X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=2ff4a8b3922fc6e1f3ee6d1a98addf68430b32b4;hb=2d137c4d89286572fba9e1f81eee9b35e4ca4a97;hp=847377d5f0c9f78d0e886856ddfe5320e8d74a32;hpb=76c239505d13a123cc83621623aaca16e47ddb12;p=jalview.git

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 847377d..2ff4a8b 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -577,18 +577,8 @@ public class SiftsClient implements SiftsClientI
                   .equalsIgnoreCase(seqCoordSys.getName())
                   && isAccessionMatched(cRefDb.getDbAccessionId()))
           {
-            String resNumIndexString = cRefDb.getDbResNum()
-                    .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
-                    : cRefDb.getDbResNum();
-            try
-            {
-              currSeqIndex = Integer.valueOf(resNumIndexString);
-            } catch (NumberFormatException nfe)
-            {
-              currSeqIndex = Integer.valueOf(resNumIndexString
-                      .split("[a-zA-Z]")[0]);
-              continue;
-            }
+            currSeqIndex = getLeadingIntegerValue(
+                    cRefDb.getDbResNum(), UNASSIGNED);
             if (pdbRefDb != null)
             {
               break;// exit loop if pdb and uniprot are already found
@@ -601,19 +591,11 @@ public class SiftsClient implements SiftsClientI
         }
         if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
         {
-          int resNum;
-          try
-          {
-            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
-                    .getDbResNum()) : Integer.valueOf(pdbRefDb
-                    .getDbResNum());
-          } catch (NumberFormatException nfe)
-          {
-            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
-                    .getDbResNum()) : Integer.valueOf(pdbRefDb
-                    .getDbResNum().split("[a-zA-Z]")[0]);
-            continue;
-          }
+
+          int resNum = (pdbRefDb == null) ? getLeadingIntegerValue(
+                  residue.getDbResNum(), UNASSIGNED)
+                  : getLeadingIntegerValue(pdbRefDb.getDbResNum(),
+                          UNASSIGNED);
 
           if (isResidueObserved(residue)
                   || seqCoordSys == CoordinateSys.UNIPROT)
@@ -636,6 +618,30 @@ public class SiftsClient implements SiftsClientI
   }
 
   /**
+   * Get the leading integer part of a string that begins with an integer.
+   * 
+   * @param input
+   *          - the string input to process
+   * @param failValue
+   *          - value returned if unsuccessful
+   * @return
+   */
+  static int getLeadingIntegerValue(String input, int failValue)
+  {
+    if (input == null)
+    {
+      return failValue;
+    }
+    String[] parts = input.split("(?=\\D)(?<=\\d)");
+    if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
+    {
+      return Integer.valueOf(parts[0]);
+    }
+    return failValue;
+  }
+
+
+  /**
    * 
    * @param chainId
    *          Target chain to populate mapping of its atom positions.