From 87018985bd993952fd848fd6b6a57d1a50aef484 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 11 Jan 2022 16:04:49 +0000
Subject: [PATCH] close filehandles straight after parse, without setting an
 error

Conflicts:
	src/jalview/project/Jalview2XML.java
(locale aware PDBID string compare)
---
 src/jalview/io/AlignFile.java        |   15 ++++++++-------
 src/jalview/project/Jalview2XML.java |    8 +++++---
 2 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 497f0a5..338c4b2 100755
--- 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!
  * 
@@ -192,6 +192,7 @@ 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 0e062ac..4f92736 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -53,6 +53,7 @@ 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;
@@ -2071,9 +2072,9 @@ 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()
-                      .startsWith(pdbId.toLowerCase())))
+      if (!pdbId.equals(entry.getId()) && !(entry.getId().length() > 4
+              && entry.getId().toLowerCase(Locale.ROOT)
+                      .startsWith(pdbId.toLowerCase(Locale.ROOT))))
       {
         /*
          * not interested in a binding to a different PDB entry here
@@ -2898,6 +2899,7 @@ public class Jalview2XML
           entryCount++;
         }
       } while (jarentry != null);
+      jin.close();
       resolveFrefedSequences();
     } catch (IOException ex)
     {
-- 
1.7.10.2