From f1671000d7556b46d63e676b83b3f7b6e9179849 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Nov 2005 11:08:31 +0000
Subject: [PATCH] OnlyAddPDBEntries

---
 src/jalview/io/SequenceFeatureFetcher.java |   22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 8bd9bab..5ecb417 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -196,7 +196,6 @@ public class SequenceFeatureFetcher implements Runnable
       return;
 
     SequenceI sequence = null;
-    //       String pdb = null;
 
     Vector entries = getUniprotEntries(file);
 
@@ -217,7 +216,7 @@ public class SequenceFeatureFetcher implements Runnable
 
       if (sequence == null)
       {
-        System.out.println("not found");
+        System.out.println(idmatch+" not found");
         continue;
       }
 
@@ -229,7 +228,6 @@ public class SequenceFeatureFetcher implements Runnable
       int absStart = entry.getUniprotSequence().getContent().indexOf(
           nonGapped.toString());
 
-      int residueOffset = 0;
       if (absStart == -1)
       {
         // Is UniprotSequence contained in dataset sequence?
@@ -244,9 +242,9 @@ public class SequenceFeatureFetcher implements Runnable
         }
         else
         {
-          if(entry.getFeatures()!=null)
+          if(entry.getFeature()!=null)
           {
-            Enumeration e = entry.getFeatures().elements();
+            Enumeration e = entry.getFeature().elements();
             while (e.hasMoreElements())
             {
               SequenceFeature sf = (SequenceFeature) e.nextElement();
@@ -266,7 +264,19 @@ public class SequenceFeatureFetcher implements Runnable
       int absEnd = absStart + nonGapped.toString().length();
       absStart += 1;
 
-      sequence.setSequenceFeatures(entry.getFeatures());
+      Enumeration e = entry.getDbReference().elements();
+      Vector onlyPdbEntries = new Vector();
+      while(e.hasMoreElements())
+      {
+        PDBEntry pdb = (PDBEntry)e.nextElement();
+        if(!pdb.getType().equals("PDB"))
+          continue;
+
+        onlyPdbEntries.addElement(pdb);
+      }
+
+      sequence.setPDBId(onlyPdbEntries);
+      sequence.setSequenceFeatures(entry.getFeature());
       sequence.setStart(absStart);
       sequence.setEnd(absEnd);
 
-- 
1.7.10.2