/*******************************************************************************
* GenPlay, Einstein Genome Analyzer
* Copyright (C) 2009, 2014 Albert Einstein College of Medicine
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
* Authors: Julien Lajugie <julien.lajugie@einstein.yu.edu>
* Nicolas Fourel <nicolas.fourel@einstein.yu.edu>
* Eric Bouhassira <eric.bouhassira@einstein.yu.edu>
*
* Website: <http://genplay.einstein.yu.edu>
******************************************************************************/
package edu.yu.einstein.genplay.core.IO.dataReader;
import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.dataStructure.enums.GeneScoreType;
import edu.yu.einstein.genplay.dataStructure.enums.Strand;
import edu.yu.einstein.genplay.dataStructure.gene.Gene;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;
import edu.yu.einstein.genplay.dataStructure.scoredChromosomeWindow.ScoredChromosomeWindow;
/**
* Interface defining method for data readers that can read elements needed to create {@link Gene} objects.
* @author Julien Lajugie
*/
public interface GeneReader extends DataReader, ChromosomeWindowReader, SCWReader {
@Override
public Chromosome getChromosome();
/**
* @return the exons of the last extracted item
*/
public ListView<ScoredChromosomeWindow> getExons();
/**
* @return the URL of the database containing informations on the genes
*/
public String getGeneDBURL();
/**
* @return the type of the scores of the genes and exons of this list (RPKM, max, sum)
*/
public GeneScoreType getGeneScoreType();
/**
* @return the name of the last extracted item
*/
public String getName();
@Override
public Float getScore();
@Override
public Integer getStart();
@Override
public Integer getStop();
/**
* @return the strand of the last extracted item
*/
public Strand getStrand();
/**
* @return the UTR3 boundary position of the last extracted item
*/
public Integer getUTR3Bound();
/**
* @return the UTR5 boundary position of the last extracted item
*/
public Integer getUTR5Bound();
}