Compound.java

package gov.nih.ncgc.bard.entity;

import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.databind.ObjectMapper;
import gov.nih.ncgc.bard.rest.BARDConstants;
import gov.nih.ncgc.bard.tools.BARDJsonRequired;

import java.io.IOException;
import java.io.StringWriter;
import java.io.Writer;
import java.util.List;

/**
 * Represents a compound.
 * <p/>
 * Currently, a compound is simply referred to by its CID in the database. I think
 * we should at least include the SMILES.
 * <p/>
 *
 * @author Rajarshi Guha
 */
public class Compound extends BaseEntity {

    @BARDJsonRequired
    Long cid;

    @JsonIgnore
    List<Long> sids;

    String probeId = null;
    String url = null;
    String smiles = null;
    String name;
    String iupacName;
    Double mwt;
    Double tpsa;
    Double exactMass;
    Double xlogp;
    Integer complexity;
    Integer rotatable;
    Integer hbondAcceptor;
    Integer hbondDonor;
    String compoundClass;


    // number of assays compound is tested in
    Integer numAssay;
    // number of assays compound is tested in and is active
    Integer numActiveAssay;

//    Map<String, String> probeDetails = null;
    List probeAnnotations;

    @JsonIgnore
    String[] anno_val, anno_key;

    String highlight;

    public Compound(Long cid, String probeId, String url) {
        this.cid = cid;
        this.probeId = probeId;
        this.url = url;
    }

    public Compound() {
    }

    public List getProbeAnnotations() {
        return probeAnnotations;
    }

    public void setProbeAnnotations(List probeAnnotations) {
        this.probeAnnotations = probeAnnotations;
    }

    public String getCompoundClass() {
        return compoundClass;
    }

    public void setCompoundClass(String compoundClass) {
        this.compoundClass = compoundClass;
    }

    public Integer getNumAssay() {
        return numAssay;
    }

    public void setNumAssay(Integer numAssay) {
        this.numAssay = numAssay;
    }

    public Integer getNumActiveAssay() {
        return numActiveAssay;
    }

    public void setNumActiveAssay(Integer numActiveAssay) {
        this.numActiveAssay = numActiveAssay;
    }

    public String[] getAnno_val() {
        return anno_val;
    }

    public void setAnno_val(String[] anno_val) {
        this.anno_val = anno_val;
    }

    public String[] getAnno_key() {
        return anno_key;
    }

    public void setAnno_key(String[] anno_key) {
        this.anno_key = anno_key;
    }

    public List<Long> getSids() {
        return sids;
    }

    public void setSids(List<Long> sids) {
        this.sids = sids;
    }

    public String getSmiles() {
        return smiles;
    }

    public void setSmiles(String smiles) {
        this.smiles = smiles;
    }

    public Long getCid() {
        return cid;
    }

    public String getProbeId() {
        return probeId;
    }

    public String getUrl() {
        return url;
    }

    public void setCid(Long cid) {
        this.cid = cid;
    }

    public void setProbeId(String probeId) {
        this.probeId = probeId;
    }

    public void setUrl(String url) {
        this.url = url;
    }

    public void setName (String name) { this.name = name; }
    public String getName () { return name; }

    public void setIupacName (String iupac) { this.iupacName = iupac; }
    public String getIupacName () { return iupacName; }

    public void setMwt (Double mwt) { this.mwt = mwt; }
    public Double getMwt () { return mwt; }

    public void setTpsa (Double tpsa) { this.tpsa = tpsa; }
    public Double getTpsa () { return tpsa; }

    public void setExactMass (Double exactMass) { this.exactMass= exactMass; }
    public Double getExactMass () { return exactMass; }

    public void setXlogp (Double xlogp) { this.xlogp = xlogp; }
    public Double getXlogp () { return xlogp; }

    public void setComplexity (Integer complexity) { 
        this.complexity = complexity; 
    }
    public Integer getComplexity () { return complexity; }

    public void setRotatable (Integer rotatable) { 
        this.rotatable = rotatable; 
    }
    public Integer getRotatable () { return rotatable; }

    public void setHbondAcceptor (Integer hbondAcceptor) {
        this.hbondAcceptor = hbondAcceptor;
    }
    public Integer getHbondAcceptor () { return hbondAcceptor; }

    public void setHbondDonor (Integer hbondDonor) {
        this.hbondDonor = hbondDonor;
    }
    public Integer getHbondDonor () { return hbondDonor; }

    public void setHighlight (String highlight) {
        this.highlight = highlight;
    }
    public String getHighlight () { return highlight; }

    public String toJson() throws IOException {
        ObjectMapper mapper = new ObjectMapper();
        Writer writer = new StringWriter();
        mapper.writeValue(writer, this);
        return writer.toString();
    }

    /**
     * Return the path for this resource in the REST API.
     * <p/>
     * The actual resource can be accessed by prepending the hostname of the server
     * hosting the REST API.
     *
     * @return The path to this resource. <code>null</code> if the object is not meant
     *         to be publically available via the REST API
     */
    public String getResourcePath() {
        return BARDConstants.API_BASE + "/compounds/" + cid;
    }

    // this is a dummy setter, so that Jackson is happy during deserialization
    public void setResourcePath(String resourcePath) {
    }
}