From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Mon, 1 May 2017 14:16:24 +0000 (+0100)
Subject: resolved merge conflict
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8feb5f87bd94e5d49c9dbc5fd7ec7e866ef80e9d;hp=-c;p=jalview.git

resolved merge conflict
---

8feb5f87bd94e5d49c9dbc5fd7ec7e866ef80e9d
diff --combined src/jalview/ws/sifts/SiftsClient.java
index 30ac0ae,5825a26..7b26214
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@@ -79,10 -79,6 +79,10 @@@ public class SiftsClient extends Struct
     */
    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;
@@@ -93,6 -89,10 +93,6 @@@
  
    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 +604,12 @@@
                      .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;
            }