com.ohnosequences.xml.model.gb.GenBankXML.java Source code

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Here is the source code for com.ohnosequences.xml.model.gb.GenBankXML.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.gb;

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

public class GenBankXML extends XMLElement {

    public static final String TAG_NAME = "gen_bank_xml";

    public static final String LOCUS_NAME_TAG_NAME = "locus_name";
    public static final String SEQUENCE_LENGTH_TAG_NAME = "sequence_length";
    public static final String MOLECULE_TYPE_TAG_NAME = "molecule_type";
    public static final String GEN_BANK_DIVISION_TAG_NAME = "gen_bank_division";
    public static final String STRANDED_TYPE_TAG_NAME = "stranded_type";
    public static final String DNA_TYPE_TAG_NAME = "dna_type";
    public static final String MODIFICATION_DATE_TAG_NAME = "modification_date";
    public static final String DEFINITION_TAG_NAME = "definition";
    public static final String LINEAR_TAG_NAME = "linear";
    public static final String ACCESSION_TAG_NAME = "accession";
    public static final String VERSION_TAG_NAME = "version";
    public static final String KEYWORDS_TAG_NAME = "keywords";
    public static final String SOURCE_TAG_NAME = "source";
    public static final String ORGANISM_TAG_NAME = "organism";
    public static final String COMMENT_TAG_NAME = "comment";
    public static final String ORGANISM_COMPLETE_TAXONOMY_LINEAGE_TAG_NAME = "organism_complete_taxonomy_lineage";

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

    }

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

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

    //----------------GETTERS-------------------

    public boolean getLinear() {
        return Boolean.parseBoolean(getNodeText(LINEAR_TAG_NAME));
    }

    public String getKeywords() {
        return getNodeText(KEYWORDS_TAG_NAME);
    }

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

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

    public int getSequenceLength() {
        return Integer.parseInt(getNodeText(SEQUENCE_LENGTH_TAG_NAME));
    }

    public String getLocusName() {
        return getNodeText(LOCUS_NAME_TAG_NAME);
    }

    public String getMoleculeType() {
        return getNodeText(MOLECULE_TYPE_TAG_NAME);
    }

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

    public String getVersion() {
        return getNodeText(VERSION_TAG_NAME);
    }

    public String getSource() {
        return getNodeText(SOURCE_TAG_NAME);
    }

    public String getDnaType() {
        return getNodeText(DNA_TYPE_TAG_NAME);
    }

    public String getAccession() {
        return getNodeText(ACCESSION_TAG_NAME);
    }

    public String getGenBankDivision() {
        return getNodeText(GEN_BANK_DIVISION_TAG_NAME);
    }

    public String getComment() {
        return getNodeText(COMMENT_TAG_NAME);
    }

    public String getModificationDate() {
        return getNodeText(MODIFICATION_DATE_TAG_NAME);
    }

    public String getStrandedType() {
        return getNodeText(STRANDED_TYPE_TAG_NAME);
    }

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

    public void setLinear(boolean value) {
        setNodeText(LINEAR_TAG_NAME, String.valueOf(value));
    }

    public void setKeywords(String value) {
        setNodeText(KEYWORDS_TAG_NAME, value);
    }

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

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

    public void setSequenceLength(int value) {
        setNodeText(SEQUENCE_LENGTH_TAG_NAME, String.valueOf(value));
    }

    public void setLocusName(String value) {
        setNodeText(LOCUS_NAME_TAG_NAME, value);
    }

    public void setMoleculeType(String value) {
        setNodeText(MOLECULE_TYPE_TAG_NAME, value);
    }

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

    public void setVersion(String value) {
        setNodeText(VERSION_TAG_NAME, value);
    }

    public void setSource(String value) {
        setNodeText(SOURCE_TAG_NAME, value);
    }

    public void setDnaType(String value) {
        setNodeText(DNA_TYPE_TAG_NAME, value);
    }

    public void setAccession(String value) {
        setNodeText(ACCESSION_TAG_NAME, value);
    }

    public void setGenBankDivision(String value) {
        setNodeText(GEN_BANK_DIVISION_TAG_NAME, value);
    }

    public void setComment(String value) {
        setNodeText(COMMENT_TAG_NAME, value);
    }

    public void setModificationDate(String value) {
        setNodeText(MODIFICATION_DATE_TAG_NAME, value);
    }

    public void setStrandedType(String value) {
        setNodeText(STRANDED_TYPE_TAG_NAME, value);
    }
}