X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=f3d8e291dc8fb35e32a96732adb8d21db1f0bf70;hb=76b6b31c53b099a3034e0622ec78d4c2b455a309;hp=75e69c260f2667f338e9e9b4b81d6e7cad04b2ea;hpb=f01e51c0c24a706409590174696ae72c4d573b7f;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 75e69c2..f3d8e29 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -250,8 +250,8 @@ public class SequenceFetcher
     EBIFetchClient ebi = new EBIFetchClient();
     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
 
-    SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
-    Vector entries = sff.getUniprotEntries(file);
+    DBRefFetcher dbref = new DBRefFetcher();
+    Vector entries = dbref.getUniprotEntries(file);
 
     if (entries != null)
     {
@@ -327,17 +327,18 @@ public class SequenceFetcher
     }
 
     EBIFetchClient ebi = new EBIFetchClient();
-    String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
-    if (reply == null)
+    String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+    if (file == null)
       return null;
     try
     {
-      PDBfile pdbfile = new PDBfile(reply);
+      PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
       for (int i = 0; i < pdbfile.chains.size(); i++)
       {
         if (chain == null ||
             ( (PDBChain) pdbfile.chains.elementAt(i)).id.
             toUpperCase().equals(chain))
+
           result.append("\n>PDB|" + id + "|" +
                         ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
                         getName() +
@@ -363,7 +364,7 @@ public class SequenceFetcher
     String format = new IdentifyFile().Identify(result, "Paste");
     SequenceI[] sequences = null;
 
-    if (FormatAdapter.formats.contains(format))
+    if (FormatAdapter.isValidFormat(format))
     {
       sequences = null;
       try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",