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org.molgenis.omx.xgap.Variant Maven / Gradle / Ivy
/* File: org.molgenis.omx/model/Variant.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;
/**
* Variant: 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 = "Variant"
)
@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 Variant 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 = "Variant";
// 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 MUTATIONPOSITION = "MutationPosition";
public final static String CDNAPOSITION = "CdnaPosition";
public final static String AAPOSITION = "AaPosition";
public final static String VARIANTLENGTH = "VariantLength";
public final static String EVENT = "Event";
public final static String NTCHANGE = "NtChange";
public final static String CODONCHANGE = "Codonchange";
public final static String CDNANOTATION = "CdnaNotation";
public final static String GDNANOTATION = "GdnaNotation";
public final static String AANOTATION = "AaNotation";
public final static String EXON = "Exon";
public final static String CONSEQUENCE = "Consequence";
public final static String INHERITANCE = "Inheritance";
public final static String REPORTEDSNP = "ReportedSNP";
public final static String EFFECTONSPLICING = "EffectOnSplicing";
public final static String PATHOGENICITY = "Pathogenicity";
public final static String GENE = "Gene";
public final static String IDMUTATION = "IdMutation";
public final static String DETAILSFORMUTATION = "DetailsForMutation";
public final static String TRACK = "Track";
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;
//todo[type=string]
@javax.persistence.Column(name="Symbol", length=255)
@javax.xml.bind.annotation.XmlElement(name="symbol")
private String symbol = null;
//[type=int]
@javax.persistence.Column(name="MutationPosition")
@javax.xml.bind.annotation.XmlElement(name="mutationPosition")
private Integer mutationPosition = null;
//[type=int]
@javax.persistence.Column(name="CdnaPosition")
@javax.xml.bind.annotation.XmlElement(name="cdnaPosition")
private Integer cdnaPosition = null;
//[type=int]
@javax.persistence.Column(name="AaPosition")
@javax.xml.bind.annotation.XmlElement(name="aaPosition")
private Integer aaPosition = null;
//[type=int]
@javax.persistence.Column(name="VariantLength")
@javax.xml.bind.annotation.XmlElement(name="variantLength")
private Integer variantLength = null;
//[type=string]
@javax.persistence.Column(name="Event", length=255)
@javax.xml.bind.annotation.XmlElement(name="event")
private String event = null;
//[type=string]
@javax.persistence.Column(name="NtChange", length=255)
@javax.xml.bind.annotation.XmlElement(name="ntChange")
private String ntChange = null;
//[type=string]
@javax.persistence.Column(name="Codonchange", length=255)
@javax.xml.bind.annotation.XmlElement(name="codonchange")
private String codonchange = null;
//[type=string]
@javax.persistence.Column(name="CdnaNotation", length=255)
@javax.xml.bind.annotation.XmlElement(name="cdnaNotation")
private String cdnaNotation = null;
//[type=string]
@javax.persistence.Column(name="GdnaNotation", length=255)
@javax.xml.bind.annotation.XmlElement(name="gdnaNotation")
private String gdnaNotation = null;
//[type=string]
@javax.persistence.Column(name="AaNotation", length=255)
@javax.xml.bind.annotation.XmlElement(name="aaNotation")
private String aaNotation = null;
//[type=string]
@javax.persistence.Column(name="Exon", length=255)
@javax.xml.bind.annotation.XmlElement(name="exon")
private String exon = null;
//[type=string]
@javax.persistence.Column(name="Consequence", length=255)
@javax.xml.bind.annotation.XmlElement(name="consequence")
private String consequence = null;
//[type=string]
@javax.persistence.Column(name="Inheritance", length=255)
@javax.xml.bind.annotation.XmlElement(name="inheritance")
private String inheritance = null;
//[type=bool]
@javax.persistence.Column(name="ReportedSNP")
@javax.xml.bind.annotation.XmlElement(name="reportedSNP")
private Boolean reportedSNP = null;
//[type=bool]
@javax.persistence.Column(name="EffectOnSplicing")
@javax.xml.bind.annotation.XmlElement(name="effectOnSplicing")
private Boolean effectOnSplicing = null;
//[type=string]
@javax.persistence.Column(name="Pathogenicity", length=255)
@javax.xml.bind.annotation.XmlElement(name="pathogenicity")
private String pathogenicity = null;
//[type=string]
@javax.persistence.Column(name="Gene", length=255)
@javax.xml.bind.annotation.XmlElement(name="gene")
private String gene = null;
//[type=int]
@javax.persistence.Column(name="IdMutation")
@javax.xml.bind.annotation.XmlElement(name="idMutation")
private Integer idMutation = null;
//[type=hyperlink]
@javax.persistence.Column(name="DetailsForMutation")
@javax.xml.bind.annotation.XmlElement(name="detailsForMutation")
private String detailsForMutation = null;
//[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="Track", nullable=false)
@javax.validation.constraints.NotNull
private org.molgenis.omx.xgap.Track track = null;
//automatically generated internal id, only for internal use.[type=int]
//constructors
public Variant()
{
//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 todo.
