/*******************************************************************************
 * Copyright 2015 EMBL - European Bioinformatics Institute
 *
 * Licensed under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License. You may obtain a copy of the License at
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
 * either express or implied. See the License for the specific
 * language governing permissions and limitations under the
 * License.
 *******************************************************************************/
package uk.ac.ebi.phenotype.chart;

import java.util.ArrayList;
import java.util.List;

import org.mousephenotype.cda.db.pojo.BiologicalModel;
import org.mousephenotype.cda.db.pojo.CategoricalResult;
import org.mousephenotype.cda.db.pojo.StatisticalResult;
import org.mousephenotype.cda.solr.service.dto.ExperimentDTO;

/**
 * Class to hold all data, charts and tables pertaining to a Categorical Result Stats set so for male and female data combined
 * @author jwarren
 *
 */
public class CategoricalResultAndCharts {

	List<CategoricalChartDataObject> maleAndFemale=new ArrayList<CategoricalChartDataObject>();
	ExperimentDTO experiment;
	List<BiologicalModel> biologicalModels=new ArrayList<BiologicalModel>();
	private List<CategoricalResult> statsResults;
	private String organisation="placeHolder";
	
	private double combinedPValue;//male and female controls and experimental data combined to get an overall p value

	public double getCombinedPValue() {
		return combinedPValue;
	}

	public void setCombinedPValue(double combinedPValue) {
		this.combinedPValue = combinedPValue;
	}

	public List<CategoricalResult> getStatsResults() {
		return statsResults;
	}

	public void setStatsResults(List<? extends StatisticalResult> list) {
		this.statsResults = (List<CategoricalResult>) list;
	}

	public List<CategoricalChartDataObject> getMaleAndFemale() {
		return maleAndFemale;
	}

	public void setMaleAndFemale(List<CategoricalChartDataObject> maleAndFemale) {
		this.maleAndFemale = maleAndFemale;
	}

	public List<BiologicalModel> getBiologicalModels() {
		return biologicalModels;
	}

	public void setBiologicalModels(List<BiologicalModel> biologicalModels) {
		this.biologicalModels = biologicalModels;
	}

	public void addBiologicalModel(BiologicalModel biologicalModel) {
		this.biologicalModels.add(biologicalModel);
	}

	public void add(CategoricalChartDataObject chartData) {
		this.maleAndFemale.add(chartData);

	}

	public String getOrganisation() {
		 return organisation;
	}

	public void setOrganisation(String organisation) {
		this.organisation=organisation;

	}

	/**
	 * @return the experiment
	 */
	public ExperimentDTO getExperiment() {
		return experiment;
	}

	/**
	 * @param experiment the experiment to set
	 */
	public void setExperiment(ExperimentDTO experiment) {
		this.experiment = experiment;
	}
	
	

}

@@ -809,60 +809,8 @@
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@@ -1037,16 +1037,68 @@
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@@ -1585,17 +1585,17 @@
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 dPValue(
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Use object Double instead of primitive double to avoid default value