pdb fetchDataAsFile

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 795276b..99c1d5e 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -327,17 +327,18 @@ 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