X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=95912fe7125cb13b6c667fc3a26f4fbffeecf2e6;hb=3596077c79b7aa2051b9aaa978481004b513101c;hp=89a7bfc5aaf51fa2ca3b946eaeabfaab956dae68;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 89a7bfc..95912fe 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,590 +1,1389 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
+
+import jalview.schemes.*;
+
+import jalview.gui.*;
+
 import java.io.*;
+
+import java.net.*;
+
 import java.util.*;
+
 import java.util.jar.*;
 
-import jalview.binding.*;
-import jalview.schemes.*;
-import javax.swing.JInternalFrame;
-import java.net.URL;
-import jalview.io.SequenceFeatureFetcher;
+import javax.swing.*;
 
+import org.exolab.castor.xml.*;
 
+import jalview.schemabinding.version2.*;
+
+
+
+
+/**
+ * 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();
 
-  // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
-  public static void SaveState(File statefile)
-  {
-      long creation = System.currentTimeMillis();
-      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-      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();
-        //REVERSE ORDER
-        for (int i = frames.length-1; i > -1; i--)
-        {
-          if (frames[i] instanceof AlignFrame)
-          {
-            AlignFrame af = (AlignFrame) frames[i];
+        if (frames == null)
+        {
+            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;
-            while( shortNames.contains(shortName) )
+            Vector shortNames = new Vector();
+
+            //REVERSE ORDER
+            for (int i = frames.length - 1; i > -1; i--)
             {
-              if(shortName.endsWith("_"+(count-1)))
-                shortName = shortName.substring(0, shortName.lastIndexOf("_"));
+                if (frames[i] instanceof AlignFrame)
+                {
+                    AlignFrame af = (AlignFrame) frames[i];
+
+                    String shortName = af.getTitle();
+
+                    if (shortName.indexOf(File.separatorChar) > -1)
+                    {
+                        shortName = shortName.substring(shortName.lastIndexOf(
+                                    File.separatorChar) + 1);
+                    }
+
+                    int count = 1;
+
+                    while (shortNames.contains(shortName))
+                    {
+                        if (shortName.endsWith("_" + (count - 1)))
+                        {
+                            shortName = shortName.substring(0,
+                                    shortName.lastIndexOf("_"));
+                        }
 
-              shortName = shortName.concat("_"+count);
-              count++;
+                        shortName = shortName.concat("_" + count);
+                        count++;
+                    }
+
+                    shortNames.addElement(shortName);
+
+                    if (!shortName.endsWith(".xml"))
+                    {
+                        shortName = shortName + ".xml";
+                    }
+
+                    SaveState(af, creation, shortName, jout, out);
+                }
             }
-            shortNames.addElement(shortName);
 
-            if(!shortName.endsWith(".xml"))
-              shortName = shortName+".xml";
+            out.close();
+            jout.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
+
+    // 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);
 
-            SaveState( af, creation, shortName, jout, out);
-           }
+            //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+            ////////////////////////////////////////////////////
+            PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+                        "UTF-8"));
+
+            SaveState(af, System.currentTimeMillis(), fileName, jout, out);
+            out.close();
+            jout.close();
         }
-        out.close();
-        jout.close();
-      }
-      catch(Exception ex){ex.printStackTrace();}
-  }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+    }
 
-  // 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);
-      //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-      ////////////////////////////////////////////////////
-      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));
+    /**
+     * 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();
 
-      SaveState(af, System.currentTimeMillis(), fileName, jout, out);
-      out.close();
-      jout.close();
-    }catch(Exception ex){}
-  }
+        AlignViewport av = af.viewport;
 
-  public static void SaveState( AlignFrame af, long timeStamp,
-      String fileName, JarOutputStream jout, PrintWriter out)
-  {
+        JalviewModel object = new JalviewModel();
+        object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 
-    Vector seqids = new Vector();
-    Vector userColours = new Vector();
+        object.setCreationDate(new java.util.Date(timeStamp));
+        object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 
-    AlignViewport av = af.viewport;
+        jalview.datamodel.AlignmentI jal = af.viewport.alignment;
+        jalview.datamodel.AlignmentI jalhidden = null;
 
-    JalviewModel object = new JalviewModel();
-    object.setVamsasModel( new VamsasModel() );
+        if(av.hasHiddenRows)
+        {
+          jalhidden = jal;
+          jal = jal.getHiddenSequences().getFullAlignment();
+        }
 
-    object.setCreationDate( new java.util.Date(timeStamp) );
 
