From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 4 Jun 2020 16:22:29 +0000 (+0100)
Subject: JAL-1191 reduce logging level for warnings
X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~15^2~4
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=4908e9c9b03343aa38e7b2234bb0f9cf79c51a31

JAL-1191 reduce logging level for warnings
---

diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index 0d631e6..89b2415 100644
--- 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 + "'");
             }