PatientSummaryVO.java

package org.molgenis.mutation.vo;

import java.io.Serializable;
import java.util.List;

import org.molgenis.core.vo.PublicationVO;

public class PatientSummaryVO implements Serializable
{
	private static final long serialVersionUID = -8983436185205230071L;
	private String patientIdentifier;
	private String patientName;
	private String patientNumber;
	private String patientConsent;
	private String patientAge;
	private String patientGender;
	private String patientEthnicity;
	private String patientDeceased;
	private String patientDeathCause;
	private String patientMmp1Allele1;
	private String patientMmp1Allele2;
	private List<MutationSummaryVO> variantSummaryVOList;
	private Integer cdnaPosition; // for sorting
	private Integer aaPosition; // for sorting
	private Integer exonNumber; // for sorting
	private String variantComment;
	private Integer phenotypeId;
	private String phenotypeMajor;
	private String phenotypeSub;
	private List<String> patientMaterialList;
	private java.util.Date submissionDate;
	private String submitterDepartment;
	private String submitterInstitute;
	private String submitterCity;
	private String submitterCountry;
	private List<PublicationVO> publicationVOList;
	private List<ObservedValueVO> observedValueVOList;

	// TODO: remove old code with persistent objects
	// private Patient patient;
	// private Mutation mutation1;
	// private Mutation mutation2;
	// private MutationPhenotype phenotype;
	// private PhenotypeDetails phenotypeDetails;
	private String pubmedURL;

	// private List<Publication> publications;
	// private Submission submission;
	// private MolgenisUser submitter;
	// private I_F if_;
	// private E_M em_;
	// private List<String> material;

	public PatientSummaryVO()
	{
		// this.mutation1 = new Mutation();
		// this.mutation2 = new Mutation();
		// this.patient = new Patient();
		// this.phenotype = new MutationPhenotype();
		// this.phenotypeDetails = new PhenotypeDetails();
		// this.publications = new ArrayList<Publication>();
		// this.submission = new Submission();
		// this.submitter = new MolgenisUser();
		// this.if_ = new I_F();
		// this.em_ = new E_M();
	}

	public String getPatientIdentifier()
	{
		return patientIdentifier;
	}

	public void setPatientIdentifier(String patientIdentifier)
	{
		this.patientIdentifier = patientIdentifier;
	}

	public String getPatientName()
	{
		return patientName;
	}

	public void setPatientName(String patientName)
	{
		this.patientName = patientName;
	}

	public String getPatientNumber()
	{
		return patientNumber;
	}

	public void setPatientNumber(String patientNumber)
	{
		this.patientNumber = patientNumber;
	}

	public String getPatientConsent()
	{
		return patientConsent;
	}

	public void setPatientConsent(String patientConsent)
	{
		this.patientConsent = patientConsent;
	}

	public String getPatientAge()
	{
		return patientAge;
	}

	public void setPatientAge(String patientAge)
	{
		this.patientAge = patientAge;
	}

	public String getPatientGender()
	{
		return patientGender;
	}

	public void setPatientGender(String patientGender)
	{
		this.patientGender = patientGender;
	}

	public String getPatientEthnicity()
	{
		return patientEthnicity;
	}

	public void setPatientEthnicity(String patientEthnicity)
	{
		this.patientEthnicity = patientEthnicity;
	}

	public String getPatientDeceased()
	{
		return patientDeceased;
	}

	public void setPatientDeceased(String patientDeceased)
	{
		this.patientDeceased = patientDeceased;
	}

	public String getPatientDeathCause()
	{
		return patientDeathCause;
	}

	public void setPatientDeathCause(String patientDeathCause)
	{
		this.patientDeathCause = patientDeathCause;
	}

	public String getPatientMmp1Allele1()
	{
		return patientMmp1Allele1;
	}

	public void setPatientMmp1Allele1(String patientMmp1Allele1)
	{
		this.patientMmp1Allele1 = patientMmp1Allele1;
	}

	public String getPatientMmp1Allele2()
	{
		return patientMmp1Allele2;
	}

	public void setPatientMmp1Allele2(String patientMmp1Allele2)
	{
		this.patientMmp1Allele2 = patientMmp1Allele2;
	}

	public List<MutationSummaryVO> getVariantSummaryVOList()
	{
		return variantSummaryVOList;
	}

	public void setVariantSummaryVOList(List<MutationSummaryVO> variantSummaryVOList)
	{
		this.variantSummaryVOList = variantSummaryVOList;
	}

	public Integer getCdnaPosition()
	{
		return cdnaPosition;
	}

	public void setCdnaPosition(Integer cdnaPosition)
	{
		this.cdnaPosition = cdnaPosition;
	}

	public Integer getAaPosition()
	{
		return aaPosition;
	}

	public void setAaPosition(Integer aaPosition)
	{
		this.aaPosition = aaPosition;
	}

	public Integer getExonNumber()
	{
		return exonNumber;
	}

	public void setExonNumber(Integer exonNumber)
	{
		this.exonNumber = exonNumber;
	}

	public String getVariantComment()
	{
		return variantComment;
	}

	public void setVariantComment(String variantComment)
	{
		this.variantComment = variantComment;
	}

	public Integer getPhenotypeId()
	{
		return phenotypeId;
	}

	public void setPhenotypeId(Integer phenotypeId)
	{
		this.phenotypeId = phenotypeId;
	}

