X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=b7629c48d9b35e09620780f0dc4d0aa3677be007;hb=4e486a5e888bc3844a94f27480e3383a5b4be005;hp=bd8bc534e718429ac4a2b840343120a1ee0f5e43;hpb=10eedfb43dacd4cf32d4b5fe27d8d5987c70eaf8;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index bd8bc53..b7629c4 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -345,12 +345,16 @@ public class FileLoader implements Runnable
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
               UrlDownloadClient.download(file, tempStructureFileStr);
-              file = tempStructureFileStr;
-              protocol = DataSourceType.FILE;
+              al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+                      format);
+              source = fa.getAlignFile();
+            }
+            else
+            {
+              al = fa.readFile(file, protocol, format);
+              source = fa.getAlignFile(); // keep reference for later if
+                                          // necessary.
             }
-            al = fa.readFile(file, protocol, format);
-            source = fa.getAlignFile(); // keep reference for later if
-                                        // necessary.
           }
         } catch (java.io.IOException ex)
         {