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org.molgenis.omx.xgap.SNP Maven / Gradle / Ivy
/* File: org.molgenis.omx/model/SNP.java
* Generator: org.molgenis.generators.DataTypeGen 4.0.0-testing
*
* THIS FILE HAS BEEN GENERATED, PLEASE DO NOT EDIT!
*/
package org.molgenis.omx.xgap;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;
import org.molgenis.data.AttributeMetaData;
import org.molgenis.data.support.MapEntity;
import org.molgenis.data.Entity;
/**
* SNP: A SNP is a special kind of Marker, but can also be seen as a phenotype to map against in some cases. A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in an individual..
* @author MOLGENIS generator
*/
@javax.persistence.Entity
@javax.persistence.Table(name = "SNP"
)
@javax.xml.bind.annotation.XmlAccessorType(javax.xml.bind.annotation.XmlAccessType.FIELD)
@edu.umd.cs.findbugs.annotations.SuppressWarnings(value={"EI_EXPOSE_REP", "EI_EXPOSE_REP2"}, justification="Exposing internal representation is accepted")
public class SNP extends org.molgenis.omx.xgap.Marker implements org.molgenis.data.Entity
{
/** default serial version ID */
private static final long serialVersionUID = 1L;
public final static String ENTITY_NAME = "SNP";
// fieldname constants
public final static String STATUS = "Status";
public final static String POLYMORPHISM = "Polymorphism";
public final static String ID = "id";
// member variables (including setters.getters for interface)
public String getEntityName()
{
return ENTITY_NAME;
}
//The status of this SNP, eg 'confirmed'.[type=string]
@javax.persistence.Column(name="Status", length=255)
@javax.xml.bind.annotation.XmlElement(name="status")
private String status = null;
//The polymorphism that belongs to this SNP.[type=mref]
@javax.persistence.OrderColumn
@javax.persistence.ManyToMany(fetch=javax.persistence.FetchType.LAZY /*cascade={javax.persistence.CascadeType.MERGE, javax.persistence.CascadeType.PERSIST, javax.persistence.CascadeType.REFRESH}*/)
@javax.persistence.JoinColumn(name="Polymorphism", insertable=true, updatable=true, nullable=true)
@javax.persistence.JoinTable(name="SNP_Polymorphism",
[email protected] (name="SNP"), [email protected] (name="Polymorphism"))
private java.util.List polymorphism = new java.util.ArrayList();
//automatically generated internal id, only for internal use.[type=int]
//constructors
public SNP()
{
//set the type for a new instance
set__Type(this.getClass().getSimpleName());
}
//getters and setters
/**
* Get the The status of this SNP, eg 'confirmed'..
* @return status.
*/
public String getStatus()
{
return this.status;
}
/**
* Set the The status of this SNP, eg 'confirmed'..
* @param status
*/
public void setStatus( String status)
{
this.status = status;
}
/**
* Get the The polymorphism that belongs to this SNP..
* @return polymorphism.
*/
public java.util.List getPolymorphism()
{
return this.polymorphism;
}
/**
* Set the The polymorphism that belongs to this SNP..
* @param polymorphism
*/
public void setPolymorphism( java.util.List polymorphism)
{
this.polymorphism = polymorphism;
}
/**
* Generic getter. Get the property by using the name.
