org.mzd.shap.analysis.hmmer.bean.Hmmpfam.java Source code

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Here is the source code for org.mzd.shap.analysis.hmmer.bean.Hmmpfam.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.hmmer.bean;

import java.util.ArrayList;
import java.util.List;

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

import com.thoughtworks.xstream.annotations.XStreamAlias;

@XStreamAlias("hmmpfam")
public class Hmmpfam {
    @XStreamAlias("database-file")
    private String databaseFile;
    @XStreamAlias("sequence-file")
    private String sequenceFile;
    @XStreamAlias("results")
    private List<Result> results;

    public Hmmpfam() {
        this(null, null, new ArrayList<Result>());
    }

    public Hmmpfam(String databaseFile, String sequenceFile) {
        this(databaseFile, sequenceFile, new ArrayList<Result>());
    }

    public Hmmpfam(String databaseFile, String sequenceFile, List<Result> results) {
        this.databaseFile = databaseFile;
        this.sequenceFile = sequenceFile;
        this.results = results;
    }

    @Override
    public String toString() {
        return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE).append("databaseFile", getDatabaseFile())
                .append("sequenceFile", getSequenceFile()).append("results", getResults()).toString();
    }

    @Override
    public boolean equals(Object obj) {
        if (obj instanceof Hmmpfam == false) {
            return false;
        }
        if (obj == this) {
            return true;
        }

        Hmmpfam rhs = (Hmmpfam) obj;
        return new EqualsBuilder().append(getDatabaseFile(), rhs.getDatabaseFile())
                .append(getSequenceFile(), rhs.getSequenceFile()).append(getResults(), rhs.getResults()).isEquals();
    }

    public String getDatabaseFile() {
        return databaseFile;
    }

    public void setDatabaseFile(String databaseFile) {
        this.databaseFile = databaseFile;
    }

    public List<Result> getResults() {
        return results;
    }

    public void setResults(List<Result> results) {
        this.results = results;
    }

    public void addResult(Result result) {
        getResults().add(result);
    }

    public String getSequenceFile() {
        return sequenceFile;
    }

    public void setSequenceFile(String sequenceFile) {
        this.sequenceFile = sequenceFile;
    }

}