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

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Here is the source code for org.mzd.shap.analysis.blast.bean.Parameters.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("Parameters")
public class Parameters {
    @XStreamAlias("Parameters_matrix")
    private String matrix;
    @XStreamAlias("Parameters_expect")
    private Double expectation;
    @XStreamAlias("Parameters_include")
    private Double include;
    @XStreamAlias("Parameters_sc-match")
    private Integer matchScore;
    @XStreamAlias("Parameters_sc-mismatch")
    private Integer mismatchScore;
    @XStreamAlias("Parameters_gap-open")
    private Integer gapOpenCost;
    @XStreamAlias("Parameters_gap-extend")
    private Integer gapExtensionCost;
    @XStreamAlias("Parameters_filter")
    private String filterOptions;
    @XStreamAlias("Parameters_pattern")
    private String phiBlastPattern;
    @XStreamAlias("Parameters_entrez-query")
    private String requestLimit;

    @Override
    public String toString() {
        return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE).append("matrix", getMatrix())
                .append("expectation", getExpectation()).append("include", getInclude())
                .append("matchScore", getMatchScore()).append("mismatchScore", getMismatchScore())
                .append("gapOpenCost", getGapOpenCost()).append("gapExtensionCost", getGapExtensionCost())
                .append("filterOptions", getFilterOptions()).append("phiBlastPattern", getPhiBlastPattern())
                .append("requestLimit", getRequestLimit()).toString();
    }

    public String getMatrix() {
        return matrix;
    }

    public void setMatrix(String matrix) {
        this.matrix = matrix;
    }

    public Double getExpectation() {
        return expectation;
    }

    public void setExpectation(Double expectation) {
        this.expectation = expectation;
    }

    public Double getInclude() {
        return include;
    }

    public void setInclude(Double include) {
        this.include = include;
    }

    public Integer getMatchScore() {
        return matchScore;
    }

    public void setMatchScore(Integer matchScore) {
        this.matchScore = matchScore;
    }

    public Integer getMismatchScore() {
        return mismatchScore;
    }

    public void setMismatchScore(Integer mismatchScore) {
        this.mismatchScore = mismatchScore;
    }

    public Integer getGapOpenCost() {
        return gapOpenCost;
    }

    public void setGapOpenCost(Integer gapOpenCost) {
        this.gapOpenCost = gapOpenCost;
    }

    public Integer getGapExtensionCost() {
        return gapExtensionCost;
    }

    public void setGapExtensionCost(Integer gapExtensionCost) {
        this.gapExtensionCost = gapExtensionCost;
    }

    public String getFilterOptions() {
        return filterOptions;
    }

    public void setFilterOptions(String filterOptions) {
        this.filterOptions = filterOptions;
    }

    public String getPhiBlastPattern() {
        return phiBlastPattern;
    }

    public void setPhiBlastPattern(String phiBlastPattern) {
        this.phiBlastPattern = phiBlastPattern;
    }

    public String getRequestLimit() {
        return requestLimit;
    }

    public void setRequestLimit(String requestLimit) {
        this.requestLimit = requestLimit;
    }

}