package org.pdxfinder.dao;

import org.neo4j.ogm.annotation.GraphId;
import org.neo4j.ogm.annotation.NodeEntity;

/**
 * Created by csaba on 25/04/2017.
 */
@NodeEntity
public class MarkerAssociation {

    @GraphId
    Long id;

    String description;
    Marker marker;
    
    private String chromosome;
    private String seqPosition;
    private String refAllele;
    private String altAllele;
    private String consequence;
    private String aminoAcidChange;
    private String rsVariants;
    private String readDepth;
    private String alleleFrequency;
    private String refAssembly;

    public MarkerAssociation() {
    }

    public MarkerAssociation(String name, Marker marker) {
        this.description = name;
        this.marker = marker;
    }

    public Long getId() {
        return id;
    }

    public String getDescription() {
        return description;
    }

    public void setId(Long id) {
        this.id = id;
    }

    public void setDescription(String description) {
        this.description = description;
    }

    public Marker getMarker() {
        return marker;
    }

    public void setMarker(Marker marker) {
        this.marker = marker;
    }

    /**
     * @return the chromosome
     */
    public String getChromosome() {
        return chromosome;
    }

    /**
     * @param chromosome the chromosome to set
     */
    public void setChromosome(String chromosome) {
        this.chromosome = chromosome;
    }

    /**
     * @return the seqPosition
     */
    public String getSeqPosition() {
        return seqPosition;
    }

    /**
     * @param seqPosition the seqPosition to set
     */
    public void setSeqPosition(String seqPosition) {
        this.seqPosition = seqPosition;
    }

    /**
     * @return the refAllele
     */
    public String getRefAllele() {
        return refAllele;
    }

    /**
     * @param refAllele the refAllele to set
     */
    public void setRefAllele(String refAllele) {
        this.refAllele = refAllele;
    }

    /**
     * @return the consequence
     */
    public String getConsequence() {
        return consequence;
    }

    /**
     * @param consequence the consequence to set
     */
    public void setConsequence(String consequence) {
        this.consequence = consequence;
    }

    /**
     * @return the aminoAcidChange
     */
    public String getAminoAcidChange() {
        return aminoAcidChange;
    }

    /**
     * @param aminoAcidChange the aminoAcidChange to set
     */
    public void setAminoAcidChange(String aminoAcidChange) {
        this.aminoAcidChange = aminoAcidChange;
    }

    /**
     * @return the rsVariants
     */
    public String getRsVariants() {
        return rsVariants;
    }

    /**
     * @param rsVariants the rsVariants to set
     */
    public void setRsVariants(String rsVariants) {
        this.rsVariants = rsVariants;
    }

    /**
     * @return the readDepth
     */
    public String getReadDepth() {
        return readDepth;
    }

    /**
     * @param readDepth the readDepth to set
     */
    public void setReadDepth(String readDepth) {
        this.readDepth = readDepth;
    }

    /**
     * @return the alleleFrequency
     */
    public String getAlleleFrequency() {
        return alleleFrequency;
    }

    /**
     * @param alleleFrequency the alleleFrequency to set
     */
    public void setAlleleFrequency(String alleleFrequency) {
        this.alleleFrequency = alleleFrequency;
    }

    /**
     * @return the altAllele
     */
    public String getAltAllele() {
        return altAllele;
    }

    /**
     * @param altAllele the altAllele to set
     */
    public void setAltAllele(String altAllele) {
        this.altAllele = altAllele;
    }

    /**
     * @return the refAssembly
     */
    public String getRefAssembly() {
        return refAssembly;
    }

    /**
     * @param refAssembly the refAssembly to set
     */
    public void setRefAssembly(String refAssembly) {
        this.refAssembly = refAssembly;
    }


}

@@ -421,24 +421,58 @@
 consequence;
+ // variant_classification in ircc
 %0A    private
@@ -491,24 +491,61 @@
 oAcidChange;
+ //use hgvsp short, remove p. in ircc
 %0A    private
@@ -661,16 +661,138 @@
 ssembly;
+ //NCBI_build in ircc%0A%0A    private String seqStartPosition;%0A    private String seqEndPosition;%0A    private String strand;%0A
 %0A%0A    pu
@@ -4222,11 +4222,543 @@
 %0A    %7D%0A%0A
+    public String getSeqStartPosition() %7B%0A        return seqStartPosition;%0A    %7D%0A%0A    public void setSeqStartPosition(String seqStartPosition) %7B%0A        this.seqStartPosition = seqStartPosition;%0A    %7D%0A%0A    public String getSeqEndPosition() %7B%0A        return seqEndPosition;%0A    %7D%0A%0A    public void setSeqEndPosition(String seqEndPosition) %7B%0A        this.seqEndPosition = seqEndPosition;%0A    %7D%0A%0A    public String getStrand() %7B%0A        return strand;%0A    %7D%0A%0A    public void setStrand(String strand) %7B%0A        this.strand = strand;%0A    %7D
 %0A%7D%0A

Add seqStartPosition, seqEndPosition and strand placeholders