* @return symbol.
*/
public String getSymbol()
{
return this.symbol;
}
/**
* Set the todo.
* @param symbol
*/
public void setSymbol( String symbol)
{
this.symbol = symbol;
}
/**
* Get the .
* @return mutationPosition.
*/
public Integer getMutationPosition()
{
return this.mutationPosition;
}
/**
* Set the .
* @param mutationPosition
*/
public void setMutationPosition( Integer mutationPosition)
{
this.mutationPosition = mutationPosition;
}
/**
* Get the .
* @return cdnaPosition.
*/
public Integer getCdnaPosition()
{
return this.cdnaPosition;
}
/**
* Set the .
* @param cdnaPosition
*/
public void setCdnaPosition( Integer cdnaPosition)
{
this.cdnaPosition = cdnaPosition;
}
/**
* Get the .
* @return aaPosition.
*/
public Integer getAaPosition()
{
return this.aaPosition;
}
/**
* Set the .
* @param aaPosition
*/
public void setAaPosition( Integer aaPosition)
{
this.aaPosition = aaPosition;
}
/**
* Get the .
* @return variantLength.
*/
public Integer getVariantLength()
{
return this.variantLength;
}
/**
* Set the .
* @param variantLength
*/
public void setVariantLength( Integer variantLength)
{
this.variantLength = variantLength;
}
/**
* Get the .
* @return event.
*/
public String getEvent()
{
return this.event;
}
/**
* Set the .
* @param event
*/
public void setEvent( String event)
{
this.event = event;
}
/**
* Get the .
* @return ntChange.
*/
public String getNtChange()
{
return this.ntChange;
}
/**
* Set the .
* @param ntChange
*/
public void setNtChange( String ntChange)
{
this.ntChange = ntChange;
}
/**
* Get the .
* @return codonchange.
*/
public String getCodonchange()
{
return this.codonchange;
}
/**
* Set the .
* @param codonchange
*/
public void setCodonchange( String codonchange)
{
this.codonchange = codonchange;
}
/**
* Get the .
* @return cdnaNotation.
*/
public String getCdnaNotation()
{
return this.cdnaNotation;
}
/**
* Set the .
* @param cdnaNotation
*/
public void setCdnaNotation( String cdnaNotation)
{
this.cdnaNotation = cdnaNotation;
}
/**
* Get the .
* @return gdnaNotation.
*/
public String getGdnaNotation()
{
return this.gdnaNotation;
}
/**
* Set the .
* @param gdnaNotation
*/
public void setGdnaNotation( String gdnaNotation)
{
this.gdnaNotation = gdnaNotation;
}
/**
* Get the .
* @return aaNotation.
*/
public String getAaNotation()
{
return this.aaNotation;
}
/**
* Set the .
* @param aaNotation
*/
public void setAaNotation( String aaNotation)
{
this.aaNotation = aaNotation;
}
/**
* Get the .
* @return exon.
*/
public String getExon()
{
return this.exon;
}
/**
* Set the .
* @param exon
*/
public void setExon( String exon)
{
this.exon = exon;
}
/**
* Get the .
* @return consequence.
*/
public String getConsequence()
{
return this.consequence;
}
/**
* Set the .
* @param consequence
*/
public void setConsequence( String consequence)
{
this.consequence = consequence;
}
/**
* Get the .
* @return inheritance.
*/
public String getInheritance()
{
return this.inheritance;
}
/**
* Set the .
* @param inheritance
*/
public void setInheritance( String inheritance)
{
this.inheritance = inheritance;
}
/**
* Get the .
* @return reportedSNP.
*/
public Boolean getReportedSNP()
{
return this.reportedSNP;
}
/**
* Set the .
