X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=4a5019619263d58d9bfc76832c85f49014b7c637;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=c75a36f9d9c78b8a5913572943171802c9c66ab0;hpb=fe72160257543fca39f7959fc1347665e95764a2;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index c75a36f..4a50196 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -140,7 +140,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
         {
           String chid = null;
           // Mapping map=null;
-          for (PDBEntry pid : pdbcs.getPDBId())
+          for (PDBEntry pid : pdbcs.getAllPDBEntries())
           {
             if (pid.getFile() == file)
             {
@@ -189,9 +189,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
         for (SequenceI pdbcs : toremove)
         {
           pdbfile.deleteSequence(pdbcs);
-          if (pdbcs.getAnnotation()!=null)
+          if (pdbcs.getAnnotation() != null)
           {
-            for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+            for (AlignmentAnnotation aa : pdbcs.getAnnotation())
             {
               pdbfile.deleteAnnotation(aa);
             }
@@ -201,7 +201,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
 
       if (pdbfile == null || pdbfile.getHeight() < 1)
       {
-        throw new Exception(MessageManager.formatMessage("exception.no_pdb_records_for_chain", new String[]{id, ((chain == null) ? "' '" : chain)}));
+        throw new Exception(MessageManager.formatMessage(
+                "exception.no_pdb_records_for_chain", new String[] { id,
+                    ((chain == null) ? "' '" : chain) }));
       }
 
     } catch (Exception ex) // Problem parsing PDB file