com.ohnosequences.xml.model.embl.EmblXML.java Source code

Java tutorial

Introduction

Here is the source code for com.ohnosequences.xml.model.embl.EmblXML.java

Source

/*
 * 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.embl;

import com.ohnosequences.xml.api.model.XMLElement;
import com.ohnosequences.xml.api.model.XMLElementException;
import org.jdom2.Element;

public class EmblXML extends XMLElement {

    public static final String TAG_NAME = "embl_xml";
    public static final String STRAIN_TAG_NAME = "strain";
    public static final String ID_TAG_NAME = "id";
    public static final String MOL_TYPE_TAG_NAME = "mol_type";
    public static final String DEFINITION_TAG_NAME = "definition";
    public static final String ORGANISM_TAG_NAME = "organism";
    public static final String ORGANISM_COMPLETE_TAXONOMY_LINEAGE_TAG_NAME = "organism_complete_taxonomy_lineage";
    public static final String LOCUS_TAG_PREFIX_TAG_NAME = "locus_tag_prefix";

    public EmblXML() {
        super(new Element(TAG_NAME));

    }

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

    public EmblXML(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 getDefinition() {
        return getNodeText(DEFINITION_TAG_NAME);
    }

    public String getLocusTagPrefix() {
        return getNodeText(LOCUS_TAG_PREFIX_TAG_NAME);
    }

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

    public String getMolType() {
        return getNodeText(MOL_TYPE_TAG_NAME);
    }

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

    public String getStrain() {
        return getNodeText(STRAIN_TAG_NAME);
    }

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

    //----------------SETTERS-------------------

    public void setDefinition(String value) {
        setNodeText(DEFINITION_TAG_NAME, value);
    }

    public void setLocusTagPrefix(String value) {
        setNodeText(LOCUS_TAG_PREFIX_TAG_NAME, value);
    }

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

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

    public void setMolType(String value) {
        setNodeText(MOL_TYPE_TAG_NAME, value);
    }

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

    public void setStrain(String value) {
        setNodeText(STRAIN_TAG_NAME, value);
    }
}