com.ohnosequences.xml.model.uniprot.FeatureXML.java Source code

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Here is the source code for com.ohnosequences.xml.model.uniprot.FeatureXML.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.uniprot;

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 FeatureXML extends XMLElement {

    public static final String TAG_NAME = "feature";

    public static final String TYPE_TAG_NAME = "type";
    public static final String ID_TAG_NAME = "id";
    public static final String DESCRIPTION_TAG_NAME = "description";
    public static final String STATUS_TAG_NAME = "status";
    public static final String EVIDENCE_TAG_NAME = "evidence";
    public static final String BEGIN_TAG_NAME = "begin";
    public static final String END_TAG_NAME = "end";
    public static final String ORIGINAL_TAG_NAME = "original";
    public static final String VARIATION_TAG_NAME = "variation";
    public static final String REF_TAG_NAME = "ref";

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

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

    public FeatureXML(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 setType(String value) {
        setNodeText(TYPE_TAG_NAME, value);
    }

    public void setId(String value) {
        setNodeText(ID_TAG_NAME, value);
    }

    public void setStatus(String value) {
        setNodeText(STATUS_TAG_NAME, value);
    }

    public void setEvidence(String value) {
        setNodeText(EVIDENCE_TAG_NAME, value);
    }

    public void setBegin(int value) {
        setNodeText(BEGIN_TAG_NAME, String.valueOf(value));
    }

    public void setEnd(int value) {
        setNodeText(END_TAG_NAME, String.valueOf(value));
    }

    public void setDescription(String value) {
        setNodeText(DESCRIPTION_TAG_NAME, value);
    }

    public void setOriginal(String value) {
        setNodeText(ORIGINAL_TAG_NAME, value);
    }

    public void setVariation(String value) {
        setNodeText(VARIATION_TAG_NAME, value);
    }

    public void setRef(String value) {
        setNodeText(REF_TAG_NAME, value);
    }

    //----------------GETTERS---------------------
    public String getType() {
        return getNodeText(TYPE_TAG_NAME);
    }

    public String getId() {
        return getNodeText(ID_TAG_NAME);
    }

    public String getStatus() {
        return getNodeText(STATUS_TAG_NAME);
    }

    public String getEvidence() {
        return getNodeText(EVIDENCE_TAG_NAME);
    }

    public int getBegin() {
        return Integer.parseInt(getNodeText(BEGIN_TAG_NAME));
    }

    public int getEnd() {
        return Integer.parseInt(getNodeText(END_TAG_NAME));
    }

    public String getDescription() {
        return getNodeText(DESCRIPTION_TAG_NAME);
    }

    public String getOriginal() {
        return getNodeText(ORIGINAL_TAG_NAME);
    }

    public String getVariation() {
        return getNodeText(VARIATION_TAG_NAME);
    }

    public String getRef() {
        return getNodeText(REF_TAG_NAME);
    }

}