X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=d652da2a5aec05c6abeda173a8c290f6019d2211;hb=92f2bdf5a7a89ceefe2bff76ca75414cf0fb633c;hp=7018ef0e79d673453270e74c70f9f185ef355ae8;hpb=96589f3091facee1b50db52995b3a13425f0e96b;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7018ef0..d652da2 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -18,21 +18,27 @@
  */
 package jalview.gui;
 
-import jalview.binding.*;
-
-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 org.exolab.castor.xml.*;
+
+import jalview.schemabinding.version2.*;
+
+
+
 
 /**
  * DOCUMENT ME!
@@ -43,7 +49,7 @@ import javax.swing.*;
 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();
@@ -156,7 +162,7 @@ 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"));
@@ -182,6 +188,7 @@ public class Jalview2XML
             vamsasSeq.setId(id + "");
             vamsasSeq.setName(jal.getSequenceAt(i).getName());
             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
+            vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
 
             jseq = new JSeq();
             jseq.setStart(jal.getSequenceAt(i).getStart());
@@ -191,6 +198,58 @@ public class Jalview2XML
 
             jseq.setId(id);
 
+            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.setStatus(sf[index].getStatus());
+                features.setType(sf[index].getType());
+                features.setFeatureGroup(sf[index].getFeatureGroup());
+                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.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++;
@@ -221,8 +280,11 @@ public class Jalview2XML
                   tree.setThreshold(tp.treeCanvas.threshold);
 
                   tree.setFitToWindow(tp.fitToWindow.getState());
-                  tree.setFontSize(tp.treeCanvas.fontSize);
+                  tree.setFontName(tp.getTreeFont().getName());
+                  tree.setFontSize(tp.getTreeFont().getSize());
+                  tree.setFontStyle(tp.getTreeFont().getStyle());
                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+
                   tree.setShowBootstrap(tp.bootstrapMenu.getState());
                   tree.setShowDistances(tp.distanceMenu.getState());
 
@@ -254,7 +316,22 @@ public class Jalview2XML
 
                 Annotation an = new Annotation();
                 an.setDescription(aa[i].description);
-                an.setGraph(aa[i].isGraph);
+                if(aa[i].graph>0)
+                {
+                  an.setGraph(true);
+                  an.setGraphType(aa[i].graph);
+                  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;
@@ -312,6 +389,12 @@ 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,
@@ -342,6 +425,7 @@ public class Jalview2XML
             jms.setJGroup(groups);
         }
 
+
         ///////////SAVE VIEWPORT
         Viewport view = new Viewport();
         view.setTitle(af.getTitle());
@@ -357,6 +441,26 @@ 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(
@@ -390,15 +494,42 @@ 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;
+          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);
+
+          }
+          jms.setFeatureSettings(fs);
+
+        }
+
         jms.addViewport(view);
 
+
         object.setJalviewModelSequence(jms);
         object.getVamsasModel().addSequenceSet(vamsasSet);
 
@@ -420,7 +551,7 @@ public class Jalview2XML
         }
     }
 
-    static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+    String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
         Vector userColours, JalviewModelSequence jms)
     {
         String id = null;
@@ -431,12 +562,12 @@ 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);
             }
@@ -450,7 +581,7 @@ public class Jalview2XML
         return id;
     }
 
-    static jalview.schemes.UserColourScheme GetUserColourScheme(
+   jalview.schemes.UserColourScheme GetUserColourScheme(
         JalviewModelSequence jms, String id)
     {
         UserColours[] uc = jms.getUserColours();
@@ -483,9 +614,9 @@ public class Jalview2XML
      *
      * @param file DOCUMENT ME!
      */
-    public static AlignFrame LoadJalviewAlign(String file)
+    public AlignFrame LoadJalviewAlign(String file)
     {
-        JalviewModel object = new JalviewModel();
+
         jalview.gui.AlignFrame af = null;
 
