FindRootUtil.java

package net.sourceforge.solexatools.util;

import java.util.Set;

import net.sourceforge.seqware.common.model.Experiment;
import net.sourceforge.seqware.common.model.Lane;
import net.sourceforge.seqware.common.model.Processing;
import net.sourceforge.seqware.common.model.Sample;
import net.sourceforge.seqware.common.model.SequencerRun;
import net.sourceforge.seqware.common.model.Study;
import net.sourceforge.seqware.common.util.Log;

/**
 * <p>
 * FindRootUtil class.
 * </p>
 * 
 * @author boconnor
 * @version $Id: $Id
 */
public class FindRootUtil {

    /**
     * <p>
     * getStudy.
     * </p>
     * 
     * @param experiment
     *            a {@link net.sourceforge.seqware.common.model.Experiment} object.
     * @return a {@link net.sourceforge.seqware.common.model.Study} object.
     */
    public static Study getStudy(Experiment experiment) {
        Study study = experiment.getStudy();
        return study;
    }

    /**
     * <p>
     * getStudy.
     * </p>
     * 
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @return a {@link net.sourceforge.seqware.common.model.Study} object.
     */
    public static Study getStudy(Sample sample) {
        Study study = getStudy(sample.getExperiment());
        return study;
    }

    /**
     * <p>
     * getStudy.
     * </p>
     * 
     * @param lane
     *            a {@link net.sourceforge.seqware.common.model.Lane} object.
     * @return a {@link net.sourceforge.seqware.common.model.Study} object.
     */
    public static Study getStudy(Lane lane) {
        Study study = getStudy(lane.getSample());
        return study;
    }

    /**
     * <p>
     * getStudy.
     * </p>
     * 
     * @param processing
     *            a {@link net.sourceforge.seqware.common.model.Processing} object.
     * @return a {@link net.sourceforge.seqware.common.model.Study} object.
     */
    public static Study getStudy(Processing processing) {
        // Study study = getStudy(lane.getSample());
        Set<Lane> lanes = processing.getLanes();
        if (lanes != null && lanes.size() > 0) {
            Log.info("Lane!=null");
            for (Lane lane : lanes) {
                Log.info("Lane_ID = " + lane.getLaneId());
                return getStudy(lane);
            }
        } else {
            Log.info("Lane==null");
            Set<Processing> parents = processing.getParents();
            for (Processing parent : parents) {
                return getStudy(parent);
            }
        }
        Log.info("RETURN NULL");
        return null;
    }

    // FOR SEQUENCER RUN
    /**
     * <p>
     * getSequencerRun.
     * </p>
     * 
     * @param lane
     *            a {@link net.sourceforge.seqware.common.model.Lane} object.
     * @return a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     */
    public static SequencerRun getSequencerRun(Lane lane) {
        SequencerRun sequencerRun = lane.getSequencerRun();
        return sequencerRun;
    }

    /**
     * <p>
     * getSequencerRun.
     * </p>
     * 
     * @param processing
     *            a {@link net.sourceforge.seqware.common.model.Processing} object.
     * @return a {@link net.sourceforge.seqware.common.model.SequencerRun} object.
     */
    public static SequencerRun getSequencerRun(Processing processing) {
        // Study study = getStudy(lane.getSample());
        Set<Lane> lanes = processing.getLanes();
        if (lanes != null && lanes.size() > 0) {
            for (Lane lane : lanes) {
                return getSequencerRun(lane);
            }
        } else {
            Set<Processing> parents = processing.getParents();
            for (Processing parent : parents) {
                return getSequencerRun(parent);
            }
        }
        return null;
    }

    // FOR ANALYSIS WORKFLOW
}