X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=fe3a25b822575c8dea7c6ea1302a057276fa7c4c;hb=95b34183f11c22462b60bc5c0254d66eba1c1f19;hp=37388d3c1a18d56c580b382db224501093bb33e1;hpb=0ed5b947087f831b8673f4c4e423bd4ef2238a89;p=jalview.git

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 37388d3..fe3a25b 100644
--- 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);
   }
 
@@ -573,18 +575,8 @@ 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
@@ -597,19 +589,11 @@ 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)
@@ -632,6 +616,30 @@ 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.