/*
* 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 java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.bio.ReadSequence;
/**
* This class define a read filter that filter reads with a regex on of the name
* of the read.
* @since 1.2
* @author Laurent Jourdren
*/
public class ReadNameRegexReadFilter extends AbstractReadFilter {
private Pattern allowedPattern;
private Pattern forbiddenPattern;
@Override
public String getName() {
return "readnameregex";
}
@Override
public String getDescription() {
return "Filter reads names with regex";
}
@Override
public void setParameter(final String key, final String value)
throws EoulsanException {
if (key == null || value == null) {
return;
}
if ("forbidden.regex".equals(key.trim())) {
try {
this.forbiddenPattern = Pattern.compile(value);
} catch (PatternSyntaxException e) {
throw new EoulsanException("Invalid forbidden regex expression in "
+ getName() + " read filter: " + value);
}
} else if ("allowed.regex".equals(key.trim())) {
try {
this.allowedPattern = Pattern.compile(value);
} catch (PatternSyntaxException e) {
throw new EoulsanException("Invalid forbidden regex expression in "
+ getName() + " read filter: " + value);
}
} else {
throw new EoulsanException(
"Unknown parameter for " + getName() + " read filter: " + key);
}
}
@Override
public boolean accept(final ReadSequence read) {
if (read == null) {
return false;
}
final String name = read.getName();
if (name == null) {
return false;
}
if (this.allowedPattern != null
&& !this.allowedPattern.matcher(name).find()) {
return false;
}
if (this.forbiddenPattern != null
&& this.forbiddenPattern.matcher(name).find()) {
return false;
}
return true;
}
}