X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=68a73287cf1114c699bfbd59bab5f636f5234bac;hb=c932f0e85a8852824cdd8ce790af68682732c85c;hp=982c399a62b7aeab93cd37ed9cac6bcc679682bb;hpb=48f7c55f44b0526c5f7be8ebf986052ca7dae245;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 982c399..68a7328 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -138,7 +138,7 @@ public class Pdb extends EbiFileRetrievedProxy
 
     if (!isValidReference(id))
     {
-      System.err.println("Ignoring invalid pdb query: '" + id + "'");
+      jalview.bin.Console.errPrintln("Ignoring invalid pdb query: '" + id + "'");
       stopQuery();
       return null;
     }
@@ -165,7 +165,7 @@ public class Pdb extends EbiFileRetrievedProxy
       // todo get rid of Type and use FileFormatI instead?
       FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
               : FileFormat.MMCif;
-      pdbAlignment = new FormatAdapter().readFile(file,
+      pdbAlignment = new FormatAdapter().readFile(tmpFile,
               DataSourceType.FILE, fileFormat);
       if (pdbAlignment != null)
       {
@@ -182,15 +182,14 @@ public class Pdb extends EbiFileRetrievedProxy
 
             }
           }
-          if (chain == null
-                  || (chid != null && (chid.equals(chain)
-                          || chid.trim().equals(chain.trim()) || (chain
-                          .trim().length() == 0 && chid.equals("_")))))
+          if (chain == null || (chid != null && (chid.equals(chain)
+                  || chid.trim().equals(chain.trim())
+                  || (chain.trim().length() == 0 && chid.equals("_")))))
           {
             // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
             // TODO: suggest simplify naming to 1qip|A as default name defined
-            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR
-                    + id + SEPARATOR + pdbcs.getName());
+            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
+                    + SEPARATOR + pdbcs.getName());
             // Might need to add more metadata to the PDBEntry object
             // like below
             /*
@@ -236,8 +235,8 @@ public class Pdb extends EbiFileRetrievedProxy
       if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
       {
         throw new Exception(MessageManager.formatMessage(
-                "exception.no_pdb_records_for_chain", new String[] { id,
-                    ((chain == null) ? "' '" : chain) }));
+                "exception.no_pdb_records_for_chain", new String[]
+                { id, ((chain == null) ? "' '" : chain) }));
       }
 
     } catch (Exception ex) // Problem parsing PDB file