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

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

    public static final String TAG_NAME = "Hit";

    public static final String HIT_HSPS_TAG_NAME = "Hit_hsps";
    public static final String HIT_DEF_TAG_NAME = "Hit_def";
    public static final String HIT_LEN_TAG_NAME = "Hit_len";
    public static final String HIT_ID_TAG_NAME = "Hit_id";
    public static final String HIT_NUM_TAG_NAME = "Hit_num";
    public static final String HIT_ACCESSION_TAG_NAME = "Hit_accession";
    public static final String UNIPROT_ID_TAG_NAME = "uniprot_id";
    public static final String GI_ID_TAG_NAME = "gi_id";

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

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

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

    //----------------GETTERS---------------------
    public ArrayList<Hsp> getHitHsps() throws XMLElementException {
        ArrayList<Hsp> array = new ArrayList<Hsp>();
        Element hsps = initHitHspsTag();
        List<Element> tempList = hsps.getChildren(Hsp.TAG_NAME);
        for (Element elem : tempList) {
            array.add(new Hsp(elem));
        }
        return array;

    }

    public String getHitDef() {
        return getNodeText(HIT_DEF_TAG_NAME);
    }

    public int getHitLen() {
        return Integer.parseInt(getNodeText(HIT_LEN_TAG_NAME));
    }

    public String getHitId() {
        return getNodeText(HIT_ID_TAG_NAME);
    }

    public String getUniprotID() {
        return getNodeText(UNIPROT_ID_TAG_NAME);
    }

    public String getScaffoldIDFromHitDef() {
        return getHitDef().split(" ")[0];
    }

    public int getHitNum() {
        return Integer.parseInt(getNodeText(HIT_NUM_TAG_NAME));
    }

    public String getHitAccession() {
        return getNodeText(HIT_ACCESSION_TAG_NAME);
    }

    public int getGiId() {
        return Integer.parseInt(getNodeText(GI_ID_TAG_NAME));
    }

    //----------------SETTERS---------------------
    public void setHitId(String value) {
        setNodeText(HIT_ID_TAG_NAME, value);
    }

    public void setHitDef(String value) {
        setNodeText(HIT_DEF_TAG_NAME, value);
    }

    public void setHitLen(int value) {
        setNodeText(HIT_LEN_TAG_NAME, String.valueOf(value));
    }

    public void setUniprotID(String value) {
        setNodeText(UNIPROT_ID_TAG_NAME, value);
    }

    public void setHitNum(int value) {
        setNodeText(HIT_NUM_TAG_NAME, String.valueOf(value));
    }

    public void setHitAccession(String value) {
        setNodeText(HIT_ACCESSION_TAG_NAME, value);
    }

    public void setGiId(int value) {
        setNodeText(GI_ID_TAG_NAME, String.valueOf(value));
    }

    public void addHsp(Hsp hsp) {
        Element hsps = initHitHspsTag();
        hsps.addContent(hsp.getRoot());
    }

    protected Element initHitHspsTag() {
        Element hsps = root.getChild(HIT_HSPS_TAG_NAME);
        if (hsps == null) {
            root.addContent(new Element(HIT_HSPS_TAG_NAME));
            hsps = root.getChild(HIT_HSPS_TAG_NAME);
        }
        return hsps;
    }
}