From 6efabb12ac7f2ed3bb6bb9e47505cf0112784837 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 5 Dec 2005 13:39:01 +0000
Subject: [PATCH] Allow for uniprot in name

---
 src/jalview/io/SequenceFeatureFetcher.java |   19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index b766627..d980b0a 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -48,6 +48,7 @@ public class SequenceFeatureFetcher implements Runnable
   ArrayList unknownSequences;
   CutAndPasteTransfer output = new CutAndPasteTransfer();
   StringBuffer sbuffer = new StringBuffer();
+  boolean uniprotFlag = false;
 
   public SequenceFeatureFetcher()
   {}
@@ -129,6 +130,12 @@ public class SequenceFeatureFetcher implements Runnable
           StringBuffer remainingIds = new StringBuffer("uniprot:");
           for (int i = 0; i < ids.size(); i++)
            {
+             if(ids.get(i).toString().indexOf("|")>-1)
+             {
+               remainingIds.append(ids.get(i).toString().substring(
+                   ids.get(i).toString().lastIndexOf("|") + 1));
+               uniprotFlag = true;
+             }
              remainingIds.append(ids.get(i) + ";");
            }
           EBIFetchClient ebi = new EBIFetchClient();
@@ -218,13 +225,21 @@ public class SequenceFeatureFetcher implements Runnable
         sequence = dataset.findName(idmatch);
       }
 
-      if (sequence == null)
+      if(sequence!=null)
+        ids.remove(sequence.getName());
+
+      else  if (sequence == null && uniprotFlag)
+      {
+          sequence = dataset.findName("UniProt/Swiss-Prot|"+entry.getAccession().elementAt(0)+"|"+idmatch);
+          ids.remove(idmatch);
+      }
+
+      if(sequence ==null)
       {
         System.out.println(idmatch+" not found");
         continue;
       }
 
-      ids.remove(sequence.getName());
       unknownSequences.remove(sequence);
 
       String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());
-- 
1.7.10.2