*/
@Override
public Object get(String name)
{
name = name.toLowerCase();
if (name.equals("id"))
return getId();
if (name.equals("identifier"))
return getIdentifier();
if (name.equals("name"))
return getName();
if (name.equals("__type"))
return get__Type();
if(name.equals("__type_label"))
return get__TypeLabel();
if (name.equals("description"))
return getDescription();
if (name.equals("chromosome"))
return getChromosome();
if (name.equals("cm"))
return getCM();
if (name.equals("bpstart"))
return getBpStart();
if (name.equals("bpend"))
return getBpEnd();
if (name.equals("seq"))
return getSeq();
if (name.equals("symbol"))
return getSymbol();
if (name.equals("reportsfor"))
return getReportsFor();
if (name.equals("status"))
return getStatus();
if (name.equals("polymorphism"))
return getPolymorphism();
return null;
}
@Override
public void set(org.molgenis.data.Entity entity, boolean strict)
{
//set Id
// query formal name, else lowercase name
if(entity.getInt("id") != null) this.setId(entity.getInt("id"));
else if(entity.getInt("id") != null) this.setId(entity.getInt("id"));
else if(strict) this.setId(entity.getInt("id")); // setting null is not an option due to function overloading
if( entity.getInt("snp_id") != null) this.setId(entity.getInt("snp_id"));
else if( entity.getInt("SNP_id") != null) this.setId(entity.getInt("SNP_id"));
//set Identifier
// query formal name, else lowercase name
if(entity.getString("identifier") != null) this.setIdentifier(entity.getString("identifier"));
else if(entity.getString("Identifier") != null) this.setIdentifier(entity.getString("Identifier"));
else if(strict) this.setIdentifier(entity.getString("identifier")); // setting null is not an option due to function overloading
if( entity.getString("snp_identifier") != null) this.setIdentifier(entity.getString("snp_identifier"));
else if( entity.getString("SNP_Identifier") != null) this.setIdentifier(entity.getString("SNP_Identifier"));
//set Name
// query formal name, else lowercase name
if(entity.getString("name") != null) this.setName(entity.getString("name"));
else if(entity.getString("Name") != null) this.setName(entity.getString("Name"));
else if(strict) this.setName(entity.getString("name")); // setting null is not an option due to function overloading
if( entity.getString("snp_name") != null) this.setName(entity.getString("snp_name"));
else if( entity.getString("SNP_Name") != null) this.setName(entity.getString("SNP_Name"));
//set __Type
// query formal name, else lowercase name
if(entity.getString("__type") != null) this.set__Type(entity.getString("__type"));
else if(entity.getString("__Type") != null) this.set__Type(entity.getString("__Type"));
else if(strict) this.set__Type(entity.getString("__type")); // setting null is not an option due to function overloading
if( entity.getString("snp___type") != null) this.set__Type(entity.getString("snp___type"));
else if( entity.getString("SNP___Type") != null) this.set__Type(entity.getString("SNP___Type"));
//set Description
// query formal name, else lowercase name
if(entity.getString("description") != null) this.setDescription(entity.getString("description"));
else if(entity.getString("description") != null) this.setDescription(entity.getString("description"));
else if(strict) this.setDescription(entity.getString("description")); // setting null is not an option due to function overloading
if( entity.getString("snp_description") != null) this.setDescription(entity.getString("snp_description"));
else if( entity.getString("SNP_description") != null) this.setDescription(entity.getString("SNP_description"));
//set Chromosome
// query formal name, else lowercase name
if( entity.getEntity("Chromosome", org.molgenis.omx.xgap.Chromosome.class) != null) {
this.setChromosome(entity.getEntity("Chromosome", org.molgenis.omx.xgap.Chromosome.class));
}
else if( entity.getEntity("chromosome", org.molgenis.omx.xgap.Chromosome.class) != null) {
this.setChromosome(entity.getEntity("chromosome", org.molgenis.omx.xgap.Chromosome.class));
}
