com.ohnosequences.xml.model.BlastOutputParam.java Source code

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Here is the source code for com.ohnosequences.xml.model.BlastOutputParam.java

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/*
 * Copyright (C) 2010-2012  "Oh no sequences!"
 *
 * This is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 * This program 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 Affero General Public License for more details.
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>
 */

package com.ohnosequences.xml.model;

import com.ohnosequences.xml.api.model.XMLElement;
import com.ohnosequences.xml.api.model.XMLElementException;
import org.jdom2.Element;

/**
 *
 * @author <a href="mailto:ppareja@ohnosequences.com">Pablo Pareja-Tobes</a>
 */
public class BlastOutputParam extends XMLElement {

    public static final String TAG_NAME = "BlastOutput_param";

    public static final String PARAMETERS_TAG_NAME = "Parameters";

    public static final String MATRIX_TAG_NAME = "Parameters_matrix";
    public static final String EXPECT_TAG_NAME = "Parameters_expect";
    public static final String GAP_OPEN_TAG_NAME = "Parameters_gap-open";
    public static final String GAP_EXTEND_TAG_NAME = "Parameters_gap-extend";
    public static final String FILTER_TAG_NAME = "Parameters_filter";

    public BlastOutputParam() {
        super(new Element(TAG_NAME));
    }

    public BlastOutputParam(Element elem) throws XMLElementException {
        super(elem);
        if (!elem.getName().equals(TAG_NAME)) {
            throw new XMLElementException(XMLElementException.WRONG_TAG_NAME, new XMLElement(elem));
        }
    }

    public BlastOutputParam(String value) throws Exception {
        super(value);
        if (!root.getName().equals(TAG_NAME)) {
            throw new XMLElementException(XMLElementException.WRONG_TAG_NAME, new XMLElement(value));
        }
    }

    //----------------SETTERS-------------------
    public void setMatrix(String value) {
        initParametersTag();
        setNodeText(MATRIX_TAG_NAME, value);
    }

    public void setExpect(String value) {
        initParametersTag();
        setNodeText(EXPECT_TAG_NAME, value);
    }

    public void setGapOpen(String value) {
        initParametersTag();
        setNodeText(GAP_OPEN_TAG_NAME, value);
    }

    public void setGapExtend(String value) {
        initParametersTag();
        setNodeText(GAP_EXTEND_TAG_NAME, value);
    }

    public void setFilter(String value) {
        initParametersTag();
        setNodeText(FILTER_TAG_NAME, value);
    }

    //----------------GETTERS---------------------
    public String getMatrix() {
        return getNodeText(MATRIX_TAG_NAME);
    }

    public String getExpect() {
        return getNodeText(EXPECT_TAG_NAME);
    }

    public String getGapOpen() {
        return getNodeText(GAP_OPEN_TAG_NAME);
    }

    public String getGapExtend() {
        return getNodeText(GAP_EXTEND_TAG_NAME);
    }

    public String getFilter() {
        return getNodeText(FILTER_TAG_NAME);
    }

    public BlastOutputParam getBlastOutputParam() throws XMLElementException {
        Element elem = root.getChild(BlastOutputParam.TAG_NAME);
        if (elem == null) {
            return null;
        } else {
            return new BlastOutputParam(elem);
        }
    }

    private void initParametersTag() {
        Element paramsTagName = root.getChild(PARAMETERS_TAG_NAME);
        if (paramsTagName == null) {
            paramsTagName = new Element(PARAMETERS_TAG_NAME);
        }
    }

}