JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...

[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 a658089..797726f 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -138,7 +138,8 @@ 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;
     }
@@ -165,8 +166,8 @@ 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(tmpFile, DataSourceType.FILE,
-              fileFormat);
+      pdbAlignment = new FormatAdapter().readFile(tmpFile,
+              DataSourceType.FILE, fileFormat);
       if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();