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

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Here is the source code for com.ohnosequences.xml.model.Hsp.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 org.jdom2.Element;

/**
 *
 * @author Pablo Pareja Tobes
 */
public class Hsp extends XMLElement {

    public static final String TAG_NAME = "Hsp";

    public static final String NUM_TAG_NAME = "Hsp_num";
    public static final String BIT_SCORE_TAG_NAME = "Hsp_bit-score";
    public static final String SCORE_TAG_NAME = "Hsp_score";
    public static final String EVALUE_TAG_NAME = "Hsp_evalue";
    public static final String QUERY_FROM_TAG_NAME = "Hsp_query-from";
    public static final String QUERY_TO_TAG_NAME = "Hsp_query-to";
    public static final String QUERY_FRAME_TAG_NAME = "Hsp_query-frame";
    public static final String HIT_FROM_TAG_NAME = "Hsp_hit-from";
    public static final String HIT_TO_TAG_NAME = "Hsp_hit-to";
    public static final String HIT_FRAME_TAG_NAME = "Hsp_hit-frame";
    public static final String POSITIVE_TAG_NAME = "Hsp_positive";
    public static final String IDENTITY_TAG_NAME = "Hsp_identity";
    public static final String GAPS_TAG_NAME = "Hsp_gaps";
    public static final String ALIGN_LEN_TAG_NAME = "Hsp_align-len";
    public static final String QSEQ_TAG_NAME = "Hsp_qseq";
    public static final String HSEQ_TAG_NAME = "Hsp_hseq";
    public static final String MIDLINE_TAG_NAME = "Hsp_midline";

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

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

    public Hsp(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 setNum(String value) {
        setNodeText(NUM_TAG_NAME, value);
    }

    public void setScore(String value) {
        setNodeText(SCORE_TAG_NAME, value);
    }

    public void setBitScore(String value) {
        setNodeText(BIT_SCORE_TAG_NAME, value);
    }

    public void setEvalue(String value) {
        setNodeText(EVALUE_TAG_NAME, value);
    }

    public void setQueryFrom(int value) {
        setNodeText(QUERY_FROM_TAG_NAME, String.valueOf(value));
    }

    public void setQueryTo(int value) {
        setNodeText(QUERY_TO_TAG_NAME, String.valueOf(value));
    }

    public void setQueryFrame(int value) {
        setNodeText(QUERY_FRAME_TAG_NAME, String.valueOf(value));
    }

    public void setHitFrom(int value) {
        setNodeText(HIT_FROM_TAG_NAME, String.valueOf(value));
    }

    public void setHitTo(int value) {
        setNodeText(HIT_TO_TAG_NAME, String.valueOf(value));
    }

    public void setHitFrame(int value) {
        setNodeText(HIT_FRAME_TAG_NAME, String.valueOf(value));
    }

    public void setIdentity(String value) {
        setNodeText(IDENTITY_TAG_NAME, value);
    }

    public void setPositive(String value) {
        setNodeText(POSITIVE_TAG_NAME, value);
    }

    public void setGaps(String value) {
        setNodeText(GAPS_TAG_NAME, value);
    }

    public void setAlignLen(String value) {
        setNodeText(ALIGN_LEN_TAG_NAME, value);
    }

    public void setQSeq(String value) {
        setNodeText(QSEQ_TAG_NAME, value);
    }

    public void setHSeq(String value) {
        setNodeText(HSEQ_TAG_NAME, value);
    }

    public void setMidline(String value) {
        setNodeText(MIDLINE_TAG_NAME, value);
    }

    //----------------GETTERS---------------------
    public String getNum() {
        return getNodeText(NUM_TAG_NAME);
    }

    public String getScore() {
        return getNodeText(SCORE_TAG_NAME);
    }

    public String getBitScore() {
        return getNodeText(BIT_SCORE_TAG_NAME);
    }

    public String getEvalue() {
        return getNodeText(EVALUE_TAG_NAME);
    }

    public double getEvalueDoubleFormat() {
        String[] array = getEvalue().split("e");
        if (array.length < 2) {
            //System.out.println("evalue = " + getEvalue());
            return Double.valueOf(array[0]);
        } else {
            return Double.valueOf(array[0]) * Math.pow(10.0, Double.valueOf(array[1]));
        }
    }

    public int getQueryFrom() {
        return Integer.parseInt(getNodeText(QUERY_FROM_TAG_NAME));
    }

    public int getQueryTo() {
        return Integer.parseInt(getNodeText(QUERY_TO_TAG_NAME));
    }

    public int getQueryFrame() {
        return Integer.parseInt(getNodeText(QUERY_FRAME_TAG_NAME));
    }

    public int getHitFrom() {
        return Integer.parseInt(getNodeText(HIT_FROM_TAG_NAME));
    }

    public int getHitTo() {
        return Integer.parseInt(getNodeText(HIT_TO_TAG_NAME));
    }

    public int getHitFrame() {
        return Integer.parseInt(getNodeText(HIT_FRAME_TAG_NAME));
    }

    public String getIdentity() {
        return getNodeText(IDENTITY_TAG_NAME);
    }

    public boolean getOrientation() {
        return getHitFrame() > 0;
    }

    public String getPositive() {
        return getNodeText(POSITIVE_TAG_NAME);
    }

    public String getGaps() {
        return getNodeText(GAPS_TAG_NAME);
    }

    public String getAlignLen() {
        return getNodeText(ALIGN_LEN_TAG_NAME);
    }

    public String getQSeq() {
        return getNodeText(QSEQ_TAG_NAME);
    }

    public String getHSeq() {
        return getNodeText(HSEQ_TAG_NAME);
    }

    public String getMidline() {
        return getNodeText(MIDLINE_TAG_NAME);
    }

}