X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=c69581ff9e3605c0e42d0f761f36edc9b544ea19;hb=5a74603b846dae238eaca8c1a8aa5bab64ab3c2c;hp=8bae5ba727e1e531f6ab49e3aba6aee36bf11de3;hpb=f1ad88cc8d9b26244086e5c24b73fb80b0ff0a38;p=jalview.git

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 8bae5ba..c69581f 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -74,6 +74,12 @@ import MCview.PDBChain;
 
 public class SiftsClient implements SiftsClientI
 {
+  /*
+   * for use in mocking out file fetch for tests only
+   * - reset to null after testing!
+   */
+  private static File mockSiftsFile;
+
   private Entry siftsEntry;
 
   private StructureFile pdb;
@@ -187,6 +193,14 @@ public class SiftsClient implements SiftsClientI
    */
   public static File getSiftsFile(String pdbId) throws SiftsException
   {
+    /*
+     * return mocked file if it has been set
+     */
+    if (mockSiftsFile != null)
+    {
+      return mockSiftsFile;
+    }
+
     String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
             + pdbId.toLowerCase() + ".xml.gz";
     File siftsFile = new File(siftsFileName);
@@ -593,8 +607,12 @@ public class SiftsClient implements SiftsClientI
                     .getDbResNum());
           } catch (NumberFormatException nfe)
           {
-            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
-                    .getDbResNum()) : Integer.valueOf(pdbRefDb
+            if (pdbRefDb == null || pdbRefDb.getDbResNum().equals("null"))
+            {
+              resNum = UNASSIGNED;
+              continue;
+            }
+            resNum = Integer.valueOf(pdbRefDb
                     .getDbResNum().split("[a-zA-Z]")[0]);
             continue;
           }
@@ -1097,4 +1115,9 @@ public class SiftsClient implements SiftsClientI
     return siftsEntry.getDbVersion();
   }
 
+  public static void setMockSiftsFile(File file)
+  {
+    mockSiftsFile = file;
+  }
+
 }