X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=addba63ec5ebb6c0eb5c8c9d2e6ad505af235bbe;hb=0a5c25233b642021bec70224aff9d405b70a3f72;hp=12f2cb20640daf23751f617cd02c13317b8e049d;hpb=b12384aa7fdffd3167a83de75d2a560356ee65f1;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 12f2cb2..addba63 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,92 +1,143 @@
+/*
+ * 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 java.io.*;
+import java.net.*;
 import java.util.*;
 import java.util.jar.*;
 
+import javax.swing.*;
+
 import jalview.binding.*;
+import jalview.io.*;
 import jalview.schemes.*;
-import javax.swing.JInternalFrame;
-
 
 public class Jalview2XML
 {
-
   // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
   public static void SaveState(File statefile)
   {
-      long creation = System.currentTimeMillis();
-      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-      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();
-        for (int i = 0; i < frames.length; i++)
+    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)
         {
-          if (frames[i] instanceof AlignFrame)
-          {
-            AlignFrame af = (AlignFrame) frames[i];
+          AlignFrame af = (AlignFrame) frames[i];
 
-            String shortName = af.getTitle();
+          String shortName = af.getTitle();
 
-            shortName = shortName.replace('/', '_');
-            shortName = shortName.replace('\\', '_');
+          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("_"));
+          int count = 1;
 
-              shortName = shortName.concat("_"+count);
-              count++;
+          while (shortNames.contains(shortName))
+          {
+            if (shortName.endsWith("_" + (count - 1)))
+            {
+              shortName = shortName.substring(0,
+                                              shortName.lastIndexOf("_"));
             }
-            shortNames.addElement(shortName);
 
-            if(!shortName.endsWith(".xml"))
-              shortName = shortName+".xml";
+            shortName = shortName.concat("_" + count);
+            count++;
+          }
 
-            SaveState( af, creation, shortName, jout, out);
-           }
+          shortNames.addElement(shortName);
+
+          if (!shortName.endsWith(".xml"))
+          {
+            shortName = shortName + ".xml";
+          }
+
+          SaveState(af, creation, shortName, jout, out);
         }
-        out.close();
-        jout.close();
       }
-      catch(Exception ex){ex.printStackTrace();}
+
+      out.close();
+      jout.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
   }
 
   // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-  public static void SaveState( AlignFrame af, String jarFile, String fileName)
+  public static void SaveState(AlignFrame af, String jarFile, String fileName)
   {
-    try{
+    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"));
+      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+          "UTF-8"));
 
       SaveState(af, System.currentTimeMillis(), fileName, jout, out);
       out.close();
       jout.close();
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {
+    }
   }
 
-  public static void SaveState( AlignFrame af, long timeStamp,
-      String fileName, JarOutputStream jout, PrintWriter out)
+  public static void SaveState(AlignFrame af, long timeStamp,
+                               String fileName, JarOutputStream jout,
+                               PrintWriter out)
   {
-
     Vector seqids = new Vector();
+    Vector userColours = new Vector();
 
     AlignViewport av = af.viewport;
 
     JalviewModel object = new JalviewModel();
-    object.setVamsasModel( new VamsasModel() );
+    object.setVamsasModel(new VamsasModel());
 
-    object.setCreationDate( new java.util.Date(timeStamp) );
+    object.setCreationDate(new java.util.Date(timeStamp));
 
     jalview.datamodel.AlignmentI jal = af.viewport.alignment;
 
@@ -94,19 +145,19 @@ public class Jalview2XML
     Sequence vamsasSeq;
     JalviewModelSequence jms = new JalviewModelSequence();
 
-    vamsasSet.setGapChar(jal.getGapCharacter()+"");
+    vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
     JSeq jseq;
 
-
     //SAVE SEQUENCES
     int id = 0;
-    for(int i=0; i<jal.getHeight(); i++)
+
+    for (int i = 0; i < jal.getHeight(); i++)
     {
       seqids.add(jal.getSequenceAt(i));
 
-      vamsasSeq = new Sequence( );
-      vamsasSeq.setId(id+"");
+      vamsasSeq = new Sequence();
+      vamsasSeq.setId(id + "");
       vamsasSeq.setName(jal.getSequenceAt(i).getName());
       vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
 
