org.opencb.cellbase.core.variant

Class AnnotationBasedPhasedQueryManager<T>

java.lang.Object

org.opencb.cellbase.core.variant.PhasedQueryManager

org.opencb.cellbase.core.variant.AnnotationBasedPhasedQueryManager<T>

Direct Known Subclasses:

ClinicalPhasedQueryManager, PopulationFrequencyPhasedQueryManager

public abstract class AnnotationBasedPhasedQueryManager<T>
extends PhasedQueryManager

Field Summary

Fields

Modifier and Type	Field and Description
protected org.slf4j.Logger	logger

Fields inherited from class org.opencb.cellbase.core.variant.PhasedQueryManager

GENOTYPE_TAG, PHASE_SET_TAG, PHASED_GENOTYPE_SEPARATOR, UNPHASED_GENOTYPE_SEPARATOR

Constructor Summary

Constructors

Constructor and Description
AnnotationBasedPhasedQueryManager()

Method Summary

Modifier and Type	Method and Description
protected abstract List<T>	getAnnotationObjectList(org.opencb.biodata.models.variant.Variant variant)
protected abstract List<org.opencb.biodata.models.variant.Variant>	getHaplotype(T annotationObject, org.opencb.biodata.models.variant.Variant variant)
List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>>	run(List<org.opencb.biodata.models.variant.Variant> variantList, List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> variantCellBaseDataResultList)

Methods inherited from class org.opencb.cellbase.core.variant.PhasedQueryManager

getSampleAttribute, isMissing, reset, sameHaplotype

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

protected org.slf4j.Logger logger

Constructor Detail

AnnotationBasedPhasedQueryManager

public AnnotationBasedPhasedQueryManager()

Method Detail

run

public List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> run(List<org.opencb.biodata.models.variant.Variant> variantList,
                                                                               List<CellBaseDataResult<org.opencb.biodata.models.variant.Variant>> variantCellBaseDataResultList)

getHaplotype

protected abstract List<org.opencb.biodata.models.variant.Variant> getHaplotype(T annotationObject,
                                                                                org.opencb.biodata.models.variant.Variant variant)

getAnnotationObjectList

protected abstract List<T> getAnnotationObjectList(org.opencb.biodata.models.variant.Variant variant)