*/\r
package eu.etaxonomy.cdm.model.molecular;\r
\r
-import java.util.HashSet;\r
-import java.util.Set;\r
-\r
-import javax.persistence.Column;\r
import javax.persistence.Entity;\r
import javax.persistence.FetchType;\r
import javax.persistence.JoinColumn;\r
import javax.persistence.ManyToOne;\r
-import javax.persistence.OneToMany;\r
import javax.validation.constraints.Size;\r
import javax.xml.bind.annotation.XmlAccessType;\r
import javax.xml.bind.annotation.XmlAccessorType;\r
-import javax.xml.bind.annotation.XmlAttribute;\r
import javax.xml.bind.annotation.XmlElement;\r
-import javax.xml.bind.annotation.XmlElementWrapper;\r
import javax.xml.bind.annotation.XmlIDREF;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlSchemaType;\r
import eu.etaxonomy.cdm.model.common.DefinedTerm;\r
import eu.etaxonomy.cdm.model.common.EventBase;\r
import eu.etaxonomy.cdm.model.common.TermType;\r
-import eu.etaxonomy.cdm.model.media.Media;\r
import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;\r
\r
/**\r
*/\r
@XmlAccessorType(XmlAccessType.FIELD)\r
@XmlType(name = "Amplification", propOrder = {\r
- "dnaSample",\r
"dnaMarker",\r
"forwardPrimer",\r
"reversePrimer",\r
"purification",\r
"institution",\r
- "cloning",\r
- "successful",\r
- "successText",\r
"ladderUsed",\r
"electrophoresisVoltage",\r
"gelRunningTime",\r
"gelConcentration",\r
- "gelPhoto",\r
- "singleReads"\r
})\r
@XmlRootElement(name = "Amplification")\r
@Entity\r
@Audited\r
public class Amplification extends EventBase implements Cloneable{\r
- private static final long serialVersionUID = -8614860617229484621L;\r
- private static final Logger logger = Logger.getLogger(Amplification.class);\r
+ private static final long serialVersionUID = -6382383300974316261L;\r
\r
-\r
- /** @see #getDnaSample() */\r
- @XmlElement( name = "DnaSample")\r
- @XmlIDREF\r
- @XmlSchemaType(name = "IDREF")\r
- @ManyToOne(fetch = FetchType.LAZY)\r
- @IndexedEmbedded\r
- private DnaSample dnaSample;\r
-\r
- @XmlElementWrapper(name = "SingleReads")\r
- @XmlElement(name = "SingleRead")\r
- @XmlIDREF\r
- @XmlSchemaType(name = "IDREF")\r
- @OneToMany(fetch = FetchType.LAZY)\r
- @Cascade({CascadeType.SAVE_UPDATE})\r
- private Set<SingleRead> singleReads = new HashSet<SingleRead>();\r
+ private static final Logger logger = Logger.getLogger(Amplification.class);\r
\r
/** @see #getDnaMarker()*/\r
@XmlElement(name = "DnaMarker")\r
@ManyToOne(fetch=FetchType.LAZY)\r
@Cascade({CascadeType.SAVE_UPDATE})\r
private MaterialOrMethodEvent purification;\r
-\r
- @XmlElement(name = "Cloning")\r
- @XmlIDREF\r
- @XmlSchemaType(name = "IDREF")\r
- @ManyToOne(fetch=FetchType.LAZY)\r
- @Cascade({CascadeType.SAVE_UPDATE})\r
- private Cloning cloning;\r
- \r
+ \r
@XmlElement(name = "Institution")\r
@XmlIDREF\r
@XmlSchemaType(name = "IDREF")\r
@JoinColumn(name="institution_id")\r
private Institution institution;\r
\r
- /** @see #getSuccessful() */\r
- @XmlAttribute(name = "successful")\r
- private Boolean successful;\r
-\r
- /** @see #getSuccessText() */\r
- @XmlElement(name = "successText")\r
- @Field\r
- @Size(max=255)\r
- private String successText;\r
-\r
/** @see #getLadderUsed() */\r
@XmlElement(name = "ladderUsed")\r
@Field\r
@NumericField\r
private Double gelConcentration;\r
\r
- @XmlElement(name = "GelPhoto")\r
- @XmlIDREF\r
