/*
* 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.core.workflow;
import static com.google.common.base.Preconditions.checkArgument;
import static com.google.common.base.Preconditions.checkNotNull;
import java.io.Serializable;
import fr.ens.biologie.genomique.eoulsan.bio.FastqFormat;
import fr.ens.biologie.genomique.eoulsan.data.DataMetadata;
/**
* This class define an abstract class for metadata of data objects.
* @since 2.0
* @author Laurent Jourdren
*/
abstract class AbstractDataMetadata implements DataMetadata, Serializable {
private static final long serialVersionUID = -6869029697238897073L;
@Override
public boolean isPairedEnd() {
if (!containsKey(PAIRED_END_KEY)) {
return false;
}
return Boolean.parseBoolean(get(PAIRED_END_KEY));
}
@Override
public void setPairedEnd(final boolean pairedEnd) {
set(PAIRED_END_KEY, Boolean.toString(pairedEnd));
}
@Override
public FastqFormat getFastqFormat() {
return getFastqFormat(FastqFormat.FASTQ_SANGER);
}
@Override
public FastqFormat getFastqFormat(final FastqFormat defaultValue) {
if (!containsKey(FASTQ_FORMAT_KEY)) {
return defaultValue;
}
final FastqFormat result =
FastqFormat.getFormatFromName(get(FASTQ_FORMAT_KEY));
return result == null ? defaultValue : result;
}
@Override
public void setFastqFormat(final FastqFormat fastqFormat) {
checkNotNull(fastqFormat, "fastqFormat argument cannot be null");
set(FASTQ_FORMAT_KEY, fastqFormat.getName());
}
@Override
public String getSampleName() {
return get(SAMPLE_NAME_KEY);
}
@Override
public void setSampleName(final String sampleName) {
checkNotNull(sampleName, "sampleName argument cannot be null");
set(SAMPLE_NAME_KEY, sampleName);
}
@Override
public String getSampleId() {
if (!containsKey(SAMPLE_ID_KEY)) {
return null;
}
return get(SAMPLE_ID_KEY);
}
@Override
public void setSampleId(final String sampleId) {
checkNotNull(sampleId, "sampleId argument cannot be null");
set(SAMPLE_ID_KEY, sampleId);
}
@Override
public int getSampleNumber() {
if (!containsKey(SAMPLE_NUMBER_KEY)) {
return -1;
}
try {
return Integer.parseInt(get(SAMPLE_NUMBER_KEY));
} catch (NumberFormatException e) {
return -1;
}
}
@Override
public void setSampleNumber(final int sampleNumber) {
checkArgument(sampleNumber > 0,
"sampleNumber argument must be greater than 0: " + sampleNumber);
set(SAMPLE_NUMBER_KEY, Integer.toString(sampleNumber));
}
}