X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;fp=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=b0b5e92dd802fab265b67a3359d0c4426a1e21dc;hb=408b2821c8daf99245bf6358d06760701d90ddd8;hp=4a089f7583db040921adfe53d7ffb8ab865c12e9;hpb=f8e603128476ca6e093ea2fc65435d1294978c53;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 4a089f7..b0b5e92 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,3 +1,4 @@
+
 /*
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
@@ -53,7 +54,7 @@ public class Pdb extends EbiFileRetrievedProxy
 
   public static final String FEATURE_RES_NUM = "RESNUM";
 
-  private static String currentDefaultFomart = DBRefSource.PDB;
+  private static String currentDefaultFormat = DBRefSource.PDB;
 
   /*
    * (non-Javadoc)
@@ -132,11 +133,11 @@ public class Pdb extends EbiFileRetrievedProxy
       stopQuery();
       return null;
     }
-    String ext = getCurrentDefaultFomart().equalsIgnoreCase("mmcif") ? ".cif"
+    String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif"
             : ".xml";
     EBIFetchClient ebi = new EBIFetchClient();
     file = ebi.fetchDataAsFile("pdb:" + id,
-            getCurrentDefaultFomart().toLowerCase(), "raw", ext)
+            getCurrentDefaultFormat().toLowerCase(), ext)
             .getAbsolutePath();
     stopQuery();
     if (file == null)
@@ -148,7 +149,7 @@ public class Pdb extends EbiFileRetrievedProxy
 
       pdbAlignment = new FormatAdapter().readFile(file,
               jalview.io.AppletFormatAdapter.FILE,
-              getCurrentDefaultFomart());
+              getCurrentDefaultFormat());
       if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();
@@ -243,12 +244,12 @@ public class Pdb extends EbiFileRetrievedProxy
   }
 
   /**
-   * obtain human glyoxalase chain A sequence
+   * human glyoxalase
    */
   @Override
   public String getTestQuery()
   {
-    return "1QIPA";
+    return "1QIP";
   }
 
   @Override
@@ -263,14 +264,14 @@ public class Pdb extends EbiFileRetrievedProxy
     return 0;
   }
 
-  public static String getCurrentDefaultFomart()
+  public static String getCurrentDefaultFormat()
   {
-    return currentDefaultFomart;
+    return currentDefaultFormat;
   }
 
-  public static void setCurrentDefaultFomart(String currentDefaultFomart)
+  public static void setCurrentDefaultFormat(String currentDefaultFomart)
   {
-    Pdb.currentDefaultFomart = currentDefaultFomart;
+    Pdb.currentDefaultFormat = currentDefaultFomart;
   }
 
   /**