PatientSummaryDTO.java

package org.molgenis.mutation.dto;

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

import org.apache.commons.collections.CollectionUtils;
import org.molgenis.core.dto.PublicationDTO;
import org.molgenis.pheno.dto.ObservedValueDTO;

public class PatientSummaryDTO implements Comparable<PatientSummaryDTO>, Serializable
{
	/* The serial version UID of this class. Needed for serialization. */
	private static final long serialVersionUID = -8983436185205230071L;

	private Integer patientId;
	private String patientIdentifier;
	private String patientName;
	private String patientLocalId;
	private String patientConsent;
	private List<VariantDTO> variantDTOList;
	private Integer gdnaStart; // for sorting
	private Integer exonNumber; // for sorting
	private String variantComment;
	private Integer phenotypeId;
	private String phenotypeMajor;
	private String phenotypeSub;
	private java.util.Date submissionDate;
	private String submitterDepartment;
	private String submitterInstitute;
	private String submitterCity;
	private String submitterCountry;
	private List<PublicationDTO> publicationDTOList;
	private List<ObservedValueDTO> observedValueDTOList;
	private String pubmedURL;

	public PatientSummaryDTO()
	{
		this.init();
	}

	private void init()
	{
		this.patientId = 0;
		this.patientIdentifier = "";
		this.patientName = "";
		this.patientLocalId = "";
		this.patientConsent = "";
		this.variantDTOList = new ArrayList<VariantDTO>();
		this.gdnaStart = 0;
		this.exonNumber = 0;
		this.variantComment = "";
		this.phenotypeId = 0;
		this.phenotypeMajor = "";
		this.phenotypeSub = "";
		this.submissionDate = new Date();
		this.submitterDepartment = "";
		this.submitterInstitute = "";
		this.submitterCity = "";
		this.submitterCountry = "";
		this.publicationDTOList = new ArrayList<PublicationDTO>();
		this.observedValueDTOList = new ArrayList<ObservedValueDTO>();
		this.pubmedURL = "";
	}

	public Integer getPatientId()
	{
		return patientId;
	}

	public void setPatientId(Integer patientId)
	{
		this.patientId = patientId;
	}

	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 getPatientLocalId()
	{
		return patientLocalId;
	}

	public void setPatientLocalId(String patientLocalId)
	{
		this.patientLocalId = patientLocalId;
	}

	public String getPatientConsent()
	{
		return patientConsent;
	}

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

	public List<VariantDTO> getVariantDTOList()
	{
		return variantDTOList;
	}

	public void setVariantDTOList(List<VariantDTO> variantDTOList)
	{
		this.variantDTOList = variantDTOList;
	}

	public Integer getGdnaStart()
	{
		return gdnaStart;
	}

	public void setGdnaStart(Integer gdnaStart)
	{
		this.gdnaStart = gdnaStart;
	}

	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 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<PublicationDTO> getPublicationDTOList()
	{
		return publicationDTOList;
	}

	public void setPublicationDTOList(List<PublicationDTO> publicationDTOList)
	{
		this.publicationDTOList = publicationDTOList;
	}

	public String getPubmedURL()
	{
		return pubmedURL;
	}

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

	public List<ObservedValueDTO> getObservedValueDTOList()
	{
		return observedValueDTOList;
	}

	public void setObservedValueDTOList(List<ObservedValueDTO> observedValueDTOList)
	{
		this.observedValueDTOList = observedValueDTOList;
	}

	/*
	 * @Override public int compareTo(PatientSummaryDTO o) { if
	 * (CollectionUtils.isEmpty(this.getPublicationDTOList()) ||
	 * CollectionUtils.isEmpty(o.getPublicationDTOList())) return 0;
	 * 
	 * if (StringUtils.isEmpty(this.getPublicationDTOList().get(0).getYear()) ||
	 * StringUtils.isEmpty(o.getPublicationDTOList().get(0).getYear())) return
	 * 0;
	 * 
	 * Integer year1 =
	 * Integer.parseInt(this.getPublicationDTOList().get(0).getYear()); Integer
	 * year2 = Integer.parseInt(o.getPublicationDTOList().get(0).getYear());
	 * 
	 * return year2.compareTo(year1); }
	 */

	@Override
	public int compareTo(PatientSummaryDTO o)
	{
		if (CollectionUtils.isEmpty(this.getVariantDTOList())) return -1;
		if (CollectionUtils.isEmpty(o.getVariantDTOList())) return 1;

		Integer gdnaPosition1 = this.getVariantDTOList().get(0).getGdnaStart();
		Integer gdnaPosition2 = o.getVariantDTOList().get(0).getGdnaStart();

		if (gdnaPosition1.compareTo(gdnaPosition2) == 0)
		{
			if (this.getVariantDTOList().size() == 1) return -1;
			else if (o.getVariantDTOList().size() == 1) return 1;
			else
			{
				gdnaPosition1 = this.getVariantDTOList().get(1).getGdnaStart();
				gdnaPosition2 = o.getVariantDTOList().get(1).getGdnaStart();
			}
		}
		return gdnaPosition1.compareTo(gdnaPosition2) * -1; // gDNA position is
															// descending
	}
}