com.ohnosequences.xml.model.ncbi.NCBITaxonomyNodeXML.java Source code

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Here is the source code for com.ohnosequences.xml.model.ncbi.NCBITaxonomyNodeXML.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.ncbi;

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 NCBITaxonomyNodeXML extends XMLElement {

    public static final String TAG_NAME = "ncbi_taxonomy_node";

    public static final String TAX_ID_TAG_NAME = "tax_id";
    public static final String PARENT_TAX_ID_TAG_NAME = "parent_tax_id";
    public static final String SCIENTIFIC_NAME_TAG_NAME = "scientific_name";
    public static final String RANK_TAG_NAME = "rank";
    public static final String EMBL_CODE_TAG_NAME = "embl_code";
    public static final String COMMENTS_TAG_NAME = "comments";
    public static final String ABSOLUTE_FREQUENCY_TAG_NAME = "absolute_frequency";
    public static final String ACCUMULATED_ABSOLUTE_FREQUENCY_TAG_NAME = "accumulated_absolute_frequency";

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

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

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

    //----------------GETTERS---------------------
    public int getTaxId() {
        return Integer.parseInt(getNodeText(TAX_ID_TAG_NAME));
    }

    public String getParentTaxId() {
        return getNodeText(PARENT_TAX_ID_TAG_NAME);
    }

    public String getRank() {
        return getNodeText(RANK_TAG_NAME);
    }

    public String getEmblCode() {
        return getNodeText(EMBL_CODE_TAG_NAME);
    }

    public String getComments() {
        return getNodeText(COMMENTS_TAG_NAME);
    }

    public String getScientificName() {
        return getNodeText(SCIENTIFIC_NAME_TAG_NAME);
    }

    public int getAbsoluteFrequency() {
        return Integer.parseInt(getNodeText(ABSOLUTE_FREQUENCY_TAG_NAME));
    }

    public int getAccumulatedAbsoluteFrequency() {
        return Integer.parseInt(getNodeText(ACCUMULATED_ABSOLUTE_FREQUENCY_TAG_NAME));
    }

    //----------------SETTERS-------------------
    public void setTaxId(int value) {
        setNodeText(TAX_ID_TAG_NAME, String.valueOf(value));
    }

    public void setParentTaxId(String value) {
        setNodeText(PARENT_TAX_ID_TAG_NAME, value);
    }

    public void setRank(String value) {
        setNodeText(RANK_TAG_NAME, value);
    }

    public void setEmblCode(String value) {
        setNodeText(EMBL_CODE_TAG_NAME, value);
    }

    public void setComments(String value) {
        setNodeText(COMMENTS_TAG_NAME, value);
    }

    public void setScientificName(String value) {
        setNodeText(SCIENTIFIC_NAME_TAG_NAME, value);
    }

    public void setAbsoluteFrequency(int value) {
        setNodeText(ABSOLUTE_FREQUENCY_TAG_NAME, String.valueOf(value));
    }

    public void setAccumulatedAbsoluteFrequency(int value) {
        setNodeText(ACCUMULATED_ABSOLUTE_FREQUENCY_TAG_NAME, String.valueOf(value));
    }

}