<commit_before>package uk.ac.ebi.spot.goci.model;

import org.apache.solr.client.solrj.beans.Field;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
 * Javadocs go here!
 *
 * @author <NAME>
 * @date 16/01/15
 */
public class AssociationDocument extends OntologyEnabledDocument<Association> {
    // basic Association information
    @Field @NonEmbeddableField private String riskFrequency;
    @Field private String qualifier;

    @Field @NonEmbeddableField private Integer pValueMantissa;
    @Field @NonEmbeddableField private Integer pValueExponent;
    @Field @NonEmbeddableField private Float orPerCopyNum;
    @Field @NonEmbeddableField private Float betaNum;
    @Field @NonEmbeddableField private String betaUnit;
    @Field @NonEmbeddableField private String betaDirection;
    @Field("orDescription") @NonEmbeddableField private String description;
    @Field @NonEmbeddableField private String range;
    //    @Field @NonEmbeddableField private String orType;
    @Field @NonEmbeddableField private Boolean snpInteraction;
    @Field @NonEmbeddableField private Boolean multiSnpHaplotype;

    // additional included genetic data...
    // capture loci/risk alleles for association;
    // if many, collapse risk allele and snp into a single field and use
    // 'x' or ',' to separate SNP x SNP and haplotype associations respectively
    @Field private String rsId;
    @Field private String strongestAllele;
    @Field private String context;
    //    @Field private String region;
    @Field("region") private Set<String> region;

    // mapped genes and reported genes must be per snp -
    // if multiple, separate mapped genes with a hyphen (downstream-upstream) and reported genes with a slash,
    // and then include 'x' or ',' as designated by multiple loci/risk alleles
//    @Field("entrezMappedGenes") private Collection<String> entrezMappedGenes;
//    @Field("entrezMappedGeneLinks") private Collection<String> entrezMappedGeneLinks;<commit_msg>add default value to solr booleans<commit_after>package uk.ac.ebi.spot.goci.model;

import org.apache.solr.client.solrj.beans.Field;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
 * Javadocs go here!
 *
 * @author <NAME>
 * @date 16/01/15
 */
public class AssociationDocument extends OntologyEnabledDocument<Association> {
    // basic Association information
    @Field @NonEmbeddableField private String riskFrequency;
    @Field private String qualifier;

    @Field @NonEmbeddableField private Integer pValueMantissa;
    @Field @NonEmbeddableField private Integer pValueExponent;
    @Field @NonEmbeddableField private Float orPerCopyNum;
    @Field @NonEmbeddableField private Float betaNum;
    @Field @NonEmbeddableField private String betaUnit;
    @Field @NonEmbeddableField private String betaDirection;
    @Field("orDescription") @NonEmbeddableField private String description;
    @Field @NonEmbeddableField private String range;
    //    @Field @NonEmbeddableField private String orType;
    @Field @NonEmbeddableField private Boolean snpInteraction = false;
    @Field @NonEmbeddableField private Boolean multiSnpHaplotype = false;

    // additional included genetic data...
    // capture loci/risk alleles for association;
    // if many, collapse risk allele and snp into a single field and use
    // 'x' or ',' to separate SNP x SNP and haplotype associations respectively
    @Field private String rsId;
    @Field private String strongestAllele;
    @Field private String context;
    //    @Field private String region;
    @Field("region") private Set<String> region;

    // mapped genes and reported genes must be per snp -
    // if multiple, separate mapped genes with a hyphen (downstream-upstream) and reported genes with a slash,
    // and then include 'x' or ',' as designated by multiple loci/risk alleles
//    @Field("entrezMappedGenes") private Collection<String> entrezMappedGenes;
//    @Field("entrezMappedGeneLinks") private Collection<String> entrezMappedGeneLinks;
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