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

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Here is the source code for com.ohnosequences.xml.model.HspSet.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 HspSet {

    public static final String TAG_NAME = "hsp_set";

    public static final String HSPS_TAG_NAME = "hsps";

    private ArrayList<Hsp> array = null;
    private Hit hit = null;
    private String organism = "";

    public HspSet() {
        array = new ArrayList<Hsp>();
        hit = new Hit();
    }

    public HspSet(Element elem) throws XMLElementException {
        array = new ArrayList<Hsp>();
        hit = new Hit(elem.getChild(Hit.TAG_NAME));
        List<Element> list = elem.getChild(HSPS_TAG_NAME).getChildren(Hsp.TAG_NAME);
        for (Element temp : list) {
            array.add(new Hsp(temp));
        }
    }

    public String getOrganism() {
        return organism;
    }

    public void setOrganism(String value) {
        this.organism = value;
    }

    public XMLElement toXML() {
        XMLElement temp = new XMLElement(new Element(TAG_NAME));
        Hit tempHit = new Hit();
        tempHit.setHitDef(hit.getHitDef());
        tempHit.setUniprotID(hit.getUniprotID());
        temp.addChild(tempHit);
        temp.addChild(new XMLElement(new Element(HSPS_TAG_NAME)));
        Element hsps = temp.getRoot().getChild(HSPS_TAG_NAME);
        for (Hsp hsp : array) {
            hsps.addContent(hsp.getRoot());
        }

        return temp;
    }

    public void addHsp(Hsp hsp) {
        array.add(hsp);
    }

    public boolean hspsAreFromTheSameReadingFrame() {
        Hsp hsp = array.get(0);
        int readingFrame = hsp.getHitFrame();

        for (int i = 1; i < array.size(); i++) {
            if (array.get(i).getHitFrame() != readingFrame) {
                return false;
            }
        }

        return true;
    }

    public Hit getHit() {
        return hit;
    }

    public void setHit(Hit hitValue) {
        hit = hitValue;
    }

    public int getHspQueryFrom() {
        return array.get(0).getQueryFrom();
    }

    public int getHspQueryTo() {
        return array.get(array.size() - 1).getQueryTo();
    }

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

    //IMPORTANTE CONFIRMAR QUE ESTOS DOS METODOS SON ASI!!!! --> en principio si
    public int getHspHitFrom() {
        Hsp primero = array.get(0);
        Hsp ultimo = null;

        if (array.size() == 1) {
            ultimo = primero;
        } else {
            ultimo = array.get(array.size() - 1);
        }

        boolean orientacionNegativa = primero.getHitFrame() < 0;
        if (orientacionNegativa) {
            return ultimo.getHitFrom();
        } else {
            return primero.getHitFrom();
        }

    }

    public double getEvalue() {
        double evalue = array.get(0).getEvalueDoubleFormat();
        for (int i = 0; i < array.size(); i++) {
            double tempEvalue = array.get(i).getEvalueDoubleFormat();
            if (tempEvalue < evalue) {
                evalue = tempEvalue;
            }
        }

        return evalue;
    }

    public int getHspHitTo() {
        Hsp primero = array.get(0);
        Hsp ultimo = null;

        if (array.size() == 1) {
            ultimo = primero;
        } else {
            ultimo = array.get(array.size() - 1);
        }

        boolean orientacionNegativa = primero.getHitFrame() < 0;
        if (orientacionNegativa) {
            return primero.getHitTo();
        } else {
            return ultimo.getHitTo();
        }
    }

    public Hsp get(int i) {
        return array.get(i);
    }

    public ArrayList<Hsp> getHsps() {
        return array;
    }

    public int size() {
        return array.size();
    }

}