header updated

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 75e69c2..dc5d31a 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -250,8 +250,8 @@ public class SequenceFetcher
     EBIFetchClient ebi = new EBIFetchClient();\r
     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
 \r
-    SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
-    Vector entries = sff.getUniprotEntries(file);\r
+    DBRefFetcher dbref = new DBRefFetcher();\r
+    Vector entries = dbref.getUniprotEntries(file);\r
 \r
     if (entries != null)\r
     {\r
@@ -301,6 +301,17 @@ public class SequenceFetcher
           onlyPdbEntries.addElement(pdb);\r
         }\r
 \r
+        Enumeration en2 = entry.getAccession().elements();\r
+        while (en2.hasMoreElements())\r
+        {\r
+          sequence[i].getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,\r
+                    "0",\r
+                    en2.nextElement().toString()));\r
+        }\r
+\r
+\r
+\r
+\r
         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
         if (entry.getFeature() != null)\r
         {\r
@@ -327,17 +338,18 @@ public class SequenceFetcher
     }\r
 \r
     EBIFetchClient ebi = new EBIFetchClient();\r
-    String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
-    if (reply == null)\r
+    String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();\r
+    if (file == null)\r
       return null;\r
     try\r
     {\r
-      PDBfile pdbfile = new PDBfile(reply);\r
+      PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);\r
       for (int i = 0; i < pdbfile.chains.size(); i++)\r
       {\r
         if (chain == null ||\r
             ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
             toUpperCase().equals(chain))\r
+\r
           result.append("\n>PDB|" + id + "|" +\r
                         ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
                         getName() +\r
@@ -363,7 +375,7 @@ public class SequenceFetcher
     String format = new IdentifyFile().Identify(result, "Paste");\r
     SequenceI[] sequences = null;\r
 \r
-    if (FormatAdapter.formats.contains(format))\r
+    if (FormatAdapter.isValidFormat(format))\r
     {\r
       sequences = null;\r
       try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r