/*
* 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 static fr.ens.biologie.genomique.eoulsan.EoulsanLogger.getLogger;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.util.ReporterIncrementer;
/**
* This builder allow to create a MultiReadFilter object.
* @since 1.1
* @author Laurent Jourdren
*/
public class MultiReadFilterBuilder {
private final Map<String, ReadFilter> mapFilters = new HashMap<>();
private final List<ReadFilter> listFilter = new ArrayList<>();
private final Map<String, String> mapParameters = new LinkedHashMap<>();
/**
* Add a parameter to the builder
* @param key key of the parameter
* @param value value of the parameter
* @return true if the parameter has been successfully added
* @throws EoulsanException if the filter reference in the key does not exist
* or if an error occurs while setting the parameter in the
* dedicated filter
*/
public boolean addParameter(final String key, final String value)
throws EoulsanException {
return addParameter(key, value, false);
}
/**
* Add a parameter to the builder
* @param key key of the parameter
* @param value value of the parameter
* @param noExceptionIfFilterNotExists do not thrown an exception if the
* filter does not exists.
* @return true if the parameter has been successfully added
* @throws EoulsanException if the filter reference in the key does not exist
* or if an error occurs while setting the parameter in the
* dedicated filter
*/
public boolean addParameter(final String key, final String value,
final boolean noExceptionIfFilterNotExists) throws EoulsanException {
if (key == null || value == null) {
return false;
}
// Get first dot position
final String keyTrimmed = key.trim();
final int index = keyTrimmed.indexOf('.');
final String filterName;
final String filterKey;
// Get the the filter name and parameter name
if (index == -1) {
filterName = keyTrimmed;
filterKey = null;
} else {
filterName = keyTrimmed.substring(0, index);
filterKey = keyTrimmed.substring(index + 1);
}
final ReadFilter filter;
// Get the filter object, load it if necessary
if (this.mapFilters.containsKey(filterName)) {
filter = this.mapFilters.get(filterName);
} else {
filter = ReadFilterService.getInstance().newService(filterName);
if (filter == null) {
if (noExceptionIfFilterNotExists) {
return false;
}
throw new EoulsanException(
"Unable to find " + filterName + " read filter.");
}
this.mapFilters.put(filterName, filter);
this.listFilter.add(filter);
}
// Set the parameter
if (filterKey != null) {
final String valueTrimmed = value.trim();
filter.setParameter(filterKey, valueTrimmed);
this.mapParameters.put(keyTrimmed, valueTrimmed);
getLogger().info("Set read filter \""
+ filterName + "\" with parameter: " + filterKey + "="
+ valueTrimmed);
} else {
this.mapParameters.put(filterName, "");
getLogger()
.info("Set read filter \"" + filterName + "\" with no parameter");
}
return true;
}
/**
* Add parameters to the builder.
* @param parameters parameters to add
* @throws EoulsanException if the filter reference in the key does not exist
* or if an error occurs while setting the parameter in the
* dedicated filter
*/
public void addParameters(final Map<String, String> parameters)
throws EoulsanException {
if (parameters == null) {
return;
}
for (Map.Entry<String, String> e : parameters.entrySet()) {
addParameter(e.getKey(), e.getValue());
}
}
/**
* Create the final MultiReadFilter.
* @return a new MultiReadFilter object
* @throws EoulsanException if an error occurs while initialize one of the
* filter
*/
public MultiReadFilter getReadFilter() throws EoulsanException {
for (ReadFilter f : this.listFilter) {
f.init();
}
return new MultiReadFilter(this.listFilter);
}
/**
* Create the final MultiReadFilter.
* @param incrementer incrementer to use
* @param counterGroup counter group for the incrementer
* @return a new MultiReadFilter object
* @throws EoulsanException if an error occurs while initialize one of the
* filter
*/
public MultiReadFilter getReadFilter(final ReporterIncrementer incrementer,
final String counterGroup) throws EoulsanException {
for (ReadFilter f : this.listFilter) {
f.init();
}
return new MultiReadFilter(incrementer, counterGroup, this.listFilter);
}
/**
* Get a map with all the parameters used to create the MultiReadFilter.
* @return an ordered map object
*/
public Map<String, String> getParameters() {
return Collections.unmodifiableMap(this.mapParameters);
}
//
// Constructors
//
/**
* Public constructor.
*/
public MultiReadFilterBuilder() {
}
/**
* Public constructor.
* @param parameters parameters to add to the builder
* @throws EoulsanException if the filter reference in the key does not exist
* or if an error occurs while setting the parameter in the
* dedicated filter
*/
public MultiReadFilterBuilder(final Map<String, String> parameters)
throws EoulsanException {
addParameters(parameters);
}
}