Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

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

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 5337852..a101d82 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -20,17 +20,17 @@
  */
 package jalview.util;
 
-import java.util.Locale;
-
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
 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;
@@ -406,7 +406,7 @@ public class DBRefUtils
         }
         else
         {
-          System.err.println("Malformed PDB DR line:" + acn);
+          jalview.bin.Console.errPrintln("Malformed PDB DR line:" + acn);
         }
       }
       else
@@ -805,15 +805,18 @@ public class DBRefUtils
           }
           // and promote - not that version must be non-null here,
           // as p must have passed isPrimaryCandidate()
-          cand.setVersion(p.getVersion() + " (promoted)");
+          cand.setVersion(cand.getVersion() + " (promoted)");
           bsSelect.clear(ic);
           // selfs.remove(cand);
           // 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());
+            }
           }
         }
       }