-    jalview.datamodel.AlignmentI jal = af.viewport.alignment;
+        SequenceSet vamsasSet = new SequenceSet();
+        Sequence vamsasSeq;
+        JalviewModelSequence jms = new JalviewModelSequence();
 
-    SequenceSet vamsasSet = new SequenceSet();
-    Sequence vamsasSeq;
-    JalviewModelSequence jms = new JalviewModelSequence();
+        vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
-    vamsasSet.setGapChar(jal.getGapCharacter()+"");
+        JSeq jseq;
+        Vector pdbfiles = null;
 
-    JSeq jseq;
+        //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 = new JSeq();
+            jseq.setStart(jal.getSequenceAt(i).getStart());
+            jseq.setEnd(jal.getSequenceAt(i).getEnd());
+            jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
+
+            jseq.setId(id);
+
+            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 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());
+            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());
+                jseq.addFeatures(features);
+                index ++;
+              }
+            }
 
-      jseq = new JSeq();
-      jseq.setStart(jal.getSequenceAt(i).getStart());
-      jseq.setEnd(jal.getSequenceAt(i).getEnd());
+            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);
+              }
+            }
 
-      jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
+            jms.addJSeq(jseq);
+            vamsasSet.addSequence(vamsasSeq);
+            id++;
+        }
 
-      jseq.setId( id );
+        //SAVE TREES
+        ///////////////////////////////////
+        if (af.viewport.currentTree != null)
+        {
+          // FIND ANY ASSOCIATED TREES
+          // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
+          if (Desktop.desktop != null)
+          {
+            JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
-      jms.addJSeq(jseq);
-      vamsasSet.addSequence(vamsasSeq);
-      id++;
-    }
+            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 TREES
-    if(af.viewport.currentTree!=null)
-    {
-      object.getVamsasModel().addTree(af.viewport.currentTree.toString());
-    }
+        //SAVE ANNOTATIONS
+        if (jal.getAlignmentAnnotation() != null)
+        {
+            jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 
-    //SAVE ANNOTATIONS
-    if(jal.getAlignmentAnnotation()!=null)
-    {
+            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);
+            }
+        }
 
-      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;}
+        //SAVE GROUPS
+        if (jal.getGroups() != null)
+        {
+            JGroup[] groups = new JGroup[jal.getGroups().size()];
 
-        Annotation an = new Annotation();
-        an.setDescription(aa[i].description);
-        an.setGraph(aa[i].isGraph);
-        an.setLabel(aa[i].label);
+            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);
+        }
+
+
+        ///////////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 if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
+        {
+           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
+        {
+            view.setBgColour(ColourSchemeProperty.getColourName(
+                    av.getGlobalColourScheme()));
+        }
 
-        AnnotationElement ae;
+        ColourSchemeI cs = av.getGlobalColourScheme();
 
-        for(int a=0; a<aa[i].annotations.length; a++)
+        if(cs!=null)
         {
-          if(aa[i]==null || aa[i].annotations[a]==null)
-            continue;
+          if (cs.conservationApplied())
+          {
+            view.setConsThreshold(cs.getConservationInc());
+            if (cs instanceof jalview.schemes.UserColourScheme)
+              view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+          }
 
-          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);
+          if (cs instanceof ResidueColourScheme)
+          {
+            view.setPidThreshold(cs.getThreshold());
+          }
         }
 
-        vamsasSet.addAnnotation(an);
-      }
+        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)
+        {
+          jalview.schemabinding.version2.FeatureSettings fs
+              = new jalview.schemabinding.version2.FeatureSettings();
 
-    }
+          String [] renderOrder =
+              af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+          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()
+                );
 
-    //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());
+            setting.setDisplay(
+                av.featuresDisplayed.containsKey(renderOrder[ro])
+                );
 
-        if(sg.cs instanceof ConservationColourScheme)
-          groups[i].setConsThreshold( ((ConservationColourScheme)sg.cs).inc);
+            fs.addSetting(setting);
 
-        if (sg.cs instanceof ResidueColourScheme)
-          groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).getThreshold());
-        else if (sg.cs instanceof ScoreColourScheme)
-          groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());
+          }
+          jms.setFeatureSettings(fs);
 
+        }
 
-        if (sg.cs instanceof jalview.schemes.UserColourScheme)
-          groups[i].setColour(SetUserColourScheme(sg.cs, userColours, jms));
-        else
-          groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
+        if(av.hasHiddenColumns)
+        {
+          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.addViewport(view);
 
