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

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Here is the source code for com.ohnosequences.xml.model.PredictedGenes.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 java.util.ArrayList;
import java.util.List;
import org.jdom2.Element;

/**
 *
 * @author ppareja
 */
public class PredictedGenes extends XMLElement {

    public static final String TAG_NAME = "predicted_genes";

    public static final String DIF_SPAN_TAG_NAME = "difspan";
    public static final String GENE_THRESHOLD_TAG_NAME = "gene_threshold";
    public static final String PREFERENT_ORGANISM = "preferent_organism";

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

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

    public PredictedGenes(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 setDifSpan(int value) {
        setNodeText(DIF_SPAN_TAG_NAME, String.valueOf(value));
    }

    public void setGeneThreshold(int value) {
        setNodeText(GENE_THRESHOLD_TAG_NAME, String.valueOf(value));
    }

    public void setPreferentOrganism(String value) {
        setNodeText(PREFERENT_ORGANISM, value);
    }

    //----------------GETTERS---------------------
    public int getDifSpan() {
        return Integer.parseInt(getNodeText(DIF_SPAN_TAG_NAME));
    }

    public int getGeneThreshold() {
        return Integer.parseInt(getNodeText(GENE_THRESHOLD_TAG_NAME));
    }

    public String getPreferentOrganism() {
        return getNodeText(PREFERENT_ORGANISM);
    }

    public List<ContigXML> getContigs() throws XMLElementException {
        List<ContigXML> list = new ArrayList<ContigXML>();

        List<Element> contigs = root.getChildren(ContigXML.TAG_NAME);
        for (Element element : contigs) {
            list.add(new ContigXML(element));
        }

        return list;
    }
}