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=3fd7541fb25fbb2fa76efe29f634e16b823dca3e;hb=a6b324e3f5edac3df0b968f0037b1cc8b651598e;hp=b9fb8f336a5ba95e33ebf0c4d32b91b4dcc732b4;hpb=e0401a6563eb1fb58b2f4b6d594b4b3826135950;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index b9fb8f3..3fd7541 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -100,7 +100,7 @@ public class Pdb extends EbiFileRetrievedProxy
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    AlignmentI pdbfile = null;
+    AlignmentI pdbAlignment = null;
     Vector result = new Vector();
     String chain = null;
     String id = null;
@@ -134,12 +134,12 @@ public class Pdb extends EbiFileRetrievedProxy
     try
     {
 
-      pdbfile = new FormatAdapter().readFile(file,
+      pdbAlignment = new FormatAdapter().readFile(file,
               jalview.io.AppletFormatAdapter.FILE, "PDB");
-      if (pdbfile != null)
+      if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();
-        for (SequenceI pdbcs : pdbfile.getSequences())
+        for (SequenceI pdbcs : pdbAlignment.getSequences())
         {
           String chid = null;
           // Mapping map=null;
@@ -191,18 +191,18 @@ public class Pdb extends EbiFileRetrievedProxy
         // now remove marked sequences
         for (SequenceI pdbcs : toremove)
         {
-          pdbfile.deleteSequence(pdbcs);
+          pdbAlignment.deleteSequence(pdbcs);
           if (pdbcs.getAnnotation() != null)
           {
             for (AlignmentAnnotation aa : pdbcs.getAnnotation())
             {
-              pdbfile.deleteAnnotation(aa);
+              pdbAlignment.deleteAnnotation(aa);
             }
           }
         }
       }
 
-      if (pdbfile == null || pdbfile.getHeight() < 1)
+      if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
       {
         throw new Exception(MessageManager.formatMessage(
                 "exception.no_pdb_records_for_chain", new String[] { id,
@@ -214,7 +214,7 @@ public class Pdb extends EbiFileRetrievedProxy
       stopQuery();
       throw (ex);
     }
-    return pdbfile;
+    return pdbAlignment;
   }
 
   /*