Merge branch 'bug/JAL-1610refAnnotationsInViews' into develop

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 946181c..3773a64 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -20,18 +20,37 @@
  */
 package jalview.gui;
 
-import java.io.*;
-import java.util.*;
-import java.util.jar.*;
-
-import javax.swing.*;
-
-import org.exolab.castor.xml.*;
-import jalview.binding.*;
-import jalview.schemes.*;
+import jalview.binding.Annotation;
+import jalview.binding.AnnotationElement;
+import jalview.binding.Features;
+import jalview.binding.JGroup;
+import jalview.binding.JSeq;
+import jalview.binding.JalviewModel;
+import jalview.binding.JalviewModelSequence;
+import jalview.binding.Pdbids;
+import jalview.binding.Sequence;
+import jalview.binding.SequenceSet;
+import jalview.binding.Setting;
+import jalview.binding.Tree;
+import jalview.binding.UserColours;
+import jalview.binding.Viewport;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.jarInputStreamProvider;
 
+import java.io.InputStreamReader;
+import java.util.Hashtable;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+
+import javax.swing.JOptionPane;
+
+import org.exolab.castor.xml.IDResolver;
+
 /**
  * DOCUMENT ME!
  * 
@@ -120,7 +139,7 @@ public class Jalview2XML_V1
           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
           JalviewModel object = new JalviewModel();
 
-          object = (JalviewModel) object.unmarshal(in);
+          object = object.unmarshal(in);
 
           af = LoadFromObject(object, file);
           entryCount++;
@@ -222,6 +241,8 @@ public class Jalview2XML_V1
           entry.setId(ids[p].getId());
           entry.setType(ids[p].getType());
           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+          StructureSelectionManager.getStructureSelectionManager(
+                  Desktop.instance).registerPDBEntry(entry);
         }
 
       }
@@ -315,7 +336,7 @@ public class Jalview2XML_V1
 
         for (int s = 0; s < ids.length; s++)
         {
-          seqs.addElement((jalview.datamodel.SequenceI) seqids
+          seqs.addElement(seqids
                   .elementAt(ids[s]));
         }
 
@@ -394,7 +415,7 @@ public class Jalview2XML_V1
 
     if (jms.getFeatureSettings() != null)
     {
-      af.viewport.featuresDisplayed = new Hashtable();
+      af.viewport.setFeaturesDisplayed(new Hashtable());
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
@@ -408,7 +429,7 @@ public class Jalview2XML_V1
 
         if (setting.getDisplay())
         {
-          af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+          af.viewport.getFeaturesDisplayed().put(setting.getType(), new Integer(
                   setting.getColour()));
         }
       }