+/*
+ * 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;
*/
protected void loadOntologyZipFile(String ontologyFile)
{
+ long now = System.currentTimeMillis();
ZipInputStream zipStream = null;
try
{
String zipFile = ontologyFile + ".zip";
- System.out.println("Loading Sequence Ontology from " + zipFile);
InputStream inStream = this.getClass().getResourceAsStream(
"/" + zipFile);
zipStream = new ZipInputStream(new BufferedInputStream(inStream));
loadOboFile(zipStream);
}
}
+ long elapsed = System.currentTimeMillis() - now;
+ System.out.println("Loaded Sequence Ontology from " + zipFile + " ("
+ + elapsed + "ms)");
} catch (Exception e)
{
e.printStackTrace();
}
else
{
- System.err.println("Warning: " + term.getName()
- + " has replaced " + replaced.getName()
- + " for lookup of '" + description + "'");
+ System.err.println("Warning: " + term.getName()
+ + " has replaced " + replaced.getName()
+ + " for lookup of '" + description + "'");
}
}
termsByDescription.put(description, term);
{
try
{
- if (Boolean.TRUE.equals(ann.getProperty("is_obsolete")))
- {
+ if (Boolean.TRUE.equals(ann.getProperty("is_obsolete")))
+ {
return true;
}
} catch (NoSuchElementException e)