X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fso%2FSequenceOntology.java;h=38d98d03d961b09cb288438a75c80efcc8aecd3f;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=89b241592e9882f3acc3cfe8fbda63f427a8643b;hpb=4908e9c9b03343aa38e7b2234bb0f9cf79c51a31;p=jalview.git

diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index 89b2415..38d98d0 100644
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -42,7 +42,7 @@ import org.biojava.nbio.ontology.Triple;
 import org.biojava.nbio.ontology.io.OboParser;
 import org.biojava.nbio.ontology.utils.Annotation;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.io.gff.SequenceOntologyI;
 
 /**
@@ -115,7 +115,7 @@ public class SequenceOntology implements SequenceOntologyI
         }
       }
       long elapsed = System.currentTimeMillis() - now;
-      System.out.println("Loaded Sequence Ontology from " + zipFile + " ("
+      Console.info("Loaded Sequence Ontology from " + zipFile + " ("
               + elapsed + "ms)");
     } catch (Exception e)
     {
@@ -184,19 +184,19 @@ public class SequenceOntology implements SequenceOntologyI
             boolean oldTermIsObsolete = isObsolete(replaced);
             if (newTermIsObsolete && !oldTermIsObsolete)
             {
-              Cache.log.debug("Ignoring " + term.getName()
+              Console.debug("Ignoring " + term.getName()
                       + " as obsolete and duplicated by "
                       + replaced.getName());
               term = replaced;
             }
             else if (!newTermIsObsolete && oldTermIsObsolete)
             {
-              Cache.log.debug("Ignoring " + replaced.getName()
+              Console.debug("Ignoring " + replaced.getName()
                       + " as obsolete and duplicated by " + term.getName());
             }
             else
             {
-              Cache.log.debug("Warning: " + term.getName()
+              Console.debug("Warning: " + term.getName()
                       + " has replaced " + replaced.getName()
                       + " for lookup of '" + description + "'");
             }
@@ -337,7 +337,7 @@ public class SequenceOntology implements SequenceOntologyI
     {
       if (!termsNotFound.contains(term))
       {
-        System.err.println("SO term " + term + " invalid");
+        Console.error("SO term " + term + " invalid");
         termsNotFound.add(term);
       }
     }