Merge branch 'develop' into patch/JAL-3088_finalbracenotinrightplace

[jalview.git] / src / jalview / util / DBRefUtils.java

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index e17a336..a101d82 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -30,6 +30,7 @@ import java.util.Map;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.bin.Console;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
@@ -405,7 +406,7 @@ public class DBRefUtils
         }
         else
         {
-          System.err.println("Malformed PDB DR line:" + acn);
+          jalview.bin.Console.errPrintln("Malformed PDB DR line:" + acn);
         }
       }
       else
@@ -810,9 +811,12 @@ public class DBRefUtils
           // toPromote.add(cand);
           if (!cand.isPrimaryCandidate())
           {
-            System.out.println(
-                    "Warning: Couldn't promote dbref " + cand.toString()
-                            + " for sequence " + sequence.toString());
+            if (Console.isDebugEnabled())
+            {
+              Console.debug(
+                      "Warning: Couldn't promote dbref " + cand.toString()
+                              + " for sequence " + sequence.toString());
+            }
           }
         }
       }