/*
* Copyright (c) 2012. The Genome Analysis Centre, Norwich, UK
* MISO project contacts: Robert Davey, Mario Caccamo @ TGAC
* *********************************************************************
*
* This file is part of MISO.
*
* MISO is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MISO is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with MISO. If not, see <http://www.gnu.org/licenses/>.
*
* *********************************************************************
*/
package uk.ac.bbsrc.tgac.miso.core.data;
//import com.fasterxml.jackson.annotation.*;
//import com.fasterxml.jackson.databind.annotation.JsonSerialize;
import org.codehaus.jackson.annotate.*;
import org.codehaus.jackson.map.annotate.JsonSerialize;
import org.w3c.dom.Document;
import uk.ac.bbsrc.tgac.miso.core.data.type.KitType;
import uk.ac.bbsrc.tgac.miso.core.security.SecurableByProfile;
import java.util.Collection;
/**
* An Experiment contains design information about a sequencing experiment,
* as part of a parent {@link Study}.
*
* Experiments are associated with {@link Run} objects via {@link Pool} objects
* which contain the actual sequencable material in prepared form. A Pool is
* attached to an Experiment which is then assigned to an instrument
* {@link SequencerPoolPartition}.
*
* @author Rob Davey
* @since 0.0.2
*/
@JsonSerialize(typing = JsonSerialize.Typing.STATIC, include = JsonSerialize.Inclusion.NON_NULL)
//@JsonIdentityInfo(generator = ObjectIdGenerators.IntSequenceGenerator.class, property = "@id")
@JsonTypeInfo(use=JsonTypeInfo.Id.CLASS, include= JsonTypeInfo.As.PROPERTY, property="@class")
@JsonIgnoreProperties({"securityProfile"})
public interface Experiment extends SecurableByProfile, Submittable<Document>, Comparable, Deletable, Nameable {
/** Field UNSAVED_ID */
public static final Long UNSAVED_ID = 0L;
/** Field PREFIX */
public static final String PREFIX = "EXP";
/**
* Returns the experimentId of this Experiment object.
*
* @return Long experimentId.
*/
@Deprecated
public Long getExperimentId();
/**
* Sets the experimentId of this Experiment object.
*
* @param experimentId the id of this Experiment object.
*
*/
@Deprecated
public void setExperimentId(Long experimentId);
public void setId(long id);
/**
* Returns the study of this Experiment object.
*
* @return Study study.
*/
@JsonBackReference(value = "study")
public Study getStudy();
/**
* Sets the study of this Experiment object.
*
* @param s study.
*
*/
public void setStudy(Study s);
/**
* Returns the accession of this Experiment object.
*
* @return String accession.
*/
public String getAccession();
/**
* Sets the accession of this Experiment object.
*
* @param accession accession.
*
*/
public void setAccession(String accession);
/**
* Returns the alias of this Experiment object.
*
* @return String alias.
*/
public String getAlias();
/**
* Sets the alias of this Experiment object.
*
* @param alias alias.
*
*/
public void setAlias(String alias);
/**
* Returns the title of this Experiment object.
*
* @return String title.
*/
public String getTitle();
/**
* Sets the title of this Experiment object.
*
* @param title title.
*
*/
public void setTitle(String title);
/**
* Returns the name of this Experiment object.
*
* @return String name.
*/
public String getName();
/**
* Sets the name of this Experiment object.
*
* @param name name.
*
*/
public void setName(String name);
/**
* Returns the description of this Experiment object.
*
* @return String description.
*/
public String getDescription();
/**
* Sets the description of this Experiment object.
*
* @param description description.
*
*/
public void setDescription(String description);
/**
* Returns the platform of this Experiment object.
*
* @return Platform platform.
*/
public Platform getPlatform();
/**
* Sets the platform of this Experiment object.
*
* @param platform platform.
*
*/
public void setPlatform(Platform platform);
/**
* Returns the run of this Experiment object.
*
* @return Run run.
*/
public Run getRun();
/**
* Sets the run of this Experiment object.
*
* @param run run.
*
*/
public void setRun(Run run);
/**
* Sets the pool of this Experiment object.
*
* @param pool pool.
*
*/
public void setPool(Pool pool);
/**
* Returns the pool of this Experiment object.
*
* @return Pool pool.
*/
@JsonBackReference(value="pool")
public Pool<? extends Poolable> getPool();
/**
* Sets the kits of this Experiment object.
*
* @param kits kits.
*/
public void setKits(Collection<Kit> kits);
/**
* Add a Kit to this Experiment object
*
* @param kit of type Kit
*/
public void addKit(Kit kit);
/**
* Returns the kits used to construct this Experiment object.
*
* @return Collection<Kit> kits.
*/
public Collection<Kit> getKits();
/**
* Return kits used within this experiment of a given KitType
*
* @param kitType of type KitType
* @return Collection<Kit>
*/
@JsonIgnore
public Collection<Kit> getKitsByKitType(KitType kitType);
}