* @param reportedSNP
*/
public void setReportedSNP( Boolean reportedSNP)
{
this.reportedSNP = reportedSNP;
}
/**
* Get the .
* @return effectOnSplicing.
*/
public Boolean getEffectOnSplicing()
{
return this.effectOnSplicing;
}
/**
* Set the .
* @param effectOnSplicing
*/
public void setEffectOnSplicing( Boolean effectOnSplicing)
{
this.effectOnSplicing = effectOnSplicing;
}
/**
* Get the .
* @return pathogenicity.
*/
public String getPathogenicity()
{
return this.pathogenicity;
}
/**
* Set the .
* @param pathogenicity
*/
public void setPathogenicity( String pathogenicity)
{
this.pathogenicity = pathogenicity;
}
/**
* Get the .
* @return gene.
*/
public String getGene()
{
return this.gene;
}
/**
* Set the .
* @param gene
*/
public void setGene( String gene)
{
this.gene = gene;
}
/**
* Get the .
* @return idMutation.
*/
public Integer getIdMutation()
{
return this.idMutation;
}
/**
* Set the .
* @param idMutation
*/
public void setIdMutation( Integer idMutation)
{
this.idMutation = idMutation;
}
/**
* Get the .
* @return detailsForMutation.
*/
public String getDetailsForMutation()
{
return this.detailsForMutation;
}
/**
* Set the .
* @param detailsForMutation
*/
public void setDetailsForMutation( String detailsForMutation)
{
this.detailsForMutation = detailsForMutation;
}
/**
* Get the .
* @return track.
*/
public org.molgenis.omx.xgap.Track getTrack()
{
return this.track;
}
/**
* Set the .
* @param track
*/
public void setTrack( org.molgenis.omx.xgap.Track track)
{
this.track = track;
}
/**
* 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("mutationposition"))
return getMutationPosition();
if (name.equals("cdnaposition"))
return getCdnaPosition();
if (name.equals("aaposition"))
return getAaPosition();
if (name.equals("variantlength"))
return getVariantLength();
if (name.equals("event"))
return getEvent();
if (name.equals("ntchange"))
return getNtChange();
if (name.equals("codonchange"))
return getCodonchange();
if (name.equals("cdnanotation"))
return getCdnaNotation();
if (name.equals("gdnanotation"))
return getGdnaNotation();
if (name.equals("aanotation"))
return getAaNotation();
if (name.equals("exon"))
return getExon();
if (name.equals("consequence"))
return getConsequence();
if (name.equals("inheritance"))
return getInheritance();
if (name.equals("reportedsnp"))
return getReportedSNP();
if (name.equals("effectonsplicing"))
return getEffectOnSplicing();
if (name.equals("pathogenicity"))
return getPathogenicity();
if (name.equals("gene"))
return getGene();
if (name.equals("idmutation"))
return getIdMutation();
if (name.equals("detailsformutation"))
return getDetailsForMutation();
if (name.equals("track"))
return getTrack();
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("variant_id") != null) this.setId(entity.getInt("variant_id"));
else if( entity.getInt("Variant_id") != null) this.setId(entity.getInt("Variant_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("variant_identifier") != null) this.setIdentifier(entity.getString("variant_identifier"));
else if( entity.getString("Variant_Identifier") != null) this.setIdentifier(entity.getString("Variant_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("variant_name") != null) this.setName(entity.getString("variant_name"));
else if( entity.getString("Variant_Name") != null) this.setName(entity.getString("Variant_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("variant___type") != null) this.set__Type(entity.getString("variant___type"));
else if( entity.getString("Variant___Type") != null) this.set__Type(entity.getString("Variant___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("variant_description") != null) this.setDescription(entity.getString("variant_description"));
else if( entity.getString("Variant_description") != null) this.setDescription(entity.getString("Variant_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("Variant_Chromosome", org.molgenis.omx.xgap.Chromosome.class) != null) {
this.setChromosome(entity.getEntity("Variant_Chromosome", org.molgenis.omx.xgap.Chromosome.class));
}
else if( entity.getEntity("variant_chromosome", org.molgenis.omx.xgap.Chromosome.class) != null) {
this.setChromosome(entity.getEntity("Variant_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("variant_cm") != null) this.setCM(entity.getDouble("variant_cm"));