- @XmlSchemaType(name = "IDREF")\r
- @ManyToOne(fetch=FetchType.LAZY)\r
- @Cascade({CascadeType.SAVE_UPDATE})\r
- private Media gelPhoto;\r
-\r
\r
// ********************* FACTORY METHODS ************************/\r
\r
- public static Amplification NewInstance(DnaSample dnaSample){\r
- Amplification result = new Amplification();\r
- dnaSample.addAmplification(result);\r
- return result;\r
- }\r
-\r
- public static Amplification NewInstance(SingleRead singleRead){\r
- Amplification result = new Amplification();\r
- result.addSingleRead(singleRead);\r
- return result;\r
- }\r
-\r
public static Amplification NewInstance(){\r
return new Amplification();\r
}\r
//********************* GETTER / SETTER ************/\r
\r
\r
- /**\r
- * The {@link DnaSample dna sample} which is the input for this {@link Amplification amplification}.\r
- */\r
- public DnaSample getDnaSample() {\r
- return dnaSample;\r
- }\r
-\r
- /**\r
- * For use by DnaSample.addAmplification(ampl.) only. For now.\r
- * @see #getDnaSample()\r
- */\r
- protected void setDnaSample(DnaSample dnaSample) {\r
- this.dnaSample = dnaSample;\r
- }\r
-\r
- /**\r
- * The {@link SingleRead single sequences} created by using this amplification's result (PCR).\r
- */\r
- public Set<SingleRead> getSingleReads() {\r
- return singleReads;\r
- }\r
-\r
- public void addSingleRead(SingleRead singleRead){\r
- if (singleRead.getAmplification() != null){\r
- singleRead.getAmplification().singleReads.remove(singleRead);\r
- }\r
- this.singleReads.add(singleRead);\r
- singleRead.setAmplification(this);\r
- }\r
-\r
- public void removeSingleRead(SingleRead singleRead){\r
- if(this.singleReads.contains(singleRead)){\r
- this.singleReads.remove(singleRead);\r
- singleRead.setAmplification(null);\r
- }\r
- }\r
-\r
- /**\r
- * @see #getSingleReads()\r
- */\r
- //TODO private until it is clear how bidirectionality is handled\r
- private void setSingleReads(Set<SingleRead> singleReads) {\r
- this.singleReads = singleReads;\r
- }\r
-\r
-\r
/**\r
* The {@link TermType#DnaMarker DNA marker} used for this amplification.\r
* The DNA marker also defines the part (locality) of the DNA/RNA examined.\r
public DefinedTerm getDnaMarker() {\r
return dnaMarker;\r
}\r
-\r
- /**\r
- * @see #getDnaMarker()\r
- */\r
+ /** @see #getDnaMarker()*/\r
public void setDnaMarker(DefinedTerm marker) {\r
this.dnaMarker = marker;\r
}\r
public Primer getForwardPrimer() {\r
return forwardPrimer;\r
}\r
-\r
/**\r
* @see #getForwardPrimer()\r
* @see #getReversePrimer()\r
public Primer getReversePrimer() {\r
return reversePrimer;\r
}\r
-\r
/**\r
* @see #getReversePrimer()\r
* @see #getForwardPrimer()\r
this.reversePrimer = reversePrimer;\r
}\r
\r
- /**\r
- * Information if this amplification was successful or not. Success may be defined\r
- * by the results of the electrophoresis.\r
- *\r
- * @see #getSuccessText()\r
- */\r
- public Boolean getSuccessful() {\r
- return successful;\r
- }\r
-\r
- /**\r
- * @see #getSuccessful()\r
- * @see #getSuccessText()\r
- */\r
- public void setSuccessful(Boolean successful) {\r
- this.successful = successful;\r
- }\r
-\r
- /**\r
- * Freetext about the success of this amplification explaining\r
- * in detail why it is concidered to be successful/unsucessful\r
- *\r
- * @see #getSuccessful()\r
- */\r
- public String getSuccessText() {\r
