X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=dc5d31a937ff4b835e9472f7da2f4af7399d06da;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=75e69c260f2667f338e9e9b4b81d6e7cad04b2ea;hpb=f01e51c0c24a706409590174696ae72c4d573b7f;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 75e69c2..dc5d31a 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -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)
     {
@@ -301,6 +301,17 @@ public class SequenceFetcher
           onlyPdbEntries.addElement(pdb);
         }
 
+        Enumeration en2 = entry.getAccession().elements();
+        while (en2.hasMoreElements())
+        {
+          sequence[i].getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
+                    "0",
+                    en2.nextElement().toString()));
+        }
+
+
+
+
         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
         if (entry.getFeature() != null)
         {
@@ -327,17 +338,18 @@ 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 +375,7 @@ 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",