X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=8bae5ba727e1e531f6ab49e3aba6aee36bf11de3;hb=95ebbef7b78bf266a8252bd479510be3c80cd234;hp=f20954ee326d1d75919b248a105ab1b3f30f861a;hpb=6c43dd36929855a7907380ffb36b4df249d4a557;p=jalview.git

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index f20954e..8bae5ba 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -29,6 +29,7 @@ import jalview.datamodel.SequenceI;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.Format;
 import jalview.xml.binding.sifts.Entry;
@@ -149,7 +150,6 @@ public class SiftsClient implements SiftsClientI
     siftsEntry = parseSIFTs(siftsFile);
   }
 
-
   /**
    * Parse the given SIFTs File and return a JAXB POJO of parsed data
    * 
@@ -212,6 +212,10 @@ public class SiftsClient implements SiftsClientI
           return new File(siftsFileName);
         }
       }
+      else
+      {
+        return siftsFile;
+      }
     }
     try
     {
@@ -276,21 +280,23 @@ 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);
+    // long now = System.currentTimeMillis();
+    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
+//            + " took " + (System.currentTimeMillis() - now) + "ms");
     return new File(downloadedSiftsFile);
   }
 
@@ -391,8 +397,8 @@ 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)
@@ -471,12 +477,13 @@ 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];
 
@@ -510,13 +517,13 @@ public class SiftsClient implements SiftsClientI
     if (os != null)
     {
       MappingOutputPojo mop = new MappingOutputPojo();
-      mop.setSeqStart(pdbStart);
-      mop.setSeqEnd(pdbEnd);
+      mop.setSeqStart(seqStart);
+      mop.setSeqEnd(seqEnd);
       mop.setSeqName(seq.getName());
       mop.setSeqResidue(matchedSeq);
 
-      mop.setStrStart(seqStart);
-      mop.setStrEnd(seqEnd);
+      mop.setStrStart(pdbStart);
+      mop.setStrEnd(pdbEnd);
       mop.setStrName(structId);
       mop.setStrResidue(targetStrucSeqs.toString());
 
@@ -611,6 +618,7 @@ public class SiftsClient implements SiftsClientI
       }
     }
   }
+
   /**
    * 
    * @param chainId
@@ -762,8 +770,6 @@ public class SiftsClient implements SiftsClientI
     }
   }
 
-
-
   @Override
   public Entity getEntityById(String id) throws SiftsException
   {
@@ -827,6 +833,10 @@ public class SiftsClient implements SiftsClientI
 
     if (sPojo[0].entityId != null)
     {
+      if (sPojo[0].pid < 1)
+      {
+        return null;
+      }
       for (Entity entity : entities)
       {
         if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId))
@@ -1001,8 +1011,10 @@ public class SiftsClient implements SiftsClientI
         {
           if ((i + (j * len)) < seqRes.length())
           {
-            if (seqRes.charAt(i + (j * len)) == strRes
-                    .charAt(i + (j * len))
+            boolean sameChar = Comparison.isSameResidue(
+                    seqRes.charAt(i + (j * len)),
+                    strRes.charAt(i + (j * len)), false);
+            if (sameChar
                     && !jalview.util.Comparison.isGap(seqRes.charAt(i
                             + (j * len))))
             {