        Viewport[] views = jms.getViewport();
+        Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 
-    AlignFrame af = new AlignFrame(al);
 
-    //  af.changeColour() );
-    /////////////////////////
-    //LOAD GROUPS
-    if (jms.getJGroupCount() > 0)
-    {
-      JGroup[] groups = jms.getJGroup();
+        AlignFrame af = new AlignFrame(al);
 
-      for (int i = 0; i < groups.length; i++)
-      {
-        ColourSchemeI cs = null;
-
-        if (groups[i].getColour() != null)
+        if(hiddenSeqs!=null)
         {
-          if (groups[i].getColour().startsWith("ucs"))
-          {
-            cs = GetUserColourScheme(jms, groups[i].getColour());
-          }
-          else
+          for(int s=0; s<JSEQ.length; s++)
           {
-            cs = ColourSchemeProperty.getColour(al,
-                                                groups[i].getColour());
+            for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
+            {
+              al.getSequenceAt(s).addHiddenSequence(
+                  al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
+                  );
+            }
           }
 
-          if (cs instanceof ResidueColourScheme)
+          for(int s=0; s<hiddenSeqs.size(); s++)
           {
-            ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
+              af.viewport.hideSequence(
+                (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));
           }
-          else if (cs instanceof ScoreColourScheme)
+        }
+
+
+        if(hideConsensus || hideQuality || hideConservation)
+        {
+          int hSize = al.getAlignmentAnnotation().length;
+          for (int h = 0; h < hSize; h++)
           {
-            ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
+            if (
+                (hideConsensus &&
+                 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
+                ||
+                (hideQuality &&
+                 al.getAlignmentAnnotation()[h].label.equals("Quality"))
+                ||
+                (hideConservation &&
+                 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
+            {
+              al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
+              hSize--;
+              h--;
+            }
           }
+          af.alignPanel.adjustAnnotationHeight();
         }
 
-        jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
-            SequenceGroup(groups[i].getName(),
-                          cs, groups[i].getDisplayBoxes(),
-                          groups[i].getDisplayText(), groups[i].getColourText(),
-                          groups[i].getStart(), groups[i].getEnd());
-        sg.setOutlineColour(new java.awt.Color(
-            groups[i].getOutlineColour()));
+        af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+            view.getHeight());
+        af.viewport.setStartRes(view.getStartRes());
+        af.viewport.setStartSeq(view.getStartSeq());
+        af.viewport.setShowAnnotation(view.getShowAnnotation());
+        af.viewport.showConservation = view.getShowConservation();
+        af.viewport.showQuality = view.getShowQuality();
+        af.viewport.showIdentity = view.getShowIdentity();
+        af.viewport.setAbovePIDThreshold(view.getPidSelected());
+        af.abovePIDThreshold.setSelected(view.getPidSelected());
+        af.viewport.setColourText(view.getShowColourText());
+        af.colourTextMenuItem.setSelected(view.getShowColourText());
+        af.viewport.setConservationSelected(view.getConservationSelected());
+        af.conservationMenuItem.setSelected(view.getConservationSelected());
+
+        af.viewport.setShowJVSuffix(view.getShowFullId());
+        af.seqLimits.setSelected(view.getShowFullId());
+
+        af.viewport.setFont(new java.awt.Font(view.getFontName(),
+                view.getFontStyle(), view.getFontSize()));
+        af.alignPanel.fontChanged();
+
+        af.viewport.setRenderGaps(view.getRenderGaps());
+        af.renderGapsMenuItem.setSelected(view.getRenderGaps());
+
+        af.viewport.setWrapAlignment(view.getWrapAlignment());
+        af.wrapMenuItem.setSelected(view.getWrapAlignment());
+
+        af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+
+        af.annotationPanelMenuItem.setState(view.getShowAnnotation());
+        af.viewport.setShowAnnotation(view.getShowAnnotation());
+        af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+
+        af.viewport.setShowBoxes(view.getShowBoxes());
+        af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
+        af.viewport.setShowText(view.getShowText());
+        af.viewTextMenuItem.setSelected(view.getShowText());
 
-        int[] ids = groups[i].getSeq();
+        ColourSchemeI cs = null;
 
