/*
* #%L
* org.gitools.ui.app
* %%
* 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.ui.app.actions.data.analysis;
import com.google.common.base.Function;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.matrix.SortDirection;
import org.gitools.heatmap.HeatmapDimension;
import org.gitools.heatmap.header.HierarchicalCluster;
import org.gitools.matrix.sort.SortByLabelComparator;
import org.gitools.ui.core.Application;
import org.gitools.ui.core.commands.AbstractCommand;
import java.util.HashMap;
import java.util.Map;
public class SortByHierarchicalClusteringCommand extends AbstractCommand {
private final HeatmapDimension clusteringDimension;
private HierarchicalCluster hierarchicalCluster;
public SortByHierarchicalClusteringCommand(HeatmapDimension clusteringDimension, HierarchicalCluster hierarchicalCluster) {
this.clusteringDimension = clusteringDimension;
this.hierarchicalCluster = hierarchicalCluster;
}
@Override
public void execute(IProgressMonitor monitor) {
try {
if (getExitStatus() > 0) {
return;
}
monitor.begin("Sorting according to clustering", 1);
clusteringDimension.sort(
new SortByLabelComparator(clusteringDimension,
SortDirection.ASCENDING,
new SortByHierarchicalClusteringCommand.HierarchicalSortFunction(hierarchicalCluster),
-1,
false) {
@Override
public int compare(String idx1, String idx2) {
String v1 = transformFunction.apply(idx1);
String v2 = transformFunction.apply(idx2);
if (v1 == null && v2 == null) {
return 0;
} else if (v1 != null && v2 == null) {
return -1;
} else if (v1 == null && v2 != null) {
return 1;
}
return v1.compareTo(v2);
}
});
Application.get().refresh();
setExitStatus(0);
} catch (Exception e) {
setExitStatus(-1);
}
}
static class HierarchicalSortFunction implements Function<String, String> {
Map<String, String> map;
public HierarchicalSortFunction(HierarchicalCluster rootCluster) {
map = rootCluster.getMaxLevel(new HashMap<String, String>());
/*for (String s : map.keySet()) {
System.out.println(s + ": " + map.get(s));
}*/
}
@Override
public String apply(String identifier) {
return map.get(identifier);
}
}
}