SampleDAO.java

package net.sourceforge.seqware.common.dao;

import java.util.List;
import java.util.Map;
import net.sourceforge.seqware.common.model.File;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.Sample;
import net.sourceforge.seqware.common.model.Study;

/**
 * <p>
 * SampleDAO interface.
 * </p>
 * 
 * @author boconnor
 * @version $Id: $Id
 */
public interface SampleDAO {

    /**
     * <p>
     * insert.
     * </p>
     * 
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @return a {@link java.lang.Integer} object.
     */
    public Integer insert(Sample sample);

    /**
     * <p>
     * insert.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @return a {@link java.lang.Integer} object.
     */
    public Integer insert(Registration registration, Sample sample);

    /**
     * <p>
     * update.
     * </p>
     * 
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public void update(Sample sample);

    /**
     * <p>
     * update.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public void update(Registration registration, Sample sample);

    /**
     * <p>
     * delete.
     * </p>
     * 
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public void delete(Sample sample);

    /**
     * <p>
     * listComplete.
     * </p>
     * 
     * @return a {@link java.util.List} object.
     */
    public List<Sample> listComplete();

    /**
     * <p>
     * listIncomplete.
     * </p>
     * 
     * @return a {@link java.util.List} object.
     */
    public List<Sample> listIncomplete();

    /**
     * <p>
     * findByName.
     * </p>
     * 
     * @param name
     *            a {@link java.lang.String} object.
     * @return a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public Sample findByName(String name);

    /**
     * <p>
     * findByName.
     * </p>
     * 
     * @param name
     *            a {@link java.lang.String} object.
     * @return a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public List<Sample> matchName(String name);

    /**
     * <p>
     * findByTitle.
     * </p>
     * 
     * @param title
     *            a {@link java.lang.String} object.
     * @return a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public Sample findByTitle(String title);

    /**
     * <p>
     * findByID.
     * </p>
     * 
     * @param sampleId
     *            a {@link java.lang.Integer} object.
     * @return a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public Sample findByID(Integer sampleId);

    /**
     * <p>
     * listSample.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @return a {@link java.util.List} object.
     */
    public List<Sample> listSample(Registration registration);

    /**
     * <p>
     * getFiles.
     * </p>
     * 
     * @param sampleId
     *            a {@link java.lang.Integer} object.
     * @return a {@link java.util.List} object.
     */
    public List<File> getFiles(Integer sampleId);

    /**
     * <p>
     * isHasFile.
     * </p>
     * 
     * @param sampleId
     *            a {@link java.lang.Integer} object.
     * @return a boolean.
     */
    public boolean isHasFile(Integer sampleId);

    /**
     * <p>
     * getFiles.
     * </p>
     * 
     * @param sampleId
     *            a {@link java.lang.Integer} object.
     * @param metaType
     *            a {@link java.lang.String} object.
     * @return a {@link java.util.List} object.
     */
    public List<File> getFiles(Integer sampleId, String metaType);

    /**
     * <p>
     * isHasFile.
     * </p>
     * 
     * @param sampleId
     *            a {@link java.lang.Integer} object.
     * @param metaType
     *            a {@link java.lang.String} object.
     * @return a boolean.
     */
    public boolean isHasFile(Integer sampleId, String metaType);

    /**
     * <p>
     * getCountFiles.
     * </p>
     * 
     * @param expId
     *            a {@link java.lang.Integer} object.
     * @return a {@link java.util.Map} object.
     */
    public Map<Integer, Integer> getCountFiles(Integer expId);

    /**
     * <p>
     * getCountFiles.
     * </p>
     * 
     * @param expId
     *            a {@link java.lang.Integer} object.
     * @param metaType
     *            a {@link java.lang.String} object.
     * @return a {@link java.util.Map} object.
     */
    public Map<Integer, Integer> getCountFiles(Integer expId, String metaType);

    /**
     * <p>
     * findBySWAccession.
     * </p>
     * 
     * @param swAccession
     *            a {@link java.lang.Integer} object.
     * @return a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public Sample findBySWAccession(Integer swAccession);

    /**
     * <p>
     * updateDetached.
     * </p>
     * 
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @return a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public Sample updateDetached(Sample sample);

    /**
     * <p>
     * updateDetached.
     * </p>
     * 
     * @param registration
     *            a {@link net.sourceforge.seqware.common.model.Registration} object.
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @return a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public Sample updateDetached(Registration registration, Sample sample);

    /**
     * <p>
     * findByOwnerID.
     * </p>
     * 
     * @param registrationId
     *            a {@link java.lang.Integer} object.
     * @return a {@link java.util.List} object.
     */
    public List<Sample> findByOwnerID(Integer registrationId);

    /**
     * <p>
     * findByCriteria.
     * </p>
     * 
     * @param criteria
     *            a {@link java.lang.String} object.
     * @param isCaseSens
     *            a boolean.
     * @return a {@link java.util.List} object.
     */
    public List<Sample> findByCriteria(String criteria, boolean isCaseSens);

    /**
     * <p>
     * getRootSamples.
     * </p>
     * 
     * @param study
     *            a {@link net.sourceforge.seqware.common.model.Study} object.
     * @return a {@link java.util.List} object.
     */
    public List<Sample> getRootSamples(Study study);

    /**
     * <p>
     * getRootSample.
     * </p>
     * 
     * @param sample
     *            a {@link net.sourceforge.seqware.common.model.Sample} object.
     * @return a {@link net.sourceforge.seqware.common.model.Sample} object.
     */
    public Sample getRootSample(Sample sample);

    /**
     * <p>
     * list.
     * </p>
     * 
     * @return a {@link java.util.List} object.
     */
    public List<Sample> list();
}