- return successText;\r
- }\r
-\r
- /**\r
- * @see #getSuccessText()\r
- * @see #getSuccessful()\r
- */\r
- public void setSuccessText(String successText) {\r
- this.successText = successText;\r
- }\r
-\r
\r
/**\r
* The material and/or method used for purification.\r
public MaterialOrMethodEvent getPurification() {\r
return purification;\r
}\r
-\r
/**\r
* @see #getPurification()\r
*/\r
}\r
\r
/**\r
- * #4498\r
- * @return\r
+ * The institution in which the amplification event took place.\r
+ * Usually the {@link Amplification#getActor()} should be a person\r
+ * or team that works for this institution at the given time\r
+ * @return the institution\r
*/\r
+// #4498\r
public Institution getInstitution() {\r
return institution;\r
}\r
-\r
- public void setInstitution(Institution institution) {\r
- this.institution = institution;\r
- }\r
-\r
-\r
- /**\r
- * The {@link Cloning cloning process} involved in this amplification.\r
- */\r
- public Cloning getCloning() {\r
- return cloning;\r
- }\r
-\r
/**\r
- * @see #getCloning()\r
+ * @see #getInstitution()\r
*/\r
- public void setCloning(Cloning cloning) {\r
- this.cloning = cloning;\r
+ public void setInstitution(Institution institution) {\r
+ this.institution = institution;\r
}\r
\r
/**\r
public Double getElectrophoresisVoltage() {\r
return electrophoresisVoltage;\r
}\r
-\r
/**\r
* @see #getElectrophoresisVoltage()\r
*/\r
public Double getGelRunningTime() {\r
return gelRunningTime;\r
}\r
-\r
/**\r
* @see #getGelRunningTime()\r
*/\r
public Double getGelConcentration() {\r
return gelConcentration;\r
}\r
-\r
/**\r
* @see #getGelConcentration()\r
*/\r
public String getLadderUsed() {\r
return ladderUsed;\r
}\r
-\r
/**\r
* @see #getLadderUsed()\r
*/\r
this.ladderUsed = ladderUsed;\r
}\r
\r
- /**\r
- * The photo taken from the electrophoresis result showing the quality of the amplification.\r
- * Gelphotos often do show multiple electrophoresis results. One may either cut or mark\r
- * the part of the photo that displays <code>this</code> amplification. However, this may make\r
- * the concrete media file unusable for other amplifications also represented by the same image.\r
- * @see #getElectrophoresisVoltage()\r
- * @see #getLadderUsed()\r
- * @see #getGelConcentration()\r
- * @see #getGelRunningTime()\r
- */\r
- public Media getGelPhoto() {\r
- return gelPhoto;\r
- }\r
-\r
-\r
- /**\r
- * @param gelPhoto the gelPhoto to set\r
- */\r
- public void setGelPhoto(Media gelPhoto) {\r
- this.gelPhoto = gelPhoto;\r
- }\r
-\r
\r
// ********************** CLONE ***********************************/\r
/**\r
try{\r
Amplification result = (Amplification)super.clone();\r
\r
- result.singleReads = new HashSet<SingleRead>();\r
- for (SingleRead seq: this.singleReads){\r
- result.singleReads.add(seq);\r
-\r
- }\r
-\r
- //don't change dnaSample, marker, successful, successText, forwardPrimer,\r
- //reversePrimer, purifiaction, cloning, ladderUsed, electrophoresisVoltage,\r
- //gelRunningTime, gelPhoto, gelConcentration\r
+ //don't change marker, forwardPrimer, reversePrimer, \r
+ //purifiaction, ladderUsed, electrophoresisVoltage,\r
+ //gelRunningTime, gelConcentration\r
return result;\r
}catch (CloneNotSupportedException e) {\r
logger.warn("Object does not implement cloneable");\r
BGBM BDI Projects / cdmlib.git / blobdiff