MutationUploadVO.java

package org.molgenis.mutation.vo;

import java.io.Serializable;

import org.molgenis.mutation.Mutation;
import org.molgenis.util.ValueLabel;

public class MutationUploadVO implements Serializable
{
	private static final long serialVersionUID = 1070160510535611854L;
	private Mutation mutation;
	private Integer exonId;
	private Boolean exonIsIntron;
	private Integer geneBpStart;
	private String geneOrientation;
	private String geneSeq;
	private String geneSymbol;
	// Values that are calculated but not stored in the db
	private String refseq;
	private String nt;
	private String codon;
	private String aa;
	private String aachange;

	public MutationUploadVO()
	{
		this.mutation = new Mutation();
	}

	public Mutation getMutation()
	{
		return mutation;
	}

	public void setMutation(Mutation mutation)
	{
		this.mutation = mutation;
	}

	public Integer getExonId()
	{
		return exonId;
	}

	public void setExonId(Integer exonId)
	{
		this.exonId = exonId;
	}

	public Boolean getExonIsIntron()
	{
		return exonIsIntron;
	}

	public void setExonIsIntron(Boolean exonIsIntron)
	{
		this.exonIsIntron = exonIsIntron;
	}

	public Integer getGeneBpStart()
	{
		return geneBpStart;
	}

	public void setGeneBpStart(Integer geneBpStart)
	{
		this.geneBpStart = geneBpStart;
	}

	public String getGeneOrientation()
	{
		return geneOrientation;
	}

	public void setGeneOrientation(String geneOrientation)
	{
		this.geneOrientation = geneOrientation;
	}

	public String getGeneSeq()
	{
		return geneSeq;
	}

	public void setGeneSeq(String geneSeq)
	{
		this.geneSeq = geneSeq;
	}

	public String getGeneSymbol()
	{
		return geneSymbol;
	}

	public void setGeneSymbol(String geneSymbol)
	{
		this.geneSymbol = geneSymbol;
	}

	public String getRefseq()
	{
		return refseq;
	}

	public void setRefseq(String refseq)
	{
		this.refseq = refseq;
	}

	public String getNt()
	{
		return nt;
	}

	public void setNt(String nt)
	{
		this.nt = nt;
	}

	public String getCodon()
	{
		return codon;
	}

	public void setCodon(String codon)
	{
		this.codon = codon;
	}

	public String getAa()
	{
		return aa;
	}

	public void setAa(String aa)
	{
		this.aa = aa;
	}

	public String getAachange()
	{
		return aachange;
	}

	public void setAachange(String aachange)
	{
		this.aachange = aachange;
	}

	public java.util.List<ValueLabel> getEventOptions()
	{
		return new Mutation().getEventOptions();
	}

	public java.util.List<ValueLabel> getConsequenceOptions()
	{
		return new Mutation().getConsequenceOptions();
	}

	public java.util.List<ValueLabel> getInheritanceOptions()
	{
		return new Mutation().getInheritanceOptions();
	}

	public Mutation toMutation()
	{
		this.mutation.setExon(this.exonId);
		// this.mutation.setGene(this.gene);
		return this.mutation;
	}

	public String toString()
	{
		return "Gene: " + this.getGeneSymbol() + "\n" + "Position: " + this.getMutation().getMutationPosition() + "\n"
				+ "Nucleotide: " + this.getNt() + "\n" + "Event: " + this.getMutation().getEvent() + "\n"
				+ "Conserved AA: " + this.getMutation().getConservedAA() + "\n" + "Splicing: "
				+ this.getMutation().getEffectOnSplicing() + "\n" + "Founder mut: "
				+ this.getMutation().getFounderMutation() + "\n" + "Population: " + this.getMutation().getPopulation()
				+ "\n" + "SNP?: " + this.getMutation().getReportedSNP() + "\n" + "Inheritance: "
				+ this.getMutation().getInheritance() + "\n" + "NT change: " + this.getMutation().getNtchange() + "\n"
				+ "Codon: " + this.getCodon() + "\n" + "cDNA not: " + this.getMutation().getCdna_Notation() + "\n"
				+ "gDNA not: " + this.getMutation().getGdna_Notation() + "\n" + "AA not: "
				+ this.getMutation().getAa_Notation() + "\n" + "Consequence: " + this.getMutation().getConsequence()
				+ "\n" + "Type: " + this.getMutation().getType() + "\n";
	}
}