X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=b8466f0872e22923a9c7688fbf447c40add60d08;hb=61505ac1511435b067e647f5c7c9050e5c1eef41;hp=a90174121559ed7b2c5ddb0e557109b6703ec6cf;hpb=eab172160ce8e1f0d3ca95c1c273124a194e13e4;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a901741..b8466f0 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -18,20 +18,26 @@
  */
 package jalview.gui;
 
-import jalview.io.*;
 
 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 org.exolab.castor.xml.*;
+
+import jalview.schemabinding.version2.*;
+
+
 
 
 /**
@@ -43,7 +49,7 @@ import jalview.binding.*;
 public class Jalview2XML
 {
     // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
-    public static void SaveState(File statefile)
+    public void SaveState(File statefile)
     {
         long creation = System.currentTimeMillis();
         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -115,7 +121,7 @@ public class Jalview2XML
     }
 
     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-    public static void SaveAlignment(AlignFrame af, String jarFile,
+    public void SaveAlignment(AlignFrame af, String jarFile,
         String fileName)
     {
         try
@@ -147,7 +153,7 @@ public class Jalview2XML
      * @param jout DOCUMENT ME!
      * @param out DOCUMENT ME!
      */
-    public static void SaveState(AlignFrame af, long timeStamp,
+    public void SaveState(AlignFrame af, long timeStamp,
         String fileName, JarOutputStream jout, PrintWriter out)
     {
         Vector seqids = new Vector();
@@ -156,12 +162,20 @@ public class Jalview2XML
         AlignViewport av = af.viewport;
 
         JalviewModel object = new JalviewModel();
-        object.setVamsasModel(new VamsasModel());
+        object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 
         object.setCreationDate(new java.util.Date(timeStamp));
         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 
         jalview.datamodel.AlignmentI jal = af.viewport.alignment;
+        jalview.datamodel.AlignmentI jalhidden = null;
+
+        if(av.hasHiddenRows)
+        {
+          jalhidden = jal;
+          jal = jal.getHiddenSequences().getFullAlignment();
+        }
+
 
         SequenceSet vamsasSet = new SequenceSet();
         Sequence vamsasSeq;
@@ -170,27 +184,171 @@ public class Jalview2XML
         vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
         JSeq jseq;
+        Vector pdbfiles = null;
 
         //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])
+                      );
+                }
+              }
+            }
+
+
+            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 ++;
+              }
+            }
+
+            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);
+              }
+            }
+
             jms.addJSeq(jseq);
             vamsasSet.addSequence(vamsasSeq);
             id++;
@@ -225,6 +383,7 @@ public class Jalview2XML
                   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());
 
@@ -247,16 +406,43 @@ public class Jalview2XML
 
             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;
                 }
 
-                Annotation an = new Annotation();
+
                 an.setDescription(aa[i].description);
-                an.setGraph(aa[i].isGraph);
+
+                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;
@@ -275,6 +461,10 @@ public class Jalview2XML
                     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);
                 }
 
@@ -314,6 +504,12 @@ public class Jalview2XML
                           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,
@@ -333,7 +529,7 @@ public class Jalview2XML
                 groups[i].setDisplayText(sg.getDisplayText());
                 groups[i].setColourText(sg.getColourText());
 
-                for (int s = 0; s < sg.getSize(); s++)
+                for (int s = 0; s < sg.getSize(false); s++)
                 {
                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
                     int index = seqids.indexOf(seq);
@@ -344,6 +540,7 @@ public class Jalview2XML
             jms.setJGroup(groups);
         }
 
+
         ///////////SAVE VIEWPORT
         Viewport view = new Viewport();
         view.setTitle(af.getTitle());
@@ -359,6 +556,26 @@ public class Jalview2XML
             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(
@@ -392,15 +609,78 @@ public class Jalview2XML
         view.setShowBoxes(av.getShowBoxes());
         view.setShowColourText(av.getColourText());
         view.setShowConservation(av.showConservation);
-        view.setShowFullId(av.getShowFullId());
+        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;
+
+          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;
+
+            Setting setting = new Setting();
+            setting.setType(key);
+            setting.setColour(
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
+                );
+
+            setting.setDisplay(false);
+
+            fs.addSetting(setting);
+            settingsAdded.addElement(key);
+          }
+
+          jms.setFeatureSettings(fs);
+
+        }
+
+        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);
 
+
         object.setJalviewModelSequence(jms);
         object.getVamsasModel().addSequenceSet(vamsasSet);
 
@@ -422,7 +702,7 @@ public class Jalview2XML
         }
     }
 
-    static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+    String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
         Vector userColours, JalviewModelSequence jms)
     {
         String id = null;
@@ -433,12 +713,12 @@ public class Jalview2XML
             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();
+            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.binding.Colour col = new jalview.binding.Colour();
+                jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
                 jbucs.addColour(col);
             }
@@ -452,7 +732,7 @@ public class Jalview2XML
         return id;
     }
 
-    static jalview.schemes.UserColourScheme GetUserColourScheme(
+   jalview.schemes.UserColourScheme GetUserColourScheme(
         JalviewModelSequence jms, String id)
     {
         UserColours[] uc = jms.getUserColours();
@@ -485,11 +765,9 @@ public class Jalview2XML
      *
      * @param file DOCUMENT ME!
      */
-    public static AlignFrame LoadJalviewAlign(String file)
+    public AlignFrame LoadJalviewAlign(final String file)
     {
-        JalviewModel object = new JalviewModel();
         jalview.gui.AlignFrame af = null;
-
         try
         {
             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
@@ -520,13 +798,23 @@ public class Jalview2XML
                     jarentry = jin.getNextJarEntry();
                 }
 