         try
@@ -516,26 +647,62 @@ 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)
                 {
                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-                    object = (JalviewModel) object.unmarshal(in);
+                    JalviewModel object = new JalviewModel();
+
+                    Unmarshaller unmar = new Unmarshaller(object);
+                    unmar.setValidation(false);
+                    object = (JalviewModel) unmar.unmarshal( in );
+
                     af = LoadFromObject(object);
                     entryCount++;
                 }
             }
             while (jarentry != null);
         }
+        catch(java.net.UnknownHostException ex)
+        {
+          ex.printStackTrace();
+          System.err.println("Couldn't locate Jalview XML file : " +
+              ex + "\n");
+           JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                    "Couldn't locate " + file,
+                                    "URL not found",
+                                    JOptionPane.WARNING_MESSAGE);
+
+        }
         catch (Exception ex)
         {
+          //Is Version 1 Jar file?
+          af =  new Jalview2XML_V1().LoadJalviewAlign(file);
+
+          if(af!=null)
+          {
+            System.out.println("Successfuly loaded archive file");
+            return af;
+          }
           ex.printStackTrace();
             System.err.println("Exception whilst loading jalview XML file : " +
                 ex + "\n");
              JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                      "Couldn't locate " + file,
-                                      "URL not found",
+                                      "Error loading  " + file,
+                                      "Error loading Jalview file",
                                       JOptionPane.WARNING_MESSAGE);
 
         }
@@ -543,7 +710,7 @@ public class Jalview2XML
         return af;
     }
 
-    static AlignFrame LoadFromObject(JalviewModel object)
+    AlignFrame LoadFromObject(JalviewModel object)
     {
         Vector seqids = new Vector();
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
@@ -555,11 +722,11 @@ public class Jalview2XML
         //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].setDescription( vamsasSeq[i].getDescription() );
 
             jseqs[i].setStart(JSEQ[i].getStart());
             jseqs[i].setEnd(JSEQ[i].getEnd());
@@ -567,10 +734,44 @@ public class Jalview2XML
             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);
         /////////////////////////////////
+
+        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());
+
+              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());
+              al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+            }
+
+          }
+        }
+
+         /////////////////////////////////
         //////////////////////////////////
         //LOAD ANNOTATIONS
         if (vamsasSet.getAnnotation() != null)
@@ -586,7 +787,7 @@ 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());
                 }
 
@@ -594,8 +795,20 @@ public class Jalview2XML
 
                 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());
+
+                  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
                 {
@@ -607,6 +820,7 @@ public class Jalview2XML
             }
         }
 
+
         /////////////////////////////////
         // LOAD VIEWPORT
         Viewport[] views = jms.getViewport();
@@ -614,6 +828,7 @@ public class Jalview2XML
 
         AlignFrame af = new AlignFrame(al);
 
+
         //  af.changeColour() );
         /////////////////////////
         //LOAD GROUPS
@@ -637,7 +852,8 @@ 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();
@@ -672,10 +888,12 @@ public class Jalview2XML
         }
 
 
+
         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();
@@ -686,8 +904,8 @@ 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()));
@@ -723,6 +941,96 @@ 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());
@@ -748,12 +1056,34 @@ 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;
         }
 
+
+        Desktop.addInternalFrame(af, view.getTitle(),
+             view.getWidth(), view.getHeight());
+
         //LOAD TREES
         ///////////////////////////////////////
         if (jms.getTreeCount() > 0)
@@ -772,14 +1102,20 @@ public class Jalview2XML
 
                     tp.fitToWindow.setState(tree.getFitToWindow());
                     tp.fitToWindow_actionPerformed(null);
-                    tp.treeCanvas.fontSize = tree.getFontSize();
-                    tp.fontSize.setText("Font Size - " + tree.getFontSize());
-                    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);
+
+                    if(tree.getFontName()!=null)
+                      tp.setTreeFont(new java.awt.Font(tree.getFontName(),
+                                          tree.getFontStyle(),
+                                          tree.getFontSize()));
+                    else
+                      tp.setTreeFont(new java.awt.Font(view.getFontName(),
+                                            view.getFontStyle(),
+                                            tree.getFontSize()));
+
+                    tp.showPlaceholders(tree.getMarkUnlinked());
+                    tp.showBootstrap(tree.getShowBootstrap());
+                    tp.showDistances(tree.getShowDistances());
+
                     tp.treeCanvas.threshold = tree.getThreshold();
 
                     if (tree.getCurrentTree())
@@ -794,9 +1130,7 @@ public class Jalview2XML
 
         }
 
-        Desktop.addInternalFrame(af, view.getTitle(),
-             view.getWidth(), view.getHeight());
-
         return af;
     }
 }
+