else if( entity.getDouble("Variant_cM") != null) this.setCM(entity.getDouble("Variant_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("variant_bpstart") != null) this.setBpStart(entity.getLong("variant_bpstart"));
else if( entity.getLong("Variant_bpStart") != null) this.setBpStart(entity.getLong("Variant_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("variant_bpend") != null) this.setBpEnd(entity.getLong("variant_bpend"));
else if( entity.getLong("Variant_bpEnd") != null) this.setBpEnd(entity.getLong("Variant_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("variant_seq") != null) this.setSeq(entity.getString("variant_seq"));
else if( entity.getString("Variant_Seq") != null) this.setSeq(entity.getString("Variant_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("variant_symbol") != null) this.setSymbol(entity.getString("variant_symbol"));
else if( entity.getString("Variant_Symbol") != null) this.setSymbol(entity.getString("Variant_Symbol"));
//set MutationPosition
// query formal name, else lowercase name
if(entity.getInt("mutationposition") != null) this.setMutationPosition(entity.getInt("mutationposition"));
else if(entity.getInt("MutationPosition") != null) this.setMutationPosition(entity.getInt("MutationPosition"));
else if(strict) this.setMutationPosition(entity.getInt("mutationposition")); // setting null is not an option due to function overloading
if( entity.getInt("variant_mutationposition") != null) this.setMutationPosition(entity.getInt("variant_mutationposition"));
else if( entity.getInt("Variant_MutationPosition") != null) this.setMutationPosition(entity.getInt("Variant_MutationPosition"));
//set CdnaPosition
// query formal name, else lowercase name
if(entity.getInt("cdnaposition") != null) this.setCdnaPosition(entity.getInt("cdnaposition"));
else if(entity.getInt("CdnaPosition") != null) this.setCdnaPosition(entity.getInt("CdnaPosition"));
else if(strict) this.setCdnaPosition(entity.getInt("cdnaposition")); // setting null is not an option due to function overloading
if( entity.getInt("variant_cdnaposition") != null) this.setCdnaPosition(entity.getInt("variant_cdnaposition"));
else if( entity.getInt("Variant_CdnaPosition") != null) this.setCdnaPosition(entity.getInt("Variant_CdnaPosition"));
//set AaPosition
// query formal name, else lowercase name
if(entity.getInt("aaposition") != null) this.setAaPosition(entity.getInt("aaposition"));
else if(entity.getInt("AaPosition") != null) this.setAaPosition(entity.getInt("AaPosition"));
else if(strict) this.setAaPosition(entity.getInt("aaposition")); // setting null is not an option due to function overloading
if( entity.getInt("variant_aaposition") != null) this.setAaPosition(entity.getInt("variant_aaposition"));
else if( entity.getInt("Variant_AaPosition") != null) this.setAaPosition(entity.getInt("Variant_AaPosition"));
//set VariantLength
// query formal name, else lowercase name
if(entity.getInt("variantlength") != null) this.setVariantLength(entity.getInt("variantlength"));
else if(entity.getInt("VariantLength") != null) this.setVariantLength(entity.getInt("VariantLength"));
else if(strict) this.setVariantLength(entity.getInt("variantlength")); // setting null is not an option due to function overloading
if( entity.getInt("variant_variantlength") != null) this.setVariantLength(entity.getInt("variant_variantlength"));
else if( entity.getInt("Variant_VariantLength") != null) this.setVariantLength(entity.getInt("Variant_VariantLength"));
//set Event
// query formal name, else lowercase name
if(entity.getString("event") != null) this.setEvent(entity.getString("event"));
else if(entity.getString("Event") != null) this.setEvent(entity.getString("Event"));
else if(strict) this.setEvent(entity.getString("event")); // setting null is not an option due to function overloading
if( entity.getString("variant_event") != null) this.setEvent(entity.getString("variant_event"));
else if( entity.getString("Variant_Event") != null) this.setEvent(entity.getString("Variant_Event"));
//set NtChange
// query formal name, else lowercase name
if(entity.getString("ntchange") != null) this.setNtChange(entity.getString("ntchange"));
else if(entity.getString("NtChange") != null) this.setNtChange(entity.getString("NtChange"));
