package net.sourceforge.seqware.common.business;
import java.util.List;
import java.util.SortedSet;
import net.sourceforge.seqware.common.dao.SampleDAO;
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>
* SampleService interface.
* </p>
*
* @author boconnor
* @version $Id: $Id
*/
public interface SampleService {
/** Constant <code>NAME="sampleService"</code> */
public static final String NAME = "sampleService";
/**
* <p>
* setSampleDAO.
* </p>
*
* @param sampleDAO
* a {@link net.sourceforge.seqware.common.dao.SampleDAO} object.
*/
public void setSampleDAO(SampleDAO 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
* @param deleteRealFiles
*/
public void delete(Sample sample, boolean deleteRealFiles);
/**
* <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);
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 id
* a {@link java.lang.Integer} object.
* @return a {@link net.sourceforge.seqware.common.model.Sample} object.
*/
public Sample findByID(Integer id);
/**
* <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>
* 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>
* hasNameBeenUsed.
* </p>
*
* @param oldName
* a {@link java.lang.String} object.
* @param newName
* a {@link java.lang.String} object.
* @return a boolean.
*/
public boolean hasNameBeenUsed(String oldName, String newName);
/**
* <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 studyId
* 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 studyId, String metaType);
/**
* <p>
* isHasFile.
* </p>
*
* @param studyId
* a {@link java.lang.Integer} object.
* @param metaType
* a {@link java.lang.String} object.
* @return a boolean.
*/
public boolean isHasFile(Integer studyId, String metaType);
/**
* <p>
* setWithHasFile.
* </p>
*
* @param expId
* a {@link java.lang.Integer} object.
* @param list
* a {@link java.util.SortedSet} object.
* @return a {@link java.util.SortedSet} object.
*/
public SortedSet<Sample> setWithHasFile(Integer expId, SortedSet<Sample> list);
/**
* <p>
* listWithHasFile.
* </p>
*
* @param expId
* a {@link java.lang.Integer} object.
* @param list
* a {@link java.util.SortedSet} object.
* @param metaType
* a {@link java.lang.String} object.
* @return a {@link java.util.SortedSet} object.
*/
public SortedSet<Sample> listWithHasFile(Integer expId, SortedSet<Sample> list, String metaType);
/**
* <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 childSample
* a {@link net.sourceforge.seqware.common.model.Sample} object.
* @return a {@link net.sourceforge.seqware.common.model.Sample} object.
*/
public Sample getRootSample(Sample childSample);
/**
* <p>
* list.
* </p>
*
* @return a {@link java.util.List} object.
*/
public List<Sample> list();
}
// ex:sw=4:ts=4: