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

[jalview.git] / src / jalview / io / StockholmFile.java

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 8b26757..9ca86f2 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -23,6 +23,8 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
 import java.io.BufferedReader;
 import java.io.FileReader;
 import java.io.IOException;
@@ -32,6 +34,7 @@ import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Vector;
 
 import com.stevesoft.pat.Regex;
@@ -1007,15 +1010,11 @@ public class StockholmFile extends AlignFile
     // output database type
     if (al.getProperties() != null)
     {
-      if (!al.getProperties().isEmpty())
+      for (Entry<Object, Object> prop : al.getProperties().entrySet())
       {
-        Enumeration key = al.getProperties().keys();
-        Enumeration val = al.getProperties().elements();
-        while (key.hasMoreElements())
-        {
-          out.append("#=GF " + key.nextElement() + " " + val.nextElement());
-          out.append(newline);
-        }
+        out.append("#=GF " + prop.getKey().toString() + " "
+                + prop.getValue().toString());
+        out.append(newline);
       }
     }
 
@@ -1110,7 +1109,7 @@ public class StockholmFile extends AlignFile
         }
         else
         {
-          key = type2id(aa.label.toLowerCase());
+          key = type2id(aa.label.toLowerCase(Locale.ROOT));
           if (key == null)
           {
             label = aa.label;