else if(strict) this.setNtChange(entity.getString("ntchange")); // setting null is not an option due to function overloading
if( entity.getString("variant_ntchange") != null) this.setNtChange(entity.getString("variant_ntchange"));
else if( entity.getString("Variant_NtChange") != null) this.setNtChange(entity.getString("Variant_NtChange"));
//set Codonchange
// query formal name, else lowercase name
if(entity.getString("codonchange") != null) this.setCodonchange(entity.getString("codonchange"));
else if(entity.getString("Codonchange") != null) this.setCodonchange(entity.getString("Codonchange"));
else if(strict) this.setCodonchange(entity.getString("codonchange")); // setting null is not an option due to function overloading
if( entity.getString("variant_codonchange") != null) this.setCodonchange(entity.getString("variant_codonchange"));
else if( entity.getString("Variant_Codonchange") != null) this.setCodonchange(entity.getString("Variant_Codonchange"));
//set CdnaNotation
// query formal name, else lowercase name
if(entity.getString("cdnanotation") != null) this.setCdnaNotation(entity.getString("cdnanotation"));
else if(entity.getString("CdnaNotation") != null) this.setCdnaNotation(entity.getString("CdnaNotation"));
else if(strict) this.setCdnaNotation(entity.getString("cdnanotation")); // setting null is not an option due to function overloading
if( entity.getString("variant_cdnanotation") != null) this.setCdnaNotation(entity.getString("variant_cdnanotation"));
else if( entity.getString("Variant_CdnaNotation") != null) this.setCdnaNotation(entity.getString("Variant_CdnaNotation"));
//set GdnaNotation
// query formal name, else lowercase name
if(entity.getString("gdnanotation") != null) this.setGdnaNotation(entity.getString("gdnanotation"));
else if(entity.getString("GdnaNotation") != null) this.setGdnaNotation(entity.getString("GdnaNotation"));
else if(strict) this.setGdnaNotation(entity.getString("gdnanotation")); // setting null is not an option due to function overloading
if( entity.getString("variant_gdnanotation") != null) this.setGdnaNotation(entity.getString("variant_gdnanotation"));
else if( entity.getString("Variant_GdnaNotation") != null) this.setGdnaNotation(entity.getString("Variant_GdnaNotation"));
//set AaNotation
// query formal name, else lowercase name
if(entity.getString("aanotation") != null) this.setAaNotation(entity.getString("aanotation"));
else if(entity.getString("AaNotation") != null) this.setAaNotation(entity.getString("AaNotation"));
else if(strict) this.setAaNotation(entity.getString("aanotation")); // setting null is not an option due to function overloading
if( entity.getString("variant_aanotation") != null) this.setAaNotation(entity.getString("variant_aanotation"));
else if( entity.getString("Variant_AaNotation") != null) this.setAaNotation(entity.getString("Variant_AaNotation"));
//set Exon
// query formal name, else lowercase name
if(entity.getString("exon") != null) this.setExon(entity.getString("exon"));
else if(entity.getString("Exon") != null) this.setExon(entity.getString("Exon"));
else if(strict) this.setExon(entity.getString("exon")); // setting null is not an option due to function overloading
if( entity.getString("variant_exon") != null) this.setExon(entity.getString("variant_exon"));
else if( entity.getString("Variant_Exon") != null) this.setExon(entity.getString("Variant_Exon"));
//set Consequence
// query formal name, else lowercase name
if(entity.getString("consequence") != null) this.setConsequence(entity.getString("consequence"));
else if(entity.getString("Consequence") != null) this.setConsequence(entity.getString("Consequence"));
else if(strict) this.setConsequence(entity.getString("consequence")); // setting null is not an option due to function overloading
if( entity.getString("variant_consequence") != null) this.setConsequence(entity.getString("variant_consequence"));
else if( entity.getString("Variant_Consequence") != null) this.setConsequence(entity.getString("Variant_Consequence"));
//set Inheritance
// query formal name, else lowercase name
if(entity.getString("inheritance") != null) this.setInheritance(entity.getString("inheritance"));
else if(entity.getString("Inheritance") != null) this.setInheritance(entity.getString("Inheritance"));
