X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=bc5e1d89b2d58ea1092f1b5e3dfa32f07de8c614;hb=614b72c437f14dd2ddd72ae918dada3fd5d64468;hp=a4e5785a1a57c310e6bc0aa4d1c8c4d05d7f2d68;hpb=296572df6fc3100c1fd97f3714bb2b6628140310;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a4e5785..bc5e1d8 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -992,17 +992,16 @@ public class Jalview2XML
             }
           }
 
-          if (entry.getProperty() != null && !entry.getProperty().isEmpty())
+          Enumeration<String> props = entry.getProperties();
+          if (props.hasMoreElements())
           {
             PdbentryItem item = new PdbentryItem();
-            Hashtable properties = entry.getProperty();
-            Enumeration en2 = properties.keys();
-            while (en2.hasMoreElements())
+            while (props.hasMoreElements())
             {
               Property prop = new Property();
-              String key = en2.nextElement().toString();
+              String key = props.nextElement();
               prop.setName(key);
-              prop.setValue(properties.get(key).toString());
+              prop.setValue(entry.getProperty(key).toString());
               item.addProperty(prop);
             }
             pdb.addPdbentryItem(item);
@@ -3033,12 +3032,11 @@ public class Jalview2XML
             }
             if (ids[p].getPdbentryItem() != null)
             {
-              entry.setProperty(new Hashtable());
               for (PdbentryItem item : ids[p].getPdbentryItem())
               {
                 for (Property pr : item.getProperty())
                 {
-                  entry.getProperty().put(pr.getName(), pr.getValue());
+                  entry.setProperty(pr.getName(), pr.getValue());
                 }
               }
             }
@@ -3403,8 +3401,8 @@ public class Jalview2XML
         }
         if (jGroup.getConsThreshold() != 0)
         {
-          Conservation c = new Conservation("All", 3,
-                  sg.getSequences(null), 0, sg.getWidth() - 1);
+          Conservation c = new Conservation("All", sg.getSequences(null),
+                  0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);