*/
package jalview.ext.so;
-import jalview.io.gff.SequenceOntologyI;
-
import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.IOException;
import org.biojava.nbio.ontology.io.OboParser;
import org.biojava.nbio.ontology.utils.Annotation;
+import jalview.bin.Console;
+import jalview.io.gff.SequenceOntologyI;
+
/**
* A wrapper class that parses the Sequence Ontology and exposes useful access
* methods. This version uses the BioJava parser.
}
}
long elapsed = System.currentTimeMillis() - now;
- System.out.println("Loaded Sequence Ontology from " + zipFile + " ("
+ Console.info("Loaded Sequence Ontology from " + zipFile + " ("
+ elapsed + "ms)");
} catch (Exception e)
{
boolean oldTermIsObsolete = isObsolete(replaced);
if (newTermIsObsolete && !oldTermIsObsolete)
{
- System.err.println("Ignoring " + term.getName()
+ Console.debug("Ignoring " + term.getName()
+ " as obsolete and duplicated by "
+ replaced.getName());
term = replaced;
}
else if (!newTermIsObsolete && oldTermIsObsolete)
{
- System.err.println("Ignoring " + replaced.getName()
+ Console.debug("Ignoring " + replaced.getName()
+ " as obsolete and duplicated by " + term.getName());
}
else
{
- System.err.println("Warning: " + term.getName()
- + " has replaced " + replaced.getName()
- + " for lookup of '" + description + "'");
+ Console.debug("Warning: " + term.getName() + " has replaced "
+ + replaced.getName() + " for lookup of '"
+ + description + "'");
}
}
termsByDescription.put(description, term);
{
if (!termsNotFound.contains(term))
{
- System.err.println("SO term " + term + " invalid");
+ Console.error("SO term " + term + " invalid");
termsNotFound.add(term);
}
}