X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=562d5cbbd96b4dfdf04aaa92fb1051fe0270379e;hb=d187567c926fed31f9cd9bda0dc112bc4d1b1261;hp=eb071e2fed493306423c719c15325c8c1445cef4;hpb=1b7c19a556c0a09859e8e46cd4e55484e5f944d2;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index eb071e2..562d5cb 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -168,6 +168,14 @@ public class Jalview2XML
         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;
@@ -176,28 +184,61 @@ 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
@@ -210,7 +251,6 @@ public class Jalview2XML
                 features.setBegin(sf[index].getBegin());
                 features.setEnd(sf[index].getEnd());
                 features.setDescription(sf[index].getDescription());
-                features.setStatus(sf[index].getStatus());
                 features.setType(sf[index].getType());
                 features.setFeatureGroup(sf[index].getFeatureGroup());
                 jseq.addFeatures(features);
@@ -230,6 +270,39 @@ public class Jalview2XML
                 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();
@@ -307,19 +380,39 @@ 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);
+
+                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);
@@ -342,6 +435,10 @@ 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);
                 }
 
@@ -381,6 +478,12 @@ 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,
@@ -400,7 +503,7 @@ 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);
@@ -427,6 +530,26 @@ 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(
@@ -472,18 +595,18 @@ public class Jalview2XML
           jalview.schemabinding.version2.FeatureSettings fs
               = new jalview.schemabinding.version2.FeatureSettings();
 
-          Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
-          while (e.hasMoreElements())
+          String [] renderOrder =
+              af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+          for(int ro=0; ro<renderOrder.length; ro++)
           {
-            String type = e.nextElement().toString();
             Setting setting = new Setting();
-            setting.setType(type);
+            setting.setType(renderOrder[ro]);
             setting.setColour(
-                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
                 );
 
             setting.setDisplay(
-                av.featuresDisplayed.containsKey(type)
+                av.featuresDisplayed.containsKey(renderOrder[ro])
                 );
 
             fs.addSetting(setting);
@@ -493,6 +616,18 @@ public class Jalview2XML
 
         }
 
+        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);
 
 
@@ -582,9 +717,7 @@ public class Jalview2XML
      */
     public AlignFrame LoadJalviewAlign(String file)
     {
-
         jalview.gui.AlignFrame af = null;
-
         try
         {
             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
@@ -613,21 +746,9 @@ public class Jalview2XML
                 for (int i = 0; i < entryCount; i++)
                 {
                     jarentry = jin.getNextJarEntry();
+                }
 
-                  }
-
-
-                  class NoDescIDResolver implements IDResolver
-                  {
-                    public Object resolve(String idref)
-                    {
-                      System.out.println(idref+" used");
-                      return null;
-                    }
-                  }
-
-
-                if (jarentry != null)
+                if (jarentry != null && jarentry.getName().endsWith(".xml"))
                 {
                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
                     JalviewModel object = new JalviewModel();
@@ -636,9 +757,14 @@ public class Jalview2XML
                     unmar.setValidation(false);
                     object = (JalviewModel) unmar.unmarshal( in );
 
-                    af = LoadFromObject(object);
+                    af = LoadFromObject(object, file);
                     entryCount++;
                 }
+                else if (jarentry != null)
+                {
+                  //Some other file here.
+                  entryCount++;
+                }
             }
             while (jarentry != null);
         }
@@ -660,7 +786,7 @@ public class Jalview2XML
 
           if(af!=null)
           {
-            System.out.println("Successfuly loaded archive file");
+            System.out.println("Successfully loaded archive file");
             return af;
           }
           ex.printStackTrace();
@@ -676,7 +802,53 @@ public class Jalview2XML
         return af;
     }
 
-    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);
@@ -686,6 +858,7 @@ 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++)
@@ -694,6 +867,12 @@ public class Jalview2XML
                     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()));
@@ -707,6 +886,8 @@ public class Jalview2XML
         al.setDataset(null);
         /////////////////////////////////
 
+
+        Hashtable pdbloaded = new Hashtable();
         for (int i = 0; i < vamsasSeq.length; i++)
         {
           if (JSEQ[i].getFeaturesCount() > 0)
@@ -731,21 +912,68 @@ public class Jalview2XML
               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()];
 
@@ -755,15 +983,29 @@ public class Jalview2XML
                             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 = 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
                 {
@@ -771,19 +1013,19 @@ 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() );
         /////////////////////////
         //LOAD GROUPS
@@ -807,7 +1049,8 @@ 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();
@@ -830,7 +1073,7 @@ 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);
@@ -842,6 +1085,56 @@ 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());
@@ -895,6 +1188,96 @@ 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());
@@ -944,6 +1327,17 @@ public class Jalview2XML
          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());