/*
* #%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.Analysis;
import org.gitools.analysis.correlation.methods.PearsonCorrelationMethod;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.resource.ResourceReference;
import org.gitools.api.resource.adapter.ResourceReferenceXmlAdapter;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import java.util.Properties;
@XmlAccessorType(XmlAccessType.FIELD)
@XmlRootElement
public class CorrelationAnalysis extends Analysis {
private String method;
private Properties methodProperties;
private Double replaceNanValue;
private boolean transposeData;
private int attributeIndex;
@XmlJavaTypeAdapter(ResourceReferenceXmlAdapter.class)
private ResourceReference<IMatrix> data;
@XmlJavaTypeAdapter(ResourceReferenceXmlAdapter.class)
private ResourceReference<IMatrix> results;
public CorrelationAnalysis() {
this.method = PearsonCorrelationMethod.ID;
this.methodProperties = new Properties();
this.replaceNanValue = null;
this.transposeData = false;
this.attributeIndex = 0;
}
public String getMethod() {
return method;
}
public void setMethod(String method) {
this.method = method;
}
public Properties getMethodProperties() {
return methodProperties;
}
public void setMethodProperties(Properties methodProperties) {
this.methodProperties = methodProperties;
}
public boolean isReplaceNanValues() {
return replaceNanValue != null && !Double.isNaN(replaceNanValue);
}
public Double getReplaceNanValue() {
return replaceNanValue;
}
public void setReplaceNanValue(Double value) {
this.replaceNanValue = value;
}
public boolean isTransposeData() {
return transposeData;
}
public void setTransposeData(boolean transposeData) {
this.transposeData = transposeData;
}
public int getAttributeIndex() {
return attributeIndex;
}
public void setAttributeIndex(int attributeIndex) {
this.attributeIndex = attributeIndex;
}
public ResourceReference<IMatrix> getData() {
return data;
}
public void setData(ResourceReference<IMatrix> data) {
this.data = data;
}
public ResourceReference<IMatrix> getResults() {
return results;
}
public void setResults(ResourceReference<IMatrix> results) {
this.results = results;
}
}