-                if (jarentry != null)
+                if (jarentry != null && jarentry.getName().endsWith(".xml"))
                 {
                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-                    object = (JalviewModel) object.unmarshal(in);
-                    af = LoadFromObject(object);
+                    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);
         }
@@ -535,28 +823,94 @@ public class Jalview2XML
           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);
 
+          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)
         {
+
+          //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);
+            javax.swing.SwingUtilities.invokeLater(new Runnable()
+            {
+              public void run()
+              {
 
+                JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    "Error loading  " + file,
+                    "Error loading Jalview file",
+                    JOptionPane.WARNING_MESSAGE);
+              }});
         }
 
         return af;
     }
 
-    static AlignFrame LoadFromObject(JalviewModel object)
+    String loadPDBFile(String file, String pdbId)
+    {
+      System.out.println("load file "+file);
+      try
+      {
+        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();
+
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+
+      return null;
+    }
+
+
+    AlignFrame LoadFromObject(JalviewModel object, String file)
     {
         Vector seqids = new Vector();
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
@@ -566,32 +920,133 @@ public class Jalview2XML
 
         //////////////////////////////////
         //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() );
 
+            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]);
         }
 
+        ///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());
+
+              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);
+            }
+
+          }
+        }
+
+
+
+         /////////////////////////////////
         //////////////////////////////////
         //LOAD ANNOTATIONS
+        boolean hideQuality = true,
+            hideConservation = true,
+            hideConsensus = true;
+
         if (vamsasSet.getAnnotation() != null)
         {
             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()];
 
@@ -599,16 +1054,31 @@ public class Jalview2XML
                 {
                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
                             ae[aa].getDescription(),
-                            ae[aa].getSecondaryStructure().charAt(0),
+                            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, 1);
+                  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
                 {
@@ -616,16 +1086,18 @@ public class Jalview2XML
                             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);
             }
         }
 
-        /////////////////////////////////
-        // LOAD VIEWPORT
-        Viewport[] views = jms.getViewport();
-        Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
-
-        AlignFrame af = new AlignFrame(al);
 
         //  af.changeColour() );
         /////////////////////////
@@ -650,7 +1122,8 @@ public class Jalview2XML
                                 groups[i].getColour());
                     }
 
-                    cs.setThreshold(groups[i].getPidThreshold(), true);
+                    if(cs!=null)
+                      cs.setThreshold(groups[i].getPidThreshold(), true);
                 }
 
                 Vector seqs = new Vector();
@@ -673,7 +1146,7 @@ public class Jalview2XML
                 if (groups[i].getConsThreshold() != 0)
                 {
                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
-                            ResidueProperties.propHash, 3, sg.sequences, 0,
+                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,
                             sg.getWidth() - 1);
                     c.calculate();
                     c.verdict(false, 25);
@@ -685,10 +1158,62 @@ public class Jalview2XML
         }
 
 
+        /////////////////////////////////
+        // LOAD VIEWPORT
+        Viewport[] views = jms.getViewport();
+        Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+
+
+        AlignFrame af = new AlignFrame(al);
+
+        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)  )
+                  );
+            }
+          }
+
+          for(int s=0; s<hiddenSeqs.size(); s++)
+          {
+              af.viewport.hideSequence(
+                (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));
+          }
+        }
+
+
+        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();
+        }
+
         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();
@@ -699,8 +1224,8 @@ public class Jalview2XML
         af.viewport.setConservationSelected(view.getConservationSelected());
         af.conservationMenuItem.setSelected(view.getConservationSelected());
 
-        af.viewport.setShowFullId(view.getShowFullId());
-        af.fullSeqId.setSelected(view.getShowFullId());
+        af.viewport.setShowJVSuffix(view.getShowFullId());
+        af.seqLimits.setSelected(view.getShowFullId());
 
         af.viewport.setFont(new java.awt.Font(view.getFontName(),
                 view.getFontStyle(), view.getFontSize()));
@@ -712,16 +1237,11 @@ public class Jalview2XML
         af.viewport.setWrapAlignment(view.getWrapAlignment());
         af.wrapMenuItem.setSelected(view.getWrapAlignment());
 
-        if (view.getWrapAlignment())
-        {
-            af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-        }
-        else
-        {
-            af.annotationPanelMenuItem.setState(view.getShowAnnotation());
-            af.viewport.setShowAnnotation(view.getShowAnnotation());
-            af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
-        }
+        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());
@@ -736,6 +1256,96 @@ public class Jalview2XML
             {
                 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());
@@ -761,12 +1371,42 @@ public class Jalview2XML
 
         if (view.getShowSequenceFeatures())
         {
-            af.viewport.showSequenceFeatures = true;
-            af.sequenceFeatures.setSelected(true);
-            new SequenceFeatureFetcher(al, af.alignPanel);
-            al.featuresAdded = true;
+           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());
 
@@ -798,13 +1438,10 @@ public class Jalview2XML
                                             view.getFontStyle(),
                                             tree.getFontSize()));
 
+                    tp.showPlaceholders(tree.getMarkUnlinked());
+                    tp.showBootstrap(tree.getShowBootstrap());
+                    tp.showDistances(tree.getShowDistances());
 
-                    tp.placeholdersMenu.setState(tree.getMarkUnlinked());
-                    tp.placeholdersMenu_actionPerformed(null);
-                    tp.bootstrapMenu.setState(tree.getShowBootstrap());
-                    tp.bootstrapMenu_actionPerformed(null);
-                    tp.distanceMenu.setState(tree.getShowDistances());
-                    tp.distanceMenu_actionPerformed(null);
                     tp.treeCanvas.threshold = tree.getThreshold();
 
                     if (tree.getCurrentTree())
@@ -822,3 +1459,4 @@ public class Jalview2XML
         return af;
     }
 }
+