fixed bug in prefix extraction for application

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 40bc005..eb10375 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -51,6 +51,7 @@ public class FileParse
    * @return this.error (true if the source was invalid)
    */
   private boolean checkFileSource(String fileStr) throws IOException {
+    error=false;
     this.inFile = new File(fileStr);
     // check to see if it's a Jar file in disguise.
     if (!inFile.exists()) {
@@ -111,11 +112,16 @@ public class FileParse
     {
       if (checkFileSource(fileStr)) {  
         String suffixLess = extractSuffix(fileStr);
-        if (suffixLess!=null && checkFileSource(suffixLess))
+        if (suffixLess!=null)
+        {
+          if (checkFileSource(suffixLess))
+          {
+            throw new IOException("Problem opening "+inFile+" (also tried "+suffixLess+") : "+errormessage);
+          }
+        } else
         {
-          throw new IOException("Problem opening "+inFile+" (also tried "+fileStr+") : "+errormessage);
+          throw new IOException("Problem opening "+inFile+" : "+errormessage);
         }
-        throw new IOException("Problem opening "+inFile+" : "+errormessage);
       }
     }
     else if (type.equals(AppletFormatAdapter.URL))