	public String getPhenotypeMajor()
	{
		return phenotypeMajor;
	}

	public void setPhenotypeMajor(String phenotypeMajor)
	{
		this.phenotypeMajor = phenotypeMajor;
	}

	public String getPhenotypeSub()
	{
		return phenotypeSub;
	}

	public void setPhenotypeSub(String phenotypeSub)
	{
		this.phenotypeSub = phenotypeSub;
	}

	public List<String> getPatientMaterialList()
	{
		return patientMaterialList;
	}

	public void setPatientMaterialList(List<String> patientMaterialList)
	{
		this.patientMaterialList = patientMaterialList;
	}

	public java.util.Date getSubmissionDate()
	{
		return submissionDate;
	}

	public void setSubmissionDate(java.util.Date submissionDate)
	{
		this.submissionDate = submissionDate;
	}

	public String getSubmitterDepartment()
	{
		return submitterDepartment;
	}

	public void setSubmitterDepartment(String submitterDepartment)
	{
		this.submitterDepartment = submitterDepartment;
	}

	public String getSubmitterInstitute()
	{
		return submitterInstitute;
	}

	public void setSubmitterInstitute(String submitterInstitute)
	{
		this.submitterInstitute = submitterInstitute;
	}

	public String getSubmitterCity()
	{
		return submitterCity;
	}

	public void setSubmitterCity(String submitterCity)
	{
		this.submitterCity = submitterCity;
	}

	public String getSubmitterCountry()
	{
		return submitterCountry;
	}

	public void setSubmitterCountry(String submitterCountry)
	{
		this.submitterCountry = submitterCountry;
	}

	public List<PublicationVO> getPublicationVOList()
	{
		return publicationVOList;
	}

	public void setPublicationVOList(List<PublicationVO> publicationVOList)
	{
		this.publicationVOList = publicationVOList;
	}

	public List<ObservedValueVO> getObservedValueVOList()
	{
		return observedValueVOList;
	}

	public void setObservedValueVOList(List<ObservedValueVO> observedValueVOList)
	{
		this.observedValueVOList = observedValueVOList;
	}

	// public Patient getPatient() {
	// return patient;
	// }
	// public void setPatient(Patient patient) {
	// this.patient = patient;
	// }
	// public Mutation getMutation1() {
	// return mutation1;
	// }
	// public void setMutation1(Mutation mutation1) {
	// this.mutation1 = mutation1;
	// }
	// public Mutation getMutation2() {
	// return mutation2;
	// }
	// public void setMutation2(Mutation mutation2) {
	// this.mutation2 = mutation2;
	// }
	// public MutationPhenotype getPhenotype() {
	// return phenotype;
	// }
	// public void setPhenotype(MutationPhenotype phenotype) {
	// this.phenotype = phenotype;
	// }
	// public PhenotypeDetails getPhenotypeDetails() {
	// return phenotypeDetails;
	// }
	// public void setPhenotypeDetails(PhenotypeDetails phenotypeDetails) {
	// this.phenotypeDetails = phenotypeDetails;
	// }
	public String getPubmedURL()
	{
		return pubmedURL;
	}

	public void setPubmedURL(String pubmedURL)
	{
		this.pubmedURL = pubmedURL;
	}

	// public List<Publication> getPublications() {
	// return publications;
	// }
	// public void setPublications(List<Publication> publications) {
	// this.publications = publications;
	// }
	// public Submission getSubmission() {
	// return submission;
	// }
	// public void setSubmission(Submission submission) {
	// this.submission = submission;
	// }
	// public MolgenisUser getSubmitter() {
	// return submitter;
	// }
	// public void setSubmitter(MolgenisUser submitter) {
	// this.submitter = submitter;
	// }
	// public I_F getIf_() {
	// return if_;
	// }
	// public void setIf_(I_F if_) {
	// this.if_ = if_;
	// }
	// public E_M getEm_() {
	// return em_;
	// }
	// public void setEm_(E_M em_) {
	// this.em_ = em_;
	// }
	// public List<String> getMaterial() {
	// return material;
	// }
	// public void setMaterial(List<String> material) {
	// this.material = material;
	// }

	public String toString()
	{
		return "";
		// "Patient No: " + this.getPatient().getNumber() + "\n" +
		// "Mutation1: " + (this.getMutation1() != null ?
		// this.getMutation1().toString() : "") + "\n" +
		// "Mutation2: " + (this.getMutation2() != null ?
		// this.getMutation2().toString() : "") + "\n" +
		// "Phenotype: " + this.getPhenotype().toString() + "\n" +
		// "Pubmed ID: " + (CollectionUtils.isNotEmpty(this.getPublications()) ?
		// this.getPublications().get(0).getPubmedID_Name() : "") + "\n" +
		// // "Article: " + (CollectionUtils.isNotEmpty(this.getPublications())
		// ? this.getPublications().get(0).getPdf() : "") + "\n" +
		// "Age: " + this.getPatient().getAge() + "\n" +
		// "Deceased?: " + this.getPatient().getDeceased() + "\n" +
		// "Consent: " + this.getPatient().getConsent() + "\n" +
		// "Details: " + (this.getPhenotypeDetails() != null ?
		// this.getPhenotypeDetails().toString() : "") + "\n" +
		// "IF: " + (this.getIf_() != null ? this.getIf_().toString() : "") +
		// "\n" +
		// "EM: " + (this.getEm_() != null ? this.getEm_().toString() : "") +
		// "\n";
	}
}