com.ohnosequences.xml.model.mg7.ReadResultXML.java Source code

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Here is the source code for com.ohnosequences.xml.model.mg7.ReadResultXML.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.mg7;

import com.ohnosequences.xml.model.Hit;
import com.ohnosequences.xml.api.model.XMLElement;
import com.ohnosequences.xml.api.model.XMLElementException;
import java.util.LinkedList;
import java.util.List;
import org.jdom2.Element;

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

    public static final String TAG_NAME = "read_result";

    public static final String READ_ID_TAG_NAME = "read_id";
    public static final String QUERY_LENGTH_TAG_NAME = "query_length";
    public static final String SEQUENCE_TAG_NAME = "sequence";

    public static final String HITS_TAG_NAME = "hits";

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

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

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

    //----------------GETTERS---------------------
    public String getReadId() {
        return getNodeText(READ_ID_TAG_NAME);
    }

    public int getQueryLength() {
        return Integer.parseInt(getNodeText(QUERY_LENGTH_TAG_NAME));
    }

    public String getSequence() {
        return getNodeText(SEQUENCE_TAG_NAME);
    }

    public List<Hit> getHits() throws XMLElementException {

        Element elem = initHitsTag();
        List<Hit> resultList = new LinkedList<Hit>();
        List<Element> tempList = elem.getChildren(Hit.TAG_NAME);
        for (Element element : tempList) {
            resultList.add(new Hit(element));
        }
        return resultList;

    }

    public void addHit(Hit hit) {
        Element hits = initHitsTag();
        hits.addContent(hit.getRoot());
    }

    //----------------SETTERS---------------------
    public void setReadId(String value) {
        setNodeText(READ_ID_TAG_NAME, value);
    }

    public void setQueryLength(int value) {
        setNodeText(QUERY_LENGTH_TAG_NAME, String.valueOf(value));
    }

    public void setSequence(String value) {
        setNodeText(SEQUENCE_TAG_NAME, value);
    }

    protected Element initHitsTag() {
        Element elem = this.root.getChild(HITS_TAG_NAME);
        if (elem == null) {
            root.addContent(new Element(HITS_TAG_NAME));
            elem = this.root.getChild(HITS_TAG_NAME);
        }
        return elem;
    }

}