/*
* #%L
* org.gitools.mutex
* %%
* Copyright (C) 2013 - 2014 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.plugins.mutex.sort;
import com.google.common.collect.Lists;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.matrix.IMatrixPosition;
import org.gitools.api.matrix.SortDirection;
import org.gitools.heatmap.Heatmap;
import org.gitools.heatmap.HeatmapDimension;
import org.gitools.heatmap.HeatmapLayer;
import org.gitools.matrix.model.iterable.IdentifiersPredicate;
import org.gitools.matrix.sort.AggregationFunction;
import org.gitools.utils.aggregation.NonNullCountAggregator;
import java.beans.PropertyChangeListener;
import java.util.Set;
public class MutualExclusiveMatrixViewSorter {
public static void sortByMutualExclusion(final Heatmap heatmap, String pattern, Set<String> values, boolean regExChecked, boolean applyToColumns, IProgressMonitor monitor, boolean showProgress) {
HeatmapLayer layer = heatmap.getLayers().getTopLayer();
HeatmapDimension rows = heatmap.getRows();
HeatmapDimension columns = heatmap.getColumns();
if (applyToColumns) {
rows = heatmap.getColumns();
columns = heatmap.getRows();
}
AggregationFunction function = new AggregationFunction(layer, NonNullCountAggregator.INSTANCE, columns, layer.getEventFunction());
IdentifiersPredicate<String> annotationResolver = new IdentifiersPredicate<String>(rows, values, pattern, rows.getAnnotations());
rows.sort(new MutualExclusiveComparator(
heatmap,
layer,
rows,
annotationResolver,
function,
monitor));
monitor.begin("Sorting rows...", values.size());
PropertyChangeListener[] listeners = columns.getPropertyChangeListeners();
if (!showProgress) {
// Remove listeners to avoid heatmap refresh at each iteration
for (PropertyChangeListener listener : listeners) {
columns.removePropertyChangeListener(listener);
}
}
IMatrixPosition position = heatmap.newPosition();
for (String row : Lists.reverse(Lists.newArrayList(rows))) {
monitor.worked(1);
if (monitor.isCancelled()) {
break;
}
position.set(rows, row);
if (!annotationResolver.apply(row, position)) {
continue;
}
columns.sort(new MutualExclusiveSingleValueComparator(position, layer, columns, SortDirection.DESCENDING,
layer.getEventFunction()));
}
if (!showProgress) {
for (PropertyChangeListener listener : listeners) {
columns.addPropertyChangeListener(listener);
}
// Force to fire the events
columns.show(columns.toList());
}
}
}