@@ -116,7 +167,7 @@ public class Jalview2XML
 
       jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
 
-      jseq.setId( id );
+      jseq.setId(id);
 
       jms.addJSeq(jseq);
       vamsasSet.addSequence(vamsasSeq);
@@ -124,22 +175,24 @@ public class Jalview2XML
     }
 
     //SAVE TREES
-    if(af.viewport.currentTree!=null)
+    if (af.viewport.currentTree != null)
     {
       object.getVamsasModel().addTree(af.viewport.currentTree.toString());
     }
 
     //SAVE ANNOTATIONS
-    if(jal.getAlignmentAnnotation()!=null)
+    if (jal.getAlignmentAnnotation() != null)
     {
+      jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 
-      jalview.datamodel.AlignmentAnnotation [] aa = jal.getAlignmentAnnotation();
-      for(int i=0; i<aa.length; i++)
+      for (int i = 0; i < aa.length; i++)
       {
-        if(aa[i].label.equals("Quality")
-        || aa[i].label.equals("Conservation")
-        || aa[i].label.equals("Consensus"))
-       {    continue;}
+        if (aa[i].label.equals("Quality") ||
+            aa[i].label.equals("Conservation") ||
+            aa[i].label.equals("Consensus"))
+        {
+          continue;
+        }
 
         Annotation an = new Annotation();
         an.setDescription(aa[i].description);
@@ -148,118 +201,154 @@ public class Jalview2XML
 
         AnnotationElement ae;
 
-        for(int a=0; a<aa[i].annotations.length; a++)
+        for (int a = 0; a < aa[i].annotations.length; a++)
         {
-          if(aa[i]==null || aa[i].annotations[a]==null)
+          if ( (aa[i] == null) || (aa[i].annotations[a] == null))
+          {
             continue;
+          }
 
           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+"");
+          ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
+                                   "");
           an.addAnnotationElement(ae);
         }
 
         vamsasSet.addAnnotation(an);
       }
-
     }
 
     //SAVE GROUPS
-    if(jal.getGroups()!=null)
+    if (jal.getGroups() != null)
     {
-      JGroup [] groups = new JGroup[jal.getGroups().size()];
-      for(int i=0; i<groups.length; i++)
+      JGroup[] groups = new JGroup[jal.getGroups().size()];
+
+      for (int i = 0; i < groups.length; i++)
       {
         groups[i] = new JGroup();
-        jalview.datamodel.SequenceGroup sg
-            = (jalview.datamodel.SequenceGroup)jal.getGroups().elementAt(i);
-        groups[i].setStart( sg.getStartRes() );
-        groups[i].setEnd( sg.getEndRes() );
-        groups[i].setName( sg.getName());
 
-        if(sg.cs instanceof ConservationColourScheme)
-          groups[i].setConsThreshold( ((ConservationColourScheme)sg.cs).inc);
+        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 instanceof ConservationColourScheme)
+        {
+          groups[i].setConsThreshold( ( (ConservationColourScheme) sg.cs).inc);
+        }
 
         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());
+        {
+          groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).
+                                    getThreshold());
+        }
+        else if (sg.cs instanceof ScoreColourScheme)
+        {
+          groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());
+        }
 
+        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].setColour( ColourSchemeProperty.getColourName(sg.cs) );
         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++)
+        for (int s = 0; s < sg.getSize(); s++)
         {
-          jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence)sg.getSequenceAt(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);
-   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 );
+    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
     {
-     if(!fileName.endsWith(".xml"))
-              fileName = fileName+".xml";
+      if (!fileName.endsWith(".xml"))
+      {
+        fileName = fileName + ".xml";
+      }
 
-     JarEntry entry = new JarEntry(fileName);
-     jout.putNextEntry(entry);
+      JarEntry entry = new JarEntry(fileName);
+      jout.putNextEntry(entry);
 
       object.marshal(out);
     }
@@ -269,134 +358,252 @@ public class Jalview2XML
     }
   }
 
