From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 27 Jul 2006 10:30:33 +0000 (+0000)
Subject: Use DBRefSource.PDB
X-Git-Tag: Release_2_1~183
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1f6f0bc48cd088f8327902b257531605ba1a6055;p=jalview.git

Use DBRefSource.PDB
---

diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 92e7e4b..17526ac 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -306,23 +306,21 @@ public class DBRefFetcher implements Runnable
 
           continue;
         }
-        else
-        {
 
-          if(entry.getFeature()!=null)
+        if (entry.getFeature() != null)
+        {
+          Enumeration e = entry.getFeature().elements();
+          while (e.hasMoreElements())
           {
-            Enumeration e = entry.getFeature().elements();
-            while (e.hasMoreElements())
-            {
-              SequenceFeature sf = (SequenceFeature) e.nextElement();
-              sf.setBegin(sf.getBegin() + absStart + 1);
-              sf.setEnd(sf.getEnd() + absStart + 1);
-            }
+            SequenceFeature sf = (SequenceFeature) e.nextElement();
+            sf.setBegin(sf.getBegin() + absStart + 1);
+            sf.setEnd(sf.getEnd() + absStart + 1);
           }
 
           sbuffer.append(sequence.getName() +
-                         " HAS "+absStart+" PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"
-                        +" HAVE BEEN ADJUSTED ACCORDINGLY \n");
+                         " HAS " + absStart +
+              " PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"
+                         + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
           absStart = 0;
         }
 
@@ -338,7 +336,7 @@ public class DBRefFetcher implements Runnable
       while(e.hasMoreElements())
       {
         PDBEntry pdb = (PDBEntry)e.nextElement();
-        if(!pdb.getType().equals("PDB"))
+        if(!pdb.getType().equals(DBRefSource.PDB))
           continue;
 
         sequence.addDBRef(new DBRefEntry(DBRefSource.PDB,