-        for (int s = 0; s < ids.length; s++)
+        if (view.getBgColour() != null)
         {
-          sg.addSequence( (jalview.datamodel.SequenceI) seqids.elementAt(
-              ids[s]));
+            if (view.getBgColour().startsWith("ucs"))
+            {
+                cs = GetUserColourScheme(jms, view.getBgColour());
+            }
+            else if(view.getBgColour().startsWith("Annotation"))
+            {
+              //int find annotation
+              for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+              {
+                if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
+                    equals(view.getAnnotationColours().getAnnotation()))
+                {
+                  if (af.viewport.alignment.getAlignmentAnnotation()[i].
+                      getThreshold() == null)
+                  {
+                    af.viewport.alignment.getAlignmentAnnotation()[i].
+                        setThreshold(
+                            new jalview.datamodel.GraphLine(
+                                view.getAnnotationColours().getThreshold(),
+                                "Threshold", java.awt.Color.black)
+
+                        );
+                  }
+
+
+                  if (view.getAnnotationColours().getColourScheme().equals(
+                      "None"))
+                  {
+                    cs = new AnnotationColourGradient(
+                        af.viewport.alignment.getAlignmentAnnotation()[i],
+                        new java.awt.Color(view.getAnnotationColours().
+                                           getMinColour()),
+                        new java.awt.Color(view.getAnnotationColours().
+                                           getMaxColour()),
+                        view.getAnnotationColours().getAboveThreshold());
+                  }
+                  else if (view.getAnnotationColours().getColourScheme().
+                           startsWith("ucs"))
+                  {
+                     cs = new AnnotationColourGradient(
+                         af.viewport.alignment.getAlignmentAnnotation()[i],
+                         GetUserColourScheme(jms, view.getAnnotationColours().
+                                                        getColourScheme()),
+                         view.getAnnotationColours().getAboveThreshold()
+                         );
+                   }
+                   else
+                   {
+                     cs = new AnnotationColourGradient(
+                         af.viewport.alignment.getAlignmentAnnotation()[i],
+                         ColourSchemeProperty.getColour(al,
+                         view.getAnnotationColours().getColourScheme()),
+                         view.getAnnotationColours().getAboveThreshold()
+                         );
+                   }
+
+                  // Also use these settings for all the groups
+                  if (al.getGroups() != null)
+                    for (int g = 0; g < al.getGroups().size(); g++)
+                    {
+                      jalview.datamodel.SequenceGroup sg
+                          = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
+
+                      if(sg.cs == null)
+                        continue;
+
+
+                  /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
+                      {
+                        sg.cs = new AnnotationColourGradient(
+                            af.viewport.alignment.getAlignmentAnnotation()[i],
+                            new java.awt.Color(view.getAnnotationColours().
+                                               getMinColour()),
+                            new java.awt.Color(view.getAnnotationColours().
+                                               getMaxColour()),
+                            view.getAnnotationColours().getAboveThreshold());
+                      }
+                      else*/
+                      {
+                        sg.cs = new AnnotationColourGradient(
+                            af.viewport.alignment.getAlignmentAnnotation()[i],
+                            sg.cs,
+                            view.getAnnotationColours().getAboveThreshold()
+                            );
+                      }
+
+                    }
+
+
+                  break;
+                }
+
+              }
+            }
+            else
+            {
+                cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+            }
+
+            if(cs!=null)
+            {
+              cs.setThreshold(view.getPidThreshold(), true);
+              cs.setConsensus(af.viewport.vconsensus);
+            }
         }
 
-        if (groups[i].getConsThreshold() != 0)
+        af.setColourSelected(view.getBgColour());
+        af.viewport.setGlobalColourScheme(cs);
+        af.viewport.setColourAppliesToAllGroups(false);
+        af.changeColour(cs);
+        if (view.getConservationSelected() && cs!=null)
         {
-          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
-              "All",
-              ResidueProperties.propHash, 3, sg.sequences, 0,
-              sg.getWidth() - 1);
-          c.calculate();
-          c.verdict(false, 25);
-          cs = new ConservationColourScheme(c, cs);
-          sg.cs = cs;
+          cs.setConservationInc(view.getConsThreshold());
         }
 
-        al.addGroup(sg);
-      }
-    }
+        af.viewport.setColourAppliesToAllGroups(true);
 
-    Desktop.addInternalFrame(af, view.getTitle(),
-                             AlignFrame.NEW_WINDOW_WIDTH,
-                             AlignFrame.NEW_WINDOW_HEIGHT);
-    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
-                 view.getHeight());
-    af.viewport.setStartRes(view.getStartRes());
-    af.viewport.setStartSeq(view.getStartSeq());
-    af.viewport.showConservation = view.getShowConservation();
-    af.viewport.showQuality = view.getShowQuality();
-    af.viewport.showIdentity = view.getShowIdentity();
-    af.viewport.setAbovePIDThreshold(view.getPidSelected());
-    af.viewport.setColourText(view.getShowColourText());
-    af.viewport.setConservationSelected(view.getConservationSelected());
-    af.viewport.setShowFullId(view.getShowFullId());
-    af.viewport.setFont(new java.awt.Font(view.getFontName(),
-                                          view.getFontStyle(), view.getFontSize()));
-    af.alignPanel.fontChanged();
-
-    af.sequenceFeatures_actionPerformed(null);
-    af.viewport.setRenderGaps(view.getRenderGaps());
-
-    af.viewport.setWrapAlignment(view.getWrapAlignment());
-
-    if (view.getWrapAlignment())
-    {
-      af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-    }
-    else
-    {
-      af.viewport.setShowAnnotation(view.getShowAnnotation());
-      af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
-    }
+        if (view.getShowSequenceFeatures())
+        {
+           af.viewport.showSequenceFeatures = true;
+           af.showSeqFeatures.setSelected(true);
+        }
 
