FormatAdapter readFile

diff --git a/src/jalview/ws/Jemboss.java b/src/jalview/ws/Jemboss.java
index 7983262..3e01b77 100755 (executable)
--- a/src/jalview/ws/Jemboss.java
+++ b/src/jalview/ws/Jemboss.java
@@ -154,11 +154,11 @@ public class Jemboss
       JembossRun thisrun = new JembossRun(embossCommand,"",
                                           filesToMove,vamsas_server);
       Hashtable h = thisrun.hash();
-      Enumeration enum = h.keys();
+      Enumeration enumerator = h.keys();
       // Find the alignment generated and parse it
-      while (enum.hasMoreElements())
+      while (enumerator.hasMoreElements())
       {
-        String thiskey = (String)enum.nextElement().toString();
+        String thiskey = (String)enumerator.nextElement().toString();
         if (thiskey.endsWith(".aln"))
         {
           // FormatAdapter, and IdentifyFile use a protocol string
@@ -167,8 +167,8 @@ public class Jemboss
           String format = IdentifyFile.Identify(alfile, "Paste");
           SequenceI[] alignment = null;
 
-          if (FormatProperties.contains(format))
-            alignment = FormatAdapter.read(alfile, "Paste", format);
+          if (FormatAdapter.formats.contains(format))
+            alignment = FormatAdapter.readFile(alfile, "Paste", format);
           else
             System.out.println("jalview.Jemboss: Unknown format "+format+"\n");
           if (alignment == null)