merge of SIFTs Branch

[jalview.git] / src / jalview / ws / dbsources / Pdb.java

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 4a50196..7f8c76c 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -97,7 +97,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    AlignmentI pdbfile = null;
+    AlignmentI pdbAlignment = null;
     Vector result = new Vector();
     String chain = null;
     String id = null;
@@ -131,12 +131,12 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     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;
@@ -188,18 +188,18 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
         // 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,
@@ -211,7 +211,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
       stopQuery();
       throw (ex);
     }
-    return pdbfile;
+    return pdbAlignment;
   }
 
   /*