X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=acca50f861973ce4a593a3193efc89d0644c9429;hb=4dc7619bed1c475c35f328601b5d7d46116327a6;hp=e08b8cbfe59b94513880406db9d7301c7170806b;hpb=49321390421afef1f818b3b1ec10badd83e95cc2;p=jalview.git

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index e08b8cb..acca50f 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -149,7 +149,6 @@ public class SiftsClient implements SiftsClientI
     siftsEntry = parseSIFTs(siftsFile);
   }
 
-
   /**
    * Parse the given SIFTs File and return a JAXB POJO of parsed data
    * 
@@ -276,21 +275,21 @@ public class SiftsClient implements SiftsClientI
     {
       siftsDownloadDir.mkdirs();
     }
-      // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
-      URL url = new URL(siftsFileFTPURL);
-      URLConnection conn = url.openConnection();
-      InputStream inputStream = conn.getInputStream();
-      FileOutputStream outputStream = new FileOutputStream(
-              downloadedSiftsFile);
-      byte[] buffer = new byte[BUFFER_SIZE];
-      int bytesRead = -1;
-      while ((bytesRead = inputStream.read(buffer)) != -1)
-      {
-        outputStream.write(buffer, 0, bytesRead);
-      }
-      outputStream.close();
-      inputStream.close();
-      // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
+    // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+    URL url = new URL(siftsFileFTPURL);
+    URLConnection conn = url.openConnection();
+    InputStream inputStream = conn.getInputStream();
+    FileOutputStream outputStream = new FileOutputStream(
+            downloadedSiftsFile);
+    byte[] buffer = new byte[BUFFER_SIZE];
+    int bytesRead = -1;
+    while ((bytesRead = inputStream.read(buffer)) != -1)
+    {
+      outputStream.write(buffer, 0, bytesRead);
+    }
+    outputStream.close();
+    inputStream.close();
+    // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
     return new File(downloadedSiftsFile);
   }
 
@@ -338,11 +337,10 @@ public class SiftsClient implements SiftsClientI
       {
         continue;
       }
+      String canonicalSource = DBRefUtils.getCanonicalName(dbRef
+              .getSource());
       if (isValidDBRefEntry(dbRef)
-              && dbRef.isPrimary()
-              && (DBRefUtils.getCanonicalName(dbRef.getSource())
-                      .equalsIgnoreCase(DBRefSource.UNIPROT) || DBRefUtils
-                      .getCanonicalName(dbRef.getSource())
+              && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT) || canonicalSource
                       .equalsIgnoreCase(DBRefSource.PDB)))
       {
         return dbRef;
@@ -392,8 +390,8 @@ public class SiftsClient implements SiftsClientI
           String pdbFile, String chain) throws SiftsException
   {
     structId = (chain == null) ? pdbId : pdbId + "|" + chain;
-    System.out.println("Getting mapping for: " + pdbId + "|" + chain
-            + " : seq- " + seq.getName());
+    System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+            + seq.getName());
 
     final StringBuilder mappingDetails = new StringBuilder(128);
     PrintStream ps = new PrintStream(System.out)
@@ -472,12 +470,13 @@ public class SiftsClient implements SiftsClientI
     int pdbStart = UNASSIGNED;
     int pdbEnd = UNASSIGNED;
 
-    Integer[] keys = mapping.keySet().toArray(new Integer[0]);
-    Arrays.sort(keys);
-    if (keys.length < 1)
+    if (mapping.isEmpty())
     {
-      throw new SiftsException(">>> Empty SIFTS mapping generated!!");
+      throw new SiftsException("SIFTS mapping failed");
     }
+
+    Integer[] keys = mapping.keySet().toArray(new Integer[0]);
+    Arrays.sort(keys);
     seqStart = keys[0];
     seqEnd = keys[keys.length - 1];
 
@@ -612,6 +611,7 @@ public class SiftsClient implements SiftsClientI
       }
     }
   }
+
   /**
    * 
    * @param chainId
@@ -763,8 +763,6 @@ public class SiftsClient implements SiftsClientI
     }
   }
 
-
-
   @Override
   public Entity getEntityById(String id) throws SiftsException
   {