-    af.viewport.setShowBoxes(view.getShowBoxes());
-    af.viewport.setShowText(view.getShowText());
+        if(jms.getFeatureSettings()!=null)
+        {
+          af.viewport.featuresDisplayed = new Hashtable();
+          String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
+         for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
+         {
+           Setting setting = jms.getFeatureSettings().getSetting(fs);
+
+           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
+               new java.awt.Color(setting.getColour()));
+
+           renderOrder[fs] = setting.getType();
+
+           if(setting.getDisplay())
+             af.viewport.featuresDisplayed.put(
+                 setting.getType(), new Integer(setting.getColour()));
+         }
+         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+        }
 
-    ColourSchemeI cs = null;
+        if (view.getHiddenColumnsCount() > 0)
+        {
+          for (int c = 0; c < view.getHiddenColumnsCount(); c++)
+          {
+              af.viewport.hideColumns(
+                view.getHiddenColumns(c).getStart(),
+                view.getHiddenColumns(c).getEnd()+1
+                );
+          }
+        }
 
-    if (view.getBgColour() != null)
-    {
-      if (view.getBgColour().startsWith("ucs"))
-      {
-        cs = GetUserColourScheme(jms, view.getBgColour());
-      }
-      else
-      {
-        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
-      }
 
-      if (cs instanceof ConservationColourScheme)
-      {
-        ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
-      }
+        Desktop.addInternalFrame(af, view.getTitle(),
+             view.getWidth(), view.getHeight());
 
-      if (cs instanceof ResidueColourScheme)
-      {
-        ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
-      }
-      else if (cs instanceof ScoreColourScheme)
-      {
-        ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
-      }
-    }
+        //LOAD TREES
+        ///////////////////////////////////////
+        if (jms.getTreeCount() > 0)
+        {
+            try
+            {
+                for (int t = 0; t < jms.getTreeCount(); t++)
+                {
 
-    af.viewport.setGlobalColourScheme(cs);
+                    Tree tree = jms.getTree(t);
 
-    af.viewport.setColourAppliesToAllGroups(false);
-    af.changeColour(af.viewport.getGlobalColourScheme());
-    af.viewport.setColourAppliesToAllGroups(true);
+                    TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
+                                tree.getNewick()), tree.getTitle(),
+                                tree.getWidth(), tree.getHeight(),
+                                tree.getXpos(), tree.getYpos());
 
-    System.out.println(view.getShowSequenceFeatures());
+                    tp.fitToWindow.setState(tree.getFitToWindow());
+                    tp.fitToWindow_actionPerformed(null);
 
-    if (view.getShowSequenceFeatures())
-    {
-      ;
-    }
+                    if(tree.getFontName()!=null)
+                      tp.setTreeFont(new java.awt.Font(tree.getFontName(),
+                                          tree.getFontStyle(),
+                                          tree.getFontSize()));
+                    else
+                      tp.setTreeFont(new java.awt.Font(view.getFontName(),
+                                            view.getFontStyle(),
+                                            tree.getFontSize()));
 
-    {
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al,
-          af.alignPanel);
-    }
+                    tp.showPlaceholders(tree.getMarkUnlinked());
+                    tp.showBootstrap(tree.getShowBootstrap());
+                    tp.showDistances(tree.getShowDistances());
 
-    //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE
-    if (object.getVamsasModel().getTreeCount() > 0)
-    {
-      try
-      {
-        af.ShowNewickTree(new jalview.io.NewickFile(
-            (String) object.getVamsasModel().getTree(0)), "Tree");
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+                    tp.treeCanvas.threshold = tree.getThreshold();
+
+                    if (tree.getCurrentTree())
+                      af.viewport.setCurrentTree(tp.getTree());
+                }
+
+            }
+            catch (Exception ex)
+            {
+                ex.printStackTrace();
+            }
+
+        }
+
+        return af;
     }
-  }
 }
+