else if( entity.getEntity("SNP_Chromosome", org.molgenis.omx.xgap.Chromosome.class) != null) {
this.setChromosome(entity.getEntity("SNP_Chromosome", org.molgenis.omx.xgap.Chromosome.class));
}
else if( entity.getEntity("snp_chromosome", org.molgenis.omx.xgap.Chromosome.class) != null) {
this.setChromosome(entity.getEntity("SNP_Chromosome", org.molgenis.omx.xgap.Chromosome.class));
}
//set CM
// query formal name, else lowercase name
if(entity.getDouble("cm") != null) this.setCM(entity.getDouble("cm"));
else if(entity.getDouble("cM") != null) this.setCM(entity.getDouble("cM"));
else if(strict) this.setCM(entity.getDouble("cm")); // setting null is not an option due to function overloading
if( entity.getDouble("snp_cm") != null) this.setCM(entity.getDouble("snp_cm"));
else if( entity.getDouble("SNP_cM") != null) this.setCM(entity.getDouble("SNP_cM"));
//set BpStart
// query formal name, else lowercase name
if(entity.getLong("bpstart") != null) this.setBpStart(entity.getLong("bpstart"));
else if(entity.getLong("bpStart") != null) this.setBpStart(entity.getLong("bpStart"));
else if(strict) this.setBpStart(entity.getLong("bpstart")); // setting null is not an option due to function overloading
if( entity.getLong("snp_bpstart") != null) this.setBpStart(entity.getLong("snp_bpstart"));
else if( entity.getLong("SNP_bpStart") != null) this.setBpStart(entity.getLong("SNP_bpStart"));
//set BpEnd
// query formal name, else lowercase name
if(entity.getLong("bpend") != null) this.setBpEnd(entity.getLong("bpend"));
else if(entity.getLong("bpEnd") != null) this.setBpEnd(entity.getLong("bpEnd"));
else if(strict) this.setBpEnd(entity.getLong("bpend")); // setting null is not an option due to function overloading
if( entity.getLong("snp_bpend") != null) this.setBpEnd(entity.getLong("snp_bpend"));
else if( entity.getLong("SNP_bpEnd") != null) this.setBpEnd(entity.getLong("SNP_bpEnd"));
//set Seq
// query formal name, else lowercase name
if(entity.getString("seq") != null) this.setSeq(entity.getString("seq"));
else if(entity.getString("Seq") != null) this.setSeq(entity.getString("Seq"));
else if(strict) this.setSeq(entity.getString("seq")); // setting null is not an option due to function overloading
if( entity.getString("snp_seq") != null) this.setSeq(entity.getString("snp_seq"));
else if( entity.getString("SNP_Seq") != null) this.setSeq(entity.getString("SNP_Seq"));
//set Symbol
// query formal name, else lowercase name
if(entity.getString("symbol") != null) this.setSymbol(entity.getString("symbol"));
else if(entity.getString("Symbol") != null) this.setSymbol(entity.getString("Symbol"));
else if(strict) this.setSymbol(entity.getString("symbol")); // setting null is not an option due to function overloading
if( entity.getString("snp_symbol") != null) this.setSymbol(entity.getString("snp_symbol"));
else if( entity.getString("SNP_Symbol") != null) this.setSymbol(entity.getString("SNP_Symbol"));
//set ReportsFor
if( entity.getEntities("ReportsFor", org.molgenis.omx.xgap.Marker.class) != null || entity.getEntities("reportsfor", org.molgenis.omx.xgap.Marker.class) != null )
{
java.lang.Iterable mrefs = entity.getEntities("ReportsFor", org.molgenis.omx.xgap.Marker.class);
if(mrefs == null) mrefs = entity.getEntities("reportsfor", org.molgenis.omx.xgap.Marker.class);
if(entity.getEntities("snp_reportsfor", org.molgenis.omx.xgap.Marker.class)!= null) mrefs = entity.getEntities("snp_reportsfor", org.molgenis.omx.xgap.Marker.class);
else if(entity.getEntities("SNP_ReportsFor", org.molgenis.omx.xgap.Marker.class)!= null) mrefs = entity.getEntities("SNP_ReportsFor", org.molgenis.omx.xgap.Marker.class);
this.setReportsFor(mrefs != null ? com.google.common.collect.Lists.newArrayList(mrefs) : null);
}
//set Status
// query formal name, else lowercase name
if(entity.getString("status") != null) this.setStatus(entity.getString("status"));
else if(entity.getString("Status") != null) this.setStatus(entity.getString("Status"));
else if(strict) this.setStatus(entity.getString("status")); // setting null is not an option due to function overloading
