/*
* #%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.analysis.correlation;
import org.gitools.analysis.AnalysisException;
import org.gitools.analysis.AnalysisProcessor;
import org.gitools.analysis.MethodException;
import org.gitools.analysis.correlation.methods.CorrelationMethodFactory;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.matrix.IMatrixDimension;
import org.gitools.api.matrix.IMatrixLayer;
import org.gitools.api.matrix.IMatrixPosition;
import org.gitools.api.resource.ResourceReference;
import org.gitools.matrix.model.hashmatrix.HashMatrix;
import org.gitools.matrix.model.hashmatrix.HashMatrixDimension;
import org.gitools.matrix.model.matrix.element.LayerAdapter;
import java.util.Date;
import static org.gitools.api.matrix.MatrixDimensionKey.COLUMNS;
import static org.gitools.api.matrix.MatrixDimensionKey.ROWS;
public class CorrelationProcessor implements AnalysisProcessor {
private final CorrelationAnalysis analysis;
public CorrelationProcessor(CorrelationAnalysis analysis) {
this.analysis = analysis;
}
@Override
public void run(IProgressMonitor monitor) {
Date startTime = new Date();
CorrelationMethod method = CorrelationMethodFactory.createMethod(analysis.getMethod(), analysis.getMethodProperties());
IMatrix data = analysis.getData().get();
int layerIndex = analysis.getAttributeIndex();
IMatrixLayer<Double> layer = data.getLayers().get(layerIndex);
IMatrixDimension comparedDimension = analysis.isTransposeData() ? data.getDimension(COLUMNS) : data.getDimension(ROWS);
IMatrixDimension correlatedDimension = analysis.isTransposeData() ? data.getDimension(ROWS) : data.getDimension(COLUMNS);
monitor.begin("Running correlation analysis ...", correlatedDimension.size() * (correlatedDimension.size() - 1) / 2);
LayerAdapter<CorrelationResult> adapter = new LayerAdapter<>(CorrelationResult.class);
final IMatrix results = new HashMatrix(
adapter.getMatrixLayers(),
new HashMatrixDimension(ROWS, correlatedDimension),
new HashMatrixDimension(COLUMNS, correlatedDimension)
);
analysis.setResults(new ResourceReference<>("results", results));
IMatrixPosition positionX = data.newPosition();
IMatrixPosition positionY = data.newPosition();
for (String X : positionX.iterate(correlatedDimension)) {
if (monitor.isCancelled()) {
break;
}
for (String Y : positionY.iterate(correlatedDimension.from(X))) {
monitor.info("Correlating " + X + " with " + Y);
try {
CorrelationResult result = method.correlation(
positionX.iterate(layer, comparedDimension),
positionY.iterate(layer, comparedDimension),
analysis.getReplaceNanValue()
);
adapter.set(results, result, X, Y);
adapter.set(results, result, Y, X);
} catch (MethodException ex) {
throw new AnalysisException(ex);
}
monitor.worked(1);
}
}
analysis.setStartTime(startTime);
analysis.setElapsedTime(new Date().getTime() - startTime.getTime());
}
}