Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callba...

[jalview.git] / src / jalview / ext / so / SequenceOntology.java

diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index 0d631e6..89b2415 100644 (file)
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -20,8 +20,6 @@
  */
 package jalview.ext.so;
 
-import jalview.io.gff.SequenceOntologyI;
-
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -44,6 +42,9 @@ 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.io.gff.SequenceOntologyI;
+
 /**
  * A wrapper class that parses the Sequence Ontology and exposes useful access
  * methods. This version uses the BioJava parser.
@@ -183,19 +184,19 @@ public class SequenceOntology implements SequenceOntologyI
             boolean oldTermIsObsolete = isObsolete(replaced);
             if (newTermIsObsolete && !oldTermIsObsolete)
             {
-              System.err.println("Ignoring " + term.getName()
+              Cache.log.debug("Ignoring " + term.getName()
                       + " as obsolete and duplicated by "
                       + replaced.getName());
               term = replaced;
             }
             else if (!newTermIsObsolete && oldTermIsObsolete)
             {
-              System.err.println("Ignoring " + replaced.getName()
+              Cache.log.debug("Ignoring " + replaced.getName()
                       + " as obsolete and duplicated by " + term.getName());
             }
             else
             {
-              System.err.println("Warning: " + term.getName()
+              Cache.log.debug("Warning: " + term.getName()
                       + " has replaced " + replaced.getName()
                       + " for lookup of '" + description + "'");
             }