if( entity.getString("snp_status") != null) this.setStatus(entity.getString("snp_status"));
else if( entity.getString("SNP_Status") != null) this.setStatus(entity.getString("SNP_Status"));
//set Polymorphism
if( entity.getEntities("Polymorphism", org.molgenis.omx.xgap.Polymorphism.class) != null || entity.getEntities("polymorphism", org.molgenis.omx.xgap.Polymorphism.class) != null )
{
java.lang.Iterable mrefs = entity.getEntities("Polymorphism", org.molgenis.omx.xgap.Polymorphism.class);
if(mrefs == null) mrefs = entity.getEntities("polymorphism", org.molgenis.omx.xgap.Polymorphism.class);
if(entity.getEntities("snp_polymorphism", org.molgenis.omx.xgap.Polymorphism.class)!= null) mrefs = entity.getEntities("snp_polymorphism", org.molgenis.omx.xgap.Polymorphism.class);
else if(entity.getEntities("SNP_Polymorphism", org.molgenis.omx.xgap.Polymorphism.class)!= null) mrefs = entity.getEntities("SNP_Polymorphism", org.molgenis.omx.xgap.Polymorphism.class);
this.setPolymorphism(mrefs != null ? com.google.common.collect.Lists.newArrayList(mrefs) : null);
}
}
@Override
public String toString()
{
return this.toString(false);
}
public String toString(boolean verbose)
{
StringBuilder sb = new StringBuilder("SNP(");
sb.append("id='" + getId()+"' ");
sb.append("identifier='" + getIdentifier()+"' ");
sb.append("name='" + getName()+"' ");
sb.append("__Type='" + get__Type()+"' ");
sb.append("description='" + getDescription()+"' ");
sb.append("chromosome='" + getChromosome()+"' ");
sb.append("cM='" + getCM()+"' ");
sb.append("bpStart='" + getBpStart()+"' ");
sb.append("bpEnd='" + getBpEnd()+"' ");
sb.append("seq='" + getSeq()+"' ");
sb.append("symbol='" + getSymbol()+"' ");
sb.append("reportsFor='" + getReportsFor()+"' ");
sb.append("status='" + getStatus()+"' ");
sb.append("polymorphism='" + getPolymorphism()+"'");
sb.append(");");
return sb.toString();
}
@Override
public Integer getIdValue()
{
return getId();
}
@Override
public Iterable getAttributeNames()
{
Set attributeNames = new LinkedHashSet();
for (AttributeMetaData attr : new SNPMetaData().getAttributes())
{
attributeNames.add(attr.getName());
}
return attributeNames;
}
@Override
public java.util.List getLabelAttributeNames()
{
java.util.List result = new java.util.ArrayList();
result.add("Identifier");
return result;
}
@Override
public void set(String attributeName, Object value)
{
if("id".equalsIgnoreCase(attributeName)) {
this.setId((Integer)value);
return;
}
if("Identifier".equalsIgnoreCase(attributeName)) {
this.setIdentifier((String)value);
return;
}
if("Name".equalsIgnoreCase(attributeName)) {
this.setName((String)value);
return;
}
if("__Type".equalsIgnoreCase(attributeName)) {
this.set__Type((String)value);
return;
}
if("description".equalsIgnoreCase(attributeName)) {
this.setDescription((String)value);
return;
}
if("Chromosome".equalsIgnoreCase(attributeName)) {
org.molgenis.omx.xgap.Chromosome e = new org.molgenis.omx.xgap.Chromosome();
e.set((Entity)value);
this.setChromosome(e);
return;
}
if("cM".equalsIgnoreCase(attributeName)) {
this.setCM((Double)value);
return;
}
if("bpStart".equalsIgnoreCase(attributeName)) {
this.setBpStart((Long)value);
return;
}
if("bpEnd".equalsIgnoreCase(attributeName)) {
this.setBpEnd((Long)value);
return;
}
if("Seq".equalsIgnoreCase(attributeName)) {
this.setSeq((String)value);
return;
}
if("Symbol".equalsIgnoreCase(attributeName)) {
this.setSymbol((String)value);
return;
}
if("ReportsFor".equalsIgnoreCase(attributeName)) {
this.setReportsFor((List)value);
return;
}
if("Status".equalsIgnoreCase(attributeName)) {
this.setStatus((String)value);
return;
}
if("Polymorphism".equalsIgnoreCase(attributeName)) {
this.setPolymorphism((List)value);
return;
}
}
@Override
public boolean equals(Object obj)
{
if (this == obj) return true;
if (obj == null) return false;
if (!super.equals(obj)) return false;
if (getClass() != obj.getClass()) return false;
return true;
}
@Override
public int hashCode()
{
int result = super.hashCode();
return result;
}
@Override
public org.molgenis.data.EntityMetaData getEntityMetaData()
{
return new SNPMetaData();
}
}
