+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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.
try
{
String zipFile = ontologyFile + ".zip";
- InputStream inStream = this.getClass().getResourceAsStream(
- "/" + zipFile);
+ InputStream inStream = this.getClass()
+ .getResourceAsStream("/" + zipFile);
zipStream = new ZipInputStream(new BufferedInputStream(inStream));
ZipEntry entry;
while ((entry = zipStream.getNextEntry()) != null)
}
}
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)
{
* @throws ParseException
* @throws IOException
*/
- protected void loadOboFile(InputStream is) throws ParseException,
- IOException
+ protected void loadOboFile(InputStream is)
+ throws ParseException, IOException
{
BufferedReader oboFile = new BufferedReader(new InputStreamReader(is));
OboParser parser = new OboParser();
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);
}
}