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

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Here is the source code for org.mzd.shap.analysis.blast.bean.BlastOutput.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 java.util.ArrayList;
import java.util.List;

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

import com.thoughtworks.xstream.annotations.XStreamAlias;

@XStreamAlias("BlastOutput")
public class BlastOutput {
    @XStreamAlias("BlastOutput_program")
    private String program;
    @XStreamAlias("BlastOutput_version")
    private String version;
    @XStreamAlias("BlastOutput_reference")
    private String reference;
    @XStreamAlias("BlastOutput_db")
    private String database;
    @XStreamAlias("BlastOutput_query-ID")
    private String queryId;
    @XStreamAlias("BlastOutput_query-def")
    private String queryDefinition;
    @XStreamAlias("BlastOutput_query-len")
    private Integer queryLength;
    @XStreamAlias("BlastOutput_query-seq")
    private String querySequence;
    @XStreamAlias("BlastOutput_param")
    private Parameters parameters;
    @XStreamAlias("BlastOutput_iterations")
    private List<Iteration> iterations = new ArrayList<Iteration>();
    @XStreamAlias("BlastOutput_mbstat")
    private Statistics megablastStatistics;

    @Override
    public String toString() {
        return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE).append("program", getProgram())
                .append("version", getVersion()).append("reference", getReference())
                .append("database", getDatabase()).append("queryId", getQueryId())
                .append("queryDefinition", getQueryDefinition()).append("queryLength", getQueryLength())
                .append("querySequence", getQuerySequence()).append("parameters", getParameters())
                .append("iterations", getIterations()).append("megablastStatistics", getMegablastStatistics())
                .toString();
    }

    public String getProgram() {
        return program;
    }

    public void setProgram(String program) {
        this.program = program;
    }

    public String getVersion() {
        return version;
    }

    public void setVersion(String version) {
        this.version = version;
    }

    public String getReference() {
        return reference;
    }

    public void setReference(String reference) {
        this.reference = reference;
    }

    public String getDatabase() {
        return database;
    }

    public void setDatabase(String database) {
        this.database = database;
    }

    public String getQueryId() {
        return queryId;
    }

    public void setQueryId(String queryId) {
        this.queryId = queryId;
    }

    public String getQueryDefinition() {
        return queryDefinition;
    }

    public void setQueryDefinition(String queryDefinition) {
        this.queryDefinition = queryDefinition;
    }

    public Integer getQueryLength() {
        return queryLength;
    }

    public void setQueryLength(Integer queryLength) {
        this.queryLength = queryLength;
    }

    public Parameters getParameters() {
        return parameters;
    }

    public void setParameters(Parameters parameters) {
        this.parameters = parameters;
    }

    public List<Iteration> getIterations() {
        return iterations;
    }

    public void setIterations(List<Iteration> iterations) {
        this.iterations = iterations;
    }

    public void addIteration(Iteration iteration) {
        getIterations().add(iteration);
    }

    public String getQuerySequence() {
        return querySequence;
    }

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

    public Statistics getMegablastStatistics() {
        return megablastStatistics;
    }

    public void setMegablastStatistics(Statistics megablastStatistics) {
        this.megablastStatistics = megablastStatistics;
    }

}