org.mzd.shap.analysis.blast.bean.Hsp.java Source code

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Here is the source code for org.mzd.shap.analysis.blast.bean.Hsp.java

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/**
 *
 * Copyright 2010 Matthew Z DeMaere.
 * 
 * This file is part of SHAP.
 *
 * SHAP is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * SHAP is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with SHAP.  If not, see <http://www.gnu.org/licenses/>.
 * 
 */
package org.mzd.shap.analysis.blast.bean;

import org.apache.commons.lang.builder.ToStringBuilder;
import org.apache.commons.lang.builder.ToStringStyle;

import com.thoughtworks.xstream.annotations.XStreamAlias;

@XStreamAlias("Hsp")
public class Hsp {
    @XStreamAlias("Hsp_num")
    private Integer number;
    @XStreamAlias("Hsp_bit-score")
    private Double bitScore;
    @XStreamAlias("Hsp_score")
    private Double score;
    @XStreamAlias("Hsp_evalue")
    private Double evalue;
    @XStreamAlias("Hsp_query-from")
    private Integer queryFrom;
    @XStreamAlias("Hsp_query-to")
    private Integer queryTo;
    @XStreamAlias("Hsp_hit-from")
    private Integer hitFrom;
    @XStreamAlias("Hsp_hit-to")
    private Integer hitTo;
    @XStreamAlias("Hsp_pattern-from")
    private Integer patternFrom;
    @XStreamAlias("Hsp_pattern-to")
    private Integer patternTo;
    @XStreamAlias("Hsp_query-frame")
    private Integer queryFrame;
    @XStreamAlias("Hsp_hit-frame")
    private Integer hitFrame;
    @XStreamAlias("Hsp_identity")
    private Integer identities;
    @XStreamAlias("Hsp_positive")
    private Integer positives;
    @XStreamAlias("Hsp_gaps")
    private Integer gaps;
    @XStreamAlias("Hsp_align-len")
    private Integer alignLength;
    @XStreamAlias("Hsp_density")
    private Integer scoreDensity;
    @XStreamAlias("Hsp_qseq")
    private String querySequence;
    @XStreamAlias("Hsp_hseq")
    private String hitSequence;
    @XStreamAlias("Hsp_midline")
    private String midline;

    @Override
    public String toString() {
        return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE).append("number", getNumber())
                .append("bitScore", getBitScore()).append("score", getScore()).append("evalue", getEvalue())
                .append("queryFrom", getQueryFrom()).append("queryTo", getQueryTo()).append("hitFrom", getHitFrom())
                .append("hitTo", getHitTo()).append("patternFrom", getPatternFrom())
                .append("patternTo", getPatternTo()).append("queryFrame", getQueryFrame())
                .append("hitFrame", getHitFrame()).append("identities", getIdentities())
                .append("positives", getPositives()).append("gaps", getGaps())
                .append("alignLength", getAlignLength()).append("scoreDensity", getScoreDensity())
                .append("querySequence", getQuerySequence()).append("hitSequence", getHitSequence())
                .append("midline", getMidline()).toString();
    }

    public Integer getNumber() {
        return number;
    }

    public void setNumber(Integer number) {
        this.number = number;
    }

    public Double getBitScore() {
        return bitScore;
    }

    public void setBitScore(Double bitScore) {
        this.bitScore = bitScore;
    }

    public Double getScore() {
        return score;
    }

    public void setScore(Double score) {
        this.score = score;
    }

    public Double getEvalue() {
        return evalue;
    }

    public void setEvalue(Double evalue) {
        this.evalue = evalue;
    }

    public Integer getQueryFrom() {
        return queryFrom;
    }

    public void setQueryFrom(Integer queryFrom) {
        this.queryFrom = queryFrom;
    }

    public Integer getQueryTo() {
        return queryTo;
    }

    public void setQueryTo(Integer queryTo) {
        this.queryTo = queryTo;
    }

    public Integer getHitFrom() {
        return hitFrom;
    }

    public void setHitFrom(Integer hitFrom) {
        this.hitFrom = hitFrom;
    }

    public Integer getHitTo() {
        return hitTo;
    }

    public void setHitTo(Integer hitTo) {
        this.hitTo = hitTo;
    }

    public Integer getPatternFrom() {
        return patternFrom;
    }

    public void setPatternFrom(Integer patternFrom) {
        this.patternFrom = patternFrom;
    }

    public Integer getPatternTo() {
        return patternTo;
    }

    public void setPatternTo(Integer patternTo) {
        this.patternTo = patternTo;
    }

    public Integer getQueryFrame() {
        return queryFrame;
    }

    public void setQueryFrame(Integer queryFrame) {
        this.queryFrame = queryFrame;
    }

    public Integer getHitFrame() {
        return hitFrame;
    }

    public void setHitFrame(Integer hitFrame) {
        this.hitFrame = hitFrame;
    }

    public Integer getIdentities() {
        return identities;
    }

    public void setIdentities(Integer identities) {
        this.identities = identities;
    }

    public Integer getPositives() {
        return positives;
    }

    public void setPositives(Integer positives) {
        this.positives = positives;
    }

    public Integer getGaps() {
        return gaps;
    }

    public void setGaps(Integer gaps) {
        this.gaps = gaps;
    }

    public Integer getAlignLength() {
        return alignLength;
    }

    public void setAlignLength(Integer alignLength) {
        this.alignLength = alignLength;
    }

    public Integer getScoreDensity() {
        return scoreDensity;
    }

    public void setScoreDensity(Integer scoreDensity) {
        this.scoreDensity = scoreDensity;
    }

    public String getQuerySequence() {
        return querySequence;
    }

    public void setQuerySequence(String querySequence) {
        this.querySequence = querySequence;
    }

    public String getHitSequence() {
        return hitSequence;
    }

    public void setHitSequence(String hitSequence) {
        this.hitSequence = hitSequence;
    }

    public String getMidline() {
        return midline;
    }

    public void setMidline(String midline) {
        this.midline = midline;
    }

}