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/* File: org.molgenis.omx/model/Gene.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;
/**
* Gene: Trait annotations specific for genes..
* @author MOLGENIS generator
*/
@javax.persistence.Entity
@javax.persistence.Table(name = "Gene"
)
@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 Gene extends org.molgenis.omx.observ.ObservationTarget implements org.molgenis.data.Entity, org.molgenis.omx.xgap.Locus
{
/** default serial version ID */
private static final long serialVersionUID = 1L;
public final static String ENTITY_NAME = "Gene";
// fieldname constants
public final static String CHROMOSOME = "Chromosome";
public final static String CM = "cM";
public final static String BPSTART = "bpStart";
public final static String BPEND = "bpEnd";
public final static String SEQ = "Seq";
public final static String SYMBOL = "Symbol";
public final static String ORIENTATION = "Orientation";
public final static String CONTROL = "Control";
public final static String ID = "id";
// member variables (including setters.getters for interface)
public String getEntityName()
{
return ENTITY_NAME;
}
//Reference to the chromosome this position belongs to.[type=xref]
@javax.persistence.ManyToOne(fetch=javax.persistence.FetchType.EAGER /*cascade={javax.persistence.CascadeType.MERGE, javax.persistence.CascadeType.PERSIST, javax.persistence.CascadeType.REFRESH}*/)
@javax.persistence.JoinColumn(name="Chromosome")
private org.molgenis.omx.xgap.Chromosome chromosome = null;
//genetic map position in centi morgan (cM).[type=decimal]
@javax.persistence.Column(name="cM")
@javax.xml.bind.annotation.XmlElement(name="cM")
private Double cM = null;
//numeric basepair postion (5') on the chromosome[type=long]
@javax.persistence.Column(name="bpStart")
@javax.xml.bind.annotation.XmlElement(name="bpStart")
private Long bpStart = null;
//numeric basepair postion (3') on the chromosome[type=long]
@javax.persistence.Column(name="bpEnd")
@javax.xml.bind.annotation.XmlElement(name="bpEnd")
private Long bpEnd = null;
//The FASTA text representation of the sequence.[type=text]
@javax.persistence.Lob
@javax.persistence.Column(name="Seq")
private String seq = null;
//Main symbol this gene is known by (not necessarily unique, in constrast to 'name')[type=string]
@javax.persistence.Column(name="Symbol", length=255)
@javax.xml.bind.annotation.XmlElement(name="symbol")
private String symbol = null;
//Orientation of the gene on the genome (F=forward, R=reverse)[type=enum]
@javax.persistence.Column(name="Orientation")
@javax.xml.bind.annotation.XmlElement(name="orientation")
private String orientation = null;
@javax.persistence.Transient
private String orientation_label = null;
@javax.persistence.Transient
private static final java.util.List orientation_options;
static {
orientation_options = new java.util.ArrayList();
orientation_options.add(new org.molgenis.util.ValueLabel("F","F"));
orientation_options.add(new org.molgenis.util.ValueLabel("R","R"));
}
//Indicating whether this is a 'housekeeping' gene that can be used as control.[type=bool]
@javax.persistence.Column(name="Control")
@javax.xml.bind.annotation.XmlElement(name="control")
private Boolean control = null;
//automatically generated internal id, only for internal use.[type=int]
//constructors
public Gene()
{
//set the type for a new instance
set__Type(this.getClass().getSimpleName());
}
//getters and setters
/**
* Get the Reference to the chromosome this position belongs to..
* @return chromosome.
*/
public org.molgenis.omx.xgap.Chromosome getChromosome()
{
return this.chromosome;
}
/**
* Set the Reference to the chromosome this position belongs to..
* @param chromosome
*/
public void setChromosome( org.molgenis.omx.xgap.Chromosome chromosome)
{
this.chromosome = chromosome;
}
/**
* Get the genetic map position in centi morgan (cM)..
* @return cM.
*/
public Double getCM()
{
return this.cM;
}
/**
* Set the genetic map position in centi morgan (cM)..
* @param cM
*/
public void setCM( Double cM)
{
this.cM = cM;
}
/**
* Get the numeric basepair postion (5') on the chromosome.
* @return bpStart.
*/
public Long getBpStart()
{
return this.bpStart;
}
/**
* Set the numeric basepair postion (5') on the chromosome.
* @param bpStart
*/
public void setBpStart( Long bpStart)
{
this.bpStart = bpStart;
}
/**
* Get the numeric basepair postion (3') on the chromosome.
* @return bpEnd.
*/
public Long getBpEnd()
{
return this.bpEnd;
}
/**
* Set the numeric basepair postion (3') on the chromosome.
* @param bpEnd
*/
public void setBpEnd( Long bpEnd)
{
this.bpEnd = bpEnd;
}
/**
* Get the The FASTA text representation of the sequence..
* @return seq.
*/
public String getSeq()
{
return this.seq;
}
/**
* Set the The FASTA text representation of the sequence..
* @param seq
*/
public void setSeq( String seq)
{
this.seq = seq;
}
/**
* Get the Main symbol this gene is known by (not necessarily unique, in constrast to 'name').
* @return symbol.
*/
public String getSymbol()
{
return this.symbol;
}
/**
* Set the Main symbol this gene is known by (not necessarily unique, in constrast to 'name').
