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JAL-1191 reduce logging level for warnings
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 4 Jun 2020 16:22:29 +0000
(17:22 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 31 Aug 2020 14:56:38 +0000
(15:56 +0100)
src/jalview/ext/so/SequenceOntology.java
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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;
*/
package jalview.ext.so;
-import jalview.io.gff.SequenceOntologyI;
-
import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.IOException;
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 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.
/**
* 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)
{
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)
{
+ " 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
{
+ " 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 + "'");
}
+ " has replaced " + replaced.getName()
+ " for lookup of '" + description + "'");
}