-        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(); s++)
+        object.setJalviewModelSequence(jms);
+        object.getVamsasModel().addSequenceSet(vamsasSet);
+
+        try
         {
-          jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence)sg.getSequenceAt(s);
-          int index = seqids.indexOf(seq);
-          groups[i].addSeq(index);
+            if (!fileName.endsWith(".xml"))
+            {
+                fileName = fileName + ".xml";
+            }
+
+            JarEntry entry = new JarEntry(fileName);
+            jout.putNextEntry(entry);
+
+            object.marshal(out);
         }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
 
-      }
-      jms.setJGroup(groups);
+    String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+        Vector userColours, JalviewModelSequence jms)
+    {
+        String id = null;
+        jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 
+        if (!userColours.contains(ucs))
+        {
+            userColours.add(ucs);
+
+            java.awt.Color[] colours = ucs.getColours();
+            jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
+            jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
+
+            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);
+            }
+
+            id = "ucs" + userColours.indexOf(ucs);
+            uc.setId(id);
+            uc.setUserColourScheme(jbucs);
+            jms.addUserColours(uc);
+        }
+
+        return id;
     }
 
-    ///////////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();
-   if(cs instanceof ConservationColourScheme)
-     view.setConsThreshold( ((ConservationColourScheme)cs).inc);
-
-   if (cs instanceof ResidueColourScheme)
-     view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());
-  else if (cs instanceof ScoreColourScheme)
-     view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());
-
-
-   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
+   jalview.schemes.UserColourScheme GetUserColourScheme(
+        JalviewModelSequence jms, String id)
     {
-     if(!fileName.endsWith(".xml"))
-              fileName = fileName+".xml";
+        UserColours[] uc = jms.getUserColours();
+        UserColours colours = null;
+
+        for (int i = 0; i < uc.length; i++)
+        {
+            if (uc[i].getId().equals(id))
+            {
+                colours = uc[i];
+
+                break;
+            }
+        }
 
-     JarEntry entry = new JarEntry(fileName);
-     jout.putNextEntry(entry);
+        int csize = colours.getUserColourScheme().getColourCount();
+        java.awt.Color[] newColours = new java.awt.Color[csize];
 
-      object.marshal(out);
+        for (int i = 0; i < csize; i++)
+        {
+            newColours[i] = new java.awt.Color(Integer.parseInt(
+                        colours.getUserColourScheme().getColour(i).getRGB(), 16));
+        }
+
+        return new jalview.schemes.UserColourScheme(newColours);
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     */
+    public AlignFrame LoadJalviewAlign(String file)
     {
-      ex.printStackTrace();
+        jalview.gui.AlignFrame af = null;
+        try
+        {
+            //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+            URL url = null;
+
+            if (file.startsWith("http://"))
+            {
+                url = new URL(file);
+            }
+
+            JarInputStream jin = null;
+            JarEntry jarentry = null;
+            int entryCount = 1;
+
+            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");
+           JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                    "Couldn't locate " + file,
+                                    "URL not found",
+                                    JOptionPane.WARNING_MESSAGE);
+
+        }
+        catch (Exception ex)
+        {
+          //Is Version 1 Jar file?
+          af =  new Jalview2XML_V1().LoadJalviewAlign(file);
+
+          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");
+             JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                      "Error loading  " + file,
+                                      "Error loading Jalview file",
+                                      JOptionPane.WARNING_MESSAGE);
+
+        }
+
+        return af;
     }
-  }
-
-  static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
-                                    Vector userColours,
-                                    JalviewModelSequence jms)
-  {
-    String id=null;
-    jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)cs;
-    if (!userColours.contains(ucs))
+
+    String loadPDBFile(String file, String pdbId)
     {
-      userColours.add(ucs);
-      java.awt.Color [] colours = ucs.getColours();
-      jalview.binding.UserColours uc = new jalview.binding.UserColours();
-      jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();
-      for(int i=0; i<colours.length; i++)
+      System.out.println("load file "+file);
+      try
       {
-             jalview.binding.Colour col = new jalview.binding.Colour();
-             col.setRGB( jalview.util.Format.getHexString(colours[i]) );
-             jbucs.addColour(col);
+        JarInputStream jin = null;
+
+        if (file.startsWith("http://"))
+        {
+          jin = new JarInputStream(new URL(file).openStream());
+        }
+        else
+        {
+          jin = new JarInputStream(new FileInputStream(file));
+        }
+
+        JarEntry entry = null;
+        do
+        {
+          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;
+
+        while ( (data = in.readLine()) != null)
+        {
+          out.println(data);
+        }
+        out.close();
+        return outFile.getAbsolutePath();
+
       }
-      id = "ucs"+userColours.indexOf(ucs);
-      uc.setId(id);
-      uc.setUserColourScheme(jbucs);
-      jms.addUserColours(uc);
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+
+      return null;
     }
-    return id;
-  }
-
-  static jalview.schemes.UserColourScheme GetUserColourScheme(JalviewModelSequence jms, String id)
-  {
-    UserColours [] uc = jms.getUserColours();
-    UserColours colours=null;
-    for(int i=0; i<uc.length; i++)
+
+
+    AlignFrame LoadFromObject(JalviewModel object, String file)
     {
-       if(uc[i].getId().equals(id))
-       {  colours = uc[i]; break;  }
-    }
-    int csize = colours.getUserColourScheme().getColourCount();
-    java.awt.Color [] newColours = new java.awt.Color[csize];
+        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() );
 
