From 4908e9c9b03343aa38e7b2234bb0f9cf79c51a31 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 4 Jun 2020 17:22:29 +0100 Subject: [PATCH] JAL-1191 reduce logging level for warnings --- src/jalview/ext/so/SequenceOntology.java | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) 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 + "'"); } -- 1.7.10.2