/*
* #%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.heatmap.format;
import org.gitools.api.PersistenceException;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.persistence.FileFormat;
import org.gitools.api.resource.IResourceLocator;
import org.gitools.heatmap.Heatmap;
import org.gitools.matrix.model.hashmatrix.HashMatrix;
import org.gitools.matrix.model.hashmatrix.HashMatrixDimension;
import org.gitools.resource.AbstractXmlFormat;
import javax.enterprise.context.ApplicationScoped;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import java.io.InputStream;
import java.io.OutputStream;
@ApplicationScoped
public class HeatmapFormat extends AbstractXmlFormat<Heatmap> {
public static final String EXTENSION = "heatmap";
public static final FileFormat FILE_FORMAT = new FileFormat("Heatmap", EXTENSION, true, false, true);
public HeatmapFormat() {
super(EXTENSION, Heatmap.class);
}
@Override
public void beforeWrite(OutputStream out, IResourceLocator resourceLocator, Heatmap resource, Marshaller marshaller, IProgressMonitor progressMonitor) throws PersistenceException {
if (resource.getContents() instanceof HashMatrix) {
HashMatrixDimension rows = (HashMatrixDimension) resource.getContents().getRows();
HashMatrixDimension columns = (HashMatrixDimension) resource.getContents().getColumns();
rows.optimize(resource.getRows());
columns.optimize(resource.getColumns());
}
super.beforeWrite(out, resourceLocator, resource, marshaller, progressMonitor);
}
@Override
public void afterRead(InputStream inputStream, IResourceLocator resourceLocator, Heatmap resource, Unmarshaller unmarshaller, IProgressMonitor progressMonitor) throws PersistenceException {
// Initialize the heatmap
resource.init();
}
}