package net.sourceforge.seqware.common.dao;
import java.util.List;
import net.sourceforge.seqware.common.model.Experiment;
import net.sourceforge.seqware.common.model.File;
import net.sourceforge.seqware.common.model.Registration;
import net.sourceforge.seqware.common.model.Study;
/**
* <p>
* ExperimentDAO interface.
* </p>
*
* @author boconnor
* @version $Id: $Id
*/
public interface ExperimentDAO {
/**
* <p>
* insert.
* </p>
*
* @param sequencerRun
* a {@link net.sourceforge.seqware.common.model.Experiment} object.
* @return a {@link java.lang.Integer} object.
*/
public Integer insert(Experiment sequencerRun);
/**
* <p>
* insert.
* </p>
*
* @param registration
* a {@link net.sourceforge.seqware.common.model.Registration} object.
* @param sequencerRun
* a {@link net.sourceforge.seqware.common.model.Experiment} object.
* @return a {@link java.lang.Integer} object.
*/
public Integer insert(Registration registration, Experiment sequencerRun);
/**
* <p>
* update.
* </p>
*
* @param sequencerRun
* a {@link net.sourceforge.seqware.common.model.Experiment} object.
*/
public void update(Experiment sequencerRun);
/**
* <p>
* update.
* </p>
*
* @param registration
* a {@link net.sourceforge.seqware.common.model.Registration} object.
* @param experiment
* a {@link net.sourceforge.seqware.common.model.Experiment} object.
*/
public void update(Registration registration, Experiment experiment);
/**
* <p>
* delete.
* </p>
*
* @param sequencerRun
* a {@link net.sourceforge.seqware.common.model.Experiment} object.
*/
public void delete(Experiment sequencerRun);
/**
* <p>
* list.
* </p>
*
* @return a {@link java.util.List} object.
*/
public List<Experiment> list();
/**
* <p>
* list.
* </p>
*
* @param registration
* a {@link net.sourceforge.seqware.common.model.Registration} object.
* @return a {@link java.util.List} object.
*/
public List<Experiment> list(Registration registration);
/**
* <p>
* list.
* </p>
*
* @param study
* a {@link net.sourceforge.seqware.common.model.Study} object.
* @return a {@link java.util.List} object.
*/
public List<Experiment> list(Study study);
/**
* <p>
* findByTitle.
* </p>
*
* @param title
* a {@link java.lang.String} object.
* @return a {@link net.sourceforge.seqware.common.model.Experiment} object.
*/
public Experiment findByTitle(String title);
/**
* <p>
* findByID.
* </p>
*
* @param studyID
* a {@link java.lang.Integer} object.
* @return a {@link net.sourceforge.seqware.common.model.Experiment} object.
*/
public Experiment findByID(Integer studyID);
/**
* <p>
* findBySWAccession.
* </p>
*
* @param swAccession
* a {@link java.lang.Integer} object.
* @return a {@link net.sourceforge.seqware.common.model.Experiment} object.
*/
public Experiment findBySWAccession(Integer swAccession);
/**
* <p>
* getFiles.
* </p>
*
* @param experimentId
* a {@link java.lang.Integer} object.
* @return a {@link java.util.List} object.
*/
public List<File> getFiles(Integer experimentId);
/**
* <p>
* isHasFile.
* </p>
*
* @param experimentId
* a {@link java.lang.Integer} object.
* @return a boolean.
*/
public boolean isHasFile(Integer experimentId);
/**
* <p>
* getFiles.
* </p>
*
* @param expId
* 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 expId, String metaType);
/**
* <p>
* isHasFile.
* </p>
*
* @param expId
* a {@link java.lang.Integer} object.
* @param metaType
* a {@link java.lang.String} object.
* @return a boolean.
*/
public boolean isHasFile(Integer expId, String metaType);
/**
* <p>
* updateDetached.
* </p>
*
* @param experiment
* a {@link net.sourceforge.seqware.common.model.Experiment} object.
* @return a {@link net.sourceforge.seqware.common.model.Experiment} object.
*/
public Experiment updateDetached(Experiment experiment);
/**
* <p>
* updateDetached.
* </p>
*
* @param registration
* a {@link net.sourceforge.seqware.common.model.Registration} object.
* @param experiment
* a {@link net.sourceforge.seqware.common.model.Experiment} object.
* @return a {@link net.sourceforge.seqware.common.model.Experiment} object.
*/
public Experiment updateDetached(Registration registration, Experiment experiment);
/**
* <p>
* findByOwnerID.
* </p>
*
* @param registrationID
* a {@link java.lang.Integer} object.
* @return a {@link java.util.List} object.
*/
public List<Experiment> 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<Experiment> findByCriteria(String criteria, boolean isCaseSens);
/**
* <p>
* merge.
* </p>
*
* @param experiment
* a {@link net.sourceforge.seqware.common.model.Experiment} object.
*/
void merge(Experiment experiment);
}