else if(strict) this.setInheritance(entity.getString("inheritance")); // setting null is not an option due to function overloading
if( entity.getString("variant_inheritance") != null) this.setInheritance(entity.getString("variant_inheritance"));
else if( entity.getString("Variant_Inheritance") != null) this.setInheritance(entity.getString("Variant_Inheritance"));
//set ReportedSNP
// query formal name, else lowercase name
if(entity.getBoolean("reportedsnp") != null) this.setReportedSNP(entity.getBoolean("reportedsnp"));
else if(entity.getBoolean("ReportedSNP") != null) this.setReportedSNP(entity.getBoolean("ReportedSNP"));
else if(strict) this.setReportedSNP(entity.getBoolean("reportedsnp")); // setting null is not an option due to function overloading
if( entity.getBoolean("variant_reportedsnp") != null) this.setReportedSNP(entity.getBoolean("variant_reportedsnp"));
else if( entity.getBoolean("Variant_ReportedSNP") != null) this.setReportedSNP(entity.getBoolean("Variant_ReportedSNP"));
//set EffectOnSplicing
// query formal name, else lowercase name
if(entity.getBoolean("effectonsplicing") != null) this.setEffectOnSplicing(entity.getBoolean("effectonsplicing"));
else if(entity.getBoolean("EffectOnSplicing") != null) this.setEffectOnSplicing(entity.getBoolean("EffectOnSplicing"));
else if(strict) this.setEffectOnSplicing(entity.getBoolean("effectonsplicing")); // setting null is not an option due to function overloading
if( entity.getBoolean("variant_effectonsplicing") != null) this.setEffectOnSplicing(entity.getBoolean("variant_effectonsplicing"));
else if( entity.getBoolean("Variant_EffectOnSplicing") != null) this.setEffectOnSplicing(entity.getBoolean("Variant_EffectOnSplicing"));
//set Pathogenicity
// query formal name, else lowercase name
if(entity.getString("pathogenicity") != null) this.setPathogenicity(entity.getString("pathogenicity"));
else if(entity.getString("Pathogenicity") != null) this.setPathogenicity(entity.getString("Pathogenicity"));
else if(strict) this.setPathogenicity(entity.getString("pathogenicity")); // setting null is not an option due to function overloading
if( entity.getString("variant_pathogenicity") != null) this.setPathogenicity(entity.getString("variant_pathogenicity"));
else if( entity.getString("Variant_Pathogenicity") != null) this.setPathogenicity(entity.getString("Variant_Pathogenicity"));
//set Gene
// query formal name, else lowercase name
if(entity.getString("gene") != null) this.setGene(entity.getString("gene"));
else if(entity.getString("Gene") != null) this.setGene(entity.getString("Gene"));
else if(strict) this.setGene(entity.getString("gene")); // setting null is not an option due to function overloading
if( entity.getString("variant_gene") != null) this.setGene(entity.getString("variant_gene"));
else if( entity.getString("Variant_Gene") != null) this.setGene(entity.getString("Variant_Gene"));
//set IdMutation
// query formal name, else lowercase name
if(entity.getInt("idmutation") != null) this.setIdMutation(entity.getInt("idmutation"));
else if(entity.getInt("IdMutation") != null) this.setIdMutation(entity.getInt("IdMutation"));
else if(strict) this.setIdMutation(entity.getInt("idmutation")); // setting null is not an option due to function overloading
if( entity.getInt("variant_idmutation") != null) this.setIdMutation(entity.getInt("variant_idmutation"));
else if( entity.getInt("Variant_IdMutation") != null) this.setIdMutation(entity.getInt("Variant_IdMutation"));
//set DetailsForMutation
// query formal name, else lowercase name
if(entity.getString("detailsformutation") != null) this.setDetailsForMutation(entity.getString("detailsformutation"));
else if(entity.getString("DetailsForMutation") != null) this.setDetailsForMutation(entity.getString("DetailsForMutation"));
else if(strict) this.setDetailsForMutation(entity.getString("detailsformutation")); // setting null is not an option due to function overloading
if( entity.getString("variant_detailsformutation") != null) this.setDetailsForMutation(entity.getString("variant_detailsformutation"));
else if( entity.getString("Variant_DetailsForMutation") != null) this.setDetailsForMutation(entity.getString("Variant_DetailsForMutation"));
//set Track
// query formal name, else lowercase name
