JAL-2113 embl_mapping.xml and code updated for EMBL XML v1.2

[jalview.git] / src / jalview / ws / ebi / EBIFetchClient.java

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 9f6bc65..f55aad4 100644 (file)
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -193,20 +193,23 @@ public class EBIFetchClient
     /*
      * JAL-1855 dbfetch from ena_sequence, ena_coding
      */
-    if (dbPath.equalsIgnoreCase(DBRefSource.EMBL))
+    String url;
+    if (dbPath.equalsIgnoreCase(DBRefSource.EMBL)
+            || dbPath.equalsIgnoreCase(DBRefSource.EMBLCDS))
     {
-      dbPath = "ena_sequence";
+      url = "http://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
+              + (format != null ? "&" + format : "");
     }
-    else if (dbPath.equalsIgnoreCase(DBRefSource.EMBLCDS))
+    else
     {
-      dbPath = "ena_coding";
+      url = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
+              + dbPath.toLowerCase() + "/" + ids.toLowerCase()
+              + (format != null ? "/" + format : "");
     }
 
     try
     {
-      URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
-              + dbPath.toLowerCase() + "/" + ids.toLowerCase()
-              + (format != null ? "/" + format : ""));
+      URL rcall = new URL(url);
 
       InputStream is = new BufferedInputStream(rcall.openStream());
       if (outFile != null)