-    for(int i=0; i<csize;i++)
-      newColours[i] = new java.awt.Color(
-        Integer.parseInt( colours.getUserColourScheme().getColour(i).getRGB(), 16) );
+            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]);
+        }
 
-    return  new jalview.schemes.UserColourScheme(newColours);
+        ///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);
+        /////////////////////////////////
 
-  }
 
+        Hashtable pdbloaded = new Hashtable();
+        for (int i = 0; i < vamsasSeq.length; i++)
+        {
+          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());
 
-  public static void LoadJalviewAlign(String file)
-  {
-    JalviewModel object = new JalviewModel();
-    try{
-      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+              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);
+            }
 
-      URL url = null;
-      if( file.startsWith("http://"))
-       url = new URL(file);
+          }
+        }
 
-      JarInputStream jin = null;
-      JarEntry jarentry=null;
-      int entryCount = 1;
-      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)
+         /////////////////////////////////
+        //////////////////////////////////
+        //LOAD ANNOTATIONS
+        boolean hideQuality = true,
+            hideConservation = true,
+            hideConsensus = true;
+
+        if (vamsasSet.getAnnotation() != null)
         {
-          InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-          object = (JalviewModel) object.unmarshal(in);
-          LoadFromObject(object);
-          entryCount++;
+            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);
+            }
         }
-      }while(jarentry!=null);
 
-    }
-    catch(Exception ex)
-    {   System.err.println("Exception whilst loading jalview XML file : "+ex+"\n");
-     ex.printStackTrace(); return; }
-
-  }
-
-  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++)
-     {
-       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]);
-     }
-
-     /////////////////////////////////
-     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
-     /////////////////////////////////
-
-     //////////////////////////////////
-     //LOAD ANNOTATIONS
-     if(vamsasSet.getAnnotation()!=null)
-     {
-       Annotation[] an = vamsasSet.getAnnotation();
-       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++)
-         {
-           anot[ae[aa].getPosition()]
-               = new jalview.datamodel.Annotation(
-                   ae[aa].getDisplayCharacter(),
-                   ae[aa].getDescription(),
-                   ae[aa].getSecondaryStructure().charAt(0),
-                   ae[aa].getValue()
-               );
-         }
 
+        //  af.changeColour() );
+        /////////////////////////
+        //LOAD GROUPS
+        if (jms.getJGroupCount() > 0)
+        {
+            JGroup[] groups = jms.getJGroup();
 
-          jalview.datamodel.AlignmentAnnotation jaa = null;
-          if(an[i].getGraph())
-            jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-                                        an[i].getDescription(), anot,
-                                        0,0,1);
-          else
-            jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-                                        an[i].getDescription(), anot);
-          al.addAnnotation(jaa);
-       }
-     }
-
-      /////////////////////////////////
-      // 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();
-      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 instanceof ResidueColourScheme)
-           ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
-         else if (cs instanceof ScoreColourScheme)
-           ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
-       }
-
-        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()));
-        int [] ids = groups[i].getSeq();
-        for(int s=0; s<ids.length; s++)
-            sg.addSequence( (jalview.datamodel.SequenceI)seqids.elementAt( ids[s] ));
-
-        if(groups[i].getConsThreshold()!=0)
-        {
-          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;
-        }
-
-
-        al.addGroup(sg);
-      }
-    }
+            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);
+            }
+        }
 
 
-    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();
+        /////////////////////////////////
+        // LOAD VIEWPORT
+        Viewport[] views = jms.getViewport();
+        Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 
-    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());
-    }
+        AlignFrame af = new AlignFrame(al);
 
-    af.viewport.setShowBoxes( view.getShowBoxes() );
-    af.viewport.setShowText( view.getShowText() );
+        if(hiddenSeqs!=null)
+        {
+          for(int s=0; s<JSEQ.length; s++)
+          {
+            for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
+            {
+              al.getSequenceAt(s).addHiddenSequence(
+                  al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
+                  );
+            }
+          }
 