if( entity.getEntity("Track", org.molgenis.omx.xgap.Track.class) != null) {
this.setTrack(entity.getEntity("Track", org.molgenis.omx.xgap.Track.class));
}
else if( entity.getEntity("track", org.molgenis.omx.xgap.Track.class) != null) {
this.setTrack(entity.getEntity("track", org.molgenis.omx.xgap.Track.class));
}
else if( entity.getEntity("Variant_Track", org.molgenis.omx.xgap.Track.class) != null) {
this.setTrack(entity.getEntity("Variant_Track", org.molgenis.omx.xgap.Track.class));
}
else if( entity.getEntity("variant_track", org.molgenis.omx.xgap.Track.class) != null) {
this.setTrack(entity.getEntity("Variant_Track", org.molgenis.omx.xgap.Track.class));
}
}
@Override
public String toString()
{
return this.toString(false);
}
public String toString(boolean verbose)
{
StringBuilder sb = new StringBuilder("Variant(");
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("mutationPosition='" + getMutationPosition()+"' ");
sb.append("cdnaPosition='" + getCdnaPosition()+"' ");
sb.append("aaPosition='" + getAaPosition()+"' ");
sb.append("variantLength='" + getVariantLength()+"' ");
sb.append("event='" + getEvent()+"' ");
sb.append("ntChange='" + getNtChange()+"' ");
sb.append("codonchange='" + getCodonchange()+"' ");
sb.append("cdnaNotation='" + getCdnaNotation()+"' ");
sb.append("gdnaNotation='" + getGdnaNotation()+"' ");
sb.append("aaNotation='" + getAaNotation()+"' ");
sb.append("exon='" + getExon()+"' ");
sb.append("consequence='" + getConsequence()+"' ");
sb.append("inheritance='" + getInheritance()+"' ");
sb.append("reportedSNP='" + getReportedSNP()+"' ");
sb.append("effectOnSplicing='" + getEffectOnSplicing()+"' ");
sb.append("pathogenicity='" + getPathogenicity()+"' ");
sb.append("gene='" + getGene()+"' ");
sb.append("idMutation='" + getIdMutation()+"' ");
sb.append("detailsForMutation='" + getDetailsForMutation()+"' ");
sb.append("track='" + getTrack()+"'");
sb.append(");");
return sb.toString();
}
@Override
public Integer getIdValue()
{
return getId();
}
@Override
public Iterable getAttributeNames()
{
Set attributeNames = new LinkedHashSet();
for (AttributeMetaData attr : new VariantMetaData().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("MutationPosition".equalsIgnoreCase(attributeName)) {
this.setMutationPosition((Integer)value);
return;
}
if("CdnaPosition".equalsIgnoreCase(attributeName)) {
this.setCdnaPosition((Integer)value);
return;
}
if("AaPosition".equalsIgnoreCase(attributeName)) {
this.setAaPosition((Integer)value);
return;
}
if("VariantLength".equalsIgnoreCase(attributeName)) {
this.setVariantLength((Integer)value);
return;
}
if("Event".equalsIgnoreCase(attributeName)) {
this.setEvent((String)value);
return;
}
if("NtChange".equalsIgnoreCase(attributeName)) {
this.setNtChange((String)value);
return;
}
if("Codonchange".equalsIgnoreCase(attributeName)) {
this.setCodonchange((String)value);
return;
}
if("CdnaNotation".equalsIgnoreCase(attributeName)) {
this.setCdnaNotation((String)value);
return;
}
if("GdnaNotation".equalsIgnoreCase(attributeName)) {
this.setGdnaNotation((String)value);
return;
}
if("AaNotation".equalsIgnoreCase(attributeName)) {
this.setAaNotation((String)value);
return;
}
if("Exon".equalsIgnoreCase(attributeName)) {
this.setExon((String)value);
return;
}
if("Consequence".equalsIgnoreCase(attributeName)) {
this.setConsequence((String)value);
return;
}
if("Inheritance".equalsIgnoreCase(attributeName)) {
this.setInheritance((String)value);
return;
}
if("ReportedSNP".equalsIgnoreCase(attributeName)) {
this.setReportedSNP((Boolean)value);
return;
}
if("EffectOnSplicing".equalsIgnoreCase(attributeName)) {
this.setEffectOnSplicing((Boolean)value);
return;
}
if("Pathogenicity".equalsIgnoreCase(attributeName)) {
this.setPathogenicity((String)value);
return;
}
if("Gene".equalsIgnoreCase(attributeName)) {
this.setGene((String)value);
return;
}
if("IdMutation".equalsIgnoreCase(attributeName)) {
this.setIdMutation((Integer)value);
return;
}
if("DetailsForMutation".equalsIgnoreCase(attributeName)) {
this.setDetailsForMutation((String)value);
return;
}
if("Track".equalsIgnoreCase(attributeName)) {
org.molgenis.omx.xgap.Track e = new org.molgenis.omx.xgap.Track();
e.set((Entity)value);
this.setTrack(e);
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 VariantMetaData();
}
}
