/*
* #%L
* gitools-core
* %%
* Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* This program 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.
*
* This program 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 this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package org.gitools.matrix.geneset;
import org.gitools.api.PersistenceException;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.resource.IResourceLocator;
import org.gitools.resource.AbstractResourceFormat;
import org.gitools.utils.readers.text.CSVReader;
import javax.enterprise.context.ApplicationScoped;
import java.io.*;
@ApplicationScoped
public class GeneSetFormat extends AbstractResourceFormat<GeneSet> {
public static final String EXTENSION = "grp";
public GeneSetFormat() {
super(EXTENSION, GeneSet.class);
}
@Override
public boolean isDefaultExtension() {
return true;
}
@Override
protected GeneSet readResource(IResourceLocator resourceLocator, IProgressMonitor progressMonitor) throws PersistenceException {
progressMonitor.begin("Reading ...", 1);
GeneSet labels = new GeneSet();
try {
InputStream in = resourceLocator.openInputStream(progressMonitor);
CSVReader parser = new CSVReader(new InputStreamReader(in));
String[] fields;
// read file
while ((fields = parser.readNext()) != null) {
if (fields.length > 1) {
throw new PersistenceException("Only one column is allowed at line " + parser.getLineNumber());
}
labels.add(fields[0]);
}
in.close();
progressMonitor.info(labels.size() + " rows");
} catch (IOException e) {
throw new PersistenceException(e);
}
return labels;
}
@Override
protected void writeResource(IResourceLocator resourceLocator, GeneSet resource, IProgressMonitor progressMonitor) throws PersistenceException {
progressMonitor.begin("Saving matrix...", resource.size());
try {
OutputStream out = resourceLocator.openOutputStream(progressMonitor);
PrintWriter pw = new PrintWriter(new OutputStreamWriter(out));
for (String label : resource)
pw.println(label);
out.close();
} catch (Exception e) {
throw new PersistenceException(e);
}
}
}