de.julielab.geneexpbase.genemodel.OrthologyRecord Maven / Gradle / Ivy

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package de.julielab.geneexpbase.genemodel;

import java.io.Serializable;

/**
 * This class models lines from the gene_orthologs file.
 *
 * @see ftp://ftp.ncbi.nih.gov/gene/DATA/
 */
public class OrthologyRecord implements Serializable {
    private final String taxId;
    private final String geneId;
    private final String otherTaxId;
    private final String otherGeneId;

    /**
     * 
     * This constructor expects a line in the original gene_orthologs format.
     * 
     * Used by {@link GeneOrthologs}.
     *
     * @param geneOrthologyLine The orthology record.
     */
    OrthologyRecord(String geneOrthologyLine) {
        if (geneOrthologyLine.startsWith("#"))
            throw new IllegalArgumentException("The line " + geneOrthologyLine + " is a comment and not an orthology record.");
        String[] split = geneOrthologyLine.split("\\t");
        taxId = split[0].trim().intern();
        geneId = split[1].trim().intern();
        otherTaxId = split[3].trim().intern();
        otherGeneId = split[4].trim().intern();
    }

    @Override
    public String toString() {
        return "OrthologyRecord{" +
                "taxId='" + taxId + '\'' +
                ", geneId='" + geneId + '\'' +
                ", otherTaxId='" + otherTaxId + '\'' +
                ", otherGeneId='" + otherGeneId + '\'' +
                '}';
    }

    public String getTaxId() {
        return taxId;
    }

    public String getGeneId() {
        return geneId;
    }

    public String getOtherTaxId() {
        return otherTaxId;
    }

    public String getOtherGeneId() {
        return otherGeneId;
    }

    public String getGeneIdNotEqualTo(String geneId) {
        boolean eqGeneId = geneId.equals(this.geneId);
        boolean eqOtherGeneId = geneId.equals(this.otherGeneId);
        if (eqGeneId && eqOtherGeneId)
            throw new IllegalArgumentException("The gene ID " + geneId + " is not a part of this record: " + this);
        if (eqGeneId)
            return otherGeneId;
        return this.geneId;
    }

    public String getGeneIdForTaxId(String taxId) {
        assert taxId != null : "The passed taxonomy ID is null.";
        if (taxId.equals(this.taxId))
            return geneId;
        if (taxId.equals(otherTaxId))
            return otherGeneId;
        throw new IllegalArgumentException("The taxonomy ID " + taxId + " is not part of this record: " + this);
    }
}