JAL-722 updated from 2.11.2 develop branch - needs further work before release

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 9b6741b..985aece 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -20,8 +20,6 @@
  */
 package jalview.project;
 
-import java.util.Locale;
-
 import static jalview.math.RotatableMatrix.Axis.X;
 import static jalview.math.RotatableMatrix.Axis.Y;
 import static jalview.math.RotatableMatrix.Axis.Z;
@@ -56,6 +54,7 @@ import java.util.IdentityHashMap;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
@@ -915,13 +914,12 @@ public class Jalview2XML
     }
     if (jal.getProperties() != null)
     {
-      Enumeration en = jal.getProperties().keys();
-      while (en.hasMoreElements())
+      for (Entry<Object, Object> prop : jal.getProperties().entrySet())
       {
-        String key = en.nextElement().toString();
+        String key = prop.getKey().toString();
         SequenceSetProperties ssp = new SequenceSetProperties();
         ssp.setKey(key);
-        ssp.setValue(jal.getProperties().get(key).toString());
+        ssp.setValue(prop.getValue().toString());
         // vamsasSet.addSequenceSetProperties(ssp);
         vamsasSet.getSequenceSetProperties().add(ssp);
       }
@@ -2077,8 +2075,8 @@ public class Jalview2XML
     {
       final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
       final String pdbId = pdbentry.getId();
-      if (!pdbId.equals(entry.getId())
-              && !(entry.getId().length() > 4 && entry.getId().toLowerCase(Locale.ROOT)
+      if (!pdbId.equals(entry.getId()) && !(entry.getId().length() > 4
+              && entry.getId().toLowerCase(Locale.ROOT)
                       .startsWith(pdbId.toLowerCase(Locale.ROOT))))
       {
         /*
@@ -2922,6 +2920,7 @@ public class Jalview2XML
           entryCount++;
         }
       } while (jarentry != null);
+      jin.close();
       resolveFrefedSequences();
     } catch (IOException ex)
     {