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

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Here is the source code for com.ohnosequences.xml.model.ContigXML.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 ContigXML extends XMLElement {

    public static final String TAG_NAME = "contig";

    public static final String ID_TAG_NAME = "id";
    public static final String LENGTH_TAG_NAME = "length";
    public static final String BEGIN_TAG_NAME = "begin";
    public static final String END_TAG_NAME = "end";
    public static final String SEQUENCE_TAG_NAME = "sequence";
    public static final String GAPS_PERCENTAGE_TAG_NAME = "gaps_percentage";
    public static final String ORGANISM_TAG_NAME = "organism";
    public static final String ORGANISM_COMPLETE_TAXONOMY_LINEAGE = "organism_complete_taxonomy_lineage";

    public static final String HSPS_TAG_NAME = "hsps";

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

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

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

    public void addPredictedGene(PredictedGene gene) {
        root.addContent(gene.asJDomElement());
    }

    public void addPredictedRna(PredictedRna rna) {
        root.addContent(rna.asJDomElement());
    }

    public void addGap(Gap gap) {
        root.addContent(gap.asJDomElement());
    }

    //----------------GETTERS---------------------
    public String getId() {
        return getNodeText(ID_TAG_NAME);
    }

    public int getLength() {
        return Integer.parseInt(getNodeText(LENGTH_TAG_NAME));
    }

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

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

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

    public String getOrganism() {
        return getNodeText(ORGANISM_TAG_NAME);
    }

    public String getOrganismCompleteTaxonomyLineage() {
        return getNodeText(ORGANISM_COMPLETE_TAXONOMY_LINEAGE);
    }

    public double getGapsPercentage() {
        return Double.parseDouble(getNodeText(GAPS_PERCENTAGE_TAG_NAME));
    }

    public List<Hsp> getHsps() throws XMLElementException {
        Element hsps = root.getChild(HSPS_TAG_NAME);
        if (hsps == null) {
            return null;
        } else {
            ArrayList<Hsp> array = new ArrayList<Hsp>();
            for (Object hspElem : hsps.getChildren(Hsp.TAG_NAME)) {
                array.add(new Hsp((Element) hspElem));
            }
            return array;
        }
    }

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

    public void setLength(int value) {
        setNodeText(LENGTH_TAG_NAME, String.valueOf(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 setSequence(String value) {
        setNodeText(SEQUENCE_TAG_NAME, value);
    }

    public void setOrganism(String value) {
        setNodeText(ORGANISM_TAG_NAME, value);
    }

    public void setOrganismCompleteTaxonomyLineage(String value) {
        setNodeText(ORGANISM_COMPLETE_TAXONOMY_LINEAGE, value);
    }

    public void setGapsPercentage(double value) {
        setNodeText(GAPS_PERCENTAGE_TAG_NAME, String.valueOf(value));
    }

    public void addHsp(Hsp hsp) {
        initHspsTag();
        Element hsps = root.getChild(HSPS_TAG_NAME);
        hsps.addContent(hsp.asJDomElement());
    }

    private void initHspsTag() {
        Element hsps = root.getChild(HSPS_TAG_NAME);
        if (hsps == null) {
            hsps = new Element(HSPS_TAG_NAME);
            root.addContent(hsps);
        }
    }

}