SampleAnalysisSet.java

package com.compomics.util.experiment;

import com.compomics.util.experiment.biology.Sample;
import com.compomics.util.experiment.personalization.ExperimentObject;

import java.util.HashMap;
import java.util.ArrayList;

/**
 * A sample measurement set is a set of replicates from a common sample.
 * 
 * @author Marc Vaudel
 */
public class SampleAnalysisSet extends ExperimentObject {

    /**
     * The version UID for Serialization/Deserialization compatibility.
     */
    static final long serialVersionUID = -5399187779025810060L;
    /**
     * The reference sample.
     */
    private Sample sample;
    /**
     * The various analysis indexed by replicates indexes.
     */
    private HashMap<Integer, ProteomicAnalysis> analysis = new HashMap<Integer, ProteomicAnalysis>();

    /**
     * Contructor for an analysis of a sample without replicates.
     *
     * @param referenceSample the reference sample
     * @param replicate the analysis for this sample
     */
    public SampleAnalysisSet(Sample referenceSample, ProteomicAnalysis replicate) {
        this.sample = referenceSample;
        analysis.put(replicate.getIndex(), replicate);
    }

    /**
     * Contructor for a set of analysis of a sample.
     *
     * @param referenceSample the reference sample
     * @param replicates the set of replicates for this sample
     */
    public SampleAnalysisSet(Sample referenceSample, ArrayList<ProteomicAnalysis> replicates) {
        this.sample = referenceSample;
        for (ProteomicAnalysis replicate : replicates) {
            analysis.put(replicate.getIndex(), replicate);
        }
    }

    /**
     * Returns the analysis corresponding to the selected replicate.
     *
     * @param replicateNumber index of the replicate analyzed
     * @return the proteomic analysis of the replicate
     */
    public ProteomicAnalysis getProteomicAnalysis(int replicateNumber) {
        return analysis.get(replicateNumber);
    }

    /**
     * Returns a list containing replicate numbers.
     *
     * @return a list containing replicate numbers
     */
    public ArrayList<Integer> getReplicateNumberList() {
        return new ArrayList<Integer>(analysis.keySet());
    }
}