resolved merge conflict

[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 1328260..7b26214 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -79,6 +79,10 @@ public class SiftsClient extends StructureMappingClient implements
    */
   private static File mockSiftsFile;
 
+  private static final int UNASSIGNED = StructureMapping.UNASSIGNED; // -1
+
+  private static final int PDB_RES_POS = StructureMapping.PDB_RES_NUM_INDEX; // 0
+
   private Entry siftsEntry;
 
   private String pdbId;
@@ -89,10 +93,6 @@ public class SiftsClient extends StructureMappingClient implements
 
   private static final int BUFFER_SIZE = 4096;
 
-  public static final int UNASSIGNED = -1;
-
-  private static final int PDB_RES_POS = 0;
-
   private static final String NOT_OBSERVED = "Not_Observed";
 
   private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
@@ -604,8 +604,12 @@ public class SiftsClient extends StructureMappingClient implements
                     .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;
           }