JAL-2482 Bugfix

[jalview.git] / src / jalview / ws / sifts / SiftsClient.java

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 37388d3..13d33df 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -295,6 +295,7 @@ public class SiftsClient implements SiftsClientI
       siftsDownloadDir.mkdirs();
     }
     // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+    // long now = System.currentTimeMillis();
     URL url = new URL(siftsFileFTPURL);
     URLConnection conn = url.openConnection();
     InputStream inputStream = conn.getInputStream();
@@ -308,7 +309,8 @@ public class SiftsClient implements SiftsClientI
     }
     outputStream.close();
     inputStream.close();
-    // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
+//    System.out.println(">>> File downloaded : " + downloadedSiftsFile
+//            + " took " + (System.currentTimeMillis() - now) + "ms");
     return new File(downloadedSiftsFile);
   }
 
@@ -605,6 +607,11 @@ public class SiftsClient implements SiftsClientI
                     .getDbResNum());
           } catch (NumberFormatException nfe)
           {
+            if (pdbRefDb.getDbResNum().equals("null"))
+            {
+              resNum = UNASSIGNED;
+              continue;
+            }
             resNum = (pdbRefDb == null) ? Integer.valueOf(residue
                     .getDbResNum()) : Integer.valueOf(pdbRefDb
                     .getDbResNum().split("[a-zA-Z]")[0]);