+  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))
+    {
+      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++)
+      {
+        jalview.binding.Colour col = new jalview.binding.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;
+  }
+
+  static jalview.schemes.UserColourScheme GetUserColourScheme(
+      JalviewModelSequence jms, String id)
+  {
+    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;
+      }
+    }
+
+    int csize = colours.getUserColourScheme().getColourCount();
+    java.awt.Color[] newColours = new java.awt.Color[csize];
+
+    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);
+  }
 
   public static void LoadJalviewAlign(String file)
   {
     JalviewModel object = new JalviewModel();
-    try{
+
+    try
+    {
       //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
-      JarInputStream jin = new JarInputStream(new FileInputStream(file));
-      JarEntry jarentry=null;
+      URL url = null;
+
+      if (file.startsWith("http://"))
+      {
+        url = new URL(file);
+      }
+
+      JarInputStream jin = null;
+      JarEntry jarentry = null;
       int entryCount = 1;
-      do{
-        jin = new JarInputStream(new FileInputStream(file));
-        for(int i=0; i<entryCount; i++)
+
+      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)
+        if (jarentry != null)
         {
           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
           object = (JalviewModel) object.unmarshal(in);
           LoadFromObject(object);
           entryCount++;
         }
-      }while(jarentry!=null);
-
+      }
+      while (jarentry != null);
     }
-    catch(Exception ex)
-    {   System.out.println("HERE"+ex); return; }
+    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()
-               );
-         }
-
-
-          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() );
+    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());
+        }
+
+        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)
+    if (jms.getJGroupCount() > 0)
     {
       JGroup[] groups = jms.getJGroup();
+
       for (int i = 0; i < groups.length; i++)
       {
-       ColourSchemeI 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)
+        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());
+          }
+        }
+
+        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.sequences, 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);
@@ -404,31 +611,41 @@ public class Jalview2XML
           sg.cs = cs;
         }
 
-
         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() );
+    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.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.setShowFullId(view.getShowFullId());
+    af.fullSeqId.setSelected(view.getShowFullId());
+
+    af.viewport.setFont(new java.awt.Font(view.getFontName(),
+                                          view.getFontStyle(), view.getFontSize()));
     af.alignPanel.fontChanged();
-    af.viewport.setRenderGaps( view.getRenderGaps() );
 
-    af.viewport.setWrapAlignment( view.getWrapAlignment() );
-    if(view.getWrapAlignment())
+    af.viewport.setRenderGaps(view.getRenderGaps());
+    af.renderGapsMenuItem.setSelected(view.getRenderGaps());
+
+    af.viewport.setWrapAlignment(view.getWrapAlignment());
+    af.wrapMenuItem.setSelected(view.getWrapAlignment());
+
+    if (view.getWrapAlignment())
     {
       af.alignPanel.setWrapAlignment(view.getWrapAlignment());
     }
@@ -438,34 +655,65 @@ public class Jalview2XML
       af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
     }
 
-    af.viewport.setShowBoxes( view.getShowBoxes() );
-    af.viewport.setShowText( view.getShowText() );
+    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
+      {
+        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+      }
+
+      if (cs instanceof ConservationColourScheme)
+      {
+        ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
+      }
+
+      if (cs instanceof ResidueColourScheme)
+      {
+        ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
+      }
+      else if (cs instanceof ScoreColourScheme)
+      {
+        ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
+      }
+    }
+
+    af.viewport.setGlobalColourScheme(cs);
 
-    af.viewport.setGlobalColourScheme( ColourSchemeProperty.getColour(al, view.getBgColour()));
     af.viewport.setColourAppliesToAllGroups(false);
-    af.changeColour( af.viewport.getGlobalColourScheme() );
+    af.changeColour(af.viewport.getGlobalColourScheme());
     af.viewport.setColourAppliesToAllGroups(true);
 
-    ColourSchemeI cs = af.viewport.getGlobalColourScheme();
-    if(cs instanceof ConservationColourScheme)
-      ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
-
-    if (cs instanceof ResidueColourScheme)
-      ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
-    else if (cs instanceof ScoreColourScheme)
-      ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
+    if (view.getShowSequenceFeatures())
+    {
+      af.viewport.showSequenceFeatures = true;
+      af.sequenceFeatures.setSelected(true);
+      new SequenceFeatureFetcher(al, af.alignPanel);
+       al.featuresAdded = true;
+    }
 
     //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE
-    if(object.getVamsasModel().getTreeCount()>0)
+    if (object.getVamsasModel().getTreeCount() > 0)
     {
-      try{
+      try
+      {
         af.ShowNewickTree(new jalview.io.NewickFile(
-            (String)object.getVamsasModel().getTree(0)), "Tree");
-      }catch(Exception ex){ex.printStackTrace();}
+            (String) object.getVamsasModel().getTree(0)), "Tree");
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
     }
-
   }
 }
-
-
-