edu.scripps.fl.pubchem.db.PCAssayPanel.java Source code

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Here is the source code for edu.scripps.fl.pubchem.db.PCAssayPanel.java

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/*
 * Copyright 2010 The Scripps Research Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package edu.scripps.fl.pubchem.db;

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

import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.Table;
import javax.persistence.Transient;
import javax.persistence.UniqueConstraint;

import org.apache.commons.collections.CollectionUtils;
import org.apache.commons.collections.Predicate;
import org.apache.commons.lang.builder.ToStringBuilder;

@Entity
@Table(name = "pcassay_panel", uniqueConstraints = {
        @UniqueConstraint(columnNames = { "assay_assay_id", "panel_number" }) })
public class PCAssayPanel implements Serializable {

    private String activityOutcomeMethod = "";
    private PCAssay assay = null;
    private String comment = "";
    private String description = "";
    private Integer id = -1;
    private String name = "";
    private Integer panelNumber = -1;
    private String protocol = "";

    @Override
    public boolean equals(Object obj) {
        if (this == obj)
            return true;
        if (obj == null)
            return false;
        if (!(obj instanceof PCAssayPanel))
            return false;
        PCAssayPanel other = (PCAssayPanel) obj;
        if (panelNumber == null) {
            if (other.panelNumber != null)
                return false;
        } else if (!panelNumber.equals(other.panelNumber))
            return false;
        if (assay == null) {
            if (other.assay != null)
                return false;
        } else if (!assay.equals(other.assay))
            return false;
        return true;
    }

    @Column(name = "panel_outcome_method")
    public String getActivityOutcomeMethod() {
        return activityOutcomeMethod;
    }

    @ManyToOne(optional = false)
    @JoinColumn(name = "assay_assay_id")
    public PCAssay getAssay() {
        return assay;
    }

    @Column(name = "panel_comment", length = 500)
    public String getComment() {
        return comment;
    }

    @Column(name = "panel_description", length = 500)
    public String getDescription() {
        return description;
    }

    @Transient
    public XRef getGene() {
        List<PCAssayXRef> list = new ArrayList();
        CollectionUtils.select(assay.getAssayXRefs(), new Predicate() {
            public boolean evaluate(Object object) {
                PCAssayXRef xref = (PCAssayXRef) object;
                if (xref.getPanel() != null)
                    if (xref.getPanel().getPanelNumber() == getPanelNumber() && xref.getXRef() != null
                            && "gene".equals(xref.getXRef().getDatabase()))
                        return true;
                return false;
            }
        }, list);
        return list.size() > 0 ? list.get(0).getXRef() : null;
    }

    @Id
    @Column(name = "panel_id")
    @GeneratedValue(strategy = GenerationType.AUTO)
    public Integer getId() {
        return id;
    }

    @Column(name = "panel_name")
    public String getName() {
        return name;
    }

    @Column(name = "panel_number", nullable = false)
    public Integer getPanelNumber() {
        return panelNumber;
    }

    @Column(name = "panel_protocol", length = 500)
    public String getProtocol() {
        return protocol;
    }

    @Transient
    public XRef getTarget() {
        List<PCAssayXRef> list = new ArrayList();
        CollectionUtils.select(assay.getAssayXRefs(), new Predicate() {
            public boolean evaluate(Object object) {
                PCAssayXRef xref = (PCAssayXRef) object;
                if (xref.getPanel() != null)
                    if (xref.getPanel().getPanelNumber() == getPanelNumber() && xref.isTarget() == true)
                        return true;
                return false;
            }
        }, list);
        return list.size() > 0 ? list.get(0).getXRef() : null;
    }

    @Transient
    public XRef getTaxonomy() {
        List<PCAssayXRef> list = new ArrayList();
        CollectionUtils.select(assay.getAssayXRefs(), new Predicate() {
            public boolean evaluate(Object object) {
                PCAssayXRef xref = (PCAssayXRef) object;
                if (xref.getPanel() != null)
                    if (xref.getPanel().getPanelNumber() == getPanelNumber())
                        if (xref.getXRef() != null && "taxonomy".equals(xref.getXRef().getDatabase()))
                            return true;
                return false;
            }
        }, list);
        return list.size() > 0 ? list.get(0).getXRef() : null;
    }

    @Override
    public int hashCode() {
        final int prime = 31;
        int result = 1;
        result = prime * result + ((panelNumber == null) ? 0 : panelNumber.hashCode());
        result = prime * result + ((assay == null) ? 0 : assay.hashCode());
        return result;
    }

    public void setActivityOutcomeMethod(String activityOutcomeMethod) {
        this.activityOutcomeMethod = activityOutcomeMethod;
    }

    public void setAssay(PCAssay assay) {
        this.assay = assay;
    }

    public void setComment(String comment) {
        this.comment = comment;
    }

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

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

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

    public void setPanelNumber(Integer panelNumber) {
        this.panelNumber = panelNumber;
    }

    public void setProtocol(String protocol) {
        this.protocol = protocol;
    }

    @Override
    public String toString() {
        return ToStringBuilder.reflectionToString(this);
    }
}