close filehandles straight after parse, without setting an error

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index cea2870..9e426ab 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -20,13 +20,6 @@
  */
 package jalview.io;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Enumeration;
@@ -34,6 +27,13 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
 /**
  * DOCUMENT ME!
  * 
@@ -193,6 +193,7 @@ public abstract class AlignFile extends FileParse
     }
     parseCalled = true;
     parse();
+    dataIn.close();
   }
 
   /**

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 9b6741b..acfeb2a 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;
@@ -2077,8 +2076,8 @@ 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 +2921,7 @@ public class Jalview2XML
           entryCount++;
         }
       } while (jarentry != null);
+      jin.close();
       resolveFrefedSequences();
     } catch (IOException ex)
     {