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JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console
[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
14969fe
..
38d98d0
100644
(file)
--- 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 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;
/**
import jalview.io.gff.SequenceOntologyI;
/**
@@
-115,7
+115,7
@@
public class SequenceOntology implements SequenceOntologyI
}
}
long elapsed = System.currentTimeMillis() - now;
}
}
long elapsed = System.currentTimeMillis() - now;
- Cache.info("Loaded Sequence Ontology from " + zipFile + " ("
+ Console.info("Loaded Sequence Ontology from " + zipFile + " ("
+ elapsed + "ms)");
} catch (Exception e)
{
+ elapsed + "ms)");
} catch (Exception e)
{
@@
-184,19
+184,19
@@
public class SequenceOntology implements SequenceOntologyI
boolean oldTermIsObsolete = isObsolete(replaced);
if (newTermIsObsolete && !oldTermIsObsolete)
{
boolean oldTermIsObsolete = isObsolete(replaced);
if (newTermIsObsolete && !oldTermIsObsolete)
{
- Cache.debug("Ignoring " + term.getName()
+ Console.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)
{
- Cache.debug("Ignoring " + replaced.getName()
+ Console.debug("Ignoring " + replaced.getName()
+ " as obsolete and duplicated by " + term.getName());
}
else
{
+ " as obsolete and duplicated by " + term.getName());
}
else
{
- Cache.debug("Warning: " + term.getName()
+ Console.debug("Warning: " + term.getName()
+ " has replaced " + replaced.getName()
+ " for lookup of '" + description + "'");
}
+ " has replaced " + replaced.getName()
+ " for lookup of '" + description + "'");
}
@@
-337,7
+337,7
@@
public class SequenceOntology implements SequenceOntologyI
{
if (!termsNotFound.contains(term))
{
{
if (!termsNotFound.contains(term))
{
- Cache.error("SO term " + term + " invalid");
+ Console.error("SO term " + term + " invalid");
termsNotFound.add(term);
}
}
termsNotFound.add(term);
}
}