JAL-1645 source formatting and organise imports

[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 c75a36f..4a50196 100644 (file)
--- 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