* @param symbol
*/
public void setSymbol( String symbol)
{
this.symbol = symbol;
}
/**
* Get the Orientation of the gene on the genome (F=forward, R=reverse).
* @return orientation.
*/
public String getOrientation()
{
return this.orientation;
}
/**
* Set the Orientation of the gene on the genome (F=forward, R=reverse).
* @param orientation
*/
public void setOrientation( String orientation)
{
this.orientation = orientation;
}
/**
* Get tha label for enum Orientation.
*/
public String getOrientationLabel()
{
return this.orientation_label;
}
/**
* Orientation is enum. This method returns all available enum options.
*/
public java.util.List getOrientationOptions()
{
return orientation_options;
}
/**
* Get the Indicating whether this is a 'housekeeping' gene that can be used as control..
* @return control.
*/
public Boolean getControl()
{
return this.control;
}
/**
* Set the Indicating whether this is a 'housekeeping' gene that can be used as control..
* @param control
*/
public void setControl( Boolean control)
{
this.control = control;
}
/**
* 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("orientation"))
return getOrientation();
if(name.equals("orientation_label"))
return getOrientationLabel();
if (name.equals("control"))
return getControl();
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("gene_id") != null) this.setId(entity.getInt("gene_id"));
else if( entity.getInt("Gene_id") != null) this.setId(entity.getInt("Gene_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("gene_identifier") != null) this.setIdentifier(entity.getString("gene_identifier"));
else if( entity.getString("Gene_Identifier") != null) this.setIdentifier(entity.getString("Gene_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("gene_name") != null) this.setName(entity.getString("gene_name"));
else if( entity.getString("Gene_Name") != null) this.setName(entity.getString("Gene_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("gene___type") != null) this.set__Type(entity.getString("gene___type"));
else if( entity.getString("Gene___Type") != null) this.set__Type(entity.getString("Gene___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("gene_description") != null) this.setDescription(entity.getString("gene_description"));
else if( entity.getString("Gene_description") != null) this.setDescription(entity.getString("Gene_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("Gene_Chromosome", org.molgenis.omx.xgap.Chromosome.class) != null) {
this.setChromosome(entity.getEntity("Gene_Chromosome", org.molgenis.omx.xgap.Chromosome.class));
}
else if( entity.getEntity("gene_chromosome", org.molgenis.omx.xgap.Chromosome.class) != null) {
this.setChromosome(entity.getEntity("Gene_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("gene_cm") != null) this.setCM(entity.getDouble("gene_cm"));
else if( entity.getDouble("Gene_cM") != null) this.setCM(entity.getDouble("Gene_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("gene_bpstart") != null) this.setBpStart(entity.getLong("gene_bpstart"));
else if( entity.getLong("Gene_bpStart") != null) this.setBpStart(entity.getLong("Gene_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("gene_bpend") != null) this.setBpEnd(entity.getLong("gene_bpend"));
else if( entity.getLong("Gene_bpEnd") != null) this.setBpEnd(entity.getLong("Gene_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("gene_seq") != null) this.setSeq(entity.getString("gene_seq"));
else if( entity.getString("Gene_Seq") != null) this.setSeq(entity.getString("Gene_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("gene_symbol") != null) this.setSymbol(entity.getString("gene_symbol"));
else if( entity.getString("Gene_Symbol") != null) this.setSymbol(entity.getString("Gene_Symbol"));
//set Orientation
// query formal name, else lowercase name
if(entity.getString("orientation") != null) this.setOrientation(entity.getString("orientation"));
else if(entity.getString("Orientation") != null) this.setOrientation(entity.getString("Orientation"));
else if(strict) this.setOrientation(entity.getString("orientation")); // setting null is not an option due to function overloading
if( entity.getString("gene_orientation") != null) this.setOrientation(entity.getString("gene_orientation"));
else if( entity.getString("Gene_Orientation") != null) this.setOrientation(entity.getString("Gene_Orientation"));
//set Control
// query formal name, else lowercase name
if(entity.getBoolean("control") != null) this.setControl(entity.getBoolean("control"));
else if(entity.getBoolean("Control") != null) this.setControl(entity.getBoolean("Control"));
else if(strict) this.setControl(entity.getBoolean("control")); // setting null is not an option due to function overloading
if( entity.getBoolean("gene_control") != null) this.setControl(entity.getBoolean("gene_control"));
else if( entity.getBoolean("Gene_Control") != null) this.setControl(entity.getBoolean("Gene_Control"));
}
@Override
public String toString()
{
return this.toString(false);
}
public String toString(boolean verbose)
{
StringBuilder sb = new StringBuilder("Gene(");
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("orientation='" + getOrientation()+"' ");
sb.append("control='" + getControl()+"'");
sb.append(");");
return sb.toString();
}
@Override
public Integer getIdValue()
{
return getId();
}
@Override
public Iterable getAttributeNames()
{
Set attributeNames = new LinkedHashSet();
for (AttributeMetaData attr : new GeneMetaData().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("Orientation".equalsIgnoreCase(attributeName)) {
this.setOrientation((String)value);
return;
}
if("Control".equalsIgnoreCase(attributeName)) {
this.setControl((Boolean)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 GeneMetaData();
}
}
