bio.pih.genoogle.search.results.Hit.java Source code

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Here is the source code for bio.pih.genoogle.search.results.Hit.java

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/*
 * Genoogle: Similar DNA Sequences Searching Engine and Tools. (http://genoogle.pih.bio.br)
 * Copyright (C) 2008,2009  Felipe Fernandes Albrecht (felipe.albrecht@gmail.com)
 *
 * For further information check the LICENSE file.
 */

package bio.pih.genoogle.search.results;

import java.util.Comparator;
import java.util.List;

import com.google.common.collect.Lists;

/**
 * The class stores a Hit from a search. 
 * 
 * @author albrecht
 *
 */
public class Hit {
    private final String id;
    private final String gi;
    private final String accession;
    private final String description;
    private final int length;
    private final String databankName;
    List<HSP> hsps;

    /**
     * @param id
     * @param gi 
     * @param description
     * @param accession
     * @param hitLength
     * @param databankName
     */
    public Hit(String id, String gi, String description, String accession, int hitLength, String databankName) {
        this.id = id;
        this.gi = gi;
        this.accession = accession;
        this.description = description;
        this.length = hitLength;
        this.databankName = databankName;
        this.hsps = Lists.newLinkedList();
    }

    /**
     * @return id of the sequence target.
     */
    public String getId() {
        return id;
    }

    /**
     * @return gi of the sequence target.
     */
    public String getGi() {
        return gi;
    }

    /**
     * @return description of the sequence target.
     */
    public String getDescription() {
        return description;
    }

    /**
     * @return accession of the sequence target.
     */
    public String getAccession() {
        return accession;
    }

    /**
     * @return length of the sequence target.
     */
    public int getLength() {
        return length;
    }

    /**
     * @return {@link List} of HSP related with this Hit.
     */
    public List<HSP> getHSPs() {
        return this.hsps;
    }

    /**
     * Add a new HSP to this Hit.
     * @param hsp
     */
    public void addHSP(HSP hsp) {
        this.hsps.add(hsp);
    }

    /**
     * Add a list of HSPs to this Hit.
     * @param hsps : {@link List} of {@link HSP}. 
     */
    public void addAllHSP(List<HSP> hsps) {
        this.hsps.addAll(hsps);
    }

    /**
     * @return data bank name where the Hit happened.
     */
    public String getDatabankName() {
        return databankName;
    }

    private int totalScore = 0;

    private int getTotalScore() {
        if (totalScore == 0) {
            for (HSP hsp : hsps) {
                totalScore += hsp.getScore();
            }
        }
        return totalScore;
    }

    private double biggestScore = Double.MIN_VALUE;

    private double getBiggestScore() {
        if (biggestScore == Double.MIN_VALUE) {
            for (HSP hsp : hsps) {
                if (hsp.getScore() > biggestScore) {
                    biggestScore = hsp.getScore();
                }
            }
        }
        return biggestScore;
    }

    @Override
    public String toString() {
        StringBuilder sb = new StringBuilder();
        sb.append(getId());
        sb.append(" ");
        sb.append(getDescription());
        sb.append(" ");
        sb.append(getDatabankName());
        return sb.toString();
    }

    /**
     * Verify if the other Hit object is from the same Gi. 
     */
    @Override
    public boolean equals(Object obj) {
        if (super.equals(obj) == true) {
            return true;
        }
        if (!(obj instanceof Hit)) {
            return false;
        }

        Hit other = (Hit) obj;
        return other.gi.equals(gi);
    }

    @Override
    public int hashCode() {
        int hashCode = id.hashCode();
        hashCode *= gi.hashCode();
        hashCode *= accession.hashCode();
        hashCode *= description.hashCode();
        hashCode *= length;
        hashCode *= databankName.hashCode();
        hashCode *= hsps.hashCode();
        return hashCode;
    }

    /**
     * Comparator of two hits by them total score.
     */
    public static final Comparator<Hit> COMPARATOR = new Comparator<Hit>() {
        @Override
        public int compare(Hit o1, Hit o2) {
            int compare = Double.compare(o2.getBiggestScore(), o1.getBiggestScore());
            if (compare != 0) {
                return compare;
            }

            return o2.getTotalScore() - o1.getTotalScore();

        }
    };
}