-    ColourSchemeI cs=null;
-    if(view.getBgColour()!=null)
-    {
+          for(int s=0; s<hiddenSeqs.size(); s++)
+          {
+              af.viewport.hideSequence(
+                (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));
+          }
+        }
 
-      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();
+        if(hideConsensus || hideQuality || hideConservation)
+        {
+          int hSize = al.getAlignmentAnnotation().length;
+          for (int h = 0; h < hSize; h++)
+          {
+            if (
+                (hideConsensus &&
+                 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
+                ||
+                (hideQuality &&
+                 al.getAlignmentAnnotation()[h].label.equals("Quality"))
+                ||
+                (hideConservation &&
+                 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
+            {
+              al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
+              hSize--;
+              h--;
+            }
+          }
+          af.alignPanel.adjustAnnotationHeight();
+        }
 
-      if (cs instanceof ResidueColourScheme)
-        ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
-      else if (cs instanceof ScoreColourScheme)
-        ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
+        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.setGlobalColourScheme( cs );
+        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.setColourAppliesToAllGroups(false);
-    af.changeColour(af.viewport.getGlobalColourScheme());
-    af.viewport.setColourAppliesToAllGroups(true);
+        af.viewport.setRenderGaps(view.getRenderGaps());
+        af.renderGapsMenuItem.setSelected(view.getRenderGaps());
 
-    System.out.println(view.getShowSequenceFeatures());
-    if( view.getShowSequenceFeatures() );
-    {
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, af.alignPanel);
-    }
+        af.viewport.setWrapAlignment(view.getWrapAlignment());
+        af.wrapMenuItem.setSelected(view.getWrapAlignment());
 
-    //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();}
-    }
+        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());
+
+        ColourSchemeI cs = null;
+
+        if (view.getBgColour() != null)
+        {
+            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);
+            }
+        }
+
+        af.setColourSelected(view.getBgColour());
+        af.viewport.setGlobalColourScheme(cs);
+        af.viewport.setColourAppliesToAllGroups(false);
+        af.changeColour(cs);
+        if (view.getConservationSelected() && cs!=null)
+        {
+          cs.setConservationInc(view.getConsThreshold());
+        }
+
+        af.viewport.setColourAppliesToAllGroups(true);
+
+        if (view.getShowSequenceFeatures())
+        {
+           af.viewport.showSequenceFeatures = true;
+           af.showSeqFeatures.setSelected(true);
+        }
+
+        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;
+        }
+
+        if (view.getHiddenColumnsCount() > 0)
+        {
+          for (int c = 0; c < view.getHiddenColumnsCount(); c++)
+          {
+              af.viewport.hideColumns(
+                view.getHiddenColumns(c).getStart(),
+                view.getHiddenColumns(c).getEnd()+1
+                );
+          }
+        }
+
+
+        Desktop.addInternalFrame(af, view.getTitle(),
+             view.getWidth(), view.getHeight());
+
+        //LOAD TREES
+        ///////////////////////////////////////
+        if (jms.getTreeCount() > 0)
+        {
+            try
+            {
+                for (int t = 0; t < jms.getTreeCount(); t++)
+                {
+
+                    Tree tree = jms.getTree(t);
+
+                    TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
+                                tree.getNewick()), tree.getTitle(),
+                                tree.getWidth(), tree.getHeight(),
+                                tree.getXpos(), tree.getYpos());
+
+                    tp.fitToWindow.setState(tree.getFitToWindow());
+                    tp.fitToWindow_actionPerformed(null);
+
+                    if(tree.getFontName()!=null)
+                      tp.setTreeFont(new java.awt.Font(tree.getFontName(),
+                                          tree.getFontStyle(),
+                                          tree.getFontSize()));
+                    else
+                      tp.setTreeFont(new java.awt.Font(view.getFontName(),
+                                            view.getFontStyle(),
+                                            tree.getFontSize()));
+
+                    tp.showPlaceholders(tree.getMarkUnlinked());
+                    tp.showBootstrap(tree.getShowBootstrap());
+                    tp.showDistances(tree.getShowDistances());
+
+                    tp.treeCanvas.threshold = tree.getThreshold();
 
+                    if (tree.getCurrentTree())
+                      af.viewport.setCurrentTree(tp.getTree());
+                }
 
+            }
+            catch (Exception ex)
+            {
+                ex.printStackTrace();
+            }
+
+        }
+
+        return af;
+    }
+}