/*
* Eoulsan development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public License version 2.1 or
* later and CeCILL-C. This should be distributed with the code.
* If you do not have a copy, see:
*
* http://www.gnu.org/licenses/lgpl-2.1.txt
* http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
*
* Copyright for this code is held jointly by the Genomic platform
* of the Institut de Biologie de l'École normale supérieure and
* the individual authors. These should be listed in @author doc
* comments.
*
* For more information on the Eoulsan project and its aims,
* or to join the Eoulsan Google group, visit the home page
* at:
*
* http://outils.genomique.biologie.ens.fr/eoulsan
*
*/
package fr.ens.biologie.genomique.eoulsan.bio.readsfilters;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.bio.ReadSequence;
/**
* This interface define a filter for reads.
* @since 1.0
* @author Laurent Jourdren
*/
public interface ReadFilter {
/**
* Tests if a specified read should be keep.
* @param read read to test
*/
boolean accept(ReadSequence read);
/**
* Tests if the specified reads should be keep.
* @param read1 first read to test
* @param read2 first read to test
*/
boolean accept(ReadSequence read1, ReadSequence read2);
/**
* Get the name of the filter.
* @return the name of the filter
*/
String getName();
/**
* Get the description of the filter.
* @return the description of the filter
*/
String getDescription();
/**
* Set a parameter of the ReadFilter.
* @param key name of the parameter to set
* @param value value of the parameter to set
* @throws EoulsanException if the parameter is invalid
*/
void setParameter(String key, String value) throws EoulsanException;
/**
* Initialize the filter.
* @throws EoulsanException an error occurs while initialize the filter
*/
void init() throws EoulsanException;
}